Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1630
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: 32115
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:5551 original size:21 final size:21
Alignment explanation
Indices: 5525--5574 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5515 TCCAACTGTT
5525 TCGATACATTTGTGGAATGTA
1 TCGATACATTTGTGGAATGTA
5546 TCGATACATTTGTGGAATGTA
1 TCGATACATTTGTGGAATGTA
5567 TCGATACA
1 TCGATACA
5575 GGGTCCCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (21 bp):
TCGATACATTTGTGGAATGTA
Found at i:5634 original size:19 final size:19
Alignment explanation
Indices: 5611--5728 Score: 134
Period size: 19 Copynumber: 6.8 Consensus size: 19
5601 ATTCAACAGT
*
5611 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
5630 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
5649 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
5663 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
5681 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
5695 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
5713 CTGTATCGATACATAA
1 TTGTATCGATACATAA
5729 TTAGCTACTG
Statistics
Matches: 86, Mismatches: 1, Indels: 24
0.77 0.01 0.22
Matches are distributed among these distances:
13 22 0.26
15 4 0.05
17 4 0.05
19 56 0.65
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:5668 original size:13 final size:13
Alignment explanation
Indices: 5650--5706 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
5640 ACATAAGTGT
5650 TGTATCGATACAA
1 TGTATCGATACAA
5663 TGTATCGATACATAA
1 TGTATCGATAC--AA
5678 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
5695 TGTATCGATACA
1 TGTATCGATACA
5707 TAAGTGCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5672 original size:32 final size:32
Alignment explanation
Indices: 5631--5725 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
5621 ACATAAGTTT
5631 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
5663 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
5695 TGTATCGATACATAAGTGCTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
5726 TAATTAGCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:5792 original size:33 final size:33
Alignment explanation
Indices: 5750--5814 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5740 CAAGGAAATG
***
5750 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
5783 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
5815 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:7307 original size:32 final size:32
Alignment explanation
Indices: 7266--7338 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
7256 AGCTTTCTAG
*
7266 CGATACATTGTATCAATGCAAAACTTATGTAT
1 CGATACATTGTATCAATACAAAACTTATGTAT
* **
7298 CGATACATTGTATCGATACAGCACTTATGTAT
1 CGATACATTGTATCAATACAAAACTTATGTAT
7330 CGATACATT
1 CGATACATT
7339 TACCGTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCAATACAAAACTTATGTAT
Found at i:7311 original size:13 final size:13
Alignment explanation
Indices: 7293--7317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7283 GCAAAACTTA
7293 TGTATCGATACAT
1 TGTATCGATACAT
7306 TGTATCGATACA
1 TGTATCGATACA
7318 GCACTTATGT
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:8328 original size:55 final size:55
Alignment explanation
Indices: 8130--9167 Score: 1134
Period size: 55 Copynumber: 18.3 Consensus size: 55
8120 ATAAAGTGCA
* * *
8130 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
** *
8191 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGGAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-G-AA-AG---GCG
* * *
8252 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTATATGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
8307 TCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * ** * *
8362 TCCTGGTCTTTGAGGACTAGAAGGTGCCACCGACTTGTGTGGGCTTCGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
8417 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
8472 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
8527 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * ** * * *
8582 TCTTGCTCTTTGAGGACTAGAAGGTGCCACCGACTTGTATGGGCTTTGAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
8637 TCCTACTCTTTAAGGACTGGAAAATGCCACCAACTTATGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
8692 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
* *** * *
8753 TCCTGCTCCTTGAGGACTGGAGGGTGCCACCAACTCGTATGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
8808 TTCTGCTCTTT-AGGGACT-GAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGA-GGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* * *
8869 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCGTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * *
8930 TCCTGCTCTTTGAGGACTGAAAAATGCCAGCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
8985 TCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
9040 TCCTACTATTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
** ** *
9095 TCCTATTCTTTGAGGACT-GAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAA-AATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
9150 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
9168 AAAGGGTGAA
Statistics
Matches: 842, Mismatches: 103, Indels: 70
0.83 0.10 0.07
Matches are distributed among these distances:
54 9 0.01
55 582 0.69
56 10 0.01
57 3 0.00
58 4 0.00
59 2 0.00
60 6 0.01
61 217 0.26
62 9 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:10258 original size:1 final size:1
Alignment explanation
Indices: 10252--10317 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
10242 CTTTTCTCTC
* * * * * ** *
10252 TTTTTTTTTTGTTTTTTGTTTTTTGTTTTTGTTTTTGTTTTTTTTTTTTTGCTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10317 T
1 T
10318 AAAGAGAATG
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:10275 original size:20 final size:20
Alignment explanation
Indices: 10252--10317 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
10242 CTTTTCTCTC
10252 TTTTTTTTTTGTTTTTTGTT
1 TTTTTTTTTTGTTTTTTGTT
*
10272 TTTTGTTTTTG-TTTTTGTT
1 TTTTTTTTTTGTTTTTTGTT
*
10291 TTTTTTTTTT-TGCTTTTGTT
1 TTTTTTTTTTGT-TTTTTGTT
10311 TTTTTTT
1 TTTTTTT
10318 AAAGAGAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTGTTTTTTGTT
Found at i:10281 original size:26 final size:27
Alignment explanation
Indices: 10252--10315 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
10242 CTTTTCTCTC
10252 TTTTTTTTTTGTTTTTTGTTTTTTG-T
1 TTTTTTTTTTGTTTTTTGTTTTTTGCT
* *
10278 TTTTGTTTTTGTTTTTTTTTTTTTGCT
1 TTTTTTTTTTGTTTTTTGTTTTTTGCT
10305 TTTGTTTTTTT
1 TTT-TTTTTTT
10316 TTAAAGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 4 0.12
28 6 0.18
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (27 bp):
TTTTTTTTTTGTTTTTTGTTTTTTGCT
Found at i:25212 original size:19 final size:19
Alignment explanation
Indices: 25188--25250 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
25178 AGCGATACAT
25188 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
25207 TGTATCGAT---ATA--T-
1 TGTATCGATACAAAACTTA
*
25220 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
25239 TGTATCGATACA
1 TGTATCGATACA
25251 TTTACCGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
16 4 0.11
18 1 0.03
19 21 0.58
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:25222 original size:32 final size:32
Alignment explanation
Indices: 25180--25252 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
25170 AGCTTTCTAG
25180 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
25212 CGATATATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
25244 CGATACATT
1 CGATACATT
25253 TACCGTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:28708 original size:18 final size:18
Alignment explanation
Indices: 28667--28710 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28657 TGATAAAATT
* * *
28667 TAAATAAATATATTAAAC
1 TAAAAAAATAAATTAAAA
*
28685 TCAAAAAATAAATTAAAA
1 TAAAAAAATAAATTAAAA
28703 TAAAAAAA
1 TAAAAAAA
28711 AGTGAAATCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAAATAAATTAAAA
Found at i:29293 original size:26 final size:26
Alignment explanation
Indices: 29241--29311 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 26
29231 TTTTTGAGTT
* *
29241 TAATATATTATTTAAATTTTATCATAAT
1 TAATATATT-TTTAAA-TTTATAATAAA
29269 TAAATATATTTTTAAATTTA-AATAAA
1 T-AATATATTTTTAAATTTATAATAAA
*
29295 TAATTTAATTTTTAAAT
1 TAATAT-ATTTTTAAAT
29312 AAATTTCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.11
26 15 0.39
27 4 0.11
28 7 0.18
29 8 0.21
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATATATTTTTAAATTTATAATAAA
Done.