Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1514
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: 52527
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1627 original size:4 final size:4
Alignment explanation
Indices: 1611--1641 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1601 ATTGTAAAGT
1611 TTTA TTT- TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1642 AGTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5090 original size:102 final size:103
Alignment explanation
Indices: 4886--5091 Score: 264
Period size: 102 Copynumber: 2.0 Consensus size: 103
4876 AAAACTCAAG
* * * *
4886 AGAGAATTCTTGGAGAAAAACTCAAGAGAGAATTCTACACTTAAACAAATTTGAATTTTTTGATT
1 AGAGAATTCTTGGAGAAAAACTCAAAAGAGAATTCTACACTTAAACAAATCTGAATTTTTTAATG
4951 TAATTGAAAGGAATACAAGAGTGGCCGCCATCATTTAA
66 TAATTGAAAGGAATACAAGAGTGGCCGCCATCATTTAA
4989 AGAGAA-TCTTGGAGAAAAACT-AAAAGAGAA-T-TAC-CTTAAACAAATCTGAAATTTTTTTTA
1 AGAGAATTCTTGGAGAAAAACTCAAAAGAGAATTCTACACTTAAACAAATCTG-AA--TTTTTT-
*
5049 AATGTAATTGAGAAGTGAATACAAG-GTGGCGGCCATC-TTTAA
62 AATGTAATTGA-AAG-GAATACAAGAGTGGCCGCCATCATTTAA
5091 A
1 A
5092 TAGGCCTCAT
Statistics
Matches: 92, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
98 13 0.14
99 5 0.05
100 1 0.01
101 14 0.15
102 30 0.33
103 20 0.22
104 9 0.10
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.29
Consensus pattern (103 bp):
AGAGAATTCTTGGAGAAAAACTCAAAAGAGAATTCTACACTTAAACAAATCTGAATTTTTTAATG
TAATTGAAAGGAATACAAGAGTGGCCGCCATCATTTAA
Found at i:34599 original size:14 final size:12
Alignment explanation
Indices: 34577--34613 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
34567 TAGTAGTTTC
34577 TTCAAAAAAAAT
1 TTCAAAAAAAAT
34589 TTCGAAAAAAAAT
1 TTC-AAAAAAAAT
34602 ATTCAAAAAAAA
1 -TTCAAAAAAAA
34614 ATTTGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (12 bp):
TTCAAAAAAAAT
Found at i:34614 original size:14 final size:13
Alignment explanation
Indices: 34580--34617 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
34570 TAGTTTCTTC
*
34580 AAAAAAAATTTCG
1 AAAAAAAATTTCA
34593 AAAAAAAATATTCA
1 AAAAAAAAT-TTCA
34607 AAAAAAAATTT
1 AAAAAAAATTT
34618 GGTTTCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAAAAATTTCA
Found at i:34675 original size:14 final size:14
Alignment explanation
Indices: 34656--34688 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
34646 TATCAAGTTG
34656 AAAAAAAATCGTGA
1 AAAAAAAATCGTGA
34670 AAAAAAAATCGTGA
1 AAAAAAAATCGTGA
34684 AAAAA
1 AAAAA
34689 GAAGAAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.70, C:0.06, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAAAAATCGTGA
Found at i:35771 original size:19 final size:18
Alignment explanation
Indices: 35743--35788 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
35733 TGAGTTTTCA
* *
35743 AAAAACAAAGAGATTGTGG
1 AAAAAGAAAGAGA-AGTGG
*
35762 AAAAAGAAAGAGAAGTTG
1 AAAAAGAAAGAGAAGTGG
35780 AAAAAGAAA
1 AAAAAGAAA
35789 TGAGTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAGAGAAGTGG
Found at i:38005 original size:15 final size:16
Alignment explanation
Indices: 37987--38025 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37977 TCTTTTCTCG
*
37987 CTTTCTTTT-CATTTT
1 CTTTCTTTTGAATTTT
38002 CTTT-TTTTGAATTTT
1 CTTTCTTTTGAATTTT
38017 CTTTCTTTT
1 CTTTCTTTT
38026 TTTCATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (16 bp):
CTTTCTTTTGAATTTT
Found at i:38021 original size:19 final size:20
Alignment explanation
Indices: 37992--38045 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
37982 TCTCGCTTTC
*
37992 TTTTCATTTTCTTTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
38013 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
38032 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
38046 GTATTTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 17 0.57
20 8 0.27
21 5 0.17
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:40589 original size:23 final size:23
Alignment explanation
Indices: 40563--40627 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
40553 TCGGTTTAGG
*
40563 TTTGTTACGAAATGGTAATATGA
1 TTTGTTACGAAATGGTAATACGA
*
40586 TTTGGTT-CGAAATGGTATTACGA
1 TTT-GTTACGAAATGGTAATACGA
*
40609 TTTGGTACGAAATGGTAAT
1 TTTGTTACGAAATGGTAAT
40628 GGTTCAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.06
23 31 0.86
24 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAATACGA
Found at i:44184 original size:79 final size:81
Alignment explanation
Indices: 44082--44266 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
44072 GCTCCTCGTT
* *
44082 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
44145 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
44162 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
44226 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
44242 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44267 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:44266 original size:40 final size:40
Alignment explanation
Indices: 44082--44266 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
44072 GCTCCTCGTT
* *
44082 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
44122 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
44162 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
44201 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
44242 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44267 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:52080 original size:38 final size:38
Alignment explanation
Indices: 52036--52138 Score: 97
Period size: 40 Copynumber: 2.7 Consensus size: 38
52026 ATAGCTCCTC
* *
52036 AACTCGCACAAATGCTTCGGACTTTAG-CTGTGTTTAGT
1 AACTCGCACAAATGCTTCGGACTTTAGCCCG-GATTAGT
*
52074 AACTCGCGTACAAATGCCTTCGGGC-TTAGCCCGGATTAGT
1 AACTCGC--ACAAATG-CTTCGGACTTTAGCCCGGATTAGT
* *
52114 ATCTCGCACAAA-CCTTCGGA-TTTAG
1 AACTCGCACAAATGCTTCGGACTTTAG
52139 TTCCGATCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
36 10 0.19
38 12 0.22
40 23 0.43
41 9 0.17
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (38 bp):
AACTCGCACAAATGCTTCGGACTTTAGCCCGGATTAGT
Done.