Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2356
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: 14833
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Found at i:1615 original size:40 final size:40
Alignment explanation
Indices: 1531--1714 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1521 TTGAATGCTG
* * * *
1531 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
1570 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
1611 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
1651 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
1691 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1715 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:1668 original size:80 final size:81
Alignment explanation
Indices: 1531--1711 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
1521 TTGAATGCTG
* * *
1531 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
1595 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
1611 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
1672 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
1691 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
1712 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:1735 original size:39 final size:38
Alignment explanation
Indices: 1612--1761 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 38
1602 GTTATTAATT
* ** * *
1612 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACT-ATA
** * *
1652 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-ATA
*
1691 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAT-A
* *
1731 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
1762 GAGCTATATC
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.35
40 60 0.65
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTATA
Found at i:9510 original size:40 final size:39
Alignment explanation
Indices: 9382--9507 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 39
9372 TTGAATGCTG
*
9382 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGA-T-ACTAAT
* * * *
9421 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGCTAAG-TCCCGAAGG-CTTTGTGCGAGATACTAAT
*
9462 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCGAGATACTAAT
9502 TCCGGG
1 TCCGGG
9508 TTACTAATTC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
39 1 0.01
40 57 0.81
41 12 0.17
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGATACTAAT
Found at i:9514 original size:14 final size:14
Alignment explanation
Indices: 9495--9524 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9485 TTGTGCGAGA
9495 TACTAATTCCGGGT
1 TACTAATTCCGGGT
9509 TACTAATTCCGGGT
1 TACTAATTCCGGGT
9523 TA
1 TA
9525 AGTCCCGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (14 bp):
TACTAATTCCGGGT
Found at i:9560 original size:54 final size:54
Alignment explanation
Indices: 9453--9564 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
9443 ATTTGTGCGA
* * * *
9453 GTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATTCCGG
1 GTTACTAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGG
**
9507 GTTACTAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAATCCGG
1 GTTACTAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACT-AAATCCGG
9561 GTTA
1 GTTA
9565 AGTCCCGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (54 bp):
GTTACTAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGG
Found at i:9600 original size:39 final size:39
Alignment explanation
Indices: 9516--9626 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 39
9506 GGTTACTAAT
** *
9516 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* *
9556 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
9596 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
9627 GAGCTAATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 25 0.41
40 36 0.59
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:12701 original size:39 final size:39
Alignment explanation
Indices: 12656--12776 Score: 224
Period size: 39 Copynumber: 3.1 Consensus size: 39
12646 AAGCAAGACA
*
12656 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
12695 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
12734 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
12773 CTGG
1 CTGG
12777 TAACATAATT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Done.