Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3492
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: 49364
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1024 original size:21 final size:23
Alignment explanation
Indices: 979--1025 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
969 TCACCTGCAA
* *
979 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
1002 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
1023 TAA
1 TAA
1026 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:6448 original size:12 final size:13
Alignment explanation
Indices: 6428--6463 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
6418 ATGGAAACCA
*
6428 AATTTTTTTTTTG
1 AATTTTTTTTTCG
6441 AATTTTTTTTTCG
1 AATTTTTTTTTCG
*
6454 AGTTTTTTTT
1 AATTTTTTTT
6464 CGAGAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:7494 original size:21 final size:23
Alignment explanation
Indices: 7449--7495 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7439 TCACCTGCAA
* *
7449 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
7472 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
7493 TAA
1 TAA
7496 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:9108 original size:24 final size:23
Alignment explanation
Indices: 9064--9108 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
9054 TTCTTAGGAC
* *
9064 TTTCTTTATTTTATTGTTGTTCG
1 TTTCTTTAATTTATTGCTGTTCG
*
9087 TTTCTTTTAATTTCTTGCTGTT
1 TTTC-TTTAATTTATTGCTGTT
9109 TGCGTCAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (23 bp):
TTTCTTTAATTTATTGCTGTTCG
Found at i:11252 original size:21 final size:22
Alignment explanation
Indices: 11216--11257 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11206 AACAAGTGAG
11216 GAAAAAGAAAAGTGAAAAAGAA
1 GAAAAAGAAAAGTGAAAAAGAA
*
11238 GAAAATGAAAA-TGAAAAAGA
1 GAAAAAGAAAAGTGAAAAAGA
11258 CAAAAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (22 bp):
GAAAAAGAAAAGTGAAAAAGAA
Found at i:11263 original size:21 final size:20
Alignment explanation
Indices: 11217--11264 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
11207 ACAAGTGAGG
11217 AAAAAGAAAAGTGAAAAAGA
1 AAAAAGAAAAGTGAAAAAGA
11237 AGAAAATGAAAA-TGAAAAAGA
1 A-AAAA-GAAAAGTGAAAAAGA
11258 CAAAAAG
1 -AAAAAG
11265 GGAAGCGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (20 bp):
AAAAAGAAAAGTGAAAAAGA
Found at i:11370 original size:33 final size:33
Alignment explanation
Indices: 11302--11371 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
11292 GTGAATGAAG
* **
11302 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTCAAACAACAAA
* *
11335 TGAGTGAAGAAGAAGAGAGTGCTCAAA-AACAAA
1 TGAGTGAAAAAG-AGAGAGAGCTCAAACAACAAA
11368 TGAG
1 TGAG
11372 GAATATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 19 0.61
34 12 0.39
ACGTcount: A:0.50, C:0.07, G:0.30, T:0.13
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTCAAACAACAAA
Found at i:19143 original size:22 final size:23
Alignment explanation
Indices: 19118--19166 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
19108 ATCAGCTTCT
19118 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
19140 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
19162 TTAAT
1 TTAAT
19167 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:20587 original size:104 final size:103
Alignment explanation
Indices: 20407--20629 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
20397 TGTATATAAA
** * *
20407 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
20472 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGA-TCCCCCG
* *
20511 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
20575 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATCCCCCG
20614 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
20630 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 23 0.21
104 88 0.79
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATCCCCCG
Found at i:20649 original size:71 final size:71
Alignment explanation
Indices: 20549--20699 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
20539 TCATTGGTGG
* *
20549 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGA-TCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
20613 GAGGGGT
65 GAGGGGT
***
20620 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
20685 AGGGGT
66 AGGGGT
20691 TGCTAAGTG
1 TGCTAAGTG
20700 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 22 0.30
71 52 0.70
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:26393 original size:24 final size:23
Alignment explanation
Indices: 26353--26397 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
26343 TTTTTAGGAC
*
26353 TTTCTTTATTTTATTGTTGTTCA
1 TTTCTTTAATTTATTGTTGTTCA
*
26376 TTTCTTTTAATTTCTTGTTGTT
1 TTTC-TTTAATTTATTGTTGTT
26398 TGCGTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (23 bp):
TTTCTTTAATTTATTGTTGTTCA
Found at i:34560 original size:18 final size:16
Alignment explanation
Indices: 34522--34564 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
34512 ACAAAAATCA
*
34522 TAAAAAAAATTTGTAT
1 TAAAAAAAATTTGAAT
*
34538 AAAAAAAGAATTTCGAAT
1 TAAAAAA-AATTT-GAAT
34556 TAAAAAAAA
1 TAAAAAAAA
34565 GTTGCAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (16 bp):
TAAAAAAAATTTGAAT
Found at i:36633 original size:19 final size:19
Alignment explanation
Indices: 36609--36646 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
36599 TGGCTTAGAA
36609 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
36628 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
36647 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:39029 original size:19 final size:18
Alignment explanation
Indices: 38993--39032 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38983 GTTCCACTCG
*
38993 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
39011 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
39030 TTT
1 TTT
39033 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:47474 original size:11 final size:12
Alignment explanation
Indices: 47448--47473 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47438 AAAAGAGAAG
47448 AAATTCAAAAAA
1 AAATTCAAAAAA
47460 AAATTCAAAAAA
1 AAATTCAAAAAA
47472 AA
1 AA
47474 TGAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:48404 original size:14 final size:14
Alignment explanation
Indices: 48382--48418 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
48372 AATAGTGAGA
48382 GAAAAAAGAAAA-T
1 GAAAAAAGAAAATT
48395 GAAGAAAAGAAAATT
1 GAA-AAAAGAAAATT
48410 GAAAAAAGA
1 GAAAAAAGA
48419 TGAATTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (14 bp):
GAAAAAAGAAAATT
Done.