Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold602
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: 54778
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:9717 original size:2 final size:2
Alignment explanation
Indices: 9710--9751 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
9700 TGTTTCGAGA
9710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9752 TCAAAAAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14892 original size:45 final size:46
Alignment explanation
Indices: 14823--14921 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 46
14813 GCAATTTTGG
14823 ACTG-TTTTTGTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
1 ACTGCTTTTTGTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
*
14868 ATTGCTTTTT-TTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
1 ACTGCTTTTTGTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
14913 ACTGCTTTT
1 ACTGCTTTT
14922 GCCTAATATG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
45 46 0.90
46 5 0.10
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (46 bp):
ACTGCTTTTTGTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
Found at i:18268 original size:15 final size:16
Alignment explanation
Indices: 18248--18280 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18238 ACATATTATT
*
18248 TTTTTGTTATATA-AA
1 TTTTTGATATATATAA
18263 TTTTTGATATATATAA
1 TTTTTGATATATATAA
18279 TT
1 TT
18281 GTATCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTTGATATATATAA
Found at i:21473 original size:15 final size:15
Alignment explanation
Indices: 21430--21476 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
21420 CTTTTATTAG
*
21430 AAAAATAAAAATTTA
1 AAAAATAAAAATATA
*
21445 AAAAATATTAAATATA
1 AAAAATA-AAAATATA
21461 AAAAATAAAAATATA
1 AAAAATAAAAATATA
21476 A
1 A
21477 TATATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAAAATATA
Found at i:22218 original size:16 final size:18
Alignment explanation
Indices: 22199--22239 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
22189 AGAGAAAAAG
22199 AAAATAATAAT-AGTA-C
1 AAAATAATAATAAGTATC
*
22215 AAAATAA-AATAAGTATG
1 AAAATAATAATAAGTATC
22232 AAAATAAT
1 AAAATAAT
22240 TCTTTTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAATAATAATAAGTATC
Found at i:22521 original size:110 final size:110
Alignment explanation
Indices: 22358--22575 Score: 427
Period size: 110 Copynumber: 2.0 Consensus size: 110
22348 ATATTTTAAA
22358 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
1 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
*
22423 TAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
66 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
22468 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
1 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
22533 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACT
66 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACT
22576 GCCTTTTGAT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (110 bp):
CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
Found at i:24374 original size:19 final size:20
Alignment explanation
Indices: 24352--24402 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
24342 TATTTTAATT
24352 TTTTTAATTTTTTCTTTT-A
1 TTTTTAATTTTTTCTTTTCA
*
24371 TTTTT-ATATTTTCTTTTCA
1 TTTTTAATTTTTTCTTTTCA
24390 TTTCTTAATTTTT
1 TTT-TTAATTTTT
24403 AGCAACTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 9 0.33
20 2 0.07
21 5 0.19
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTAATTTTTTCTTTTCA
Found at i:24580 original size:34 final size:34
Alignment explanation
Indices: 24501--24582 Score: 89
Period size: 37 Copynumber: 2.4 Consensus size: 34
24491 GATATTTTTT
*
24501 AAAAAATAAAA--AACCTTAACAATTGTTTAAAA
1 AAAAAATAAAATCAACCTAAACAATTGTTTAAAA
* *
24533 ATAAAAATAAAAATCAATCCTAAATAATTGTTT-TAA
1 A-AAAAAT-AAAATCAA-CCTAAACAATTGTTTAAAA
24569 AAAAAATAAAATCA
1 AAAAAATAAAATCA
24583 TTTTTGCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
32 1 0.02
33 6 0.14
34 11 0.26
35 6 0.14
36 5 0.12
37 13 0.31
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAAAATAAAATCAACCTAAACAATTGTTTAAAA
Found at i:24743 original size:2 final size:2
Alignment explanation
Indices: 24736--24770 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24726 TTTATAATTA
24736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24771 GAGATTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26394 original size:15 final size:15
Alignment explanation
Indices: 26374--26406 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
26364 TATTTTCTAT
26374 ATTCATCACAATTAA
1 ATTCATCACAATTAA
26389 ATTCATCACAATTAA
1 ATTCATCACAATTAA
26404 ATT
1 ATT
26407 ACCGAGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTCATCACAATTAA
Found at i:26586 original size:91 final size:91
Alignment explanation
Indices: 26431--26613 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
26421 TCTTGCATTG
26431 TCTTAGTTGTTTTTGCCCCCGTACTTTTTCCTTATCATATTTAGATTTAAATGTATGTGTTGGAT
1 TCTTAGTTGTTTTTGCCCCCGTACTTTTTCCTTATCATATTTAGATTTAAATGTATGTGTTGGAT
26496 GTAAGTATATATTTAACATGAATATA
66 GTAAGTATATATTTAACATGAATATA
26522 TCTTAGTTGTTTTTGCCCCCGTACTTTTTCCTTATCATATTTAGATTTAAATGTATGTGTTGGAT
1 TCTTAGTTGTTTTTGCCCCCGTACTTTTTCCTTATCATATTTAGATTTAAATGTATGTGTTGGAT
26587 GTAAGTATATATTTAACATGAATATA
66 GTAAGTATATATTTAACATGAATATA
26613 T
1 T
26614 TCACATATTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (91 bp):
TCTTAGTTGTTTTTGCCCCCGTACTTTTTCCTTATCATATTTAGATTTAAATGTATGTGTTGGAT
GTAAGTATATATTTAACATGAATATA
Found at i:28438 original size:16 final size:16
Alignment explanation
Indices: 28417--28447 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28407 TATTTATACA
*
28417 TTCATGTTATGTTTTT
1 TTCATGTTATCTTTTT
28433 TTCATGTTATCTTTT
1 TTCATGTTATCTTTT
28448 AATTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.68
Consensus pattern (16 bp):
TTCATGTTATCTTTTT
Found at i:31367 original size:19 final size:20
Alignment explanation
Indices: 31343--31402 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
31333 TTTGAATTTC
31343 AACAAT-TTGTATCGATACA
1 AACAATATTGTATCGATACA
*
31362 AACAATAAATGTATCGATACA
1 AACAAT-ATTGTATCGATACA
* *
31383 TA-AGTATTGTATCGATACA
1 AACAATATTGTATCGATACA
31402 A
1 A
31403 TGTATCGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (20 bp):
AACAATATTGTATCGATACA
Found at i:33504 original size:82 final size:81
Alignment explanation
Indices: 33362--33523 Score: 306
Period size: 82 Copynumber: 2.0 Consensus size: 81
33352 TTTTTAGATC
33362 GACCCTCATCGAGTTACCTTTCCAAGGGTACTTTTCCACCCTCTAGAAGCTTTAAATCAATCCGA
1 GACCCTCATCGAGTTACCTTTCCAAGGGTACTTTTCCACCCTCTAGAAGCTTTAAATCAATCCGA
33427 AATAAATTCAAAAAGT
66 AATAAATTCAAAAAGT
33443 GACCCTCATCGAGTTACCTTTCCAAGGGTACCTTTTCCACCCTCTAGAAGCTTTAAATCAATCCG
1 GACCCTCATCGAGTTACCTTTCCAAGGGTA-CTTTTCCACCCTCTAGAAGCTTTAAATCAATCCG
*
33508 AAATAAATTCAGAAAG
65 AAATAAATTCAAAAAG
33524 CGAGACAACG
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 30 0.38
82 49 0.62
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (81 bp):
GACCCTCATCGAGTTACCTTTCCAAGGGTACTTTTCCACCCTCTAGAAGCTTTAAATCAATCCGA
AATAAATTCAAAAAGT
Found at i:37041 original size:161 final size:162
Alignment explanation
Indices: 36867--37184 Score: 518
Period size: 162 Copynumber: 2.0 Consensus size: 162
36857 AAATGATGAG
* *
36867 TTTTGTATTATAGACCAATTAACATCAATTAAATTAAAAA-TTATTTGAAATTTTATATAATAAA
1 TTTTGTATTATAGACCAAATAACATCAATTAAATTAAAAATTTATTTAAAATTTTATATAAT-AA
*
36931 ATAAAAATATATAAATTTTAAAAACACCTTTATCTTTTAAC-TTTTT-AAAAAAAATAAAAAT-T
65 AT-AAAATATATAAATTTTAAAAACACCTTTATCTTTTAACTTTTTTAAAAAAAAATAAAAATCG
36993 GAGTTAAATACTTTCAACCAGAATGCTCTCATGGA
129 GA-TTAAATACTTTCAACCAGAATGCTCTCATGGA
*
37028 TTTTGTATTATAGACCAAATAATATCAATTAAATTAAAAATTTATTTAAAATTTTATATAATAAA
1 TTTTGTATTATAGACCAAATAACATCAATTAAATTAAAAATTTATTTAAAATTTTATATAATAAA
* * *
37093 TAAAATATATAAATTTTAAAAATATCTTTATCTTTTAACTTTTTTAAAAAAAAATAAAACTCGGA
66 TAAAATATATAAATTTTAAAAACACCTTTATCTTTTAACTTTTTTAAAAAAAAATAAAAATCGGA
37158 TTAAATACTTTCAACCAGAATGCTCTC
131 TTAAATACTTTCAACCAGAATGCTCTC
37185 GTGAAAGTCG
Statistics
Matches: 146, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
160 36 0.25
161 47 0.32
162 61 0.42
163 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (162 bp):
TTTTGTATTATAGACCAAATAACATCAATTAAATTAAAAATTTATTTAAAATTTTATATAATAAA
TAAAATATATAAATTTTAAAAACACCTTTATCTTTTAACTTTTTTAAAAAAAAATAAAAATCGGA
TTAAATACTTTCAACCAGAATGCTCTCATGGA
Found at i:42567 original size:22 final size:22
Alignment explanation
Indices: 42542--42606 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
42532 TATTAAAATC
42542 AATATAAATATAAAATATTTTA
1 AATATAAATATAAAATATTTTA
* * **
42564 AATACT-ATTAT-AAATAATAAA
1 AATA-TAAATATAAAATATTTTA
42585 ATATATAAATATAAAAT-TTTTA
1 A-ATATAAATATAAAATATTTTA
42607 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
21 9 0.29
22 17 0.55
23 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATAAATATAAAATATTTTA
Found at i:42593 original size:16 final size:15
Alignment explanation
Indices: 42543--42601 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
42533 ATTAAAATCA
42543 ATATAAATATAAAAT
1 ATATAAATATAAAAT
* * **
42558 ATTTTAA-ATACTAT
1 ATATAAATATAAAAT
42572 -TATAAATAATAAAAT
1 ATATAAAT-ATAAAAT
42587 ATATAAATATAAAAT
1 ATATAAATATAAAAT
42602 TTTTATTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 17 0.52
16 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAATATAAAAT
Found at i:42682 original size:18 final size:17
Alignment explanation
Indices: 42645--42685 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
42635 GTAATATTTT
* *
42645 TATTTAAAATTTTATCA
1 TATTTAAAATTATATAA
42662 TATTTAATAATTATATAA
1 TATTTAA-AATTATATAA
42680 TATTTA
1 TATTTA
42686 TTTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTAAAATTATATAA
Found at i:43091 original size:2 final size:2
Alignment explanation
Indices: 43084--43118 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43074 ATTAAAGAGC
43084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43119 CATTGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43335 original size:18 final size:18
Alignment explanation
Indices: 43312--43346 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43302 CAAAAATTAT
43312 ATTTTTCAAACTTGAATA
1 ATTTTTCAAACTTGAATA
43330 ATTTTTCAAACTTGAAT
1 ATTTTTCAAACTTGAAT
43347 GTAAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTTCAAACTTGAATA
Found at i:44259 original size:35 final size:35
Alignment explanation
Indices: 44213--44284 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
44203 TTCTTGCCAT
44213 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
1 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
44248 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
1 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
44283 AA
1 AA
44285 CACAGCCAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (35 bp):
AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
Found at i:46889 original size:79 final size:80
Alignment explanation
Indices: 46779--46932 Score: 226
Period size: 79 Copynumber: 1.9 Consensus size: 80
46769 AAAAAAAAAA
*
46779 ACAAATTCCTACTACAGCAATTGTAGCCAATAAAACCCCAGTTACTGCCAAATCTGTGT-AA-CA
1 ACAAATTCCTACTACAGCAATGGTAGCCAATAAAACCCCAGTTACTGCCAAA--TGTGTCAAGCA
46842 AAGCAAACAACTTTTCC
64 AAGCAAACAACTTTTCC
* *
46859 ACAAATTCCTA-TACAGCACA-GGTAGCCAATAAAACCCCAGTTATTGCCAAATGTGTCAAGGAA
1 ACAAATTCCTACTACAGCA-ATGGTAGCCAATAAAACCCCAGTTACTGCCAAATGTGTCAAGCAA
46922 AGCAAACAACT
65 AGCAAACAACT
46933 CTTAGCCAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
77 5 0.07
78 2 0.03
79 49 0.72
80 12 0.18
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (80 bp):
ACAAATTCCTACTACAGCAATGGTAGCCAATAAAACCCCAGTTACTGCCAAATGTGTCAAGCAAA
GCAAACAACTTTTCC
Found at i:49267 original size:46 final size:47
Alignment explanation
Indices: 49182--49276 Score: 104
Period size: 46 Copynumber: 2.0 Consensus size: 47
49172 CTATTTGTAT
* * * **
49182 ATTTTATTATATTATAATTATATTTAAATTATTTTTATATGT-ATAA
1 ATTTTAATATAATATAATAATATTTAAATTATTCCTATATGTAATAA
* *
49228 ATTTTAATATAATATAATAAATTTTTAAA-TATTCCTATATTTAATAA
1 ATTTTAATATAATATAAT-AATATTTAAATTATTCCTATATGTAATAA
49275 AT
1 AT
49277 AATTAATGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
46 26 0.65
47 14 0.35
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (47 bp):
ATTTTAATATAATATAATAATATTTAAATTATTCCTATATGTAATAA
Found at i:54647 original size:16 final size:16
Alignment explanation
Indices: 54626--54666 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
54616 TACTTTTTAC
*
54626 TTTAATTAATAGGGTT
1 TTTAATTAATAGGATT
*
54642 TTTAATTAGTAGGATT
1 TTTAATTAATAGGATT
*
54658 TTTATTTAA
1 TTTAATTAA
54667 ACTTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (16 bp):
TTTAATTAATAGGATT
Done.