Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003840.1 Corchorus capsularis cultivar CVL-1 contig03848, 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: 8837
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:4746 original size:4 final size:4
Alignment explanation
Indices: 4737--4787 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
4727 GAGGTCTTGT
4737 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4785 ATA
1 ATA
4788 TATATCAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:5690 original size:26 final size:28
Alignment explanation
Indices: 5651--5714 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
5641 GTATCATTTT
5651 TTAAAT-ATATTTTTAATT-TGT-CACTA
1 TTAAATAATATTTTTAATTAT-TCCACTA
5677 TTAAATAATA-TTTTAATTATTCCACTA
1 TTAAATAATATTTTTAATTATTCCACTA
5704 TTAAAATAATA
1 TT-AAATAATA
5715 GAAATTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.44
27 11 0.32
28 8 0.24
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAAATAATATTTTTAATTATTCCACTA
Found at i:6360 original size:27 final size:30
Alignment explanation
Indices: 6310--6364 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6300 TTTTCAAATA
*
6310 TATTTGTAAATTGACATTATTAAAATTTAT
1 TATTTGAAAATTGACATTATTAAAATTTAT
6340 TATTTGAAAATT-A-ATTA-TAAAATTT
1 TATTTGAAAATTGACATTATTAAAATTT
6365 CAATTTAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 1 0.04
30 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
TATTTGAAAATTGACATTATTAAAATTTAT
Found at i:6643 original size:19 final size:20
Alignment explanation
Indices: 6619--6656 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6609 TACTATTATT
6619 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAATATTTTAC
*
6638 TTTTAATTTCAATTTTTTA
1 TTTTAATTTCAATATTTTA
6657 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTAATTTCAATATTTTAC
Found at i:6898 original size:66 final size:67
Alignment explanation
Indices: 6818--7035 Score: 232
Period size: 66 Copynumber: 3.3 Consensus size: 67
6808 TCTTGTCTCT
* * * *
6818 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTT-TATGAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATGGTTATTAAAATTTCTATGAGGAAGTTATCAAAATTTCA
6882 TA
66 TA
* ** *
6884 GTGTGGTTACCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATATGA--AAGTTACCAAAATTT
1 GTGTGGTTACCAAAATTTCATAAG-ATGGTTATTAAAATTTC-TATGAGGAAGTTATCAAAATTT
6946 CATA
64 CATA
* **
6950 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCT-T-AGGAATGTTATTGAAATT
1 GTGTGGTTACCAAAATTTCATAAGAT--GGTTATTAAAATTTCTATGAGGAA-GTTATCAAAATT
7013 TCATA
63 TCATA
* *
7018 GTGTGGTTATCACAATTT
1 GTGTGGTTACCAAAATTT
7036 TATAGAAATG
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
65 3 0.02
66 71 0.56
67 4 0.03
68 48 0.38
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (67 bp):
GTGTGGTTACCAAAATTTCATAAGATGGTTATTAAAATTTCTATGAGGAAGTTATCAAAATTTCA
TA
Found at i:7040 original size:22 final size:22
Alignment explanation
Indices: 6818--7040 Score: 170
Period size: 22 Copynumber: 10.0 Consensus size: 22
6808 TCTTGTCTCT
6818 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * * *
6841 G-ATGGTTATTATAATTTTATGA
1 GTGTGGTTATCAAAATTTCAT-A
* *
6863 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
*
6884 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
6906 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
** *
6928 -TGAAAGTTACCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
6950 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* *
6972 G-GATCAGGTTATTAAAATTTCTTA
1 GTG-T--GGTTATCAAAATTTCATA
**
6996 G-GAAT-GTTATTGAAATTTCATA
1 GTG--TGGTTATCAAAATTTCATA
* *
7018 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
7040 G
1 G
7041 AAATGTTATC
Statistics
Matches: 164, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
21 6 0.04
22 135 0.82
23 4 0.02
24 17 0.10
25 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:7094 original size:22 final size:20
Alignment explanation
Indices: 7058--7175 Score: 76
Period size: 22 Copynumber: 5.5 Consensus size: 20
7048 ATCAAAGAGA
*
7058 TTATCAAAATGTCATAGCGAGG
1 TTAT-AAAATTTCATAG-GAGG
*
7080 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAG-GAGG
* *
7102 TTAACAAAATTTCATAAGGAGA
1 TT-ATAAAATTTCAT-AGGAGG
* *
7124 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCAT-AGGAGG
*
7146 TTATCAAAATTTCATATGAAGG
1 TTAT-AAAATTTCATA-GGAGG
7168 TTA-AAAAT
1 TTATAAAAT
7176 CTCAATTTCA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
20 5 0.07
21 4 0.05
22 62 0.82
23 5 0.07
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (20 bp):
TTATAAAATTTCATAGGAGG
Found at i:7117 original size:44 final size:43
Alignment explanation
Indices: 7062--7161 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 43
7052 AAGAGATTAT
* * * *
7062 CAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAG-GAGATTACTAA-AATTTCATAGGGAGGTTAA
* * *
7106 CAAAATTTCATAAGGAGATTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCAT-AGGAGATTACTAAAATTTCATAGGGAGGTTAA
7150 CAAAATTTCATA
1 CAAAATTTCATA
7162 TGAAGGTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 1 0.02
44 41 0.87
45 5 0.11
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (43 bp):
CAAAATTTCATAGGAGATTACTAAAATTTCATAGGGAGGTTAA
Found at i:7322 original size:22 final size:22
Alignment explanation
Indices: 7297--7423 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 22
7287 AATTCATAGT
*
7297 GTTATCAAAATTTCAAAGCGAG
1 GTTATCAAAATTTCAAAGAGAG
* *
7319 GTTATCAAAATTGCATAATGTGA-
1 GTTATCAAAATTTCA-AA-GAGAG
* * *
7342 -ATATCAAAATTTCATAGAGGG
1 GTTATCAAAATTTCAAAGAGAG
* * * * *
7363 GTCAACCAAATTTTATAGAGAG
1 GTTATCAAAATTTCAAAGAGAG
7385 GTTATCAAAATTTCATAA-AGAG
1 GTTATCAAAATTTCA-AAGAGAG
**
7407 GTTATCAATTTTTCAAA
1 GTTATCAAAATTTCAAA
7424 ATGTGATTAC
Statistics
Matches: 80, Mismatches: 20, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.03
21 3 0.04
22 69 0.86
23 3 0.04
24 3 0.04
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (22 bp):
GTTATCAAAATTTCAAAGAGAG
Found at i:7575 original size:22 final size:22
Alignment explanation
Indices: 7547--8026 Score: 191
Period size: 22 Copynumber: 21.7 Consensus size: 22
7537 TCAGGCAGGA
*
7547 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATATGAAGGT
**
7569 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7591 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
7613 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
7634 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
7657 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
7679 TATCAAAATTTTATATGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
7702 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
7725 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
7747 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7769 TATCAAAATTTCAGATTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
7791 TA-CTAACAA-TTCATAT-ATAGGT
1 TATC-AA-AATTTCATATGA-AGGT
* * * * *
7813 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
7835 TATCAATATATT-ATATGGAGGT
1 TATCAAAAT-TTCATATGAAGGT
* **
7857 TATCAACATTTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
**
7880 TATCAAAATTTCGCAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7902 CT-TCAAAA-TTCGTTAGGGAGGT
1 -TATCAAAATTTC-ATATGAAGGT
* *
7924 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** ** *
7946 TAAAAGAAATTT-ATAAAAAAGT
1 TATCA-AAATTTCATATGAAGGT
* * * **
7968 TCTCGAAATTCCATAAT-ATCGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
7990 TATTAAAATTTCAAAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
8012 TATCAAAATTTCATA
1 TATCAAAATTTCATA
8027 GGGAAATCAT
Statistics
Matches: 347, Mismatches: 80, Indels: 62
0.71 0.16 0.13
Matches are distributed among these distances:
21 24 0.07
22 240 0.69
23 82 0.24
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:7640 original size:66 final size:66
Alignment explanation
Indices: 7547--7781 Score: 230
Period size: 66 Copynumber: 3.5 Consensus size: 66
7537 TCAGGCAGGA
* **
7547 TATCAAAATTTCATATGAATGT-TATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGG
1 TATCAAAATTTCATATGTATGTATATCAAAATTTCATAG-GAAGTTTTCAAAATTTCATAAGAGG
7611 GT
65 GT
* * **
7613 TATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA-
1 TATCAAAATTTCATATGTATGTATATCAAAATTTCATAGGAAG-TTTTCAAAATTTCATAA-GAG
7676 GGT
64 GGT
* * * * * *
7679 TATCAAAATTTTATATGGAGGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTCAT-AGCG
1 TATCAAAATTTCATATGTATGTATATCAAAATTTCATAGGAA-GTTT-TCAAAATTTCATAAGAG
7743 AGGT
64 -GGT
* *
7747 TATCACAATTTCATA-GTGTG-ATTATCAAAATTTCA
1 TATCAAAATTTCATATGTATGTA-TATCAAAATTTCA
7782 GATTGTGATT
Statistics
Matches: 137, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
65 7 0.05
66 63 0.46
67 39 0.28
68 28 0.20
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (66 bp):
TATCAAAATTTCATATGTATGTATATCAAAATTTCATAGGAAGTTTTCAAAATTTCATAAGAGGG
T
Found at i:7897 original size:23 final size:23
Alignment explanation
Indices: 7854--7897 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
7844 ATTATATGGA
* *
7854 GGTTATCAACATTTCATAGTGTT
1 GGTTATCAAAATTTCACAGTGTT
*
7877 GGTTATCAAAATTTCGCAGTG
1 GGTTATCAAAATTTCACAGTG
7898 AGGTCTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (23 bp):
GGTTATCAAAATTTCACAGTGTT
Done.