Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold652
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: 24380
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Found at i:2194 original size:40 final size:39
Alignment explanation
Indices: 2113--2257 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 39
2103 CGAGCTTGGG
*
2113 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTG-TCATAACCG-ACTTAGT
2154 TTCGAAGGGCTTTTGAGCCAGTGTCATAACCAGACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGTCATAACC-GACTTAGT
* * * * *
2194 TTCGAAGGGCCTTCGAGCCAGTGGCCTAATCCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGTGTCATAA-CCGA-CTTAGT
*
2235 CTCGAAGGGC-TTTGAGCCAGTGT
1 TTCGAAGGGCTTTTGAGCCAGTGT
2258 TAAAATCGTG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
40 52 0.57
41 40 0.43
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
TTCGAAGGGCTTTTGAGCCAGTGTCATAACCGACTTAGT
Found at i:9884 original size:40 final size:40
Alignment explanation
Indices: 9800--9983 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9790 TTGAATGCTG
* * * *
9800 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
9839 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
9880 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
9920 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
9960 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9984 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:9937 original size:80 final size:81
Alignment explanation
Indices: 9800--9980 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
9790 TTGAATGCTG
* * *
9800 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
9864 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
9880 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
9941 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
9960 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
9981 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:17721 original size:40 final size:40
Alignment explanation
Indices: 17637--17820 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
17627 TTGAATGCTG
* * * *
17637 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
17676 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
17717 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
17757 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
17797 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17821 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:17774 original size:80 final size:81
Alignment explanation
Indices: 17637--17817 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
17627 TTGAATGCTG
* * *
17637 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
17701 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
17717 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
17778 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
17797 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
17818 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:17841 original size:39 final size:38
Alignment explanation
Indices: 17718--17867 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
17708 GTTATTAATT
* ** * *
17718 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
17758 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
17797 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
17837 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
17868 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:21599 original size:49 final size:48
Alignment explanation
Indices: 21419--21612 Score: 192
Period size: 49 Copynumber: 3.9 Consensus size: 48
21409 TCTATTGTGA
* * * *
21419 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTAC---CAGACTGT
* * * *** *
21470 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTTGA-TGGAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACT---GT
* *
21520 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTG-T
*
21569 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
21613 TAACTTCGGC
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 41 0.34
50 41 0.34
51 35 0.29
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (48 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGT
Found at i:23679 original size:16 final size:17
Alignment explanation
Indices: 23658--23690 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23648 GTTTACAGTA
23658 CAAACA-AACAAAATTT
1 CAAACATAACAAAATTT
*
23674 CAAACATATCAAAATTT
1 CAAACATAACAAAATTT
23691 GTATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
CAAACATAACAAAATTT
Done.