Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5971.1
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: 15394
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:3154 original size:15 final size:14
Alignment explanation
Indices: 3134--3181 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
3124 CTCATTTTCA
3134 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
3149 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
3163 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
3178 TCTT
1 TCTT
3182 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:3186 original size:22 final size:21
Alignment explanation
Indices: 3134--3192 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
3124 CTCATTTTCA
* *
3134 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
3155 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
3176 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
3193 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:4269 original size:12 final size:13
Alignment explanation
Indices: 4233--4268 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
4223 TATGCAATTT
4233 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
4247 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
4260 TTTTTTTTT
1 TTTTTTTTT
4269 CGAACTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:7656 original size:15 final size:14
Alignment explanation
Indices: 7636--7683 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
7626 CTCATTTTCA
7636 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
7651 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
7665 TCTTATTTCTTTTTT
1 TCTT-TTTCTTTTTT
7680 TCTT
1 TCTT
7684 CTCTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:7660 original size:21 final size:21
Alignment explanation
Indices: 7636--7687 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
7626 CTCATTTTCA
*
7636 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
7657 TCTTTTTCTCTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
*
7678 T-TTCTTCTCT
1 TCTTTTTCTCT
7688 CAATTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTTTTTCTCTTATTTCTTTT
Found at i:7693 original size:21 final size:21
Alignment explanation
Indices: 7648--7694 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
7638 TTTTTCTTTT
* *
7648 ATTTCTTTTTCTTTTTCTCTT
1 ATTTCTTTTTCTTCTTCTCTA
7669 ATTTCTTTTT-TTCTTCTCTCA
1 ATTTCTTTTTCTTCTTCTCT-A
7690 ATTTC
1 ATTTC
7695 ATTCAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTCTTTTTCTTCTTCTCTA
Found at i:8558 original size:81 final size:81
Alignment explanation
Indices: 8423--8586 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 81
8413 ATTTGCTGCT
8423 TGAGGGTCGGTTTCAAAATGGGTTACAATGGATAATGTCGGGTGTAGGGTAGGCTGAACAAAGAA
1 TGAGGGTCGGTTTCAAAATGGGTTACAATGGATAATGTCGGGTGTAGGGTAGGCTGAACAAAGAA
8488 GAAAATTGGTTAAAAA
66 GAAAATTGGTTAAAAA
*
8504 TGAGGGTCGGTTTCAAAATGGGTTACAATGGATAATGTCGGGTGTAGGGTAGGCTGAATAAAGAA
1 TGAGGGTCGGTTTCAAAATGGGTTACAATGGATAATGTCGGGTGTAGGGTAGGCTGAACAAAGAA
*
8569 GAAAATTGGTTTAAAA
66 GAAAATTGGTTAAAAA
8585 TG
1 TG
8587 TGGCGTTGGG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.35, C:0.07, G:0.32, T:0.26
Consensus pattern (81 bp):
TGAGGGTCGGTTTCAAAATGGGTTACAATGGATAATGTCGGGTGTAGGGTAGGCTGAACAAAGAA
GAAAATTGGTTAAAAA
Found at i:8760 original size:11 final size:11
Alignment explanation
Indices: 8720--8765 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
8710 TTGTCACTTC
*
8720 TTTTTTTT-CA
1 TTTTTTTTGAA
8730 TTTTTTTTCG-A
1 TTTTTTTT-GAA
8741 TTTTTTTTGAA
1 TTTTTTTTGAA
8752 TTTTTTTTGAA
1 TTTTTTTTGAA
8763 TTT
1 TTT
8766 CTTCTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:8859 original size:11 final size:11
Alignment explanation
Indices: 8843--8871 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
8833 CCAGCTCAAA
8843 TTTTTTTTATT
1 TTTTTTTTATT
8854 TTTTTTTTATT
1 TTTTTTTTATT
8865 TTTTTTT
1 TTTTTTT
8872 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:12487 original size:15 final size:14
Alignment explanation
Indices: 12467--12514 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
12457 CTCATTTTCA
12467 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
12482 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
12496 TCTTATTTCTTTTTT
1 TCTT-TTTCTTTTTT
12511 TCTT
1 TCTT
12515 CTCTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:12491 original size:21 final size:21
Alignment explanation
Indices: 12467--12518 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12457 CTCATTTTCA
*
12467 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
12488 TCTTTTTCTCTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
*
12509 T-TTCTTCTCT
1 TCTTTTTCTCT
12519 CAATTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTTTTTCTCTTATTTCTTTT
Found at i:12524 original size:21 final size:21
Alignment explanation
Indices: 12479--12525 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12469 TTTTTCTTTT
* *
12479 ATTTCTTTTTCTTTTTCTCTT
1 ATTTCTTTTTCTTCTTCTCTA
12500 ATTTCTTTTT-TTCTTCTCTCA
1 ATTTCTTTTTCTTCTTCTCT-A
12521 ATTTC
1 ATTTC
12526 ATTCAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTCTTTTTCTTCTTCTCTA
Found at i:13510 original size:11 final size:11
Alignment explanation
Indices: 13470--13515 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
13460 TTGTCACTTC
*
13470 TTTTTTTT-CA
1 TTTTTTTTGAA
13480 TTTTTTTTCG-A
1 TTTTTTTT-GAA
13491 TTTTTTTTGAA
1 TTTTTTTTGAA
13502 TTTTTTTTGAA
1 TTTTTTTTGAA
13513 TTT
1 TTT
13516 CTTCTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:13609 original size:11 final size:11
Alignment explanation
Indices: 13593--13621 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
13583 CCAGCTCAAA
13593 TTTTTTTTATT
1 TTTTTTTTATT
13604 TTTTTTTTATT
1 TTTTTTTTATT
13615 TTTTTTT
1 TTTTTTT
13622 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTATT
Done.