Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013642.1 Corchorus capsularis cultivar CVL-1 contig13663, 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: 55613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8928 original size:21 final size:21
Alignment explanation
Indices: 8898--8943 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
8888 GACGAGGAAG
8898 AAATAAATTACTTTTAATTTT
1 AAATAAATTACTTTTAATTTT
* * *
8919 AAATATATTATTTTTATTTTT
1 AAATAAATTACTTTTAATTTT
8940 AAAT
1 AAAT
8944 CCTAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATAAATTACTTTTAATTTT
Found at i:12548 original size:23 final size:23
Alignment explanation
Indices: 12521--12564 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12511 GGAAATCGGG
*
12521 TTGATGGTGAGACAAGAGACAGT
1 TTGATGGTCAGACAAGAGACAGT
*
12544 TTGATGGTCAGGCAAGAGACA
1 TTGATGGTCAGACAAGAGACA
12565 ATGAAGAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.20
Consensus pattern (23 bp):
TTGATGGTCAGACAAGAGACAGT
Found at i:15446 original size:20 final size:20
Alignment explanation
Indices: 15421--15458 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15411 TGACAAGTTT
15421 TTATTTAAATCATACTTTAC
1 TTATTTAAATCATACTTTAC
*
15441 TTATTTAAATCCTACTTT
1 TTATTTAAATCATACTTT
15459 TTTTTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTTAAATCATACTTTAC
Found at i:15836 original size:23 final size:23
Alignment explanation
Indices: 15810--15853 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
15800 TACTGTGAAG
15810 GCCCCATGGGAAAAGGAGAAAAT
1 GCCCCATGGGAAAAGGAGAAAAT
15833 GCCCCATGGGAAAAGGAGAAA
1 GCCCCATGGGAAAAGGAGAAA
15854 TTGATAGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.32, T:0.07
Consensus pattern (23 bp):
GCCCCATGGGAAAAGGAGAAAAT
Found at i:15999 original size:46 final size:46
Alignment explanation
Indices: 15929--16022 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
15919 TTGAACTAAA
*
15929 AATTTTAGTTTTAGGAGAGGAGTTATGACAGCATCTTCCACGCTAC
1 AATTTTAGTTTTAGGAGAGGAGTTATGACAGCATCTTCCACACTAC
* *
15975 AATTTTAGTTTTAGGAGAGTAGTTATGACAGCATCTTCCTCACTAC
1 AATTTTAGTTTTAGGAGAGGAGTTATGACAGCATCTTCCACACTAC
16021 AA
1 AA
16023 CAATCTGCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (46 bp):
AATTTTAGTTTTAGGAGAGGAGTTATGACAGCATCTTCCACACTAC
Found at i:16442 original size:75 final size:74
Alignment explanation
Indices: 16309--16455 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 74
16299 GGGTGCAAAG
* *
16309 TGTGGAAATGGTGCAACTCAGAGCAAGATTATATGCTATACTCTGTCGTGTAATATCATTCACGT
1 TGTGGAAATGGTGCAACTCAGAGCAAGACTAGATGCTATACTCTGTCGTGTAATATCATTCACGT
16374 ACAGAAAAT
66 ACAGAAAAT
*
16383 TGTGGAAATGGTGCAACTCAGAGCAAAGACTAGATGCTATGCTCTGTCGTGTAATATCATTCACG
1 TGTGGAAATGGTGCAACTCAGAGC-AAGACTAGATGCTATACTCTGTCGTGTAATATCATTCACG
*
16448 TGCAGAAA
65 TACAGAAA
16456 GTATTACACA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 24 0.35
75 44 0.65
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (74 bp):
TGTGGAAATGGTGCAACTCAGAGCAAGACTAGATGCTATACTCTGTCGTGTAATATCATTCACGT
ACAGAAAAT
Found at i:16472 original size:24 final size:23
Alignment explanation
Indices: 16440--16485 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
16430 CGTGTAATAT
16440 CATTCACGTGCAGAAAGTATTACA
1 CATTCACGTGCAGAAAGT-TTACA
16464 CATTCACGTGCAGAAAGTTTAC
1 CATTCACGTGCAGAAAGTTTAC
16486 GGGCGTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (23 bp):
CATTCACGTGCAGAAAGTTTACA
Found at i:17496 original size:2 final size:2
Alignment explanation
Indices: 17489--17514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17479 TGCATAAAGC
17489 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17515 GAATAGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24483 original size:82 final size:80
Alignment explanation
Indices: 24389--24557 Score: 239
Period size: 82 Copynumber: 2.1 Consensus size: 80
24379 AACATATCAA
* *
24389 GAAAAAACAGTAACTTGTTACCGTCTTTCCTAAACTTATAAAGATAAAATAGTAACATGTTACCA
1 GAAAAAACAGTAACTTGTTACCGTCTTTCCTAAACTTACAAAGAGAAAATAGTAACATGTTACCA
*
24454 TTTTTTCATAAAGTTTT
66 TTTTTT--TAAAGTTAT
* * * * * *
24471 TAAAAAATAGTAACTTGTTACCGTTTTTGCTAAACTTACAAAGAGAAAATTGTAACATGTTACCG
1 GAAAAAACAGTAACTTGTTACCGTCTTTCCTAAACTTACAAAGAGAAAATAGTAACATGTTACCA
24536 TTTTTTTAAAGTTAT
66 TTTTTTTAAAGTTAT
24551 GAAAAAA
1 GAAAAAA
24558 AAATCATACT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 14 0.18
82 63 0.82
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (80 bp):
GAAAAAACAGTAACTTGTTACCGTCTTTCCTAAACTTACAAAGAGAAAATAGTAACATGTTACCA
TTTTTTTAAAGTTAT
Found at i:38502 original size:28 final size:28
Alignment explanation
Indices: 38450--38503 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
38440 AACTTGTATG
*
38450 ATTTTGACATTTTGTCTTCTAAACTTTA
1 ATTTTGACATTTTGTCTTATAAACTTTA
*
38478 ATTTTGGACATTTTG-CTTATGAACTT
1 ATTTT-GACATTTTGTCTTATAAACTT
38504 GCAATTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (28 bp):
ATTTTGACATTTTGTCTTATAAACTTTA
Found at i:38509 original size:29 final size:28
Alignment explanation
Indices: 38450--38510 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
38440 AACTTGTATG
* *
38450 ATTTTGACATTTTGTCTTCTAAACTTTA
1 ATTTTGACATTTTGTCTTATAAACTTCA
*
38478 ATTTTGGACATTTTG-CTTATGAACTTGCA
1 ATTTT-GACATTTTGTCTTATAAACTT-CA
38507 ATTT
1 ATTT
38511 GGAGCCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (28 bp):
ATTTTGACATTTTGTCTTATAAACTTCA
Found at i:51362 original size:3 final size:3
Alignment explanation
Indices: 51356--51387 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
51346 ATAAAGTTAT
51356 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
51388 TGTGCCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54728 original size:29 final size:31
Alignment explanation
Indices: 54696--54762 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
54686 ATGCAATTTG
*
54696 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAATCAAGCAAATAA
*
54725 GGATATAACGTTACGAAAATCGAGCAAATAA
1 GGATATAACGTTACGAAAATCAAGCAAATAA
54756 GGATATA
1 GGATATA
54763 GTCCGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAATCAAGCAAATAA
Done.