Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 400853
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:346979 original size:20 final size:19
Alignment explanation
Indices: 346930--346979 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
346920 GGGCACACAC
*
346930 CCGTGTGGCCTGGGACATG
1 CCGTGTGGCCTAGGACATG
346949 CCAGTGTGGCCTAGGACATGG
1 CC-GTGTGGCCTAGGACAT-G
*
346970 CCGTGGGGCC
1 CCGTGTGGCC
346980 AGGCCGTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.12, C:0.28, G:0.42, T:0.18
Consensus pattern (19 bp):
CCGTGTGGCCTAGGACATG
Found at i:348763 original size:12 final size:12
Alignment explanation
Indices: 348723--348756 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
348713 AAAACCCTAT
*
348723 TTTTTCCTT-TC
1 TTTTTCTTTCTC
348734 TTTTTCTTTCTC
1 TTTTTCTTTCTC
348746 TTTTTCTTTCT
1 TTTTTCTTTCT
348757 TTCTTTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:364746 original size:20 final size:20
Alignment explanation
Indices: 364709--364746 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
364699 TTCTTTGAAT
*
364709 TTGTCTTTAAAATGAAAAGG
1 TTGTCTTTAAAATAAAAAGG
*
364729 TTGTTTTTAAAATAAAAA
1 TTGTCTTTAAAATAAAAA
364747 AAATAGGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGTCTTTAAAATAAAAAGG
Found at i:368586 original size:13 final size:13
Alignment explanation
Indices: 368564--368600 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
368554 TATTGACAAG
*
368564 TTTTTGGTTTTTT
1 TTTTTTGTTTTTT
368577 TTTTTTG-TTTTT
1 TTTTTTGTTTTTT
368589 TTTTTTGTTTTT
1 TTTTTTGTTTTT
368601 CTGATGACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:378994 original size:33 final size:33
Alignment explanation
Indices: 378952--379019 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
378942 ACATAGAGTG
378952 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
1 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
378985 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
1 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
379018 GA
1 GA
379020 TCTTTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.34, T:0.15
Consensus pattern (33 bp):
GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
Found at i:379493 original size:41 final size:40
Alignment explanation
Indices: 379406--379492 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
379396 ATACAAATAA
*
379406 GAAAAAGGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
1 GAAAAAAGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
*
379446 GAAAAAAGAAAAC-CTAAAAATTAGCTATGAATTTAAGCTT
1 GAAAAAAGAAAACTC-AAAAATTAGCTACGAATTTAAGCTT
379486 GAAAAAA
1 GAAAAAA
379493 AATGAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (40 bp):
GAAAAAAGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
Found at i:382590 original size:30 final size:31
Alignment explanation
Indices: 382537--382594 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
382527 CATGTAAAAA
382537 CCTTTAAAATAATAATAAAAATTAACAAATG
1 CCTTTAAAATAATAATAAAAATTAACAAATG
382568 CCTTTAAAATAA-AA-ACAAAATTAACAA
1 CCTTTAAAATAATAATA-AAAATTAACAA
382595 TAAAATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 1 0.04
30 13 0.50
31 12 0.46
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (31 bp):
CCTTTAAAATAATAATAAAAATTAACAAATG
Found at i:383128 original size:25 final size:25
Alignment explanation
Indices: 383089--383146 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
383079 TAGCCCTTTC
* *
383089 GAGCTTTCCGTTATATGGTTCTTAT
1 GAGCTTCCCATTATATGGTTCTTAT
*
383114 GAGTTTCCCATTATATGGTTCTTAT
1 GAGCTTCCCATTATATGGTTCTTAT
383139 GAGCTTCC
1 GAGCTTCC
383147 TGTTAATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGTTCTTAT
Found at i:386561 original size:20 final size:20
Alignment explanation
Indices: 386536--386605 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
386526 CTTTTGGACA
386536 TAATTGCAATTACTATAGTC
1 TAATTGCAATTACTATAGTC
* * * * *
386556 TAATTGGAACGATACTTTTGGAC
1 TAATTGCAA--TTAC-TATAGTC
386579 ATAATTGCAATTACTATAGTC
1 -TAATTGCAATTACTATAGTC
386600 TAATTG
1 TAATTG
386606 TATATGTTCA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 14 0.39
21 4 0.11
22 6 0.17
23 4 0.11
24 8 0.22
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (20 bp):
TAATTGCAATTACTATAGTC
Found at i:386581 original size:44 final size:44
Alignment explanation
Indices: 386518--386605 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
386508 CGAATTATCA
386518 GAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATTG
1 GAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATTG
386562 GAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATTG
1 GAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATTG
386606 TATATGTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (44 bp):
GAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATTG
Found at i:395728 original size:79 final size:79
Alignment explanation
Indices: 395593--395739 Score: 267
Period size: 79 Copynumber: 1.9 Consensus size: 79
395583 TTTGGGTTGA
395593 TTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCATTTCTA
1 TTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCATTTCTA
395658 GAATTTTTCTTTTT
66 GAATTTTTCTTTTT
* * *
395672 TTTAGTTTGCTGTTAGAGACATGTAAAGGTGACGACTTTTCATGATCTTTGGATAGTCATTTCTA
1 TTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCATTTCTA
395737 GAA
66 GAA
395740 AATTTTTGGG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (79 bp):
TTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCATTTCTA
GAATTTTTCTTTTT
Found at i:399794 original size:30 final size:30
Alignment explanation
Indices: 399762--399821 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
399752 TGACATCCTT
*
399762 AAACTATGATTCAGATTTTTAAATTGGTTTAA
1 AAACTATGATTCAGA-TTCTAAATTGGTTT-A
* *
399794 AAATTATGATTGAGATTCTAAATTGGTT
1 AAACTATGATTCAGATTCTAAATTGGTT
399822 CAGAGAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
AAACTATGATTCAGATTCTAAATTGGTTTA
Done.