Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1774
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: 16489
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Found at i:1591 original size:3 final size:3
Alignment explanation
Indices: 1585--1623 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1575 AAACTCCTCC
*
1585 ATA ATA ATA ATA ATA CTA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1624 ATTTTATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4516 original size:2 final size:2
Alignment explanation
Indices: 4509--4552 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4499 TAGATTTGTG
4509 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4550 TA T
1 TA T
4553 GTCATGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5135 original size:36 final size:33
Alignment explanation
Indices: 5112--5177 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
5102 AATATATATA
* * *
5112 TATTTTATATTTAATATATTAAAAAATATATTTTA
1 TATTTTATAATTAA-ATA-TAAAAAAAATATTATA
5147 TATTTTATAATTAAATATAAATAAAAATATT
1 TATTTTATAATTAAATATAAA-AAAAATATT
5178 TTATTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 11 0.39
35 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TATTTTATAATTAAATATAAAAAAAATATTATA
Found at i:5149 original size:28 final size:27
Alignment explanation
Indices: 5109--5161 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
5099 AAAAATATAT
5109 ATATATTTTATATTTAATATATTAAAAA
1 ATATATTTTATATTTAATA-ATTAAAAA
*
5137 ATATATTTTATATTTTATAATTAAA
1 ATATATTTTATATTTAATAATTAAA
5162 TATAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATATTTTATATTTAATAATTAAAAA
Found at i:5537 original size:2 final size:2
Alignment explanation
Indices: 5530--5570 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5520 TAGGCATTAT
*
5530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5571 GGGGTTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6134 original size:36 final size:37
Alignment explanation
Indices: 6063--6134 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
6053 GTTATTCAAA
* * * * *
6063 TTTAAATATTAAATATATATATATATATTTTAAATAT
1 TTTAAATATTAAAAATAAATAAAAATATTTAAAATAT
6100 TTTAAATA-TAAAAATAAATAAAAATATTTAAAATA
1 TTTAAATATTAAAAATAAATAAAAATATTTAAAATA
6135 AATGAGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 22 0.73
37 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
TTTAAATATTAAAAATAAATAAAAATATTTAAAATAT
Found at i:6656 original size:42 final size:42
Alignment explanation
Indices: 6607--6687 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
6597 ATTAAATATA
6607 ATTAATATAATTAAAAATAAATAAATTTAAT-ATTTATATGTT
1 ATTAATAT-ATTAAAAATAAATAAATTTAATAATTTATATGTT
* ** * *
6649 ATTAATATTTTAAATTTTAATATATTTAATAATTTATAT
1 ATTAATATATTAAAAATAAATAAATTTAATAATTTATAT
6688 AATATTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
ATTAATATATTAAAAATAAATAAATTTAATAATTTATATGTT
Found at i:6703 original size:17 final size:17
Alignment explanation
Indices: 6634--6705 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 17
6624 TAAATAAATT
6634 TAATATTTATATGTTAT-
1 TAATATTTATAT-TTATA
*
6651 TAATATTTTAAATTT-TA
1 TAATA-TTTATATTTATA
6668 -ATATATTTAATAATTTATA
1 TA-ATATTT-AT-ATTTATA
6687 TAATATTTATATTTATA
1 TAATATTTATATTTATA
6704 TA
1 TA
6706 TTCGATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 5 0.11
17 20 0.43
18 12 0.26
19 8 0.17
20 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TAATATTTATATTTATA
Found at i:7713 original size:15 final size:16
Alignment explanation
Indices: 7693--7722 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7683 ATATATTTTA
7693 TTTTTT-AAAAATAAC
1 TTTTTTCAAAAATAAC
7708 TTTTTTCAAAAATAA
1 TTTTTTCAAAAATAA
7723 TTTAAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTTTCAAAAATAAC
Found at i:8863 original size:12 final size:12
Alignment explanation
Indices: 8848--8885 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8838 ATTTTTAATT
8848 TTATTTTTATAA
1 TTATTTTTATAA
8860 TTATTTTTATAA
1 TTATTTTTATAA
* *
8872 ATATTATTA-AA
1 TTATTTTTATAA
8883 TTA
1 TTA
8886 GTGATAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTTTTATAA
Found at i:9339 original size:34 final size:33
Alignment explanation
Indices: 9293--9357 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
9283 AATCTTATAA
9293 TTTATAAATAAA-TAATTAAAAATAAAAAATATT
1 TTTATAAATAAATTAATT-AAAATAAAAAATATT
* **
9326 TTTATTAATTAAATTAATTTTAATAAAAAATA
1 TTTA-TAAATAAATTAATTAAAATAAAAAATA
9358 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.15
34 18 0.67
35 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TTTATAAATAAATTAATTAAAATAAAAAATATT
Found at i:15082 original size:155 final size:155
Alignment explanation
Indices: 14889--15195 Score: 614
Period size: 155 Copynumber: 2.0 Consensus size: 155
14879 GATATTCTGT
14889 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
1 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
14954 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
66 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
15019 CCGAGAATTTTCAGGGAAACCCTGA
131 CCGAGAATTTTCAGGGAAACCCTGA
15044 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
1 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
15109 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
66 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
15174 CCGAGAATTTTCAGGGAAACCC
131 CCGAGAATTTTCAGGGAAACCC
15196 CACCTGAACA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 152 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (155 bp):
AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
CCGAGAATTTTCAGGGAAACCCTGA
Done.