Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold213
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: 483536
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 4 of 4
Found at i:439182 original size:18 final size:19
Alignment explanation
Indices: 439161--439206 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
439151 TAATATTAAA
439161 ATATTAAAAATTAT-TTTT
1 ATATTAAAAATTATATTTT
* *
439179 ATATTAATATTTATATTTT
1 ATATTAAAAATTATATTTT
439198 ATAATTAAA
1 AT-ATTAAA
439207 TTAAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.52
19 6 0.26
20 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAAAAATTATATTTT
Found at i:440079 original size:2 final size:2
Alignment explanation
Indices: 440072--440112 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
440062 TACTTCCGTC
440072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
440113 GGGCCTAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:440178 original size:17 final size:18
Alignment explanation
Indices: 440140--440186 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
440130 TTTGTTTATA
440140 AATATAATAT-AAAATAT
1 AATATAATATAAAAATAT
*
440157 GATATAATATAAAAAT-T
1 AATATAATATAAAAATAT
440174 AATATATATATAA
1 AATATA-ATATAA
440187 TATAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATATAATATAAAAATAT
Found at i:441107 original size:33 final size:33
Alignment explanation
Indices: 441043--441107 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
441033 TATTTTTATA
* * *
441043 TTATATCATATTTTATTTTATATTTTAATTTTT
1 TTATATCATATTATATTATATAATTTAATTTTT
*
441076 TTATATGATATTCATATTATATAATTT-ATTTT
1 TTATATCATATT-ATATTATATAATTTAATTTT
441108 GTGTTCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (33 bp):
TTATATCATATTATATTATATAATTTAATTTTT
Found at i:443463 original size:3 final size:3
Alignment explanation
Indices: 443455--443485 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
443445 AGTTGACCAA
443455 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
443486 TAACTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:445968 original size:2 final size:2
Alignment explanation
Indices: 445963--445993 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
445953 TTCAAAAAAT
*
445963 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
445994 TTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:448570 original size:4 final size:4
Alignment explanation
Indices: 448561--448589 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
448551 AAAATTGACA
448561 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
448590 CATTGCTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:451144 original size:2 final size:2
Alignment explanation
Indices: 451139--451179 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
451129 AAAAAGGTGT
*
451139 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
451180 TGTATTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:453538 original size:66 final size:66
Alignment explanation
Indices: 453432--453562 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
453422 GCACTCATCC
453432 TGAACTTGTTCTTTCATATTTTGGTAATCCTGGAACTTCAGTTTTTGGTAAATAGCCTCTTTCAA
1 TGAACTTGTTCTTTCATATTTTGGTAATCCTGGAACTTCAGTTTTTGGTAAATAGCCTCTTTCAA
453497 A
66 A
*
453498 TGAACTTGTTCTTTCATATTTTGGTAATCCTGGAACTTCAGTTTTTGGTAAATGGCCTCTTTCAA
1 TGAACTTGTTCTTTCATATTTTGGTAATCCTGGAACTTCAGTTTTTGGTAAATAGCCTCTTTCAA
453563 CTCGCTTTCG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (66 bp):
TGAACTTGTTCTTTCATATTTTGGTAATCCTGGAACTTCAGTTTTTGGTAAATAGCCTCTTTCAA
A
Found at i:456452 original size:24 final size:24
Alignment explanation
Indices: 456420--456477 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
456410 CATATTGACG
456420 ATATCTTAGAAGATTTGTGAAATA
1 ATATCTTAGAAGATTTGTGAAATA
456444 ATATCTTAG-AGATTTGTGAAATA
1 ATATCTTAGAAGATTTGTGAAATA
456467 ATATCTTAGAA
1 ATATCTTAGAA
456478 AATTATAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.70
24 10 0.30
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (24 bp):
ATATCTTAGAAGATTTGTGAAATA
Found at i:461129 original size:24 final size:24
Alignment explanation
Indices: 461097--461154 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
461087 CATATTGATG
461097 ATATCTTAGAAGATTTGTGAAATA
1 ATATCTTAGAAGATTTGTGAAATA
461121 ATATCTTAG-AGATTTGTGAAATA
1 ATATCTTAGAAGATTTGTGAAATA
461144 ATATCTTAGAA
1 ATATCTTAGAA
461155 AATTATAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.70
24 10 0.30
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (24 bp):
ATATCTTAGAAGATTTGTGAAATA
Found at i:477019 original size:13 final size:13
Alignment explanation
Indices: 477001--477025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
476991 CACCAAAGTT
477001 TGTATCGATACAA
1 TGTATCGATACAA
477014 TGTATCGATACA
1 TGTATCGATACA
477026 CAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:477023 original size:33 final size:33
Alignment explanation
Indices: 476981--477045 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
476971 TAGCCAAACT
* **
476981 TGTATCGATACACCAAAGTTTGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
477014 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
477046 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:478187 original size:12 final size:12
Alignment explanation
Indices: 478170--478196 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
478160 TAAAAATTAA
478170 AAATTCAAATTC
1 AAATTCAAATTC
478182 AAATTCAAATTC
1 AAATTCAAATTC
478194 AAA
1 AAA
478197 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:478470 original size:50 final size:50
Alignment explanation
Indices: 478327--478489 Score: 274
Period size: 50 Copynumber: 3.3 Consensus size: 50
478317 AATAGAAAAT
*
478327 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
* * *
478377 GCATGCATGGGAAAACA-CAAAATTGCAATTGGAGACAAAACATGCGGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
478426 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
478476 ACATGCATGGGAAA
1 GCATGCATGGGAAA
478490 TGAAAAAAGC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 45 0.43
50 59 0.57
ACGTcount: A:0.43, C:0.15, G:0.27, T:0.15
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:480178 original size:79 final size:79
Alignment explanation
Indices: 480045--480793 Score: 1250
Period size: 79 Copynumber: 9.5 Consensus size: 79
480035 GTTAAGTTTC
480045 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
480110 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * *
480124 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
480189 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
480203 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
480268 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * *
480282 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
480347 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
480361 TCAATTTTTCATAATCGGGGATACTCCAATCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGGT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGGT
480425 TTTATTTCTAAAACA
65 TTTATTTCTAAAACA
* * *
480440 TAAATTTTTCATAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGG-T
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
480504 TTATTTCTAAAATA
66 TTATTTCTAAAACA
*
480518 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
* *
480583 TTATTTTTAAAATA
66 TTATTTCTAAAACA
* *
480597 TTAATTTTTCACAATCGGGGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
480662 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
480676 CCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
480741 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
480755 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATT
480794 ATCTCCAAAA
Statistics
Matches: 630, Mismatches: 37, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
78 77 0.12
79 549 0.87
80 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:480644 original size:315 final size:316
Alignment explanation
Indices: 480045--480793 Score: 1313
Period size: 315 Copynumber: 2.4 Consensus size: 316
480035 GTTAAGTTTC
*
480045 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGGATACTCCAACCCCGGT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCGGT
* * *
480109 TTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
65 TTTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
*
480174 ACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTT
130 ACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTT
480239 ATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGAT
195 ATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGAT
480304 ACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACA
260 ACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACA
*
480361 TCAATTTTTCATAATCGGGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTT
* *
480426 TTATTTCTAAAACATAAATTTTTCATAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATA
66 TTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
* *
480491 CTCCAACCCCGG-TTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
131 CTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
*
480555 TTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAAAATATTAATTTTTCACAATCGGGGATA
196 TTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATA
* * *
480620 CTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
261 CTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACA
* *
480676 CCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTT
* *
480741 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATT
66 TTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAACCCCGTTATT
480794 ATCTCCAAAA
Statistics
Matches: 412, Mismatches: 20, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
315 278 0.67
316 133 0.32
317 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (316 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
CTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
TTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATA
CTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACA
Done.