Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1281
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: 186375
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:156191 original size:34 final size:34
Alignment explanation
Indices: 156121--156218 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
156111 ACAAAGTTGT
*
156121 AGGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
* *
156154 AGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
* *
156188 AGGTGCCACGGAGTTGTGGACTTTGAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
156219 GATTGCCACT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 22 0.38
34 36 0.62
ACGTcount: A:0.31, C:0.11, G:0.36, T:0.22
Consensus pattern (34 bp):
AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
Found at i:164579 original size:13 final size:13
Alignment explanation
Indices: 164561--164585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
164551 CAAAGATCAG
164561 TGTATCGATACAA
1 TGTATCGATACAA
164574 TGTATCGATACA
1 TGTATCGATACA
164586 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:164663 original size:33 final size:33
Alignment explanation
Indices: 164626--164692 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
164616 AGTAGCTTAA
164626 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
164659 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
164692 A
1 A
164693 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:164666 original size:13 final size:13
Alignment explanation
Indices: 164648--164672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
164638 CAAAAAAATA
164648 TGTATCGATACAT
1 TGTATCGATACAT
164661 TGTATCGATACA
1 TGTATCGATACA
164673 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:170454 original size:23 final size:23
Alignment explanation
Indices: 170427--170472 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
170417 AACATTATAC
170427 AAATATTTGT-TATTTCAATAATT
1 AAATATTT-TATATTTCAATAATT
170450 AAATATTTTATATTTCAATAATT
1 AAATATTTTATATTTCAATAATT
170473 TTGTGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATATTTTATATTTCAATAATT
Found at i:171030 original size:22 final size:22
Alignment explanation
Indices: 171005--171101 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
170995 TAAGCTCTTA
171005 ATAATATAATAATAAATAATTT
1 ATAATATAATAATAAATAATTT
* *
171027 ATAATATAAGAATAAAAAAATATT
1 ATAATATAATAAT-AAATAAT-TT
* * * *
171051 GATAAAATAATAGTAAATGATAT
1 -ATAATATAATAATAAATAATTT
* * * *
171074 ACAATAT-ATAAAAAATTATTG
1 ATAATATAATAATAAATAATTT
171095 ATAATAT
1 ATAATAT
171102 GGTAATAGAT
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
21 15 0.27
22 17 0.30
23 7 0.12
24 7 0.12
25 10 0.18
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (22 bp):
ATAATATAATAATAAATAATTT
Found at i:171067 original size:25 final size:26
Alignment explanation
Indices: 171004--171067 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 26
170994 ATAAGCTCTT
*
171004 AATAATATAATAATAAATAATTTATAA
1 AATAATATAA-AATAAATAATTGATAA
* *
171031 TATAAGAATAAAA-AAAT-ATTGATAA
1 AATAA-TATAAAATAAATAATTGATAA
171056 AATAATAGTAAA
1 AATAATA-TAAA
171068 TGATATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
24 1 0.03
25 15 0.50
26 4 0.13
27 6 0.20
28 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (26 bp):
AATAATATAAAATAAATAATTGATAA
Found at i:174627 original size:26 final size:25
Alignment explanation
Indices: 174584--174645 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
174574 AATTAATTTA
**
174584 TAATTTAAAA-AAATTAATTTTTTT
1 TAATTTAAAATAAATTAATTTAATT
*
174608 TAATTTAAAATGAATCTAATTTAATT
1 TAATTTAAAATAAAT-TAATTTAATT
174634 TAATTTTAAAAT
1 TAA-TTTAAAAT
174646 TTTATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.31
25 3 0.09
26 11 0.34
27 8 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATTTAAAATAAATTAATTTAATT
Found at i:179120 original size:16 final size:17
Alignment explanation
Indices: 179099--179133 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
179089 GCTAAGTGAG
179099 TTTATAT-AATAAAAAT
1 TTTATATCAATAAAAAT
*
179115 TTTATATCCATAAAAAT
1 TTTATATCAATAAAAAT
179132 TT
1 TT
179134 GATAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATATCAATAAAAAT
Found at i:179744 original size:29 final size:31
Alignment explanation
Indices: 179696--179759 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
179686 TAGCGAAAAA
* *
179696 AATATTTTAATGTTTGTATTATT-AAATT-T
1 AATATATTAATGTTTATATTATTAAAATTAT
* *
179725 AATATATTAATTTTTATATTTTTAAAATTAT
1 AATATATTAATGTTTATATTATTAAAATTAT
179756 AATA
1 AATA
179760 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 19 0.66
30 5 0.17
31 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
AATATATTAATGTTTATATTATTAAAATTAT
Found at i:179822 original size:13 final size:13
Alignment explanation
Indices: 179804--179828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179794 TTGAATGTTG
179804 ATAAAATTTTAAC
1 ATAAAATTTTAAC
179817 ATAAAATTTTAA
1 ATAAAATTTTAA
179829 ATTTATATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAAATTTTAAC
Found at i:181374 original size:13 final size:13
Alignment explanation
Indices: 181356--181385 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
181346 GGTTGTAATA
181356 TTTTTTTCTCTTC
1 TTTTTTTCTCTTC
*
181369 TTTTTTTCTTTTC
1 TTTTTTTCTCTTC
181382 TTTT
1 TTTT
181386 CTCTTGGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTCTTC
Found at i:185383 original size:10 final size:10
Alignment explanation
Indices: 185364--185520 Score: 120
Period size: 10 Copynumber: 15.0 Consensus size: 10
185354 ACCCAAGGGC
*
185364 GTATGTATAT
1 GTATATATAT
*
185374 GTATACATAT
1 GTATATATAT
185384 GTAATATATAT
1 GT-ATATATAT
* *
185395 ATATATGTAT
1 GTATATATAT
185405 GTATATATAT
1 GTATATATAT
185415 GTATATATATAT
1 G--TATATATAT
185427 GTTTATATATGTAT
1 G--TATATA--TAT
*
185441 GTTATATGTAT
1 G-TATATATAT
*
185452 GTTATATAGAT
1 G-TATATATAT
*
185463 GTATGT-TAT
1 GTATATATAT
*
185472 GTATGTATAT
1 GTATATATAT
*
185482 GTATGTAT-T
1 GTATATATAT
*
185491 GTATACATAT
1 GTATATATAT
185501 GTATATATAT
1 GTATATATAT
*
185511 GTGTATATAT
1 GTATATATAT
185521 ATATTACTAA
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
9 15 0.12
10 60 0.49
11 21 0.17
12 17 0.14
13 6 0.05
14 4 0.03
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (10 bp):
GTATATATAT
Found at i:185394 original size:2 final size:2
Alignment explanation
Indices: 185369--185524 Score: 61
Period size: 2 Copynumber: 80.5 Consensus size: 2
185359 AGGGCGTATG
* * * * *
185369 TA TA TG TA TA CA TA TG TA -A TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
185410 TA TA TG TA TA TA TA TA TG TT TA TA TA TG TA TG T- TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
185451 TG T- TA TA TA GA TG TA TG T- TA TG TA TG TA TA TG TA TG TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
185490 TG TA TA CA TA TG TA TA TA TA TG TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
185525 TACTAAAGGA
Statistics
Matches: 108, Mismatches: 41, Indels: 10
0.68 0.26 0.06
Matches are distributed among these distances:
1 5 0.05
2 103 0.95
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.50
Consensus pattern (2 bp):
TA
Found at i:185482 original size:15 final size:15
Alignment explanation
Indices: 185402--185495 Score: 50
Period size: 15 Copynumber: 6.1 Consensus size: 15
185392 TATATATATG
*
185402 TATGTATATATATGTA
1 TATGT-TATGTATGTA
* * *
185418 TATATATATGTTTATA
1 TATGT-TATGTATGTA
* *
185434 TATG-TATGTTATATG
1 TATGTTATG-TATGTA
* *
185449 TATGTTATATA-GATG
1 TATGTTATGTATG-TA
185464 TATGTTATGTATGTA
1 TATGTTATGTATGTA
185479 TATG-TATGTATTGTA
1 TATGTTATGTA-TGTA
185494 TA
1 TA
185496 CATATGTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
14 10 0.16
15 33 0.53
16 19 0.31
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (15 bp):
TATGTTATGTATGTA
Done.