Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008869.1 Corchorus capsularis cultivar CVL-1 contig08890, 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: 40448
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:3423 original size:27 final size:27
Alignment explanation
Indices: 3393--3446 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3383 AATTCTTTTA
3393 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
3420 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
3447 TGTTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAAAATTCAGTTAAGAAATGAAATTT
Found at i:3439 original size:13 final size:14
Alignment explanation
Indices: 3390--3438 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
3380 ATAAATTCTT
3390 TTAAGAAAATTCAG
1 TTAAGAAAATTCAG
** *
3404 TTAAG-AAATGAAA
1 TTAAGAAAATTCAG
*
3417 TTTAGAAAATTCAG
1 TTAAGAAAATTCAG
3431 TTAAGAAA
1 TTAAGAAA
3439 TGAAATTTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (14 bp):
TTAAGAAAATTCAG
Found at i:4234 original size:170 final size:170
Alignment explanation
Indices: 3952--4405 Score: 863
Period size: 170 Copynumber: 2.7 Consensus size: 170
3942 TAATAGGTTT
3952 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAAGAAATATA
1 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAAGAAATATA
4017 TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAACTGAAAAATAGTAAAAT
66 TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAACTGAAAAATAGTAAAAT
4082 AGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTG
131 AGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTG
*
4122 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGGCATTTAAGAAATATA
1 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAAGAAATATA
4187 TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAACTGAAAAATAGTAAAAT
66 TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAACTGAAAAATAGTAAAAT
*
4252 GGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTG
131 AGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTG
*
4292 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAACAAATATA
1 AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAAGAAATATA
* *
4357 TTTGACAAATAAGGTTATAATAGGTGATTCAAAAGTTTTACAGGTGAAC
66 TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAAC
4406 GTACTTTTTA
Statistics
Matches: 278, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 278 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (170 bp):
AATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTAAGCAATGACATTTAAGAAATATA
TTTGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGGTGAACTGAAAAATAGTAAAAT
AGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTG
Found at i:6295 original size:2 final size:2
Alignment explanation
Indices: 6288--6326 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
6278 TCAAGTGTCA
6288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
6327 TATTTTTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9065 original size:6 final size:6
Alignment explanation
Indices: 9054--9086 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
9044 CTTATATAAT
*
9054 ATAAAG ATAAAG ATAAAG ATAAAG ATAACG ATA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA
9087 TGAAAGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.64, C:0.03, G:0.15, T:0.18
Consensus pattern (6 bp):
ATAAAG
Found at i:10811 original size:15 final size:15
Alignment explanation
Indices: 10792--10840 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
10782 CACAAGAAAC
* *
10792 AGAAATCCCAGAATT
1 AGAAACCCCACAATT
*
10807 CGAAACCCCACAATT
1 AGAAACCCCACAATT
10822 AGAAACCCCACAATT
1 AGAAACCCCACAATT
10837 AGAA
1 AGAA
10841 TTCTCATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.47, C:0.29, G:0.10, T:0.14
Consensus pattern (15 bp):
AGAAACCCCACAATT
Found at i:16891 original size:58 final size:58
Alignment explanation
Indices: 16822--16943 Score: 226
Period size: 58 Copynumber: 2.1 Consensus size: 58
16812 GTATAGAAAG
*
16822 AAATGTATGAATTAGCAGTCACTTTTGAATTCATGAATTGTCCTGCTAGAAAGCCATAA
1 AAAT-TATGAATTAGCAGTCACTTTGGAATTCATGAATTGTCCTGCTAGAAAGCCATAA
16881 AAATTATGAATTAGCAGTCACTTTGGAATTCATGAATTGTCCTGCTAGAAAGCCATAA
1 AAATTATGAATTAGCAGTCACTTTGGAATTCATGAATTGTCCTGCTAGAAAGCCATAA
16939 AAATT
1 AAATT
16944 CTTAGGAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 58 0.94
59 4 0.06
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (58 bp):
AAATTATGAATTAGCAGTCACTTTGGAATTCATGAATTGTCCTGCTAGAAAGCCATAA
Found at i:24144 original size:12 final size:12
Alignment explanation
Indices: 24127--24158 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
24117 CATCTCTTAC
24127 GGCAGGCTGTAT
1 GGCAGGCTGTAT
24139 GGCAGGCTGTAT
1 GGCAGGCTGTAT
24151 GGCAGGCT
1 GGCAGGCT
24159 TAAGAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.44, T:0.22
Consensus pattern (12 bp):
GGCAGGCTGTAT
Found at i:40389 original size:76 final size:77
Alignment explanation
Indices: 40301--40445 Score: 240
Period size: 78 Copynumber: 1.9 Consensus size: 77
40291 AGTTTTTAAT
* *
40301 TAAAATAGTAAAATGGTAAAATAT-A-AGTAATAAGGATATTAGATTTAATTATATTAAAATAGA
1 TAAAATAATAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATA-TAAAATAGA
40364 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
40377 TAAAATAATAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAATAGAG
1 TAAAATAATAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAATAGAG
40442 TTTT
66 TTTT
40446 AGT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
76 22 0.34
77 15 0.23
78 27 0.42
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAATAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAATAGAG
TTTTTAGTTGAG
Done.