Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3732
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: 42516
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:3420 original size:30 final size:30
Alignment explanation
Indices: 3384--3443 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3374 TTCTCGATCC
* *
3384 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATATAATTATGCAAAAGTT
* *
3414 TAGGGGCAAAAATATAATTTTGCCAAAGTT
1 TAGGGGCAAAAATATAATTATGCAAAAGTT
3444 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATATAATTATGCAAAAGTT
Found at i:7510 original size:27 final size:28
Alignment explanation
Indices: 7480--7541 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
7470 TAAAATAGTA
*
7480 ACCCCTGAGTATG-AAAATTACCATTAT
1 ACCCCTAAGTATGCAAAATTACCATTAT
7507 ACCCCTAAGTATGCAAAATTACCATTAT
1 ACCCCTAAGTATGCAAAATTACCATTAT
7535 ACCCCTA
1 ACCCCTA
7542 GGGCATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27
Consensus pattern (28 bp):
ACCCCTAAGTATGCAAAATTACCATTAT
Found at i:7661 original size:28 final size:27
Alignment explanation
Indices: 7621--7731 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
7611 GGAGGAAGCG
7621 TTCTGGTGGCTATGCCACAATTATCTGT
1 TTCTGGTGGCTATGCCACAA-TATCTGT
*
7649 TTCTGGTGGCTATGCAACAATTATCTG-
1 TTCTGGTGGCTATGCCACAA-TATCTGT
*
7676 TTCTGGTGGCTCTGCCACAATATCTGT
1 TTCTGGTGGCTATGCCACAATATCTGT
* * * *
7703 ATCTGGTGACTCTGTCACAATATCTGT
1 TTCTGGTGGCTATGCCACAATATCTGT
7730 TT
1 TT
7732 TGGCAGCCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.08
27 43 0.57
28 26 0.35
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.39
Consensus pattern (27 bp):
TTCTGGTGGCTATGCCACAATATCTGT
Found at i:26591 original size:47 final size:46
Alignment explanation
Indices: 26529--26651 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 46
26519 CTTGAGGCTG
*
26529 ATGCATGTCCCAGACATGCCTTACACTAGCGCTCGTC-TCAA-TGCCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCGCTC-TCAT-AAGTGCCA
*
26575 ATGACATGTCCCAGACATGGTCTTACACTA--GCTCTCATAATGTGCCC
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCGCTCTCATAA-GTGCCA
*
26622 ATGCAAGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
26652 TCACACAAGT
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
45 15 0.22
46 21 0.31
47 21 0.31
48 10 0.15
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCGCTCTCATAAGTGCCA
Found at i:33903 original size:80 final size:80
Alignment explanation
Indices: 33686--33950 Score: 349
Period size: 80 Copynumber: 3.3 Consensus size: 80
33676 TTGAATGATG
* * *
33686 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAATCCGGACTAAGATCCGAAGGCATT
* * *
33750 TGTGAGAGATACTAAT
65 TGTGCGAGTTACTAAA
* * *
33766 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATTCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGACTAAGATCCGAAGGCATTT
33830 GTGCGAGTTACTAAA
66 GTGCGAGTTACTAAA
* **
33845 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
33909 TGTGCAAGTTACTATAA
65 TGTGCGAGTTACTA-AA
*
33926 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33951 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
79 63 0.39
80 98 0.60
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:33964 original size:40 final size:40
Alignment explanation
Indices: 33686--33950 Score: 315
Period size: 40 Copynumber: 6.7 Consensus size: 40
33676 TTGAATGATG
* * * *
33686 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
33726 TCCGGACTAAGAT-CCGAAGGCATTTGTGAGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
33766 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
33805 TCCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
33845 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
33885 TCCGGGTTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
33926 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33951 AACGAGTAGC
Statistics
Matches: 194, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
39 34 0.18
40 151 0.78
41 9 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.