Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1881
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: 32819
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:3361 original size:40 final size:39
Alignment explanation
Indices: 3315--3544 Score: 277
Period size: 40 Copynumber: 5.8 Consensus size: 39
3305 TATAACCACA
* * *
3315 AGCACAATTGCCTTCGGGTCTTAACCCGGGAT-TAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAACCC-GGATAAAAC-ACT
* * * *
3355 CGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAAC-ACT
* *
3395 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAA-CACT
3435 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAA-CACT
*
3475 AGCATAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAA-CACT
* *
3515 AG--CAAATGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATA
3545 TCATTCAAAT
Statistics
Matches: 176, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
38 25 0.14
39 4 0.02
40 146 0.83
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (39 bp):
AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAACACT
Found at i:10515 original size:24 final size:24
Alignment explanation
Indices: 10483--10528 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
10473 AGTGTTATGA
* *
10483 GGAGGAAATCAATGAGAGGATTGG
1 GGAGAAAATCAAGGAGAGGATTGG
10507 GGAGAAAATCAAGGAGAGGATT
1 GGAGAAAATCAAGGAGAGGATT
10529 ATGGAGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.39, T:0.15
Consensus pattern (24 bp):
GGAGAAAATCAAGGAGAGGATTGG
Found at i:10534 original size:24 final size:24
Alignment explanation
Indices: 10483--10535 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10473 AGTGTTATGA
* * *
10483 GGAGGAAATCAATGAGAGGATTGG
1 GGAGAAAATCAAGGAGAGGATTAG
*
10507 GGAGAAAATCAAGGAGAGGATTAT
1 GGAGAAAATCAAGGAGAGGATTAG
10531 GGAGA
1 GGAGA
10536 GATTTTAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.40, T:0.15
Consensus pattern (24 bp):
GGAGAAAATCAAGGAGAGGATTAG
Found at i:11969 original size:27 final size:27
Alignment explanation
Indices: 11939--11992 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
11929 ATGACCAAAA
*
11939 TACCCCTATAGGGTAAAATGACT-ATTT
1 TACCCCTAGAGGGT-AAATGACTGATTT
*
11966 TACCCCTCGAGGGTAAATGACTGATTT
1 TACCCCTAGAGGGTAAATGACTGATTT
11993 GTGCTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (27 bp):
TACCCCTAGAGGGTAAATGACTGATTT
Found at i:12156 original size:26 final size:26
Alignment explanation
Indices: 12119--12199 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
12109 TTTGCCACAT
*
12119 ATACTAATACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * * * **
12145 TTACTGTTACTGGCAACTCTGCTAAG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
12171 ATATTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
12197 ATA
1 ATA
12200 TTGGTGTGTT
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:18595 original size:56 final size:56
Alignment explanation
Indices: 18504--18626 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
18494 GAGATTGGCG
* * *
18504 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
18561 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
18616 CTGAGTGTGCG
1 CTAAGTGTGCG
18627 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:18613 original size:27 final size:28
Alignment explanation
Indices: 18504--18626 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
18494 GAGATTGGCG
* * * *
18504 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
18533 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
18561 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
18589 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
18616 CTGAGTGTGCG
1 CTAAGTGTGCG
18627 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:18637 original size:27 final size:27
Alignment explanation
Indices: 18529--18639 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
18519 TAAATTGTAC
* * *
18529 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18557 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18585 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
18612 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
18639 A
1 A
18640 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:26693 original size:29 final size:28
Alignment explanation
Indices: 26649--26716 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
26639 GAGATTGGCG
*
26649 CTAAGTGTGCGGGTTTAAAT-TGTACAGCA
1 CTAAGTGTGCGAGTTTAAATATGT--AGCA
* *
26678 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATATGTAGCA
26706 CTAAGTGTGCG
1 CTAAGTGTGCG
26717 GACTTAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.43
29 17 0.49
30 3 0.09
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTAAATATGTAGCA
Found at i:31819 original size:28 final size:28
Alignment explanation
Indices: 31782--31839 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
31772 CGTTATCCTT
* * *
31782 AAAATCGTATATGGTGTAAACTAGTTTA
1 AAAATCGTATATGGCGTAAACCAATTTA
31810 AAAATCGTATATGGCGTAAACCAATTTA
1 AAAATCGTATATGGCGTAAACCAATTTA
31838 AA
1 AA
31840 CTACAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (28 bp):
AAAATCGTATATGGCGTAAACCAATTTA
Done.