Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2599
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: 40702
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:1199 original size:35 final size:34
Alignment explanation
Indices: 1158--1251 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
1148 TCTGAAGACT
*
1158 TAAAATTTCCATTAATAAAACCAAAATCAAAGAAG
1 TAAAATTTCCATTAATAAAACCAAAAT-AAAGAAC
* * *
1193 TAAAATTTCCATGAATAAAACCAAAAATGAAGACC
1 TAAAATTTCCATTAATAAAACC-AAAATAAAGAAC
* *
1228 TAAATTTTCCATTAATAAAGCCAA
1 TAAAATTTCCATTAATAAAACCAA
1252 GTCAAGACTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.04
35 44 0.86
36 5 0.10
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.24
Consensus pattern (34 bp):
TAAAATTTCCATTAATAAAACCAAAATAAAGAAC
Found at i:5274 original size:8 final size:9
Alignment explanation
Indices: 5247--5275 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5237 ATCCTAGTTC
5247 AATTGTTAA
1 AATTGTTAA
5256 AATTGTTAA
1 AATTGTTAA
5265 AATT-TTAA
1 AATTGTTAA
5273 AAT
1 AAT
5276 AGTTTGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (9 bp):
AATTGTTAA
Found at i:11012 original size:3 final size:3
Alignment explanation
Indices: 10993--11063 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
10983 TAATATTAAT
* *
10993 TTA TCA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
11041 CTA CTA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
11064 TTTTTATCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13226 original size:18 final size:19
Alignment explanation
Indices: 13188--13229 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
13178 TTTGGGTTAA
*
13188 AAGTTTTTTTACACTGCAG
1 AAGTGTTTTTACACTGCAG
*
13207 AAGTGTTTTTCCACTG-AG
1 AAGTGTTTTTACACTGCAG
13225 AAGTG
1 AAGTG
13230 ATGAAGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (19 bp):
AAGTGTTTTTACACTGCAG
Found at i:14383 original size:17 final size:18
Alignment explanation
Indices: 14355--14389 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
14345 TATGCAAAAA
14355 AATTTCAAAGTAAATAAT
1 AATTTCAAAGTAAATAAT
14373 AATTT-AAAGTAAATAAT
1 AATTTCAAAGTAAATAAT
14390 TTATAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AATTTCAAAGTAAATAAT
Found at i:14467 original size:23 final size:24
Alignment explanation
Indices: 14441--14494 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
14431 TAAACAGTAT
*
14441 ATAAAAACTTAAAATGAAT-AATA
1 ATAAAAACTTAAAATAAATAAATA
* **
14464 ATAACAGTTTAAAATAAATAAATA
1 ATAAAAACTTAAAATAAATAAATA
*
14488 AGAAAAA
1 ATAAAAA
14495 TACAACAGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24
Consensus pattern (24 bp):
ATAAAAACTTAAAATAAATAAATA
Found at i:14617 original size:26 final size:24
Alignment explanation
Indices: 14524--14657 Score: 81
Period size: 26 Copynumber: 5.4 Consensus size: 24
14514 AATATATATG
* *
14524 TATATAAAAATTTAAAAGATAATGTA
1 TATATAAAAATTTAAAATA-AAT-AA
* *** *
14550 CATATAATGGTTTAAAATGAATAA
1 TATATAAAAATTTAAAATAAATAA
* *
14574 TATATAAAAATTTTAAATAAATAG
1 TATATAAAAATTTAAAATAAATAA
*
14598 TATGTAAAACAATTTAAAATAAATGATA
1 TATAT-AAA-AATTTAAAATAAAT-A-A
* * * *
14626 AATAAAAAAACTTAAAACAAATAA
1 TATATAAAAATTTAAAATAAATAA
14650 TA-ATAAAA
1 TATATAAAA
14658 GAGTTTTTTA
Statistics
Matches: 80, Mismatches: 24, Indels: 11
0.70 0.21 0.10
Matches are distributed among these distances:
23 5 0.06
24 24 0.30
25 7 0.09
26 38 0.47
27 4 0.05
28 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (24 bp):
TATATAAAAATTTAAAATAAATAA
Found at i:17364 original size:23 final size:22
Alignment explanation
Indices: 17337--17390 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
17327 CCAAAAAGTA
17337 ATTAATTATTATTAGATAAAATT
1 ATTAATTATTATT-GATAAAATT
*
17360 ATTAA-TATTTATTTATAAAATT
1 ATTAATTA-TTATTGATAAAATT
*
17382 -TTCATTATT
1 ATTAATTATT
17391 TATTTTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.19
22 12 0.44
23 10 0.37
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTAATTATTATTGATAAAATT
Found at i:17377 original size:22 final size:22
Alignment explanation
Indices: 17352--17395 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17342 TTATTATTAG
17352 ATAAAATTATT-AATATTTATTT
1 ATAAAATT-TTCAATATTTATTT
*
17374 ATAAAATTTTCATTATTTATTT
1 ATAAAATTTTCAATATTTATTT
17396 TACTAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAAAATTTTCAATATTTATTT
Found at i:27829 original size:91 final size:91
Alignment explanation
Indices: 27671--27838 Score: 291
Period size: 91 Copynumber: 1.8 Consensus size: 91
27661 GAGATGTCCG
* * *
27671 GGGTGTTTCGATTTCAAATGTTTTCTGTAGACTGGTGATTGATTGGAGGCTTATCGTTGAGCGCA
1 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCGCA
*
27736 CTTATGATGATGTATGATGTATGAAA
66 CTTATAATGATGTATGATGTATGAAA
*
27762 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCTCA
1 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCGCA
27827 CTTATAATGATG
66 CTTATAATGATG
27839 GTACATTCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (91 bp):
GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCGCA
CTTATAATGATGTATGATGTATGAAA
Found at i:39811 original size:24 final size:24
Alignment explanation
Indices: 39765--39812 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39755 TTAGTTTTGA
* *
39765 TGTCATATATATAATAACGGTTAT
1 TGTCATAAATATAATAACAGTTAT
39789 TGTCATAAATATTAATAA-AGTTAT
1 TGTCATAAATA-TAATAACAGTTAT
39813 ATCATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (24 bp):
TGTCATAAATATAATAACAGTTAT
Done.