MOTIFSIM - MOTIF SIMilarity Detection Tool

Version 2.0

INPUT

Input Parameters
Number of files: 4
Number of top significant motifs: 10
Number of best matches: 5
Similarity cutoff >= 0.75
Output file type: All
Output file format: All

Input files and motif counts
File name Count of motifs Dataset number
DREME_DM01.txt 51 1
MEME-CHIP_DM01.txt 9 2
PScanChIP_DM01.txt 27 3
RSAT_peak-motifs_DM01.txt 40 4

RESULTS

Top 10 Significant Motifs - Global Matching (Highest to Lowest)

Dataset #: 3 Motif ID: 69 Motif name: NKX3-1

Original motif     Consensus sequence: ATACTTA Reverse complement motif     Consensus sequence: TAAGTAT

Best Matches for Top Significant Motif ID 69 (Highest to Lowest)

Dataset #: 4
Motif ID: 90
Motif name: ymTACATAyw
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 3
Number of overlap: 7
Similarity score: 0

Alignment:
DBTATGTAHH
--TAAGTAT-

Original motif     Consensus sequence: HHTACATABD Reverse complement motif     Consensus sequence: DBTATGTAHH


Dataset #: 1
Motif ID: 10
Motif name: Motif 10
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 7
Similarity score: 0.00274846

Alignment:
TATGTAD
TAAGTAT

Original motif     Consensus sequence: HTACATA Reverse complement motif     Consensus sequence: TATGTAD


Dataset #: 1
Motif ID: 34
Motif name: Motif 34
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 7
Similarity score: 0.00883486

Alignment:
ATATTTA
ATACTTA

Original motif     Consensus sequence: ATATTTA Reverse complement motif     Consensus sequence: TAAATAT


Dataset #: 4
Motif ID: 106
Motif name: wtAATTAAtw
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 4
Number of overlap: 7
Similarity score: 0.0100679

Alignment:
HATTAATTAD
---TAAGTAT

Original motif     Consensus sequence: DTAATTAATH Reverse complement motif     Consensus sequence: HATTAATTAD


Dataset #: 4
Motif ID: 100
Motif name: wwTAATAAww
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 3
Number of overlap: 7
Similarity score: 0.0316418

Alignment:
DDTTATTAHD
--TAAGTAT-

Original motif     Consensus sequence: DHTAATAADD Reverse complement motif     Consensus sequence: DDTTATTAHD


Dataset #: 2 Motif ID: 53 Motif name: Motif 53

Original motif     Consensus sequence: TSTGTR Reverse complement motif     Consensus sequence: MACASA

Best Matches for Top Significant Motif ID 53 (Highest to Lowest)

Dataset #: 1
Motif ID: 7
Motif name: Motif 7
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 1
Number of overlap: 6
Similarity score: 0.00228262

Alignment:
TSTSTGTG
TSTGTR--

Original motif     Consensus sequence: CACASASA Reverse complement motif     Consensus sequence: TSTSTGTG


Dataset #: 4
Motif ID: 114
Motif name: awAACAcAAwa
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 4
Number of overlap: 6
Similarity score: 0.0122629

Alignment:
DDAACACAADV
--MACASA---

Original motif     Consensus sequence: DDAACACAADV Reverse complement motif     Consensus sequence: BDTTGTGTTDD


Dataset #: 1
Motif ID: 23
Motif name: Motif 23
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 2
Number of overlap: 6
Similarity score: 0.0137023

Alignment:
MTSTGTA
-TSTGTR

Original motif     Consensus sequence: MTSTGTA Reverse complement motif     Consensus sequence: TACASAR


Dataset #: 1
Motif ID: 2
Motif name: Motif 2
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 2
Number of overlap: 6
Similarity score: 0.0252334

Alignment:
GTGTGTGT
-TSTGTR-

Original motif     Consensus sequence: ACACACAC Reverse complement motif     Consensus sequence: GTGTGTGT


Dataset #: 1
Motif ID: 12
Motif name: Motif 12
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 2
Number of overlap: 6
Similarity score: 0.0262273

Alignment:
MTGTGTGC
-TSTGTR-

Original motif     Consensus sequence: GCACACAY Reverse complement motif     Consensus sequence: MTGTGTGC


Dataset #: 1 Motif ID: 25 Motif name: Motif 25

Original motif     Consensus sequence: TTTAWW Reverse complement motif     Consensus sequence: WWTAAA

Best Matches for Top Significant Motif ID 25 (Highest to Lowest)

Dataset #: 4
Motif ID: 91
Motif name: wtATTTTAww
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 1
Number of overlap: 6
Similarity score: 0.0116421

Alignment:
HWTAAAATHD
WWTAAA----

Original motif     Consensus sequence: DHATTTTAWH Reverse complement motif     Consensus sequence: HWTAAAATHD


Dataset #: 4
Motif ID: 108
Motif name: wwATkTTTAww
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 6
Number of overlap: 6
Similarity score: 0.0118254

Alignment:
DHATKTTTAHH
-----TTTAWW

Original motif     Consensus sequence: DHATKTTTAHH Reverse complement motif     Consensus sequence: HHTAAARATHD


Dataset #: 3
Motif ID: 70
Motif name: Foxq1
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 6
Similarity score: 0.0158082

Alignment:
HATTGTTTATW
-----TTTAWW

Original motif     Consensus sequence: HATTGTTTATW Reverse complement motif     Consensus sequence: WATAAACAATH


Dataset #: 2
Motif ID: 55
Motif name: Motif 55
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 6
Similarity score: 0.0307675

Alignment:
TTTTAAA
-TTTAWW

Original motif     Consensus sequence: TTTAAAA Reverse complement motif     Consensus sequence: TTTTAAA


Dataset #: 3
Motif ID: 67
Motif name: FOXI1
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 6
Number of overlap: 6
Similarity score: 0.0347747

Alignment:
KBDTRTTTRTTT
-----TTTAWW-

Original motif     Consensus sequence: KBDTRTTTRTTT Reverse complement motif     Consensus sequence: AAAMAAAMADBY


Dataset #: 1 Motif ID: 24 Motif name: Motif 24

Original motif     Consensus sequence: CACGB Reverse complement motif     Consensus sequence: BCGTG

Best Matches for Top Significant Motif ID 24 (Highest to Lowest)

Dataset #: 2
Motif ID: 56
Motif name: Motif 56
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 5
Similarity score: 0

Alignment:
TCCGTG
-BCGTG

Original motif     Consensus sequence: CACGGA Reverse complement motif     Consensus sequence: TCCGTG


Dataset #: 4
Motif ID: 115
Motif name: ysCmAGCACwy
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 1
Number of overlap: 5
Similarity score: 0.0186397

Alignment:
DHGTGCTRGVH
BCGTG------

Original motif     Consensus sequence: HVCMAGCACHH Reverse complement motif     Consensus sequence: DHGTGCTRGVH


Dataset #: 4
Motif ID: 107
Motif name: crCGyGCRcg
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 5
Number of overlap: 5
Similarity score: 0.019278

Alignment:
CGCGTGCACG
-BCGTG----

Original motif     Consensus sequence: CGCGTGCACG Reverse complement motif     Consensus sequence: CGTGCACGCG


Dataset #: 2
Motif ID: 58
Motif name: Motif 58
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 5
Similarity score: 0.0339655

Alignment:
CACACACACACACA
CACGB---------

Original motif     Consensus sequence: CACACACACACACA Reverse complement motif     Consensus sequence: TGTGTGTGTGTGTG


Dataset #: 4
Motif ID: 93
Motif name: cmCARCACTwr
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 2
Number of overlap: 5
Similarity score: 0.0385683

Alignment:
VHAGTGCTGHB
-BCGTG-----

Original motif     Consensus sequence: BHCAGCACTHV Reverse complement motif     Consensus sequence: VHAGTGCTGHB


Dataset #: 2 Motif ID: 54 Motif name: Motif 54

Original motif     Consensus sequence: RGAAA Reverse complement motif     Consensus sequence: TTTCK

Best Matches for Top Significant Motif ID 54 (Highest to Lowest)

Dataset #: 1
Motif ID: 26
Motif name: Motif 26
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 5
Similarity score: 0

Alignment:
RGARGAAA
---RGAAA

Original motif     Consensus sequence: RGARGAAA Reverse complement motif     Consensus sequence: TTTCKTCK


Dataset #: 1
Motif ID: 28
Motif name: Motif 28
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 1
Number of overlap: 5
Similarity score: 0.0199405

Alignment:
TTTCTVT
TTTCK--

Original motif     Consensus sequence: AVAGAAA Reverse complement motif     Consensus sequence: TTTCTVT


Dataset #: 1
Motif ID: 33
Motif name: Motif 33
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 5
Similarity score: 0.0284722

Alignment:
CMTTTCC
TTTCK--

Original motif     Consensus sequence: CMTTTCC Reverse complement motif     Consensus sequence: GGAAARG


Dataset #: 1
Motif ID: 46
Motif name: Motif 46
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 5
Similarity score: 0.0284722

Alignment:
GGAAASA
RGAAA--

Original motif     Consensus sequence: GGAAASA Reverse complement motif     Consensus sequence: TSTTTCC


Dataset #: 1
Motif ID: 44
Motif name: Motif 44
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 5
Similarity score: 0.0339244

Alignment:
CATTTCT
--TTTCK

Original motif     Consensus sequence: AGAAATG Reverse complement motif     Consensus sequence: CATTTCT


Dataset #: 3 Motif ID: 64 Motif name: ARID3A

Original motif     Consensus sequence: ATYAAA Reverse complement motif     Consensus sequence: TTTMAT

Best Matches for Top Significant Motif ID 64 (Highest to Lowest)

Dataset #: 4
Motif ID: 106
Motif name: wtAATTAAtw
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 4
Number of overlap: 6
Similarity score: 0.0114914

Alignment:
DTAATTAATH
---ATYAAA-

Original motif     Consensus sequence: DTAATTAATH Reverse complement motif     Consensus sequence: HATTAATTAD


Dataset #: 1
Motif ID: 20
Motif name: Motif 20
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 3
Number of overlap: 6
Similarity score: 0.015396

Alignment:
CCTYTAAT
--TTTMAT

Original motif     Consensus sequence: ATTAMAGG Reverse complement motif     Consensus sequence: CCTYTAAT


Dataset #: 1
Motif ID: 49
Motif name: Motif 49
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 6
Similarity score: 0.0340365

Alignment:
AGATAAAR
--ATYAAA

Original motif     Consensus sequence: AGATAAAR Reverse complement motif     Consensus sequence: KTTTATCT


Dataset #: 1
Motif ID: 25
Motif name: Motif 25
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 6
Similarity score: 0.0368439

Alignment:
WWTAAA
ATYAAA

Original motif     Consensus sequence: TTTAWW Reverse complement motif     Consensus sequence: WWTAAA


Dataset #: 4
Motif ID: 100
Motif name: wwTAATAAww
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 5
Number of overlap: 6
Similarity score: 0.0394923

Alignment:
DHTAATAADD
TTTMAT----

Original motif     Consensus sequence: DHTAATAADD Reverse complement motif     Consensus sequence: DDTTATTAHD


Dataset #: 1 Motif ID: 6 Motif name: Motif 6

Original motif     Consensus sequence: CCCASCMC Reverse complement motif     Consensus sequence: GYGSTGGG

Best Matches for Top Significant Motif ID 6 (Highest to Lowest)

Dataset #: 4
Motif ID: 115
Motif name: ysCmAGCACwy
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 3
Number of overlap: 8
Similarity score: 0.0212781

Alignment:
DHGTGCTRGVH
--GYGSTGGG-

Original motif     Consensus sequence: HVCMAGCACHH Reverse complement motif     Consensus sequence: DHGTGCTRGVH


Dataset #: 4
Motif ID: 111
Motif name: ccCCmCaCCCCcc
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 3
Number of overlap: 8
Similarity score: 0.0266863

Alignment:
HBCCCCACCCCBH
---CCCASCMC--

Original motif     Consensus sequence: HBCCCCACCCCBH Reverse complement motif     Consensus sequence: DBGGGGTGGGGBD


Dataset #: 4
Motif ID: 93
Motif name: cmCARCACTwr
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 4
Number of overlap: 8
Similarity score: 0.030511

Alignment:
BHCAGCACTHV
CCCASCMC---

Original motif     Consensus sequence: BHCAGCACTHV Reverse complement motif     Consensus sequence: VHAGTGCTGHB


Dataset #: 4
Motif ID: 119
Motif name: cbCCAGCTCmyk
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 4
Number of overlap: 8
Similarity score: 0.0322039

Alignment:
BBCCAGCTCMBD
-CCCASCMC---

Original motif     Consensus sequence: BBCCAGCTCMBD Reverse complement motif     Consensus sequence: HBYGAGCTGGBB


Dataset #: 4
Motif ID: 101
Motif name: csCACCCCgg
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 8
Similarity score: 0.0415267

Alignment:
HVCACCCCBB
CCCASCMC--

Original motif     Consensus sequence: HVCACCCCBB Reverse complement motif     Consensus sequence: BBGGGGTGVD


Dataset #: 4 Motif ID: 94 Motif name: yrTCWCAAyr

Original motif     Consensus sequence: HVTCACAAYD Reverse complement motif     Consensus sequence: HKTTGTGABH

Best Matches for Top Significant Motif ID 94 (Highest to Lowest)

Dataset #: 3
Motif ID: 76
Motif name: Sox2
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 2
Number of overlap: 10
Similarity score: 0.00762497

Alignment:
CCWTTGTYATGCAAA
----HKTTGTGABH-

Original motif     Consensus sequence: CCWTTGTYATGCAAA Reverse complement motif     Consensus sequence: TTTGCATMACAAWGG


Dataset #: 3
Motif ID: 80
Motif name: Pou5f1
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 6
Number of overlap: 10
Similarity score: 0.0127574

Alignment:
CWTTGTHATGCAAAT
-----HKTTGTGABH

Original motif     Consensus sequence: CWTTGTHATGCAAAT Reverse complement motif     Consensus sequence: ATTTGCATHACAAWG


Dataset #: 3
Motif ID: 81
Motif name: Pax4
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 2
Number of overlap: 10
Similarity score: 0.0426407

Alignment:
RAAWAWTWDCMVHHVBBHHHVHMHCMCYMC
-------------------HVTCACAAYD-

Original motif     Consensus sequence: RAAWAWTWDCMVHHVBBHHHVHMHCMCYMC Reverse complement motif     Consensus sequence: GRKGRGDRHVHDDVBBHHBRGDWAWTWTTM


Dataset #: 3
Motif ID: 62
Motif name: TBP
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 5
Number of overlap: 10
Similarity score: 0.0429648

Alignment:
STATAAAWRVVVVBV
-HVTCACAAYD----

Original motif     Consensus sequence: STATAAAWRVVVVBV Reverse complement motif     Consensus sequence: VBVVVVMWTTTATAS


Dataset #: 3
Motif ID: 83
Motif name: NR2F1
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 10
Similarity score: 0.0463536

Alignment:
TGAMCTTTGMMCYT
HKTTGTGABH----

Original motif     Consensus sequence: TGAMCTTTGMMCYT Reverse complement motif     Consensus sequence: AKGYYCAAAGRTCA


Dataset #: 2 Motif ID: 55 Motif name: Motif 55

Original motif     Consensus sequence: TTTAAAA Reverse complement motif     Consensus sequence: TTTTAAA

Best Matches for Top Significant Motif ID 55 (Highest to Lowest)

Dataset #: 4
Motif ID: 120
Motif name: wtTTTwAAAaw
Matching format of first motif: Original Motif
Matching format of second motif: Original Motif
Direction: Backward
Position number: 3
Number of overlap: 7
Similarity score: 0.00286145

Alignment:
HHTTTWAAADD
--TTTAAAA--

Original motif     Consensus sequence: HHTTTWAAADD Reverse complement motif     Consensus sequence: DDTTTWAAAHH


Dataset #: 1
Motif ID: 9
Motif name: Motif 9
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 1
Number of overlap: 7
Similarity score: 0.0142562

Alignment:
TTTWWAAA
-TTTAAAA

Original motif     Consensus sequence: TTTWWAAA Reverse complement motif     Consensus sequence: TTTWWAAA


Dataset #: 4
Motif ID: 91
Motif name: wtATTTTAww
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 4
Number of overlap: 7
Similarity score: 0.036821

Alignment:
DHATTTTAWH
---TTTTAAA

Original motif     Consensus sequence: DHATTTTAWH Reverse complement motif     Consensus sequence: HWTAAAATHD


Dataset #: 4
Motif ID: 108
Motif name: wwATkTTTAww
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 7
Similarity score: 0.0428268

Alignment:
DHATKTTTAHH
----TTTTAAA

Original motif     Consensus sequence: DHATKTTTAHH Reverse complement motif     Consensus sequence: HHTAAARATHD


Dataset #: 3
Motif ID: 62
Motif name: TBP
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Forward
Position number: 8
Number of overlap: 7
Similarity score: 0.058454

Alignment:
VBVVVVMWTTTATAS
-------TTTTAAA-

Original motif     Consensus sequence: STATAAAWRVVVVBV Reverse complement motif     Consensus sequence: VBVVVVMWTTTATAS


Dataset #: 4 Motif ID: 96 Motif name: mdAAcCAACG

Original motif     Consensus sequence: VDAACCAACG Reverse complement motif     Consensus sequence: CGTTGGTTDB

Best Matches for Top Significant Motif ID 96 (Highest to Lowest)

Dataset #: 2
Motif ID: 60
Motif name: Motif 60
Matching format of first motif: Reverse Complement
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 3
Number of overlap: 10
Similarity score: 0.0244161

Alignment:
YTTTTTRTTTTDTT
--CGTTGGTTDB--

Original motif     Consensus sequence: AADAAAAMAAAAAM Reverse complement motif     Consensus sequence: YTTTTTRTTTTDTT


Dataset #: 3
Motif ID: 70
Motif name: Foxq1
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Backward
Position number: 1
Number of overlap: 10
Similarity score: 0.0266383

Alignment:
HATTGTTTATW
-CGTTGGTTDB

Original motif     Consensus sequence: HATTGTTTATW Reverse complement motif     Consensus sequence: WATAAACAATH


Dataset #: 3
Motif ID: 67
Motif name: FOXI1
Matching format of first motif: Original Motif
Matching format of second motif: Reverse Complement
Direction: Backward
Position number: 3
Number of overlap: 10
Similarity score: 0.036655

Alignment:
AAAMAAAMADBY
VDAACCAACG--

Original motif     Consensus sequence: KBDTRTTTRTTT Reverse complement motif     Consensus sequence: AAAMAAAMADBY


Dataset #: 3
Motif ID: 83
Motif name: NR2F1
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 1
Number of overlap: 10
Similarity score: 0.0376121

Alignment:
TGAMCTTTGMMCYT
CGTTGGTTDB----

Original motif     Consensus sequence: TGAMCTTTGMMCYT Reverse complement motif     Consensus sequence: AKGYYCAAAGRTCA


Dataset #: 3
Motif ID: 76
Motif name: Sox2
Matching format of first motif: Reverse Complement
Matching format of second motif: Original Motif
Direction: Forward
Position number: 6
Number of overlap: 10
Similarity score: 0.0382008

Alignment:
CCWTTGTYATGCAAA
-----CGTTGGTTDB

Original motif     Consensus sequence: CCWTTGTYATGCAAA Reverse complement motif     Consensus sequence: TTTGCATMACAAWGG


Results created by MOTIFSIM on 02-23-2016 14:17:57
Runtime: 128.484 seconds.

MOTIFSIM is written by Ngoc Tam L. Tran
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