Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold735
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: 29241
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:10704 original size:23 final size:21
Alignment explanation
Indices: 10673--10720 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
10663 CCGTATACAA
10673 TTTTTTTTTTCTTTCAAATTTT
1 TTTTTTTTTTCTTTC-AATTTT
*
10695 TTTTTGTTTTTTTTTCAATTTT
1 TTTTT-TTTTTCTTTCAATTTT
10717 TTTT
1 TTTT
10721 CAAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTCTTTCAATTTT
Found at i:10716 original size:11 final size:12
Alignment explanation
Indices: 10678--10733 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
10668 TACAATTTTT
10678 TTTTTCTTTCAAA
1 TTTTT-TTTCAAA
***
10691 TTTTTTTT-TGT
1 TTTTTTTTCAAA
10702 TTTTTTTTC-AA
1 TTTTTTTTCAAA
10713 TTTTTTTTCAAA
1 TTTTTTTTCAAA
10725 CTTTTTTTT
1 -TTTTTTTT
10734 TACGTACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 17 0.49
12 5 0.14
13 13 0.37
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:11059 original size:21 final size:21
Alignment explanation
Indices: 11033--11095 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
11023 TTGGTATTTG
*
11033 GGAATTGGTTCGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
11054 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
11075 GGTATTTTGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
11096 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.35
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:22038 original size:27 final size:27
Alignment explanation
Indices: 21971--22048 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
21961 AATACCATGC
* * * *
21971 GGCACTAAGTGTGCGAGTCTAACTATGT
1 GGCACTAAGTGTGCGA-TTTGATTACGT
*
21999 AGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
*
22026 GGCACTAAGTGTGCGAGTTGATT
1 GGCACTAAGTGTGCGATTTGATT
22049 GTATAGCACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 28 0.65
28 15 0.35
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (27 bp):
GGCACTAAGTGTGCGATTTGATTACGT
Found at i:22057 original size:27 final size:27
Alignment explanation
Indices: 21891--22068 Score: 105
Period size: 28 Copynumber: 6.6 Consensus size: 27
21881 AAATTGTTAC
*
21891 AGCACTAAGTGT-CGA-TTCGACTATGT
1 AGCACTAAGTGTGCGAGTT-GATTATGT
* ** *
21917 TGCACTAAGTGTGGCGAAATGAATATG-
1 AGCACTAAGTGT-GCGAGTTGATTATGT
* ** *
21944 ATGCACTAAGTGTGCG-GAAT-ACCATGC
1 A-GCACTAAGTGTGCGAG-TTGATTATGT
* * *
21971 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
21999 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
22026 GGCACTAAGTGTGCGAGTTGATTGTAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
22053 AGCACTGATGTGTGCG
1 AGCACT-AAGTGTGCG
22069 GCTCAATATA
Statistics
Matches: 119, Mismatches: 23, Indels: 18
0.74 0.14 0.11
Matches are distributed among these distances:
26 29 0.24
27 40 0.34
28 49 0.41
29 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Done.