Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2748
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: 21855
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1688 original size:152 final size:150
Alignment explanation
Indices: 1394--1696 Score: 498
Period size: 152 Copynumber: 2.0 Consensus size: 150
1384 AGGAAGGGGA
* * * *
1394 ATGATACGAGTCATAAAGCCCAATCCAAGTTCAAGAACGTGATGGGCTCACATACCACAAGGCCC
1 ATGATACAAGTCATAAAGCCCAATCCAAGTTAAAGAACGTGATGGGCTCAAATACCACAAGACCC
*
1459 AATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACTATTCAAGAGCTTGTTA
66 AATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTA
1524 GCAAGGCATTAGATGCATAC
131 GCAAGGCATTAGATGCATAC
*
1544 ATGATACAAGTCATAAAGGCCCAATCCAAGTTAAAGAACGTGATGGGCTCAAATTGCCACAAGAC
1 ATGATACAAGTCATAAA-GCCCAATCCAAGTTAAAGAACGTGATGGGCTCAAA-TACCACAAGAC
* *
1609 CCAATAACGAGATCAAAGGCCCGACAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGT
64 CCAATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGT
* *
1674 TAGCAAGGCCTTAGATGTATAC
129 TAGCAAGGCATTAGATGCATAC
1696 A
1 A
1697 CGAGAGAACA
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 16 0.11
151 33 0.23
152 92 0.65
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (150 bp):
ATGATACAAGTCATAAAGCCCAATCCAAGTTAAAGAACGTGATGGGCTCAAATACCACAAGACCC
AATAACAAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTA
GCAAGGCATTAGATGCATAC
Found at i:6524 original size:30 final size:30
Alignment explanation
Indices: 6490--6586 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
6480 AGCTCACTCC
6490 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
6520 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
6550 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
6580 TAGCTCA
1 TAGCTCA
6587 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:7516 original size:22 final size:20
Alignment explanation
Indices: 7484--7532 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
7474 GCCGAATTTA
7484 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
7507 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
7527 TGAACA
1 TGAACA
7533 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:8325 original size:13 final size:12
Alignment explanation
Indices: 8307--8344 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
8297 AAAGGAGAAG
8307 AAATTCAGAAAAA
1 AAATTC-GAAAAA
8320 AAATTC-AAAAA
1 AAATTCGAAAAA
8331 AAA-TCGAAAAA
1 AAATTCGAAAAA
8342 AAA
1 AAA
8345 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 16 0.67
13 6 0.25
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (12 bp):
AAATTCGAAAAA
Found at i:8331 original size:10 final size:11
Alignment explanation
Indices: 8314--8354 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
8304 AAGAAATTCA
8314 GAAAAAAAATTC
1 GAAAAAAAA-TC
8326 -AAAAAAAATC
1 GAAAAAAAATC
*
8336 GAAAAAAAA-G
1 GAAAAAAAATC
8346 GAAAAAAAA
1 GAAAAAAAA
8355 GTGACAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (11 bp):
GAAAAAAAATC
Found at i:8351 original size:22 final size:23
Alignment explanation
Indices: 8292--8354 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
8282 TATTGGATTT
* * *
8292 AAAAAAAAGGAGAAGAAATTCAG
1 AAAAAAAAGGAAAAAAAAATCAG
***
8315 AAAAAAAATTCAAAAAAAATC-G
1 AAAAAAAAGGAAAAAAAAATCAG
8337 AAAAAAAAGGAAAAAAAA
1 AAAAAAAAGGAAAAAAAA
8355 GTGACAAAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.75, C:0.05, G:0.13, T:0.08
Consensus pattern (23 bp):
AAAAAAAAGGAAAAAAAAATCAG
Found at i:9334 original size:37 final size:37
Alignment explanation
Indices: 9283--9353 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
9273 CATTCTTGTA
9283 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
9320 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
9354 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:9353 original size:6 final size:6
Alignment explanation
Indices: 9293--9342 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
9283 AAGAGAAAAC
*
9293 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
9342 A
1 A
9343 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:9435 original size:11 final size:12
Alignment explanation
Indices: 9403--9433 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
9393 TTGAGAGAAC
9403 TTGAAAAAGCCT
1 TTGAAAAAGCCT
9415 TTGAAAAAGCCT
1 TTGAAAAAGCCT
9427 TTGAAAA
1 TTGAAAA
9434 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:11645 original size:30 final size:30
Alignment explanation
Indices: 11611--11707 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
11601 AGCTCACTCC
11611 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
11641 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
11671 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
11701 TAGCTCA
1 TAGCTCA
11708 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:12636 original size:22 final size:20
Alignment explanation
Indices: 12604--12652 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
12594 GCCGAATTTA
12604 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
12627 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
12647 TGAACA
1 TGAACA
12653 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Done.