MEME

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use MEME in your research, please cite the following paper:
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.

Discovered Motifs   |   Block diagrams of Motifs   |   Program information   |   Explanation

Discovered Motifs

Motif Overview

Motif 1
  • 1.1e-133
  • 40 sites
Motif 1 Logo
Motif 2
  • 2.6e-056
  • 25 sites
Motif 2 Logo
Motif 3
  • 3.0e-055
  • 40 sites
Motif 3 Logo
Motif 4
  • 6.1e-049
  • 37 sites
Motif 4 Logo
Motif 5
  • 7.9e-037
  • 32 sites
Motif 5 Logo
Motif 6
  • 9.0e-037
  • 32 sites
Motif 6 Logo
Motif 7
  • 5.3e-025
  • 19 sites
Motif 7 Logo
Motif 8
  • 3.1e-024
  • 31 sites
Motif 8 Logo
Motif 9
  • 1.5e-022
  • 15 sites
Motif 9 Logo
Motif 10
  • 1.1e-020
  • 23 sites
Motif 10 Logo
Motif 11
  • 3.2e-017
  • 10 sites
Motif 11 Logo
Motif 12
  • 1.9e-020
  • 17 sites
Motif 12 Logo
Motif 13
  • 2.0e-016
  • 40 sites
Motif 13 Logo
Motif 14
  • 2.8e-012
  • 33 sites
Motif 14 Logo
Motif 15
  • 5.8e-012
  • 9 sites
Motif 15 Logo
Motif 16
  • 3.4e-010
  • 15 sites
Motif 16 Logo
Motif 17
  • 4.2e-009
  • 5 sites
Motif 17 Logo
Motif 18
  • 1.1e-006
  • 5 sites
Motif 18 Logo
Motif 19
  • 5.9e-008
  • 5 sites
Motif 19 Logo
Motif 20
  • 1.4e-005
  • 28 sites
Motif 20 Logo

Further Analysis

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Motif 1

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Summary

Sequence Logo

E-value 1.1e-133
Width 5
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

IWFQN

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1561 46 4.28e-08 ALSLSERQIK IWFQN RRMKSKKDR
1515 4 4.28e-08 RQIR IWFQN RRMRWRR
1514 4 4.28e-08 RQIK IWFQN RRMKWKKTYA
1513 4 4.28e-08 RQIK IWFQN RRMKWKKDIM
1512 4 4.28e-08 RQIK IWFQN RRMKWKK
1511 4 4.28e-08 RQIK IWFQN RRMKWKA
1510 4 4.28e-08 RQIK IWFQN RRMKWK
1509 4 4.28e-08 RQIK IWFQN RRMKWAK
1508 4 4.28e-08 RQIK IWFQN RRMKW
1507 4 4.28e-08 RQIK IWFQN RRMKAKK
1506 4 4.28e-08 RQIK IWFQN RRMK
1505 4 4.28e-08 RQIK IWFQN RRMAWKK
1504 4 4.28e-08 RQIK IWFQN RRM
1503 4 4.28e-08 RQIK IWFQN RRAKWKK
1502 4 4.28e-08 RQIK IWFQN RR
1501 4 4.28e-08 RQIK IWFQN RAMKWKK
1500 4 4.28e-08 RQIK IWFQN R
1499 4 4.28e-08 RQIK IWFQN MRRKWKK
1498 4 4.28e-08 RQIK IWFQN ARMKWKK
1497 4 4.28e-08 RQIK IWFQN
1487 4 4.28e-08 RQIA IWFQN RRMKWKK
1483 4 4.28e-08 RQAK IWFQN RRMKWKK
1437 4 4.28e-08 RHIK IWFQN RRMKWKK
1431 4 4.28e-08 RAIK IWFQN RRMKWKK
1420 3 4.28e-08 QIK IWFQN RRMKWKK
1319 10 4.28e-08 LIRLWSHLIH IWFQN RRLKWKKK
1225 1 4.28e-08 K IWFQN RRMKWKK
1199 0 4.28e-08 IWFQN RRMKWKK
1195 2 4.28e-08 IK IWFQN RRMKWKK
1071 47 4.28e-08 ELGLNEAQIK IWFQN KRAKIKKST
1043 5 4.28e-08 CRQIK IWFQN RRMKWKK
1031 4 4.28e-08 AQIK IWFQN RRMKWKK
1020 12 4.28e-08 ALCPPERQIK IWFQN RRMKWKKEN
1019 12 4.28e-08 ALCLTERQIK IWFQN RRMKWKKEN
1543 4 6.42e-08 RVIR VWFQN KRCKDKK
1491 4 9.51e-08 RQIK IFFQN RRMKWKK
1490 4 9.51e-08 RQIK IFFQN RRMKFKK
1488 4 2.41e-07 RQIK AWFQN RRMKWKK
1517 4 3.08e-07 RQPK IWFPN RRKPWKK
1493 4 4.44e-07 RQIK IWFAN RRMKWKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1019 4.28e-08
1020 4.28e-08
1031 4.28e-08
1043 4.28e-08
1071 4.28e-08
1195 4.28e-08
1199 4.28e-08
1225 4.28e-08
1319 4.28e-08
1420 4.28e-08
1431 4.28e-08
1437 4.28e-08
1483 4.28e-08
1487 4.28e-08
1488 2.41e-07
1490 9.51e-08
1491 9.51e-08
1493 4.44e-07
1497 4.28e-08
1498 4.28e-08
1499 4.28e-08
1500 4.28e-08
1501 4.28e-08
1502 4.28e-08
1503 4.28e-08
1504 4.28e-08
1505 4.28e-08
1506 4.28e-08
1507 4.28e-08
1508 4.28e-08
1509 4.28e-08
1510 4.28e-08
1511 4.28e-08
1512 4.28e-08
1513 4.28e-08
1514 4.28e-08
1515 4.28e-08
1517 3.08e-07
1543 6.42e-08
1561 4.28e-08
 
0
10
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30
40
50
60

Time 18.7 secs.

Motif 2

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Summary

Sequence Logo

E-value 2.6e-056
Width 5
Sites 25
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

YSPTT

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1481 6 6.87e-08 RLYMRY YSPTT RRYG
1477 6 6.87e-08 RLWMRW YSPTT RRYG
1476 6 6.87e-08 RLWMRW YSPTT RRYA
1475 6 6.87e-08 RLWMRW YSPTT RRAG
1474 6 6.87e-08 RLWMRW YSPTT RAYG
1473 6 6.87e-08 RLWMRW YSPTT ARYG
1468 6 6.87e-08 RLWMRA YSPTT RRYG
1467 6 6.87e-08 RLWMAW YSPTT RRYG
1466 6 6.87e-08 RLWARW YSPTT RRYG
1465 6 6.87e-08 RLVMRV YSPTT RRYG
1462 6 6.87e-08 RLLMRL YSPTT RRYG
1461 6 6.87e-08 RLIMRI YSPTT RRYG
1460 6 6.87e-08 RLFMRF YSPTT RRYG
1459 6 6.87e-08 RLAMRW YSPTT RRYG
1433 6 6.87e-08 RAWMRW YSPTT RRYG
1262 6 6.87e-08 KLWMRW YSPTT RRYG
1028 6 6.87e-08 ALWMRW YSPTT RRYG
1479 6 1.35e-07 RLWMRW YSPWT RRYG
1478 6 1.35e-07 RLWMRW YSPWT RRWG
1263 6 1.35e-07 KLWMRW YSPWT RRYG
1470 6 3.85e-07 RLWMRW YAPTT RRYG
1261 6 3.85e-07 KLWMRW YSATT RRYG
1471 6 6.20e-07 RLWMRW YSPAT RRYG
1472 6 7.75e-07 RLWMRW YSPTA RRYG
1469 6 1.51e-06 RLWMRW ASPTT RRYG

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1028 6.87e-08
1261 3.85e-07
1262 6.87e-08
1263 1.35e-07
1433 6.87e-08
1459 6.87e-08
1460 6.87e-08
1461 6.87e-08
1462 6.87e-08
1465 6.87e-08
1466 6.87e-08
1467 6.87e-08
1468 6.87e-08
1469 1.51e-06
1470 3.85e-07
1471 6.20e-07
1472 7.75e-07
1473 6.87e-08
1474 6.87e-08
1475 6.87e-08
1476 6.87e-08
1477 6.87e-08
1478 1.35e-07
1479 1.35e-07
1481 6.87e-08
 
0
2
4
6
8
10
12
14

Time 36.7 secs.

Motif 3

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Summary

Sequence Logo

E-value 3.0e-055
Width 5
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

MII[FY]R

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1386 0 1.81e-07 MIIYR IAASHKK
1385 0 1.81e-07 MIIYR DLISKK
1384 0 1.81e-07 MIIYR DLISH
1383 0 1.81e-07 MIIYR DLIS
1382 0 1.81e-07 MIIYR DLIA
1381 0 1.81e-07 MIIYR DLI
1380 0 1.81e-07 MIIYR DLAS
1379 0 1.81e-07 MIIYR DKKSH
1378 0 1.81e-07 MIIYR DAIS
1377 0 1.81e-07 MIIYR ALISHKK
1376 0 1.81e-07 MIIYR ALIS
1375 0 1.81e-07 MIIYR AEISH
1370 0 4.28e-07 MIIFR ILISHKK
1369 0 4.28e-07 MIIFR IAAYHKK
1368 0 4.28e-07 MIIFR IAATHKK
1367 0 4.28e-07 MIIFR IAASHKK
1366 0 4.28e-07 MIIFR DLISH
1365 0 4.28e-07 MIIFR ALISHKK
1364 0 4.28e-07 MIIFR AAASHKK
1374 0 5.16e-07 MIIYA RRAEE
1373 0 5.16e-07 MIIYA DLIS
1362 0 6.37e-07 MIIFA IAASHKK
1630 0 4.08e-06 WIIFR IAATHKK
1629 0 4.08e-06 WIIFR IAASHKK
1627 0 4.08e-06 WIIFR AAASHKK
1318 0 4.08e-06 LIIFR ILISHRR
1317 0 4.08e-06 LIIFR ILISHR
1316 0 4.08e-06 LIIFR ILISHKK
1315 0 4.08e-06 LIIFR ILISHK
1314 0 4.08e-06 LIIFR ILISHHH
1313 0 4.08e-06 LIIFR ILISH
1312 0 4.08e-06 LIIFR IAASHKK
1363 0 4.37e-06 MIIFK IAASHKK
1372 0 5.12e-06 MIISR DLISH
1079 0 5.75e-06 FIIFR IAASHKK
1360 0 6.73e-06 MIAYR DLIS
1352 0 6.73e-06 MAIYR DLIS
1361 0 8.56e-06 MIIAR DLIS
1021 0 1.04e-05 AIIYR DLIS
1371 0 1.33e-05 MIIRR DLISE

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1021 1.04e-05
1079 5.75e-06
1312 4.08e-06
1313 4.08e-06
1314 4.08e-06
1315 4.08e-06
1316 4.08e-06
1317 4.08e-06
1318 4.08e-06
1352 6.73e-06
1360 6.73e-06
1361 8.56e-06
1362 6.37e-07
1363 4.37e-06
1364 4.28e-07
1365 4.28e-07
1366 4.28e-07
1367 4.28e-07
1368 4.28e-07
1369 4.28e-07
1370 4.28e-07
1371 1.33e-05
1372 5.12e-06
1373 5.16e-07
1374 5.16e-07
1375 1.81e-07
1376 1.81e-07
1377 1.81e-07
1378 1.81e-07
1379 1.81e-07
1380 1.81e-07
1381 1.81e-07
1382 1.81e-07
1383 1.81e-07
1384 1.81e-07
1385 1.81e-07
1386 1.81e-07
1627 4.08e-06
1629 4.08e-06
1630 4.08e-06
 
0
2
4
6
8
10
12

Time 53.9 secs.

Motif 4

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Summary

Sequence Logo

E-value 6.1e-049
Width 5
Sites 37
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

MKWKK

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1625 6 1.74e-06 WFQNRR MKWKK
1514 11 1.74e-06 QIKIWFQNRR MKWKK TYADFIASGR
1513 11 1.74e-06 QIKIWFQNRR MKWKK DIMGEWGNEI
1512 11 1.74e-06 QIKIWFQNRR MKWKK
1501 11 1.74e-06 QIKIWFQNRA MKWKK
1498 11 1.74e-06 QIKIWFQNAR MKWKK
1496 11 1.74e-06 QIKIWFQARR MKWKK
1494 11 1.74e-06 QIKIWFPNRR MKWKK
1493 11 1.74e-06 QIKIWFANRR MKWKK
1492 11 1.74e-06 QIKIWAQNRR MKWKK
1491 11 1.74e-06 QIKIFFQNRR MKWKK
1489 11 1.74e-06 QIKIAFQNRR MKWKK
1488 11 1.74e-06 QIKAWFQNRR MKWKK
1487 11 1.74e-06 QIAIWFQNRR MKWKK
1483 11 1.74e-06 QAKIWFQNRR MKWKK
1437 11 1.74e-06 HIKIWFQNRR MKWKK
1431 11 1.74e-06 AIKIWFQNRR MKWKK
1422 4 1.74e-06 QNRR MKWKK
1420 10 1.74e-06 QIKIWFQNRR MKWKK
1399 3 1.74e-06 NRR MKWKK
1225 8 1.74e-06 KIWFQNRR MKWKK
1199 7 1.74e-06 IWFQNRR MKWKK
1195 9 1.74e-06 IKIWFQNRR MKWKK
1084 5 1.74e-06 FQNRR MKWKK
1043 12 1.74e-06 QIKIWFQNRR MKWKK
1042 12 1.74e-06 QIKIWFPNRR MKWKK C
1035 19 1.74e-06 QIKIWFANRR MKWKK EN
1031 11 1.74e-06 QIKIWFQNRR MKWKK
1020 19 1.74e-06 QIKIWFQNRR MKWKK EN
1019 19 1.74e-06 QIKIWFQNRR MKWKK EN
1490 11 3.00e-06 QIKIFFQNRR MKFKK
1511 11 1.30e-05 QIKIWFQNRR MKWKA
1509 11 1.30e-05 QIKIWFQNRR MKWAK
1505 11 1.30e-05 QIKIWFQNRR MAWKK
1561 53 2.88e-05 QIKIWFQNRR MKSKK DR
1507 11 5.97e-05 QIKIWFQNRR MKAKK
1319 17 5.97e-05 LIHIWFQNRR LKWKK K

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1019 1.74e-06
1020 1.74e-06
1031 1.74e-06
1035 1.74e-06
1042 1.74e-06
1043 1.74e-06
1084 1.74e-06
1195 1.74e-06
1199 1.74e-06
1225 1.74e-06
1319 5.97e-05
1399 1.74e-06
1420 1.74e-06
1422 1.74e-06
1431 1.74e-06
1437 1.74e-06
1483 1.74e-06
1487 1.74e-06
1488 1.74e-06
1489 1.74e-06
1490 3.00e-06
1491 1.74e-06
1492 1.74e-06
1493 1.74e-06
1494 1.74e-06
1496 1.74e-06
1498 1.74e-06
1501 1.74e-06
1505 1.30e-05
1507 5.97e-05
1509 1.30e-05
1511 1.30e-05
1512 1.74e-06
1513 1.74e-06
1514 1.74e-06
1561 2.88e-05
1625 1.74e-06
 
0
10
20
30
40
50
60

Time 71 secs.

Motif 5

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Summary

Sequence Logo

E-value 7.9e-037
Width 5
Sites 32
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

WRWK[CS]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1580 2 7.14e-07 SR WRWKC SKK
1579 2 7.14e-07 SR WRWKC CKK
1551 1 7.14e-07 R WRWKC CKK
1356 4 7.14e-07 MDCR WRWKC CKK
1297 2 7.14e-07 KR WRWKC CKK
1275 5 7.14e-07 KMDSR WRWKC SKK
1274 5 7.14e-07 KMDSR WRWKC CKK
1269 5 7.14e-07 KMDCR WRWKC SKK
1268 5 7.14e-07 KMDCR WRWKC KK
1267 5 7.14e-07 KMDCR WRWKC CKK
1215 4 7.14e-07 KDCR WRWKC CKK
1214 3 7.14e-07 KCR WRWKC CKK
1212 5 7.14e-07 KCGCR WRWKC GCKK
1057 3 7.14e-07 DCR WRWKC CKK
1048 2 7.14e-07 CR WRWKC SKK
1047 2 7.14e-07 CR WRWKC GCKK
1046 2 7.14e-07 CR WRWKC G
1045 2 7.14e-07 CR WRWKC CKK
1582 2 2.29e-06 SR WRWKS SKK
1581 2 2.29e-06 SR WRWKS CKK
1277 5 2.29e-06 KMDSR WRWKS SKK
1276 5 2.29e-06 KMDSR WRWKS CKK
1272 5 2.29e-06 KMDCR WRWKS SKK
1271 5 2.29e-06 KMDCR WRWKS CKK
1049 2 2.29e-06 CR WRWKS SKK
1041 2 2.81e-06 CR FRWKC CKK
1044 2 3.32e-06 CR WRFKC CKK
1206 4 4.24e-06 KCCK WRWRC K
1273 4 1.06e-05 KMDR WRWKK K
1270 5 1.06e-05 KMDCR WRWKK K
1266 5 1.96e-05 KMDCR WRPKC CKK
1040 2 5.27e-05 CR FRFKC CKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1040 5.27e-05
1041 2.81e-06
1044 3.32e-06
1045 7.14e-07
1046 7.14e-07
1047 7.14e-07
1048 7.14e-07
1049 2.29e-06
1057 7.14e-07
1206 4.24e-06
1212 7.14e-07
1214 7.14e-07
1215 7.14e-07
1266 1.96e-05
1267 7.14e-07
1268 7.14e-07
1269 7.14e-07
1270 1.06e-05
1271 2.29e-06
1272 2.29e-06
1273 1.06e-05
1274 7.14e-07
1275 7.14e-07
1276 2.29e-06
1277 2.29e-06
1297 7.14e-07
1356 7.14e-07
1551 7.14e-07
1579 7.14e-07
1580 7.14e-07
1581 2.29e-06
1582 2.29e-06
 
0
2
4
6
8
10
12
14

Time 87.3 secs.

Motif 6

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Summary

Sequence Logo

E-value 9.0e-037
Width 5
Sites 32
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

H[AC][HR]SK

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1339 13 3.54e-07 ILRRRIRKQA HAHSK
1334 13 3.54e-07 ILRRRIRKAA HAHSK
1333 13 3.54e-07 ILRRRIRAQA HAHSK
1332 14 3.54e-07 LRRRIARKQA HAHSK
1331 13 3.54e-07 ILRRRARKQA HAHSK
1330 13 3.54e-07 ILRRAIRKQA HAHSK
1329 13 3.54e-07 ILRARIRKQA HAHSK
1328 13 3.54e-07 ILARRIRKQA HAHSK
1327 13 3.54e-07 IARRRIRKQA HAHSK
1326 13 3.54e-07 ALRRRIRKQA HAHSK
1322 13 3.54e-07 ILRRRIRKQA HAHSK
1304 13 3.54e-07 ILRRRIRKQA HAHSK
1196 10 3.54e-07 ILRRRIRKQA HAHSK
1025 13 3.54e-07 ILRRRIRKQA HAHSK
1001 13 3.54e-07 AARRRIRKQA HAHSK
1577 4 1.11e-06 SRRH HCRSK AKRSAHH
1576 4 1.11e-06 SRRH HCRSK AKRARHH
1575 4 1.11e-06 SRRH HCRSK AKASRHH
1574 4 1.11e-06 SRRH HCRSK AARSRHH
1567 4 1.11e-06 SRRA HCRSK AKRSRHH
1566 4 1.11e-06 SRAH HCRSK AKRSRHH
1553 4 1.11e-06 SARH HCRSK AKRSRHH
1519 3 1.11e-06 RRH HCRSK AKRSR
1161 4 1.11e-06 GRRH HCRSK AKRSRHH
1571 4 3.79e-06 SRRH HARSK AKRSRHH
1337 13 4.51e-06 ILRRRIRKQA HAHAK
1338 13 5.62e-06 ILRRRIRKQA HAHSA
1586 6 7.61e-06 SWWTPW HVHSE S
1336 13 7.61e-06 ILRRRIRKQA HAASK
1185 3 7.72e-06 HHH HHHTK RRITPKDVID
1335 13 1.08e-05 ILRRRIRKQA AAHSK
1298 2 3.30e-05 KS HAHAQ KRIRRRLIIL

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1001 3.54e-07
1025 3.54e-07
1161 1.11e-06
1185 7.72e-06
1196 3.54e-07
1298 3.30e-05
1304 3.54e-07
1322 3.54e-07
1326 3.54e-07
1327 3.54e-07
1328 3.54e-07
1329 3.54e-07
1330 3.54e-07
1331 3.54e-07
1332 3.54e-07
1333 3.54e-07
1334 3.54e-07
1335 1.08e-05
1336 7.61e-06
1337 4.51e-06
1338 5.62e-06
1339 3.54e-07
1519 1.11e-06
1553 1.11e-06
1566 1.11e-06
1567 1.11e-06
1571 3.79e-06
1574 1.11e-06
1575 1.11e-06
1576 1.11e-06
1577 1.11e-06
1586 7.61e-06
 
0
5
10
15
20
25

Time 103.2 secs.

Motif 7

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Summary

Sequence Logo

E-value 5.3e-025
Width 5
Sites 19
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

LWMRW

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1479 1 4.08e-07 R LWMRW YSPWTRRYG
1478 1 4.08e-07 R LWMRW YSPWTRRWG
1477 1 4.08e-07 R LWMRW YSPTTRRYG
1476 1 4.08e-07 R LWMRW YSPTTRRYA
1475 1 4.08e-07 R LWMRW YSPTTRRAG
1474 1 4.08e-07 R LWMRW YSPTTRAYG
1473 1 4.08e-07 R LWMRW YSPTTARYG
1472 1 4.08e-07 R LWMRW YSPTARRYG
1471 1 4.08e-07 R LWMRW YSPATRRYG
1470 1 4.08e-07 R LWMRW YAPTTRRYG
1469 1 4.08e-07 R LWMRW ASPTTRRYG
1263 1 4.08e-07 K LWMRW YSPWTRRYG
1262 1 4.08e-07 K LWMRW YSPTTRRYG
1261 1 4.08e-07 K LWMRW YSATTRRYG
1028 1 4.08e-07 A LWMRW YSPTTRRYG
1433 1 1.11e-06 R AWMRW YSPTTRRYG
1467 1 1.36e-06 R LWMAW YSPTTRRYG
1468 1 1.10e-05 R LWMRA YSPTTRRYG
1459 1 1.10e-05 R LAMRW YSPTTRRYG

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1028 4.08e-07
1261 4.08e-07
1262 4.08e-07
1263 4.08e-07
1433 1.11e-06
1459 1.10e-05
1467 1.36e-06
1468 1.10e-05
1469 4.08e-07
1470 4.08e-07
1471 4.08e-07
1472 4.08e-07
1473 4.08e-07
1474 4.08e-07
1475 4.08e-07
1476 4.08e-07
1477 4.08e-07
1478 4.08e-07
1479 4.08e-07
 
0
2
4
6
8
10
12
14

Time 118 secs.

Motif 8

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Summary

Sequence Logo

E-value 3.1e-024
Width 4
Sites 31
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

D[LV]I[SDA]

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1596 8 4.69e-07 TKRRITPK DVID VRSVTTKINT
1595 8 4.69e-07 TKRRITPK DVID VRSVTTEINT
1594 8 4.69e-07 TKRRITPK DVID VESVTTEINT
1593 8 4.69e-07 TKRRITPK DVID V
1592 8 4.69e-07 TKRRITPD DVID VRSVTTEINT
1591 9 4.69e-07 TKAARITPK DVID VRSVTTEINT
1589 8 4.69e-07 TARRITPK DVID VRSVTTEINT
1185 14 4.69e-07 HHTKRRITPK DVID VRSVTTEINT
1419 5 7.36e-06 QIISR DLIS H
1385 5 7.36e-06 MIIYR DLIS KK
1384 5 7.36e-06 MIIYR DLIS H
1383 5 7.36e-06 MIIYR DLIS
1373 5 7.36e-06 MIIYA DLIS
1372 5 7.36e-06 MIISR DLIS H
1371 5 7.36e-06 MIIRR DLIS E
1366 5 7.36e-06 MIIFR DLIS H
1361 5 7.36e-06 MIIAR DLIS
1360 5 7.36e-06 MIAYR DLIS
1352 5 7.36e-06 MAIYR DLIS
1200 3 7.36e-06 IYR DLIS H
1194 4 7.36e-06 IIYR DLIS H
1039 5 7.36e-06 CIISR DLIS H
1021 5 7.36e-06 AIIYR DLIS
1382 5 1.92e-05 MIIYR DLIA
1229 7 1.92e-05 KKKEERA DLIA YLKKA
1170 16 1.92e-05 VGIKKKEERA DLIA YLKKA
1536 14 2.15e-05 RRRRRRRTYA DFIA SGRTGRRNAI
1514 19 2.15e-05 RRMKWKKTYA DFIA SGRTGRRNAI
1149 16 2.15e-05 QRRRPPQTYA DFIA SGRTGRRNAI
1017 24 2.15e-05 ALAKKILTYA DFIA SGRTGRRNAI
1378 5 2.71e-05 MIIYR DAIS

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1017 2.15e-05
1021 7.36e-06
1039 7.36e-06
1149 2.15e-05
1170 1.92e-05
1185 4.69e-07
1194 7.36e-06
1200 7.36e-06
1229 1.92e-05
1352 7.36e-06
1360 7.36e-06
1361 7.36e-06
1366 7.36e-06
1371 7.36e-06
1372 7.36e-06
1373 7.36e-06
1378 2.71e-05
1382 1.92e-05
1383 7.36e-06
1384 7.36e-06
1385 7.36e-06
1419 7.36e-06
1514 2.15e-05
1536 2.15e-05
1589 4.69e-07
1591 4.69e-07
1592 4.69e-07
1593 4.69e-07
1594 4.69e-07
1595 4.69e-07
1596 4.69e-07
 
0
5
10
15
20
25
30
35

Time 133.8 secs.

Motif 9

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Summary

Sequence Logo

E-value 1.5e-022
Width 5
Sites 15
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GYLLG

Further Analysis

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Data Formats

View the motif in PSPM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1346 4 3.78e-07 LNSA GYLLG KLKALAALAK
1345 4 3.78e-07 LNSA GYLLG KLKALAALAK
1344 4 3.78e-07 LNSA GYLLG KINLKALAAL
1343 4 3.78e-07 LNSA GYLLG KALAALAKKI
1178 7 3.78e-07 GWTLNSA GYLLG PHAVGNHRSF
1177 7 3.78e-07 GWTLNSA GYLLG KLKALAALAK
1176 7 3.78e-07 GWTLNSA GYLLG KINLKAPAAL
1175 7 3.78e-07 GWTLNSA GYLLG KINLKALAAL
1174 7 3.78e-07 GWTLNSA GYLLG KINLKALAAL
1173 7 3.78e-07 GWTLNSA GYLLG KFLPLILRKI
1172 7 3.78e-07 GWTLNPP GYLLG KINLKALAAL
1171 7 3.78e-07 GWTLNPA GYLLG KINLKALAAL
1018 1 3.78e-07 A GYLLG KLKALAALAK
1017 1 3.78e-07 A GYLLG KINLKALAAL
1016 1 3.78e-07 A GYLLG KINLKALAAL

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1016 3.78e-07
1017 3.78e-07
1018 3.78e-07
1171 3.78e-07
1172 3.78e-07
1173 3.78e-07
1174 3.78e-07
1175 3.78e-07
1176 3.78e-07
1177 3.78e-07
1178 3.78e-07
1343 3.78e-07
1344 3.78e-07
1345 3.78e-07
1346 3.78e-07
 
0
5
10
15
20
25
30
35

Time 149.3 secs.

Motif 10

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Summary

Sequence Logo

E-value 1.1e-020
Width 5
Sites 23
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

I[AL][AI]SH

Further Analysis

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Data Formats

View the motif in PSPM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1629 5 4.29e-07 WIIFR IAASH KK
1626 5 4.29e-07 WIIFK IAASH KK
1386 5 4.29e-07 MIIYR IAASH KK
1367 5 4.29e-07 MIIFR IAASH KK
1363 5 4.29e-07 MIIFK IAASH KK
1362 5 4.29e-07 MIIFA IAASH KK
1312 5 4.29e-07 LIIFR IAASH KK
1310 5 4.29e-07 LIIFA IAASH KK
1079 5 4.29e-07 FIIFR IAASH KK
1370 5 1.44e-06 MIIFR ILISH KK
1318 5 1.44e-06 LIIFR ILISH RR
1317 5 1.44e-06 LIIFR ILISH R
1316 5 1.44e-06 LIIFR ILISH KK
1315 5 1.44e-06 LIIFR ILISH K
1314 5 1.44e-06 LIIFR ILISH HH
1313 5 1.44e-06 LIIFR ILISH
1311 5 1.44e-06 LIIFA ILISH KK
1630 5 1.81e-06 WIIFR IAATH KK
1368 5 1.81e-06 MIIFR IAATH KK
1631 5 2.23e-06 WIIFR IAAYH KK
1369 5 2.23e-06 MIIFR IAAYH KK
1627 5 3.81e-06 WIIFR AAASH KK
1364 5 3.81e-06 MIIFR AAASH KK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1079 4.29e-07
1310 4.29e-07
1311 1.44e-06
1312 4.29e-07
1313 1.44e-06
1314 1.44e-06
1315 1.44e-06
1316 1.44e-06
1317 1.44e-06
1318 1.44e-06
1362 4.29e-07
1363 4.29e-07
1364 3.81e-06
1367 4.29e-07
1368 1.81e-06
1369 2.23e-06
1370 1.44e-06
1386 4.29e-07
1626 4.29e-07
1627 3.81e-06
1629 4.29e-07
1630 1.81e-06
1631 2.23e-06
 
0
2
4
6
8
10
12

Time 164.5 secs.

Motif 11

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Summary

Sequence Logo

E-value 3.2e-017
Width 5
Sites 10
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

SVTTE

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1597 14 3.43e-08 ITPKKVIDVR SVTTE INT
1595 14 3.43e-08 ITPKDVIDVR SVTTE INT
1594 14 3.43e-08 ITPKDVIDVE SVTTE INT
1592 14 3.43e-08 ITPDDVIDVR SVTTE INT
1591 15 3.43e-08 ITPKDVIDVR SVTTE INT
1589 14 3.43e-08 ITPKDVIDVR SVTTE INT
1540 1 3.43e-08 R SVTTE INTLFQTLTS
1185 20 3.43e-08 ITPKDVIDVR SVTTE INT
1094 17 4.07e-07 APDLFDFLDS SVTTA RTINA
1596 14 7.24e-07 ITPKDVIDVR SVTTK INT

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1094 4.07e-07
1185 3.43e-08
1540 3.43e-08
1589 3.43e-08
1591 3.43e-08
1592 3.43e-08
1594 3.43e-08
1595 3.43e-08
1596 7.24e-07
1597 3.43e-08
 
0
5
10
15
20
25

Time 179.7 secs.

Motif 12

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Summary

Sequence Logo

E-value 1.9e-020
Width 5
Sites 17
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

K[MA]D[CS][RD]

Further Analysis

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Data Formats

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     PSSM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1272 0 1.72e-07 KMDCR WRWKSSKK
1271 0 1.72e-07 KMDCR WRWKSCKK
1270 0 1.72e-07 KMDCR WRWKKK
1269 0 1.72e-07 KMDCR WRWKCSKK
1268 0 1.72e-07 KMDCR WRWKCKK
1267 0 1.72e-07 KMDCR WRWKCCKK
1266 0 1.72e-07 KMDCR WRPKCCKK
1265 0 1.72e-07 KMDCR PRPKCCKK
1255 12 2.85e-07 IKGRTPIKFG KADCD RPPKHSQNGM
1254 12 2.85e-07 IKGRTPIKFG KADCD RPPKHSQNGM
1253 12 2.85e-07 IKGRTPIKFG KADCD RPPKHSQNGK
1252 12 2.85e-07 IKGRTPIKFG KADCD RPPKHSGK
1221 9 2.85e-07 KGRTPIKFG KADCD RPPKHSQNGM
1277 0 6.30e-07 KMDSR WRWKSSKK
1276 0 6.30e-07 KMDSR WRWKSCKK
1275 0 6.30e-07 KMDSR WRWKCSKK
1274 0 6.30e-07 KMDSR WRWKCCKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1221 2.85e-07
1252 2.85e-07
1253 2.85e-07
1254 2.85e-07
1255 2.85e-07
1265 1.72e-07
1266 1.72e-07
1267 1.72e-07
1268 1.72e-07
1269 1.72e-07
1270 1.72e-07
1271 1.72e-07
1272 1.72e-07
1274 6.30e-07
1275 6.30e-07
1276 6.30e-07
1277 6.30e-07
 
0
5
10
15
20
25

Time 194.5 secs.

Motif 13

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Summary

Sequence Logo

E-value 2.0e-016
Width 5
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

LA[LA]LA

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1634 14 6.26e-06 AAVALLPAVL LALLA P
1455 23 6.26e-06 AAVALLPAVL LALLA P
1205 8 6.26e-06 KALKLKLA LALLA KLKLA
1013 10 6.26e-06 AAVALLPAVL LALLA VTDQLGEDFF
1012 10 6.26e-06 AAVALLPAVL LALLA PVQRKRQKLM
1011 10 6.26e-06 AAVALLPAVL LALLA PSGASGLDKR
1010 10 6.26e-06 AAVALLPAVL LALLA PRRRRRR
1009 10 6.26e-06 AAVALLPAVL LALLA PRKKRRQRRR
1008 10 6.26e-06 AAVALLPAVL LALLA PRKKRRQRRR
1007 10 6.26e-06 AAVALLPAVL LALLA PEILLPNNYN
1006 10 6.26e-06 AAVALLPAVL LALLA P
1005 10 6.26e-06 AAVALLPAVL LALLA KKNNLKECGL
1004 10 6.26e-06 AAVALLPAVL LALLA KKNNLKDCGL
1003 10 6.26e-06 AAVALLPAVL LALLA K
1346 13 1.21e-05 AGYLLGKLKA LAALA KIL
1345 13 1.21e-05 AGYLLGKLKA LAALA K
1344 15 1.21e-05 YLLGKINLKA LAALA KKIL
1343 11 1.21e-05 NSAGYLLGKA LAALA KKIL
1325 9 1.21e-05 LLGKINLKA LAALA KKIL
1197 5 1.21e-05 INLKA LAALA KKIL
1179 12 1.21e-05 TLNSKINLKA LAALA KKIL
1177 16 1.21e-05 AGYLLGKLKA LAALA KKIL
1175 18 1.21e-05 YLLGKINLKA LAALA KKLL
1174 18 1.21e-05 YLLGKINLKA LAALA KKIL
1172 18 1.21e-05 YLLGKINLKA LAALA KKIL
1171 18 1.21e-05 YLLGKINLKA LAALA KKIL
1104 7 1.21e-05 GKINLKA LAALA KKIL
1018 10 1.21e-05 AGYLLGKLKA LAALA KKIL
1017 12 1.21e-05 YLLGKINLKA LAALA KKILTYADFI
1016 12 1.21e-05 YLLGKINLKA LAALA KKIL
1090 4 1.39e-05 GALF LAFLA AALSLMGLWS
1421 5 1.61e-05 QLALQ LALQA LQAALQLA
1249 5 1.61e-05 KLALQ LALQA LQAALQLA
1072 5 1.74e-05 ELALE LALEA LEAALELA
1598 5 3.29e-05 TLPSP LALLT VH
1032 12 4.03e-05 TINAQQAELD SALLA AAGFGNTTAD
1243 5 5.53e-05 KLALK LALKA LKAALK
1242 5 5.53e-05 KLALK LALKA LKAA
1241 1 5.53e-05 K LALKA LKAALKLA
1354 8 1.05e-04 MANLGYWL LALFV TMWTDVGLCK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1003 6.26e-06
1004 6.26e-06
1005 6.26e-06
1006 6.26e-06
1007 6.26e-06
1008 6.26e-06
1009 6.26e-06
1010 6.26e-06
1011 6.26e-06
1012 6.26e-06
1013 6.26e-06
1016 1.21e-05
1017 1.21e-05
1018 1.21e-05
1032 4.03e-05
1072 1.74e-05
1090 1.39e-05
1104 1.21e-05
1171 1.21e-05
1172 1.21e-05
1174 1.21e-05
1175 1.21e-05
1177 1.21e-05
1179 1.21e-05
1197 1.21e-05
1205 6.26e-06
1241 5.53e-05
1242 5.53e-05
1243 5.53e-05
1249 1.61e-05
1325 1.21e-05
1343 1.21e-05
1344 1.21e-05
1345 1.21e-05
1346 1.21e-05
1354 1.05e-04
1421 1.61e-05
1455 6.26e-06
1598 3.29e-05
1634 6.26e-06
 
0
5
10
15
20
25
30
35
40

Time 210.2 secs.

Motif 14

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Summary

Sequence Logo

E-value 2.8e-012
Width 4
Sites 33
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

RQIK

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1561 42 4.44e-05 DIANALSLSE RQIK IWFQNRRMKS
1514 0 4.44e-05 RQIK IWFQNRRMKW
1513 0 4.44e-05 RQIK IWFQNRRMKW
1512 0 4.44e-05 RQIK IWFQNRRMKW
1511 0 4.44e-05 RQIK IWFQNRRMKW
1510 0 4.44e-05 RQIK IWFQNRRMKW
1509 0 4.44e-05 RQIK IWFQNRRMKW
1508 0 4.44e-05 RQIK IWFQNRRMKW
1507 0 4.44e-05 RQIK IWFQNRRMKA
1506 0 4.44e-05 RQIK IWFQNRRMK
1505 0 4.44e-05 RQIK IWFQNRRMAW
1504 0 4.44e-05 RQIK IWFQNRRM
1503 0 4.44e-05 RQIK IWFQNRRAKW
1502 0 4.44e-05 RQIK IWFQNRR
1501 0 4.44e-05 RQIK IWFQNRAMKW
1500 0 4.44e-05 RQIK IWFQNR
1499 0 4.44e-05 RQIK IWFQNMRRKW
1498 0 4.44e-05 RQIK IWFQNARMKW
1497 0 4.44e-05 RQIK IWFQN
1496 0 4.44e-05 RQIK IWFQARRMKW
1495 0 4.44e-05 RQIK IWFQ
1494 0 4.44e-05 RQIK IWFPNRRMKW
1493 0 4.44e-05 RQIK IWFANRRMKW
1492 0 4.44e-05 RQIK IWAQNRRMKW
1491 0 4.44e-05 RQIK IFFQNRRMKW
1490 0 4.44e-05 RQIK IFFQNRRMKF
1489 0 4.44e-05 RQIK IAFQNRRMKW
1488 0 4.44e-05 RQIK AWFQNRRMKW
1043 1 4.44e-05 C RQIK IWFQNRRMKW
1042 1 4.44e-05 C RQIK IWFPNRRMKW
1035 8 4.44e-05 AYALCLTE RQIK IWFANRRMKW
1020 8 4.44e-05 AHALCPPE RQIK IWFQNRRMKW
1019 8 4.44e-05 AHALCLTE RQIK IWFQNRRMKW

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1019 4.44e-05
1020 4.44e-05
1035 4.44e-05
1042 4.44e-05
1043 4.44e-05
1488 4.44e-05
1489 4.44e-05
1490 4.44e-05
1491 4.44e-05
1492 4.44e-05
1493 4.44e-05
1494 4.44e-05
1495 4.44e-05
1496 4.44e-05
1497 4.44e-05
1498 4.44e-05
1499 4.44e-05
1500 4.44e-05
1501 4.44e-05
1502 4.44e-05
1503 4.44e-05
1504 4.44e-05
1505 4.44e-05
1506 4.44e-05
1507 4.44e-05
1508 4.44e-05
1509 4.44e-05
1510 4.44e-05
1511 4.44e-05
1512 4.44e-05
1513 4.44e-05
1514 4.44e-05
1561 4.44e-05
 
0
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40
50
60

Time 224.5 secs.

Motif 15

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Summary

Sequence Logo

E-value 5.8e-012
Width 5
Sites 9
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GWTLN

Further Analysis

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Data Formats

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     PSSM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1179 0 1.51e-07 GWTLN SKINLKALAA
1178 0 1.51e-07 GWTLN SAGYLLGPHA
1177 0 1.51e-07 GWTLN SAGYLLGKLK
1176 0 1.51e-07 GWTLN SAGYLLGKIN
1175 0 1.51e-07 GWTLN SAGYLLGKIN
1174 0 1.51e-07 GWTLN SAGYLLGKIN
1173 0 1.51e-07 GWTLN SAGYLLGKFL
1172 0 1.51e-07 GWTLN PPGYLLGKIN
1171 0 1.51e-07 GWTLN PAGYLLGKIN

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1171 1.51e-07
1172 1.51e-07
1173 1.51e-07
1174 1.51e-07
1175 1.51e-07
1176 1.51e-07
1177 1.51e-07
1178 1.51e-07
1179 1.51e-07
 
0
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25
30

Time 239.6 secs.

Motif 16

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Summary

Sequence Logo

E-value 3.4e-010
Width 5
Sites 15
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

LPAVL

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1634 9 1.07e-06 WRFKAAVAL LPAVL LALLAP
1455 18 1.07e-06 RPPQCAAVAL LPAVL LALLAP
1013 5 1.07e-06 AAVAL LPAVL LALLAVTDQL
1012 5 1.07e-06 AAVAL LPAVL LALLAPVQRK
1011 5 1.07e-06 AAVAL LPAVL LALLAPSGAS
1010 5 1.07e-06 AAVAL LPAVL LALLAPRRRR
1009 5 1.07e-06 AAVAL LPAVL LALLAPRKKR
1008 5 1.07e-06 AAVAL LPAVL LALLAPRKKR
1007 5 1.07e-06 AAVAL LPAVL LALLAPEILL
1006 5 1.07e-06 AAVAL LPAVL LALLAP
1005 5 1.07e-06 AAVAL LPAVL LALLAKKNNL
1004 5 1.07e-06 AAVAL LPAVL LALLAKKNNL
1003 5 1.07e-06 AAVAL LPAVL LALLAK
1584 7 2.19e-06 SWAQHLS LPPVL
1029 18 2.19e-06 KVLKAAAKAA LNAVL VGANA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1003 1.07e-06
1004 1.07e-06
1005 1.07e-06
1006 1.07e-06
1007 1.07e-06
1008 1.07e-06
1009 1.07e-06
1010 1.07e-06
1011 1.07e-06
1012 1.07e-06
1013 1.07e-06
1029 2.19e-06
1455 1.07e-06
1584 2.19e-06
1634 1.07e-06
 
0
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25
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35
40

Time 253.9 secs.

Motif 17

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Summary

Sequence Logo

E-value 4.2e-009
Width 5
Sites 5
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

DSDCP

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1101 13 1.50e-08 CPKILKKCRR DSDCP GACICRGNGY
1100 13 1.50e-08 CPKILKACRR DSDCP GACICRGNGY
1099 13 1.50e-08 CPKILAKCRR DSDCP GACICRGNGY
1098 13 1.50e-08 CPKILAACRR DSDCP GACICRGNGY
1097 13 1.50e-08 CPAILKKCRR DSDCP GACICRGNGY

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1097 1.50e-08
1098 1.50e-08
1099 1.50e-08
1100 1.50e-08
1101 1.50e-08
 
0
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25
30

Time 267.5 secs.

Motif 18

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Summary

Sequence Logo

E-value 1.1e-006
Width 5
Sites 5
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

CF[QM]WQ

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1211 1 2.22e-08 K CFQWQ RNMRKVRGPP
1210 1 2.22e-08 K CFQWQ RNMRKVRGPP
1209 1 2.22e-08 K CFQWQ RNMRKVRGPP
1208 1 2.22e-08 K CFQWQ RNMRKVR
1207 1 4.65e-08 K CFMWQ EMLNKAGVPK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1207 4.65e-08
1208 2.22e-08
1209 2.22e-08
1210 2.22e-08
1211 2.22e-08
 
0
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20

Time 281.1 secs.

Motif 19

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Summary

Sequence Logo

E-value 5.9e-008
Width 5
Sites 5
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GNGYC

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1101 24 2.09e-08 SDCPGACICR GNGYC GSGSD
1100 24 2.09e-08 SDCPGACICR GNGYC GSGSD
1099 24 2.09e-08 SDCPGACICR GNGYC GSGSD
1098 24 2.09e-08 SDCPGACICR GNGYC GSGSD
1097 24 2.09e-08 SDCPGACICR GNGYC GSGSD

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1097 2.09e-08
1098 2.09e-08
1099 2.09e-08
1100 2.09e-08
1101 2.09e-08
 
0
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25
30

Time 295.6 secs.

Motif 20

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Summary

Sequence Logo

E-value 1.4e-005
Width 5
Sites 28
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

KKRRQ

Further Analysis

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 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1646 3 2.03e-05 YGR KKRRQ RRR
1645 4 2.03e-05 YGRK KKRRQ RRR
1455 1 2.03e-05 R KKRRQ RRRPPQCAAV
1454 1 2.03e-05 R KKRRQ RRR
1453 1 2.03e-05 R KKRRQ RRA
1452 1 2.03e-05 R KKRRQ RR
1451 1 2.03e-05 R KKRRQ RAR
1450 1 2.03e-05 R KKRRQ ARR
1307 7 2.03e-05 LGISYGR KKRRQ RRRPPQ
1235 0 2.03e-05 KKRRQ RRR
1217 17 2.03e-05 WWTEWSQPGR KKRRQ RRRPPQ
1182 4 2.03e-05 GYGR KKRRQ RRRG
1150 2 2.03e-05 GR KKRRQ RRRPWQ
1149 2 2.03e-05 GR KKRRQ RRRPPQTYAD
1147 2 2.03e-05 GR KKRRQ RRRPPQC
1146 2 2.03e-05 GR KKRRQ RRRPPQ
1145 2 2.03e-05 GR KKRRQ RRRPP
1144 2 2.03e-05 GR KKRRQ RRRC
1143 2 2.03e-05 GR KKRRQ RRR
1142 2 2.03e-05 GR KKRRQ RRPPQC
1141 2 2.03e-05 GR KKRRQ RPPQC
1140 2 2.03e-05 GR KKRRQ RARPPQC
1139 2 2.03e-05 GR KKRRQ PPQC
1138 2 2.03e-05 GR KKRRQ ARAPPQC
1081 12 2.03e-05 TKALGISYGR KKRRQ RRRPPQ
1023 1 2.03e-05 A KKRRQ RRR
1009 17 2.03e-05 AVLLALLAPR KKRRQ RRRPPQC
1008 17 2.03e-05 AVLLALLAPR KKRRQ RRRPPQ

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1008 2.03e-05
1009 2.03e-05
1023 2.03e-05
1081 2.03e-05
1138 2.03e-05
1139 2.03e-05
1140 2.03e-05
1141 2.03e-05
1142 2.03e-05
1143 2.03e-05
1144 2.03e-05
1145 2.03e-05
1146 2.03e-05
1147 2.03e-05
1149 2.03e-05
1150 2.03e-05
1182 2.03e-05
1217 2.03e-05
1235 2.03e-05
1307 2.03e-05
1450 2.03e-05
1451 2.03e-05
1452 2.03e-05
1453 2.03e-05
1454 2.03e-05
1455 2.03e-05
1645 2.03e-05
1646 2.03e-05
 
0
5
10
15
20
25
30

Time 310 secs.

All Motifs

Top

Combined Block Diagrams

Non-overlapping sites with a p-value better than 0.0001.
The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. The motif blocks have tool tips with more information.

Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Name Combined p-value Motif Location
1001 2.79e-02
1003 5.17e-03
1004 2.34e-03
1005 9.23e-03
1006 5.34e-03
1007 4.73e-04
1008 1.66e-03
1009 1.84e-03
1010 2.06e-02
1011 1.31e-02
1012 1.97e-02
1013 8.45e-04
1016 3.43e-03
1017 4.83e-05
1018 1.98e-03
1019 1.24e-06
1020 9.69e-07
1021 1.09e-03
1023 9.47e-01
1025 2.51e-02
1028 8.77e-06
1029 7.03e-03
1031 2.72e-05
1032 2.49e-05
1035 1.62e-06
1039 6.37e-04
1040 6.48e-01
1041 2.31e-01
1042 8.75e-05
1043 1.22e-05
1044 5.14e-01
1045 4.29e-01
1046 2.44e-01
1047 1.53e-01
1048 3.46e-01
1049 4.92e-01
1052 5.83e-02
1057 3.80e-01
1071 2.29e-04
1072 2.79e-01
1079 1.68e-04
1081 1.37e-01
1084 1.68e-01
1090 6.02e-03
1094 4.45e-06
1097 3.14e-07
1098 5.87e-07
1099 1.03e-06
1100 7.72e-06
1101 3.23e-06
1104 2.69e-01
1138 4.37e-01
1139 7.77e-01
1140 9.46e-01
1141 9.33e-01
1142 9.44e-01
1143 9.50e-01
1144 8.85e-01
1145 9.76e-01
1146 9.83e-01
1147 9.64e-01
1148 1.00e+00
1149 2.40e-02
1150 9.30e-01
1161 3.83e-01
1170 3.77e-02
1171 6.49e-06
1172 8.06e-06
1173 9.40e-06
1174 8.57e-07
1175 8.57e-07
1176 3.57e-06
1177 2.81e-07
1178 1.49e-05
1179 1.10e-04
1180 2.37e-02
1182 5.61e-01
1184 1.75e-02
1185 1.40e-06
1194 3.71e-03
1195 9.83e-05
1196 1.42e-01
1197 1.81e-01
1199 3.37e-05
1200 2.55e-03
1205 4.01e-01
1206 3.44e-01
1207 9.32e-02
1208 8.37e-02
1209 2.60e-02
1210 1.44e-02
1211 1.14e-02
1212 1.50e-01
1214 4.38e-01
1215 3.81e-01
1217 5.65e-01
1221 5.48e-03
1224 5.97e-01
1225 6.43e-05
1229 1.90e-02
1235 9.32e-01
1239 5.17e-01
1240 3.56e-01
1241 4.96e-01
1242 8.23e-01
1243 6.80e-01
1244 7.75e-01
1245 7.39e-01
1246 3.45e-01
1247 8.52e-01
1248 4.18e-01
1249 2.91e-01
1252 8.63e-03
1253 3.49e-03
1254 4.38e-03
1255 5.84e-03
1257 6.42e-01
1261 1.09e-06
1262 6.73e-06
1263 1.17e-04
1265 5.90e-02
1266 3.35e-03
1267 4.48e-04
1268 1.79e-04
1269 4.43e-04
1270 1.77e-04
1271 7.68e-04
1272 8.34e-04
1273 1.17e-01
1274 1.72e-03
1275 1.62e-03
1276 3.10e-03
1277 2.81e-03
1297 4.20e-01
1298 2.29e-01
1304 7.51e-03
1307 5.71e-02
1310 2.14e-05
1311 1.86e-05
1312 1.39e-04
1313 4.99e-04
1314 7.13e-04
1315 6.95e-04
1316 3.02e-04
1317 1.16e-03
1318 1.57e-03
1319 4.15e-04
1322 4.29e-03
1325 3.35e-01
1326 9.22e-03
1327 6.88e-03
1328 5.32e-03
1329 1.39e-02
1330 1.04e-02
1331 2.39e-02
1332 3.17e-02
1333 6.93e-03
1334 5.01e-03
1335 7.49e-03
1336 2.98e-02
1337 3.85e-02
1338 2.35e-02
1339 1.09e-02
1343 2.83e-04
1344 7.71e-04
1345 1.27e-04
1346 2.61e-04
1350 4.88e-03
1352 1.73e-04
1356 2.49e-01
1360 1.78e-04
1361 1.49e-03
1362 3.34e-06
1363 1.74e-04
1364 6.57e-05
1365 5.77e-05
1366 5.58e-06
1367 3.86e-05
1368 2.78e-05
1369 1.81e-04
1370 9.45e-05
1371 5.20e-04
1372 5.88e-05
1373 1.02e-06
1374 2.86e-02
1375 3.46e-04
1376 2.02e-03
1377 7.51e-05
1378 1.70e-04
1379 4.69e-03
1380 7.02e-04
1381 4.96e-03
1382 1.57e-04
1383 1.39e-04
1384 8.70e-06
1385 1.21e-04
1386 2.37e-05
1399 1.59e-01
1410 7.75e-01
1419 1.21e-03
1420 1.77e-04
1421 3.51e-01
1422 1.25e-01
1431 4.40e-05
1433 9.39e-06
1437 4.28e-05
1450 9.04e-01
1451 9.39e-01
1452 9.32e-01
1453 9.57e-01
1454 9.60e-01
1455 8.38e-04
1459 1.65e-05
1460 9.28e-05
1461 1.32e-04
1462 8.39e-04
1465 1.10e-04
1466 8.01e-04
1467 4.16e-06
1468 3.58e-05
1469 4.35e-05
1470 1.76e-04
1471 9.98e-05
1472 2.05e-04
1473 1.24e-06
1474 7.15e-06
1475 1.07e-05
1476 8.82e-06
1477 9.36e-06
1478 1.85e-04
1479 1.71e-04
1480 9.16e-01
1481 5.60e-04
1483 5.48e-05
1487 6.43e-07
1488 7.75e-06
1489 4.69e-06
1490 4.46e-05
1491 6.97e-06
1492 1.30e-04
1493 4.19e-05
1494 1.02e-04
1495 5.77e-01
1496 2.48e-04
1497 6.80e-04
1498 1.26e-07
1499 1.75e-04
1500 7.05e-04
1501 2.55e-06
1502 1.56e-03
1503 1.52e-04
1504 2.21e-03
1505 2.48e-05
1506 2.54e-03
1507 1.29e-04
1508 3.09e-03
1509 6.64e-05
1510 4.88e-03
1511 3.56e-05
1512 7.64e-06
1513 6.68e-07
1514 1.27e-08
1515 3.14e-04
1517 9.08e-02
1519 2.61e-01
1536 2.54e-01
1540 6.59e-04
1543 1.19e-03
1544 1.51e-02
1545 2.97e-02
1551 4.24e-01
1553 1.74e-01
1561 2.07e-04
1566 2.26e-01
1567 1.73e-01
1570 8.08e-01
1571 8.18e-01
1572 6.27e-01
1573 4.52e-01
1574 2.64e-01
1575 1.22e-01
1576 3.52e-01
1577 2.86e-01
1579 4.29e-01
1580 3.46e-01
1581 5.18e-01
1582 4.92e-01
1584 4.95e-02
1586 1.18e-02
1589 2.46e-05
1591 3.23e-05
1592 5.47e-06
1593 6.34e-02
1594 7.53e-06
1595 1.08e-05
1596 1.13e-04
1597 6.36e-04
1598 1.63e-02
1615 3.22e-02
1625 1.16e-01
1626 6.49e-04
1627 2.81e-04
1628 2.07e-04
1629 1.39e-04
1630 1.02e-04
1631 6.45e-04
1634 8.96e-04
1645 8.39e-01
1646 8.63e-01
1647 9.75e-01
 
0
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20
30
40
50
60
Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Top
MEME version
4.7.0 (Release date: Wed Sep 28 17:30:10 EST 2011)
Reference
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
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Command line summary

Letter frequencies in dataset
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Background letter frequencies (from dataset with add-one prior applied):
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Stopping Reason
Stopped because nmotifs = 20 reached. Program ran on crdd.imtech.res.in.
show model parameters...

Explanation of MEME Results

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The MEME results consist of

  • The overview of all discovered motifs.
  • Information on each of the motifs MEME discovered, including:
    1. A summary table showing the width, number of contributing sites, log likelihood ratio, statistical significance, information content and relative entropy of the motif.
    2. A sequence LOGO.
    3. Downloadable LOGO files suitable for publication.
    4. A regular expression describing the motif.
    5. Some further analysis that can be performed on the motif.
    6. A list of data formats describing the motif.
    7. The contributing sites of the motif sorted by p-value and aligned with each other.
    8. The block diagrams of the contributing sites of the motif within each sequence in the training set.
  • A combined block diagram showing an optimized (non-overlapping) tiling of all of the motifs onto each of the sequences in the training set.
  • The version of MEME and the date it was released.
  • The reference to cite if you use MEME in your research.
  • A description of the sequences you submitted (the "training set") showing the name, "weight" and length of each sequence.
  • The command line summary detailing the parameters with which you ran MEME.
  • The reason why MEME stopped and the name of the CPU on which it ran.
  • This explanation of how to interpret MEME results.

Motifs

For each motif that it discovers in the training set, MEME prints the following information:

Summary Table

This summary table gives the main attributes of the motif.

E-value
The statistical significance of the motif. MEME usually finds the most statistically significant (low E-value) motifs first. The E-value of a motif is based on its log likelihood ratio, width, sites, the background letter frequencies (given in the command line summary), and the size of the training set. The E-value is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and site count, that one would find in a similarly sized set of random sequences. (In random sequences each position is independent with letters chosen according to the background letter frequencies.)
Width
The width of the motif. Each motif describes a pattern of a fixed with as no gaps are allowed in MEME motifs.
Sites
The number of sites contributing to the construction of the motif.
Log Likelihood Ratio
The log likelihood ratio of the motif.The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.)
Information Content
The information content of the motif in bits. It is equal to the sum of the uncorrected information content, R(), in the columns of the LOGO. This is equal relative entropy of the motif relative to a uniform background frequency model.
Relative Entropy
The relative entropy of the motif, computed in bits and relative to the background letter frequencies given in the command line summary. It is equal to the log-likelihood ratio (llr) divided by the number of contributing sites of the motif times 1/ln(2),

re = llr / (sites * ln(2)).
Sequence LOGO

MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. These are displayed as "sequence LOGOS", containing stacks of letters at each position in the motif. The total height of the stack is the "information content" of that position in the motif in bits. The height of the individual letters in a stack is the probability of the letter at that position multiplied by the total information content of the stack.

Note: The MEME LOGO differs from those produced by the Weblogo program because a small-sample correction is NOT applied. However, MEME LOGOs in PNG and encapsulated postscript (EPS) formats with small-sample correction (SSC) are available by clicking on the download button with "SSC" set to "on" under Download LOGO. The MEME LOGOs without small sample correction are similarly available. Error bars are included in the LOGOs with small-sample correction.

Modern web browsers supporting the canvas element and it's text manipulation functions as described in the html 5 standard, can render the sequence LOGOs without needing the images. The browsers which work with this feature are:

  • Firefox 3.5 and above
  • Safari 4 and above
  • Google Chrome 4 and above

Unfortunately Internet Explorer 8 does not support any html 5 features.

The information content of each motif position is computed as described in the paper by Schneider and Stephens, "Sequence Logos: A New Way to Display Consensus Sequences" but the small-sample correction, e(n), is set to zero for the LOGO displayed in the MEME output. The corrected information content of position i is given by

            R(i) for amino acids   = log2(20) - (H(i) + e(n))   (1a) 
            R(i) for nucleic acids =    2    - (H(i) + e(n))    (1b)
          

where H(i) is the entropy of position i,

            H(l) = - (Sum f(a,i) * log2[ f(a,i) ]).             (2)
          

Here, f(a,i) is the frequency of base or amino acid a at position i, and e(n) is the small-sample correction for an alignment of n letters. The height of letter a in column i is given by

            height = f(a,i) * R(i)                              (3)
          

The approximation for the small-sample correction, e(n), is given by:

            e(n) = (s-1) / (2 * ln(2) * n),                     (4)
          

where s is 4 for nucleotides, 20 for amino acids, and n is the number of sequences in the alignment.

The letters in the logos are colored as follows.
For DNA sequences, the letter categories contain one letter each.

NUCLEIC ACIDS COLOR
A RED
C BLUE
G ORANGE
T GREEN

For proteins, the categories are based on the biochemical properties of the various amino acids.

AMINO ACIDS COLOR PROPERTIES
A, C, F, I, L, V, W and M BLUE Most hydrophobic[Kyte and Doolittle, 1982]
NQST GREEN Polar, non-charged, non-aliphatic residues
DE MAGENTA Acidic
KR RED Positively charged
H PINK  
G ORANGE  
P YELLOW  
Y TURQUOISE  

J. Kyte and R. Doolittle, 1982. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol Biol. 157, 105-132.

Note: the "text" output format of MEME preserves the historical MEME format where LOGOS are replaced by a simplified probability matrix, a relative entropy plot, and a multi-level consensus sequence.

Download LOGO

Logos can be generated on the fly by the meme webservice and you may specify a number of options to customize them to your needs. The options are:

Orientation
Only valid for nucleotide motifs. Generate the standard view or the reverse complemented view of the motif.
SSC
Use small sample correction and show errorbars on the image. Small sample correction is used by the Weblogo program.
Format
The format of the generated image. If the image is to be used on the web then png is recommend. If the image is to be published then eps is recommended.
Width
The width of the generated image in centimetres.
Height
The height of the generated image in centimetres.

Regular Expression

This is a regular expression (RE) describing the motif. In each column, all letters with observed frequencies greater than 0.2 are shown; less-frequent letters are not included in the RE. MEME regular expressions are interpreted as follows: single letters match that letter; groups of letters in square brackets match any of the letters in the group. Regular expressions can be used for searching for the motif in sequences (using, for example, PatMatch) but the search accuracy will usually be better with the PSSM (using, for example MAST.)

Further Analysis

Either as a group or individually the motifs have a number of options for further analysis.

MAST
Finds the best matching positions for a set of motifs in each sequence provided to it, ranked by the combined score of each sequence. For more information about MAST please read the introduction.
FIMO
Finds all matches for a motif. For more information about FIMO please read the introduction.
TOMTOM
Compares a single motif to a database of motifs. For more information about TOMTOM please read the introduction.
GOMO
Identifies possible roles of DNA binding motifs. For more information about GOMO please read the introduction.
BLOCKS
Submit to Blocks Multiple Alignment Processor where you can do several things like create phylogeny trees and search the blocks against a database of other blocks (protein only). For more information about BLOCKS Multiple Alignment Processor please visit the website.
Data Formats

The extracted data is avaliable in the following formats.

PSPM Format
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the observed frequency ("probability") of each possible letter. The probability matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The motif is preceded by a line starting with "letter-probability matrix:" and containing the length of the alphabet, width of the motif, number of occurrences of the motif, and the E-value of the motif.
Note: Earlier versions of MEME gave the posterior probabilities--the probability after applying a prior on letter frequencies--rather than the observed frequencies. These versions of MEME also gave the number of possible positions for the motif rather than the actual number of occurrences. The output from these earlier versions of MEME can be distinguished by "n=" rather than "nsites=" in the line preceding the matrix.
PSSM Format
The position-specific scoring matrix corresponding to the motif is printed for use by database search programs such as MAST. This matrix is a log-odds matrix calculated by taking 100 times the log (base 2) of the ratio p/f at each position in the motif where p is the probability of a particular letter at that position in the motif, and f is the background frequency of the letter (given in the command line summary section.) This is the same matrix that is used above in computing the p-values of the occurrences of the motif in the Sites and Block Diagrams sections. The scoring matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The scoring matrix is preceded by a line starting with "log-odds matrix:" and containing the length of the alphabet, width of the motif, number of characters in the training set, the scoring threshold (obsolete) and the motif E-value.
Note: The probability p used to compute the PSSM is not exactly the same as the corresponding value in the Position Specific Probability Matrix (PSPM). The values of p used to compute the PSSM take into account the motif prior, whereas the values in the PSPM are just the observed frequencies of letters in the motif sites.
BLOCKS Format
For use with BLOCKS tools.
FASTA Format
The FASTA format as described here.
Raw Format
Just the sites of the sequences that contributed to the motif. One site per line.
Sites

MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs, the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand is specified, '+' means the sequence in the training set, and '-' means the reverse complement of the training set sequence. (For '-' strands, the 'start' position is actually the position on the positive strand where the site ends.) The sites are listed in order of increasing statistical significance (p-value). The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p-value by the MAST algorithm.)

Block Diagrams

The occurrences of the motif in the training set sequences are shown as coloured blocks on a line. One diagram is printed for each sequence showing all the sites contributating to that motif in that sequence. The sequences are listed in the same order as in the input to make it easier to compare multiple block diagrams. Additionally the best p-value for the sequence/motif combination is listed though this may not be in ascending order as with the sites. The p-value of an occurrence is the probability of a single random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as the score of the occurrence. When the DNA strand is specified '+', it means the motif appears from left to right on the sequence, and '-' means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of block diagrams.

Combined Block Diagrams

The motif occurrences shown in the motif summary may not be exactly the same as those reported in each motif section because only motifs with a position p-value of 0.0001 that don't overlap other, more significant motif occurrences are shown.

See the documentation for MAST output for the definition of position and combined p-values.