Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010316.1 Corchorus capsularis cultivar CVL-1 contig10337, whole genome shotgun sequence
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: 23302
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:1379 original size:35 final size:36
Alignment explanation
Indices: 1322--1402 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
1312 ATCCTCTCCC
* * * *
1322 AATTCTAAATCATTATAATTTGCCTCGTGAATTTCCA
1 AATTC-AAAACATTATAATTTGCCCCATAAATTTCCA
* *
1359 AATTCAAAACATTA-ACTTTGCCCCATAAATTTCCC
1 AATTCAAAACATTATAATTTGCCCCATAAATTTCCA
1394 AATTCAAAA
1 AATTCAAAA
1403 TATTTTGCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 25 0.66
36 8 0.21
37 5 0.13
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (36 bp):
AATTCAAAACATTATAATTTGCCCCATAAATTTCCA
Found at i:1710 original size:28 final size:28
Alignment explanation
Indices: 1647--1726 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
1637 GCTTAATACC
* *
1647 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T--TTTTTGGGA
1678 CAAATTGGCCCCTTAACTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTGGGA
*
1706 CAAATTGACCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
1727 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.61
30 1 0.02
31 17 0.37
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGGGA
Found at i:4391 original size:15 final size:15
Alignment explanation
Indices: 4328--4396 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
4318 CTTTCCATAA
*
4328 AATCACTCTACTGAG
1 AATCACTCTCCTGAG
* * * *
4343 AATTACTTTCGTGGG
1 AATCACTCTCCTGAG
*
4358 AATCACTCTCC-CAG
1 AATCACTCTCCTGAG
*
4372 AAATCACTTTCCTGAG
1 -AATCACTCTCCTGAG
4388 AATCACTCT
1 AATCACTCT
4397 TTTATGGAAA
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
14 1 0.03
15 36 0.92
16 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (15 bp):
AATCACTCTCCTGAG
Found at i:6976 original size:3 final size:3
Alignment explanation
Indices: 6968--6994 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6958 AATATAGTAT
6968 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
6995 TATTCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7626 original size:78 final size:78
Alignment explanation
Indices: 7538--7698 Score: 234
Period size: 78 Copynumber: 2.1 Consensus size: 78
7528 CTTTAGTCTT
* ** *
7538 TATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATTTAATATCTTTATAACTATTTTA-
1 TATTTTACTCAACTAAAAACCCTATATTTATTTAATTAAACCTAATATCCTTATAACTATTTTAG
*
7602 TTTCACTATTTTAC
66 TTT-ACCATTTTAC
* * *
7616 TATTTTACTCAACTGAAAACCCTATTTTTATTTAATTAAACCTAATTTCCTTATAACTATTTTAG
1 TATTTTACTCAACTAAAAACCCTATATTTATTTAATTAAACCTAATATCCTTATAACTATTTTAG
7681 TTTACCATTTTAC
66 TTTACCATTTTAC
7694 TATTT
1 TATTT
7699 CAATTATCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 71 0.96
79 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.50
Consensus pattern (78 bp):
TATTTTACTCAACTAAAAACCCTATATTTATTTAATTAAACCTAATATCCTTATAACTATTTTAG
TTTACCATTTTAC
Found at i:11055 original size:6 final size:6
Alignment explanation
Indices: 11027--11087 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
11017 GTTTGATATC
* * *
11027 TTTTTCG TTTTT- TTTCTG TTTTTTG TTTTTG TTTTTG -TTTCG TTTTCG
1 TTTTT-G TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
11075 -TTTTG TTTTTG TT
1 TTTTTG TTTTTG TT
11088 GTGTTGTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
5 12 0.26
6 24 0.52
7 10 0.22
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:11059 original size:13 final size:12
Alignment explanation
Indices: 11029--11087 Score: 63
Period size: 11 Copynumber: 5.2 Consensus size: 12
11019 TTGATATCTT
11029 TTTC-GTTTTT-
1 TTTCTGTTTTTG
11039 TTTCTGTTTTTTG
1 TTTCTG-TTTTTG
*
11052 TTTTTGTTTTTG
1 TTTCTGTTTTTG
*
11064 TTTC-GTTTTCG
1 TTTCTGTTTTTG
11075 TTT-TGTTTTTG
1 TTTCTGTTTTTG
11086 TT
1 TT
11088 GTGTTGTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 4 0.10
11 18 0.44
12 14 0.34
13 5 0.12
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (12 bp):
TTTCTGTTTTTG
Found at i:17357 original size:24 final size:24
Alignment explanation
Indices: 17295--17348 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
17285 CATCCTCAAC
*
17295 AGGATCACCCAAGTTGACAACAGG
1 AGGATCACCCAAGTTAACAACAGG
17319 AGGATCACCCAAGTTAACAACAGG
1 AGGATCACCCAAGTTAACAACAGG
17343 AGGATC
1 AGGATC
17349 TTGCAAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (24 bp):
AGGATCACCCAAGTTAACAACAGG
Found at i:18384 original size:29 final size:28
Alignment explanation
Indices: 18322--18382 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
18312 TTTTCAAGCC
18322 ATTTTCGAAGAGAGAGAAGAGAGAGAAAG
1 ATTTTCGAAGAGAGAGAAGA-AGAGAAAG
*
18351 ATTTTC-AACGAGAGAGAAG-AGAGAAGG
1 ATTTTCGAA-GAGAGAGAAGAAGAGAAAG
18378 ATTTT
1 ATTTT
18383 TTTTTAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 12 0.40
28 2 0.07
29 16 0.53
ACGTcount: A:0.44, C:0.05, G:0.31, T:0.20
Consensus pattern (28 bp):
ATTTTCGAAGAGAGAGAAGAAGAGAAAG
Done.