Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3092
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: 20097
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Found at i:6519 original size:40 final size:40
Alignment explanation
Indices: 6435--6618 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
6425 TTGAATGCTG
* * * *
6435 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
6474 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
6515 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
6555 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
6595 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
6619 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:6572 original size:80 final size:81
Alignment explanation
Indices: 6435--6615 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
6425 TTGAATGCTG
* * *
6435 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
6499 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
6515 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
6576 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
6595 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
6616 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:6639 original size:39 final size:38
Alignment explanation
Indices: 6516--6665 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
6506 GTTATTAATT
* ** * *
6516 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
6556 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
6595 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
6635 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
6666 GAGCTAATCC
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:14357 original size:40 final size:40
Alignment explanation
Indices: 14273--14456 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
14263 TTGAATGCTG
* * * *
14273 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
14312 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
14353 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
14393 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
14433 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
14457 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:14410 original size:80 final size:81
Alignment explanation
Indices: 14273--14453 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
14263 TTGAATGCTG
* * *
14273 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
14337 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
14353 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
14414 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
14433 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
14454 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:14477 original size:39 final size:38
Alignment explanation
Indices: 14354--14503 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
14344 GTTATTAATT
* ** * *
14354 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
14394 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
14433 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
14473 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
14504 GAGCTAATCC
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
Done.