Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2769
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: 13895
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Found at i:543 original size:26 final size:26
Alignment explanation
Indices: 514--589 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
504 CATAGCTCAA
514 GTGAGCAAG-CCCATTTCACAGCTCGT
1 GTGAG-AAGACCCATTTCACAGCTCGT
* * * *
540 GTGAGTAGTCCCATTTCACAACTTGT
1 GTGAGAAGACCCATTTCACAGCTCGT
* * *
566 GTAAGTAGACCCATTTCATAGCTC
1 GTGAGAAGACCCATTTCACAGCTC
590 ATATGAGCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 2 0.05
26 39 0.95
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (26 bp):
GTGAGAAGACCCATTTCACAGCTCGT
Found at i:2651 original size:47 final size:47
Alignment explanation
Indices: 2593--2735 Score: 241
Period size: 47 Copynumber: 3.0 Consensus size: 47
2583 GTTGAATTTA
* *
2593 AAGCTTGTTAAATTTGCTCTTAATATTCCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
*
2640 AAGCCTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
* *
2687 AAGCTTGTTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTATTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
2734 AA
1 AA
2736 AGAAAATTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 90 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
Found at i:3600 original size:44 final size:45
Alignment explanation
Indices: 3536--3707 Score: 203
Period size: 44 Copynumber: 3.9 Consensus size: 45
3526 CGCACAGTAT
* *
3536 TATTCAGGCCTTTGAGCCTAGCAGACTATAATGCCGGTGATATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATAC
* *
3581 TATTC-GGCCTTTGAGCCTAGCAGGCTATAATGTCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATAC
* * *
3625 TATT-TGGGCTTTCGAGCCTAGCAGGCTATAATGCCAGTGAAATGA-
1 TATTCAGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAAAT-AC
* *
3670 TA-TCAGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTGAA
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAA
3708 CGAATTCAGG
Statistics
Matches: 112, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
42 11 0.10
43 14 0.12
44 50 0.45
45 36 0.32
46 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (45 bp):
TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATAC
Found at i:4143 original size:19 final size:21
Alignment explanation
Indices: 4114--4165 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
4104 TTGCATTACT
4114 TAAAA-CTTACTA-T-GCTTA
1 TAAAAGCTTACTATTAGCTTA
4132 TAAAAGCTTACTATTAAGCTTA
1 TAAAAGCTTACTATT-AGCTTA
*
4154 TGAAAGCTTACT
1 TAAAAGCTTACT
4166 CCATTTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 1 0.03
22 16 0.55
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAAAGCTTACTATTAGCTTA
Found at i:9475 original size:40 final size:40
Alignment explanation
Indices: 9391--9574 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9381 TTGAATGCTG
* * * *
9391 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
9430 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
9471 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
9511 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
9551 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9575 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:9528 original size:80 final size:81
Alignment explanation
Indices: 9391--9571 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
9381 TTGAATGCTG
* * *
9391 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
9455 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
9471 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
9532 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
9551 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
9572 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
Done.