Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2854
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: 38941
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:5754 original size:21 final size:22
Alignment explanation
Indices: 5719--5770 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
5709 AGGCACTTTA
5719 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
5742 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
5763 TGTGTCGT
1 TGTGTCGT
5771 TTTAGACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 20 0.69
23 9 0.31
ACGTcount: A:0.12, C:0.25, G:0.29, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:18189 original size:131 final size:131
Alignment explanation
Indices: 17892--18251 Score: 442
Period size: 131 Copynumber: 2.7 Consensus size: 131
17882 CTTAGAAAAT
** * * *
17892 ATGAGTGAAATTCCGAAGGGATATTCGATTATTTGATA-CAAACGGGAGATTGCAACCCAGCACG
1 ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTA-AGCAAACGAGAAATTGCAACCCAGCACG
* * * * ** ** *
17956 ATAGGGCACTACTCCCTGAATTGCCAAACATCGAGTATTTCCTTTGTTTTAAAGAGTTTTTAGAA
65 TTAGGGCACGATTCCC-GAATTGCCAAATATCGAGTATCGCCTTTCATTTAAAGAGTTTTTAAAA
18021 GAC
129 GAC
* *
18024 ATGAATGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACGT
1 ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACGT
*
18089 TAGGGCACGATTCCGCGAATTGCCAAATATCGCA-TATCGCC-TTCATTT-AAGGGATTTTTAAA
66 TAGGGCACGATTCC-CGAATTGCCAAATATCG-AGTATCGCCTTTCATTTAAAGAG-TTTTTAAA
18151 AGAC
128 AGAC
* *
18155 ATTG-GTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACG
1 A-TGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACG
18219 TTAGGGCACGATTCCACGAATTGCCAAAATATC
65 TTAGGGCACGATTCC-CGAATTGCC-AAATATC
18252 AAATCTCGTC
Statistics
Matches: 200, Mismatches: 22, Indels: 12
0.85 0.09 0.05
Matches are distributed among these distances:
130 4 0.02
131 98 0.49
132 96 0.48
133 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (131 bp):
ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACGT
TAGGGCACGATTCCCGAATTGCCAAATATCGAGTATCGCCTTTCATTTAAAGAGTTTTTAAAAGA
C
Found at i:21668 original size:132 final size:133
Alignment explanation
Indices: 21379--21730 Score: 494
Period size: 132 Copynumber: 2.7 Consensus size: 133
21369 GTTAAGGCAA
* * * * * * **
21379 TGGCTTGAATCTGCTTCACTGCAACTTCAAGAAGACTAGATTCATCATCTTTGATCTGCTCTTCT
1 TGGCTTAAATCTGCTTCACTGCAATTTCAGGAAGCCTAGATTCACCGTCTTTGATCTGCTCCACT
*
21444 GCAACTTCAGGGAGATA-GA-ATCTACAATCTTCAGCCTACTCCACGACAACTTTAGGGAGCTAG
66 GCAACTTCAGGGA-A-ACGAGATCTAAAATCTTCAGCCTACTCCACGACAACTTTAGGGAGCTAG
21507 GTCGG
129 GTCGG
* *
21512 TGGCTTAAATCTACTTCACTGCAATTTTAGGAAGCCTAGATTCACCGTCTTTGATCTGCTCCACT
1 TGGCTTAAATCTGCTTCACTGCAATTTCAGGAAGCCTAGATTCACCGTCTTTGATCTGCTCCACT
* *
21577 GCAACTTCAGGGAAACGAGATCTAAAAT-TTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGT
66 GCAACTTCAGGGAAACGAGATCTAAAATCTTCAGCCTACTCCACGACAACTTTAGGGAGCTAGGT
*
21641 TGG
131 CGG
* * * * *
21644 TGGTTTAAATCTGTTTTACTGCAATTTCAGGAAGCCTAGATTCACCGTCTTCGATCTACTCCACT
1 TGGCTTAAATCTGCTTCACTGCAATTTCAGGAAGCCTAGATTCACCGTCTTTGATCTGCTCCACT
21709 GCAACTTCAGGGAAACGAGATC
66 GCAACTTCAGGGAAACGAGATC
21731 CGTAGGATTC
Statistics
Matches: 196, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
131 1 0.01
132 119 0.61
133 76 0.39
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (133 bp):
TGGCTTAAATCTGCTTCACTGCAATTTCAGGAAGCCTAGATTCACCGTCTTTGATCTGCTCCACT
GCAACTTCAGGGAAACGAGATCTAAAATCTTCAGCCTACTCCACGACAACTTTAGGGAGCTAGGT
CGG
Found at i:22632 original size:3 final size:3
Alignment explanation
Indices: 22624--22664 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
22614 CTCTCCATCT
22624 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
22665 TTGAGCGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:24952 original size:23 final size:23
Alignment explanation
Indices: 24922--25008 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
24912 GCTTTACTGA
* *
24922 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
24945 TCAGGCACCTCATGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
24966 TCAGGCACCTCATGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
24988 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
25009 ACTGATTAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
21 36 0.63
22 2 0.04
23 19 0.33
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:32792 original size:23 final size:23
Alignment explanation
Indices: 32762--32848 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
32752 GCTTTACTGA
* *
32762 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
32785 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
32806 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
32828 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
32849 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Done.