Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold474
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 406844
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 3
Found at i:382111 original size:20 final size:20
Alignment explanation
Indices: 382057--382111 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
382047 AACTAATAAA
*
382057 ATAAAAT-TATAACTATTATT
1 ATAAAATATATAATTA-TATT
382077 ATAAAATATATAATTATATT
1 ATAAAATATATAATTATATT
*
382097 TTAAAA-ATATGAATT
1 ATAAAATATAT-AATT
382112 TTATAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
20 20 0.65
21 7 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAAATATATAATTATATT
Found at i:383149 original size:23 final size:22
Alignment explanation
Indices: 383099--383154 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
383089 CACATGTCAC
**
383099 ATTAAAAATT-ATTTTTAAAAA
1 ATTAAAAATTAATTTAGAAAAA
*
383120 ATAAAAAATTAATTTAGATAAAA
1 ATTAAAAATTAATTTAGA-AAAA
*
383143 ATTAAAATTTAA
1 ATTAAAAATTAA
383155 AACTTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 9 0.32
22 5 0.18
23 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTAAAAATTAATTTAGAAAAA
Found at i:383554 original size:22 final size:21
Alignment explanation
Indices: 383520--383571 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
383510 CTGTTGTTAT
* *
383520 AAAATATATAATTATATGATA
1 AAAAAATATAATTATATAATA
*
383541 AAAAAATATGAATTTTATAATA
1 AAAAAATAT-AATTATATAATA
383563 AAAAAATAT
1 AAAAAATAT
383572 TTAGACTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAAAATATAATTATATAATA
Found at i:384491 original size:3 final size:3
Alignment explanation
Indices: 384483--384517 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
384473 TTGGTTTTTT
* *
384483 ATA ATA ATA ATA ATA ATA CTC ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
384518 TTTTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:385161 original size:166 final size:164
Alignment explanation
Indices: 384931--385386 Score: 526
Period size: 166 Copynumber: 2.7 Consensus size: 164
384921 AAATTTTTTT
* * * * *
384931 ATTGAAATTCAAAAGATGAGATTAATGCATAGATTTTATTTTTGAATAAATATGATAAATGCATA
1 ATTGGAATTCAAAAAATGAGACTAATGCATGGATTTTGTTTTTGAATAAATATGATAAATGCATA
* * *
384996 AATTATTAATGGAAAACAAATTCTTTATGATATAAAAAGAGTTGAAAAGACTAATGCATGGATTG
66 GATTATTAATGGAAATCAAATTCTTT-TGATAT-AAAAGAGTTGATAAGACTAATGCATGGATTG
* * *
385061 TAAATGTTAAACTGTAAGGAATAAACTAATGCATAG
129 TAAATGTCAAACTATAAGGAATAAACTAACGCATAG
** *
385097 ATT-GAAGTTTGAAAAATGAGACTAATGCATGGATTTTGTTTTTGAACAAATATGATAAATGCAT
1 ATTGGAA-TTCAAAAAATGAGACTAATGCATGGATTTTGTTTTTGAATAAATATGATAAATGCAT
* * * *
385161 AGATTCTTAATAGG-AATCAGATTCTTTTTTATATGAAAGAAGTTGATAAGACTAATGCATGGAT
65 AGATTATTAAT-GGAAATCAAATTC-TTTTGATATAAAAG-AGTTGATAAGACTAATGCATGGAT
* * *
385225 TGTAAATGTCAGACTATAAGGAATATACTAACGCATGG
127 TGTAAATGTCAAACTATAAGGAATAAACTAACGCATAG
* * * *
385263 ATTGGAATTCAAAAAATGAGACTAATGCATGGATTCTG-TTTTGAAATAAATGTGATTAATTCAT
1 ATTGGAATTCAAAAAATGAGACTAATGCATGGATTTTGTTTTTG-AATAAATATGATAAATGCAT
** *
385327 AGATTGCTGAT-GAGAATCAAATTCCTTTTGATATGGAAAA-AGTTGATAAGACTAATGCAT
65 AGATTATTAATGGA-AATCAAATT-CTTTTGATAT--AAAAGAGTTGATAAGACTAATGCAT
385387 TATACATAGA
Statistics
Matches: 245, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
164 1 0.00
165 11 0.04
166 221 0.90
167 9 0.04
168 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (164 bp):
ATTGGAATTCAAAAAATGAGACTAATGCATGGATTTTGTTTTTGAATAAATATGATAAATGCATA
GATTATTAATGGAAATCAAATTCTTTTGATATAAAAGAGTTGATAAGACTAATGCATGGATTGTA
AATGTCAAACTATAAGGAATAAACTAACGCATAG
Found at i:385405 original size:67 final size:67
Alignment explanation
Indices: 385324--385453 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 67
385314 GTGATTAATT
* * *
385324 CATAGATTGCTGATGAGAATCAAATTCCTTTTGATATGGAAAAAGTTGATAAGACTAATGCATTA
1 CATAGATTGCTGATGAGAATCAAATTCCTTTTGATATGAAAAAAATTCATAAGACTAATGCATTA
385389 TA
66 TA
** * * * *
385391 CATAGATTTTTGATGGGATTCAAATTCTTTTTTATATGAAAAAAATTCATAAGACTAATGCAT
1 CATAGATTGCTGATGAGAATCAAATTCCTTTTGATATGAAAAAAATTCATAAGACTAATGCAT
385454 AATTGTAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (67 bp):
CATAGATTGCTGATGAGAATCAAATTCCTTTTGATATGAAAAAAATTCATAAGACTAATGCATTA
TA
Found at i:388846 original size:80 final size:79
Alignment explanation
Indices: 388737--388931 Score: 212
Period size: 79 Copynumber: 2.5 Consensus size: 79
388727 GGTTGGGGTG
* * * * * *
388737 TCCCCTTGAAAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGGAAAAAAA
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGG-AAAAAA
*
388801 AATCGGGATTGGAGTA
64 AACCGGGATTGGAGTA
* * * * * *
388817 TCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAG
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAA
*
388882 CCGGGGTTGGAGTA
66 CCGGGATTGGAGTA
* **
388896 TCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
388932 GAAATAACGA
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 49 0.52
80 46 0.48
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAA
CCGGGATTGGAGTA
Found at i:388939 original size:28 final size:28
Alignment explanation
Indices: 388883--388959 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
388873 GGAATAAAGC
*** **
388883 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
388911 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
388939 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
388960 TGTGAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:389058 original size:52 final size:51
Alignment explanation
Indices: 388942--389119 Score: 155
Period size: 52 Copynumber: 3.4 Consensus size: 51
388932 GAAATAACGA
* * *
388942 GGTTGGAGTATCCTCGATTGTGAAA--AAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGA-T-T-AAAGGAAAATTGGTG-TTTTAGAAAT-AAATCGG
* * *
388996 AGCTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAGAAATAAA-TCGG
** * *
389048 GGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTGTTTTAGCAATGAAATCGG
1 GGTTGGAGTATCCCCGATTAAAGG-AAAATTGGTGTTTTAGAAAT-AAATCGG
* *
389100 GGTTGGAGTAACCCCAATTA
1 GGTTGGAGTATCCCCGATTA
389120 TGAGAAATCA
Statistics
Matches: 103, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
51 8 0.08
52 67 0.65
53 14 0.14
54 14 0.14
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAGAAATAAATCGG
Found at i:389211 original size:27 final size:27
Alignment explanation
Indices: 389149--389223 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
389139 GAATAAAGCA
389149 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTAT-CCC-CGATAAATAAC
* * *
389177 TGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATAAATAAC
389204 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
389224 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 27 0.64
28 12 0.29
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATAAATAAC
Found at i:389287 original size:53 final size:51
Alignment explanation
Indices: 389207--389328 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 51
389197 GATTAACGGG
* *
389207 GTTGGAGTATCCCCGATTGTGAAAAATTTGTGTTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGAAAATAAAATCGGA
389260 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* *
389311 GATGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
389329 GCAGAGAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
51 35 0.55
52 1 0.02
53 28 0.44
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:391712 original size:13 final size:13
Alignment explanation
Indices: 391694--391719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
391684 ACAAAGATCC
391694 ATGTATCGATACA
1 ATGTATCGATACA
391707 ATGTATCGATACA
1 ATGTATCGATACA
391720 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:391715 original size:33 final size:33
Alignment explanation
Indices: 391673--391739 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
391663 AAAATTTCCA
***
391673 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
391706 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
391739 A
1 A
391740 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:391859 original size:21 final size:20
Alignment explanation
Indices: 391830--391908 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 20
391820 GTTGGGACCC
391830 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTA-AA
* **
391851 TGCATCGATACATTTCACAAA
1 TGTATCGATACATTT-GTAAA
*
391872 TGTATCGATACATTCTATAAA
1 TGTATCGATACATT-TGTAAA
391893 TGTATCGATACATTTG
1 TGTATCGATACATTTG
391909 AATTTTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 47 0.94
22 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTTGTAAA
Found at i:392969 original size:59 final size:59
Alignment explanation
Indices: 392652--393486 Score: 1227
Period size: 59 Copynumber: 14.3 Consensus size: 59
392642 ATAAAGTGTA
* **
392652 TCCTGATCTTTGAGGACT-AAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAG--GTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* *
392713 TCCTGCTCTCTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
392768 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
392823 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AGAGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
392878 TCCTGTTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
392937 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
392996 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
393055 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
393114 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAATGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
393173 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
393232 TCCTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
393291 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
393350 TCCCGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
**
393409 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
393469 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
393487 AAAAAGCGGA
Statistics
Matches: 725, Mismatches: 35, Indels: 29
0.92 0.04 0.04
Matches are distributed among these distances:
53 1 0.00
54 34 0.05
55 107 0.15
56 2 0.00
58 2 0.00
59 512 0.71
60 25 0.03
61 40 0.06
64 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:394488 original size:20 final size:20
Alignment explanation
Indices: 394463--394502 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
394453 TTTTTCTCTT
394463 TTTTTTTGTTTTATTTTTTG
1 TTTTTTTGTTTTATTTTTTG
*
394483 TTTTTTTGTTTTTTTTTTTG
1 TTTTTTTGTTTTATTTTTTG
394503 AAGAGAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (20 bp):
TTTTTTTGTTTTATTTTTTG
Found at i:394502 original size:12 final size:12
Alignment explanation
Indices: 394461--394501 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
394451 GATTTTTCTC
394461 TTTTTTTTTGTT
1 TTTTTTTTTGTT
*
394473 TTATTTTTTGTT
1 TTTTTTTTTGTT
394485 TTTTTGTTTT-TT
1 TTTTT-TTTTGTT
394497 TTTTT
1 TTTTT
394502 GAAGAGAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTGTT
Done.