Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011316.1 Corchorus capsularis cultivar CVL-1 contig11337, 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: 9817
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:370 original size:28 final size:28
Alignment explanation
Indices: 338--393 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
328 AGAGGTTTAT
* *
338 AGGGTTTAAGAATTAAGCCATAGAGTCG
1 AGGGTTTAAGAATTAAGCAACAGAGTCG
366 AGGGTTTAAGAATTAAGCAACAGAGTCG
1 AGGGTTTAAGAATTAAGCAACAGAGTCG
394 CTGCTGCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.23
Consensus pattern (28 bp):
AGGGTTTAAGAATTAAGCAACAGAGTCG
Found at i:4379 original size:31 final size:31
Alignment explanation
Indices: 4344--4405 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4334 TTATGTTTTT
*
4344 CAATTGTACCCTTATTTTTAAAATATATTTC
1 CAATTGTACCCTTATTTTTAAAACATATTTC
*
4375 CAATTGTACCCTTTTTTTTAAAACATATTTC
1 CAATTGTACCCTTATTTTTAAAACATATTTC
4406 TAAATTGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (31 bp):
CAATTGTACCCTTATTTTTAAAACATATTTC
Found at i:4642 original size:19 final size:20
Alignment explanation
Indices: 4615--4652 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4605 TACTATTAGT
4615 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
4635 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
4653 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:4846 original size:22 final size:22
Alignment explanation
Indices: 4818--4942 Score: 73
Period size: 22 Copynumber: 5.7 Consensus size: 22
4808 TGTCTCTATG
*
4818 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGAA
* * *
4840 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGAA
* *
4863 -GATTATCAAAATTAT-ATA-ATG
1 TGGTTATCAAAATT-TCATAGA-A
4884 TGGTTA-CTAAAATTTCATATGGAA
1 TGGTTATC-AAAATTTCATA--GAA
**
4908 --GTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAGAA
*
4928 TGGTTACCAAAATTT
1 TGGTTATCAAAATTT
4943 TTAGTATCAG
Statistics
Matches: 77, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 68 0.88
23 4 0.05
25 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGAA
Found at i:4888 original size:44 final size:44
Alignment explanation
Indices: 4820--4942 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
4810 TCTCTATGTG
** * *
4820 GTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GG-A
1 GTTATCAAAATTTCATAATGTGGTTACTAAAATTTCAT-ATGGAA
4863 GATTATCAAAATTAT-ATAATGTGGTTACTAAAATTTCATATGGAA
1 G-TTATCAAAATT-TCATAATGTGGTTACTAAAATTTCATATGGAA
* *
4908 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTT
1 GTTATCAAAATTTCATAATGTGGTTACTAAAATTT
4943 TTAGTATCAG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.04
44 63 0.91
45 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (44 bp):
GTTATCAAAATTTCATAATGTGGTTACTAAAATTTCATATGGAA
Found at i:4980 original size:22 final size:22
Alignment explanation
Indices: 4883--5000 Score: 85
Period size: 22 Copynumber: 5.3 Consensus size: 22
4873 ATTATATAAT
* * *
4883 GTGGTTACTAAAATTTCATATG
1 GTGGTTATTAAAATTTCTTAGG
** * * *
4905 GAAGTTATCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCTTAGG
** *
4927 GTGGTTACCAAAATTT-TTAGT
1 GTGGTTATTAAAATTTCTTAGG
*
4948 ATCAGGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCTTAGG
* *
4972 TTGGTTATTGAAATTTCTTAGG
1 GTGGTTATTAAAATTTCTTAGG
4994 GTGGTTA
1 GTGGTTA
5001 ATTTTCACAA
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 5 0.07
22 54 0.71
23 12 0.16
24 5 0.07
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCTTAGG
Found at i:5171 original size:22 final size:22
Alignment explanation
Indices: 5036--5175 Score: 78
Period size: 22 Copynumber: 6.4 Consensus size: 22
5026 GTTAAAAAGA
* *
5036 TTATCAAAATGTCATA-GCGAGT
1 TTATCAAAATTTCATATG-GAGG
*
5058 TTAT-AAGAATTTCATAGTGTA-G
1 TTATCAA-AATTTCATA-TGGAGG
*
5080 TTAACAAAATTTCAT-TAGGAGG
1 TTATCAAAATTTCATAT-GGAGG
* **
5102 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATATGGAGG
* * *
5124 TTATAAAAATTTTATAAT-GTGG
1 TTATCAAAATTTCAT-ATGGAGG
*
5146 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGGAGG
5168 TTAT-AAAA
1 TTATCAAAA
5176 GTCTCAATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
20 1 0.01
21 11 0.12
22 74 0.82
23 3 0.03
24 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Found at i:5413 original size:22 final size:22
Alignment explanation
Indices: 5321--5426 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
5311 AATTAAAAGC
* *
5321 GAGGTTATCAAAATTACATAAT
1 GAGGTTATCAAAATTTCATAAA
* * *
5343 GTGATTATCATAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
* * *
5365 G-GTGTCAACAAAATTTTATAAA
1 GAG-GTTATCAAAATTTCATAAA
*
5387 AAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
*
5409 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
5427 AAATGTGATT
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 64 0.97
23 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAA
Found at i:5757 original size:23 final size:25
Alignment explanation
Indices: 5695--5765 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 25
5685 ATTTCACAAG
5695 AAAG-TTATCAAAATTTTATAGGGATC
1 AAAGTTTATCAAAATTTTATA-GGA-C
*
5721 AAAGTGTATCAAAATTTTATAGGA-
1 AAAGTTTATCAAAATTTTATAGGAC
* *
5745 AGA-TTTATCAAAATTTCATAG
1 AAAGTTTATCAAAATTTTATAG
5766 CGAGGTTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 16 0.40
24 2 0.05
26 7 0.17
27 15 0.38
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (25 bp):
AAAGTTTATCAAAATTTTATAGGAC
Found at i:5811 original size:22 final size:22
Alignment explanation
Indices: 5727--5941 Score: 97
Period size: 22 Copynumber: 9.7 Consensus size: 22
5717 GATCAAAGTG
* *
5727 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* * *
5750 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
5772 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
5794 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
5816 TA-CTAACAA-TTCATA-TG-GAGGT
1 TATC-AA-AATTTCATAGTGTGA--T
* * * ** *
5838 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGTGTGAT
* *
5860 TATCAATATATCATA-TG-GAAGT
1 TATCAAAATTTCATAGTGTG-A-T
* * *
5882 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
*
5905 TATCAAAATTTCAT--TGGGAAGT
1 TATCAAAATTTCATAGTGTG-A-T
5927 TATCAAAATTTCATA
1 TATCAAAATTTCATA
5942 TTAAGGTCTT
Statistics
Matches: 147, Mismatches: 28, Indels: 34
0.70 0.13 0.16
Matches are distributed among these distances:
20 4 0.03
21 7 0.05
22 98 0.67
23 35 0.24
24 2 0.01
25 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:5925 original size:45 final size:45
Alignment explanation
Indices: 5856--5941 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
5846 TTTCATAACG
* *
5856 TGGTTATCAATATATCATATGGAAGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
5901 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
5942 TTAAGGTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:7680 original size:25 final size:25
Alignment explanation
Indices: 7650--7699 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
7640 CAGGGAATGC
7650 AAAAGAAATGAGCAAACTATTAGTT
1 AAAAGAAATGAGCAAACTATTAGTT
7675 AAAAGAAATGAGCAAACTATTAGTT
1 AAAAGAAATGAGCAAACTATTAGTT
7700 TCTCTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (25 bp):
AAAAGAAATGAGCAAACTATTAGTT
Done.