Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1203
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: 39311
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:9742 original size:13 final size:13
Alignment explanation
Indices: 9724--9749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9714 ACATTTTATG
9724 GTGTATCGATACA
1 GTGTATCGATACA
9737 GTGTATCGATACA
1 GTGTATCGATACA
9750 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:9747 original size:33 final size:32
Alignment explanation
Indices: 9705--9768 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
9695 TACAAGCCAA
**
9705 TGTATCGATACATTTTATGGTGTATCGATACAG
1 TGTATCGATACATACTAT-GTGTATCGATACAG
*
9738 TGTATCGATACATACTGTGTGTATCGATACA
1 TGTATCGATACATACTATGTGTATCGATACA
9769 AGTTTAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATACTATGTGTATCGATACAG
Found at i:9844 original size:20 final size:20
Alignment explanation
Indices: 9798--9851 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
9788 ATTGCCAACG
*
9798 ACATGTATCGATACAATGCA
1 ACATGTATCGATACAATGAA
*
9818 ACATGTATCGATACAATTAA
1 ACATGTATCGATACAATGAA
**
9838 ATGTGTATCGATAC
1 ACATGTATCGATAC
9852 TTTTCAGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
ACATGTATCGATACAATGAA
Found at i:28379 original size:2 final size:2
Alignment explanation
Indices: 28365--28411 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
28355 GATCCAAAGA
28365 AT AT AT A- AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28405 AT AT AT A
1 AT AT AT A
28412 ACCCATATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29785 original size:26 final size:24
Alignment explanation
Indices: 29734--29785 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
29724 TAAATAACTT
* * *
29734 AAAAATTAAAAAAATATTATTTTA
1 AAAAATTAAAAAAATATCAATATA
29758 AAAAATTATAAAATAATATCAATATA
1 AAAAATTA-AAAA-AATATCAATATA
29784 AA
1 AA
29786 TTTACCACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 4 0.17
26 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAATTAAAAAAATATCAATATA
Found at i:30102 original size:27 final size:26
Alignment explanation
Indices: 30037--30102 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
30027 TAATATTTTT
* *
30037 ATAAATTATAAA-TATCAAATATACTA
1 ATAAATTA-AAATTAACAAATATAATA
* *
30063 ATATTATTTAAATTAACAAATATTAATA
1 ATA-AATTAAAATTAACAAATA-TAATA
30091 ATAAATTAAAAT
1 ATAAATTAAAAT
30103 AATTAACATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 6 0.19
27 18 0.58
28 7 0.23
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (26 bp):
ATAAATTAAAATTAACAAATATAATA
Found at i:30997 original size:3 final size:3
Alignment explanation
Indices: 30976--31015 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
30966 TCACTGCCAG
* *
30976 CAA CAA CAG TAA CACA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CA-A CAA CAA CAA CAA CAA CAA CAA CAA
31016 GAACCAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.33, G:0.03, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:33806 original size:1 final size:1
Alignment explanation
Indices: 33800--33868 Score: 66
Period size: 1 Copynumber: 69.0 Consensus size: 1
33790 GGGAATTGAA
* * * * * * * *
33800 GGGGGGGGAGGAGGGAGGGAGGGGGGGGGGGCGGGAGGGGGGGGGGGGGGGGGAGAGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
33865 GGGG
1 GGGG
33869 AAATTAATAA
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.10, C:0.01, G:0.88, T:0.00
Consensus pattern (1 bp):
G
Found at i:33824 original size:20 final size:18
Alignment explanation
Indices: 33799--33869 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 18
33789 TGGGAATTGA
33799 AGGGGGGGGAGGAGGGAGGG
1 AGGGGGGGG-GG-GGGAGGG
33819 AGGGGGGGGGGGCGGGAGGG
1 A-GGGGGGGGGG-GGGAGGG
*
33839 -GGGGGGGGGGGGG-GAG
1 AGGGGGGGGGGGGGAGGG
33855 AGGGGGGGGGGGGGA
1 AGGGGGGGGGGGGGA
33870 AATTAATAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.04
17 16 0.35
18 10 0.22
20 10 0.22
21 8 0.17
ACGTcount: A:0.13, C:0.01, G:0.86, T:0.00
Consensus pattern (18 bp):
AGGGGGGGGGGGGGAGGG
Found at i:33836 original size:24 final size:21
Alignment explanation
Indices: 33800--33868 Score: 95
Period size: 20 Copynumber: 3.2 Consensus size: 21
33790 GGGAATTGAA
33800 GGGGGGGGAGGAGGGAGGGAGGG
1 GGGGGGGGAGGAGGG-GGG-GGG
*
33823 GGGGGGGGCGGGAGGGGGGGGG
1 GGGGGGGG-AGGAGGGGGGGGG
33845 GGGGGGGGA-GAGGGGGGGGG
1 GGGGGGGGAGGAGGGGGGGGG
33865 GGGG
1 GGGG
33869 AAATTAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 15 0.35
22 11 0.26
23 11 0.26
24 6 0.14
ACGTcount: A:0.10, C:0.01, G:0.88, T:0.00
Consensus pattern (21 bp):
GGGGGGGGAGGAGGGGGGGGG
Found at i:34588 original size:25 final size:25
Alignment explanation
Indices: 34547--34597 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
34537 GAATTTAATC
*
34547 ATAAAATAAATAGAAAACTAATTTA
1 ATAAAATAAATAGAAAAATAATTTA
*
34572 ATAAAATTAAATA-AAAAATATTTTA
1 ATAAAA-TAAATAGAAAAATAATTTA
34597 A
1 A
34598 AACTTAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
ATAAAATAAATAGAAAAATAATTTA
Done.