Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold910
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: 27442
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:8148 original size:39 final size:39
Alignment explanation
Indices: 8091--8241 Score: 184
Period size: 39 Copynumber: 3.9 Consensus size: 39
8081 ATATAGCAAC
* *
8091 CACTCGCACAAATGCCTTCGGGTCTTAGCCGGATATAGT
1 CACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
** *
8130 CACTAGCATGAATGCCTTCGGGACTTAGCCCGATATAGT
1 CACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
8169 CACTAGCACAAATGCC-TCGGGACTTAGCCCGG-TATAG-
1 CACTAGCACAAATGCCTTCGGGACTTAG-CCGGATATAGT
*
8206 AACTACTGCACAAATGCCTTC-GGACTTAGCCCGGAT
1 CACTA--GCACAAATGCCTTCGGGACTTAG-CCGGAT
8242 TCACTCCGAA
Statistics
Matches: 98, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.04
38 16 0.16
39 75 0.77
40 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
Found at i:18553 original size:49 final size:47
Alignment explanation
Indices: 18390--18826 Score: 651
Period size: 47 Copynumber: 9.2 Consensus size: 47
18380 AATTCTAAAT
18390 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
18437 TGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
18483 TGTGATAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
18532 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
18581 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
18628 TGCGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
18677 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
18724 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
18771 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
18818 TGTGATAAG
1 TGTGATAAG
18827 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
46 45 0.13
47 174 0.49
49 138 0.39
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:18626 original size:96 final size:94
Alignment explanation
Indices: 18390--18826 Score: 651
Period size: 96 Copynumber: 4.6 Consensus size: 94
18380 AATTCTAAAT
18390 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
18454 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
* *
18483 TGTGATAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
18548 GGCCGATGTGATGAATGTGAAAGTGTATATATA
64 GGCCGATGTGATGAATGTGAAAGTG--TATATA
* * * *
18581 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGCGATAAGGCCTAATAG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
18646 CCGATGTGATGAATGTGAAAGTGTATATATA
66 CCGATGTGATGAATGTGAAAGTG--TATATA
* ** *
18677 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
18742 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
18771 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
18827 TCCCGAAGGG
Statistics
Matches: 314, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
93 39 0.12
94 51 0.16
95 16 0.05
96 164 0.52
98 44 0.14
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATA
Found at i:18999 original size:37 final size:37
Alignment explanation
Indices: 18943--19021 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
18933 TCGAGCTCTA
* * *
18943 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
18980 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
19017 AAGAC
1 AAGAC
19022 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20930 original size:43 final size:43
Alignment explanation
Indices: 20882--21070 Score: 342
Period size: 43 Copynumber: 4.4 Consensus size: 43
20872 TTGGTTTTCA
*
20882 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
*
20925 GCACTAAGTGTGCGGGCAATCAGTGTTCACGGTTGCGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
20968 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
* *
21011 GCACTAAGTGTGCGGGCAATAAGTATTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
21054 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
21071 TTGAAATGCA
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 141 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGCGAGATTG
Found at i:21085 original size:29 final size:29
Alignment explanation
Indices: 21052--21125 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
21042 GTTGTGAGAT
* *
21052 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
21081 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
21110 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
21126 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:21461 original size:40 final size:40
Alignment explanation
Indices: 21417--21684 Score: 242
Period size: 40 Copynumber: 6.7 Consensus size: 40
21407 CATTTGAATG
*
21417 ATATCCGGGCTAAGTCCCGAAGGCAATT-GAGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCAATTCGTGCTAGTGA-T
* * * *
21457 ATATCCGGGCTAAGACCCGAAGGC-ATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGTCCCGAAGGCAATTCGTGC-TAGTGAT
* *
21497 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTGAT
1 ATATCCGGGCTAAGTCCCGAAGGCAATTCGTGCTAG-TGAT
* * * *
21537 ATATCCGGGCTAAGACCCGAAGGC-ATTGGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCAATTCGTGCTAGTGA-T
* * * *
21577 AAATCCGGGCTAAATTCCGAAGAGC-ATTCGTGCTAGTGAG
1 ATATCCGGGCTAAGTCCCGAAG-GCAATTCGTGCTAGTGAT
* * * * *
21617 GTATCCGGACTAAGTTCCGAAGAGC-ATTCGTGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAG-GCAATTCGTGCTAGTGAT
*
21657 ATATCCGGGCTAGGTCCCGAAGAGCAAT
1 ATATCCGGGCTAAGTCCCGAAG-GCAAT
21685 CATGCTGGTG
Statistics
Matches: 194, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
39 10 0.05
40 162 0.84
41 22 0.11
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCAATTCGTGCTAGTGAT
Found at i:21630 original size:120 final size:120
Alignment explanation
Indices: 21417--21684 Score: 276
Period size: 120 Copynumber: 2.2 Consensus size: 120
21407 CATTTGAATG
* * *
21417 ATATCCGGGCTAAGTCCCGAAGGCAATTGAGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCAATTGAGCGAGTGACTAAATCCGGGCTAAGACCCGAAGGCA
* * * * *
21482 TTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAG-GCAATT-GTGCAAGTTGAT
66 TTCGTGCGAAGTGAGATATCCGGACTAAGACCCGAAGAGC-ATTCGTGC-AGGTGAT
* * * *
21537 ATATCCGGGCTAAGACCCGAAGGC-ATTGGTGCGAGTTACTAAATCCGGGCTAA-ATTCCGAAGA
1 ATATCCGGGCTAAGTCCCGAAGGCAATT-GAGCGAGTGACTAAATCCGGGCTAAGA-CCCGAAG-
* * ** * *
21600 GCATTCGTGC-TAGTGAGGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTT
63 GCATTCGTGCGAAGTGAGATATCCGGACTAAGACCCGAAGAGCATTCGTGCAGGTGAT
*
21657 ATATCCGGGCTAGGTCCCGAAGAGCAAT
1 ATATCCGGGCTAAGTCCCGAAG-GCAAT
21685 CATGCTGGTG
Statistics
Matches: 121, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
119 4 0.03
120 98 0.81
121 17 0.14
122 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAGTCCCGAAGGCAATTGAGCGAGTGACTAAATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAAGTGAGATATCCGGACTAAGACCCGAAGAGCATTCGTGCAGGTGAT
Found at i:21691 original size:40 final size:40
Alignment explanation
Indices: 21618--21694 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
21608 GCTAGTGAGG
* * *
21618 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTTA
1 TATCCGGACTAAGTCCCGAAGAGCAATCATGCTGGTGTTA
* *
21658 TATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 TATCCGGACTAAGTCCCGAAGAGCAATCATGCTGGTG
21695 ACATGTATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (40 bp):
TATCCGGACTAAGTCCCGAAGAGCAATCATGCTGGTGTTA
Found at i:25227 original size:49 final size:47
Alignment explanation
Indices: 25021--25504 Score: 729
Period size: 47 Copynumber: 10.2 Consensus size: 47
25011 AATTCTAAAT
25021 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
25068 TGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
25114 TGTGA-ATAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATA-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
25161 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
*
25210 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* * *
25259 TGTGACAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
25306 TGCGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
25355 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
25402 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
25449 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
25496 TGTGATAAG
1 TGTGATAAG
25505 TCCCGAAGGG
Statistics
Matches: 404, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.00
46 44 0.11
47 221 0.55
48 1 0.00
49 137 0.34
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:25304 original size:96 final size:94
Alignment explanation
Indices: 25021--25504 Score: 729
Period size: 96 Copynumber: 5.1 Consensus size: 94
25011 AATTCTAAAT
25021 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
25085 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
25114 TGTGA-ATAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
1 TGTGATA-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
25178 GCCGATGTGATGAATGTGAAAGTGTATATATA
65 GCCGATGTGATGAATGTGAAAGTG--TATATA
* * *
25210 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGACAAGGCTTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
*
25275 GGCCGATGTGATGAATGTGAAAGTGTATATG
64 GGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
25306 TGCGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
*
25371 GGCCGATGTGATGAATGTGAAAGTGTATATG
64 GGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * *
25402 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
* * * *
25467 CCAATGTGATGGATGTGAAAGTGCATAAA
66 CCGATGTGATGAATGTGAAAGTGTATATA
25496 TGTGATAAG
1 TGTGATAAG
25505 TCCCGAAGGG
Statistics
Matches: 361, Mismatches: 23, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.00
93 55 0.15
94 81 0.22
96 178 0.49
97 1 0.00
98 45 0.12
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (94 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATA
Found at i:25676 original size:37 final size:37
Alignment explanation
Indices: 25620--25698 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
25610 TCGAGCTCTA
* * *
25620 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
25657 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
25694 AAGAC
1 AAGAC
25699 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:27252 original size:42 final size:37
Alignment explanation
Indices: 27172--27320 Score: 140
Period size: 41 Copynumber: 3.8 Consensus size: 37
27162 TAGCAACTCA
* *
27172 CACAAATGCCTTCGGTCTTAGCCCGGATATAGTCTAG
1 CACAAATGCCTTCGGACTTAGCCCGGATATAATCTAG
**
27209 CATGAATGCCTTCGGGACTTAGCGCCGCGATATAATCACTAG
1 CACAAATGCCTTC-GGACTTAGC-CCG-GATATAAT--CTAG
* *
27251 CACAAATGCCTTCGGACTTAGCCCGGGTATAGCAACTACTCG
1 CACAAATGCCTTCGGACTTAGCCC-GG-ATA-TAA-T-CTAG
27293 CAC-AATGCCTTCGGACTTAGCCC-GATAT
1 CACAAATGCCTTCGGACTTAGCCCGGATAT
27321 CATGAACCGA
Statistics
Matches: 94, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
37 11 0.12
38 11 0.12
39 4 0.04
40 10 0.11
41 33 0.35
42 24 0.26
43 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (37 bp):
CACAAATGCCTTCGGACTTAGCCCGGATATAATCTAG
Done.