Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011373.1 Corchorus capsularis cultivar CVL-1 contig11394, 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: 65460
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3022 original size:16 final size:16
Alignment explanation
Indices: 3001--3032 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2991 ATTCCTACGT
3001 GAACAAACAAACAAAA
1 GAACAAACAAACAAAA
*
3017 GAACAAGCAAACAAAA
1 GAACAAACAAACAAAA
3033 AGAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.19, G:0.09, T:0.00
Consensus pattern (16 bp):
GAACAAACAAACAAAA
Found at i:5098 original size:35 final size:36
Alignment explanation
Indices: 5058--5132 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
5048 AGGGCAATCA
*
5058 GTAAAAAGTAAAAAGGT-ATCTG-AAAGGGTAAAATG
1 GTAAAAAGT-AAAAGGTAATCAGTAAAGGGTAAAATG
5093 GTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAATG
1 GTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAATG
5129 GTAA
1 GTAA
5133 TTAGTAAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
34 7 0.19
35 13 0.35
36 17 0.46
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (36 bp):
GTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAATG
Found at i:5131 original size:22 final size:22
Alignment explanation
Indices: 5093--5346 Score: 167
Period size: 22 Copynumber: 11.6 Consensus size: 22
5083 GGGTAAAATG
*
5093 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
5114 GTAAAGGGTAAAATGGTAATTA
1 GTAAAGAGTAAAATGGTAATCA
5136 GTAAAGAGTAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
5158 GTGAAA-ATTAAAA-GAGTAATTTA
1 GT-AAAGAGTAAAATG-GTAA-TCA
*
5181 GTAGAA-AGT--AATAGTAATCA
1 GTA-AAGAGTAAAATGGTAATCA
* *
5201 GT-AAGAAGCAATA-GGTAATACA
1 GTAAAG-AGTAAAATGGTAAT-CA
*
5223 GTAAAAAGTAGAAA-GGTAAATACA
1 GTAAAGAGTA-AAATGGT-AAT-CA
*
5247 GTAAA-AGGTAAAATAGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
*
5269 GTAAAGGGTAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* **
5291 GTAAAAAGTACGA-GAGTAATCA
1 GTAAAGAGTAAAATG-GTAATCA
5313 GTAAAGAG-AAAATGGT-A-CA
1 GTAAAGAGTAAAATGGTAATCA
5332 GGGTAAAGAGTAAAA
1 --GTAAAGAGTAAAA
5347 GAGTATTCAG
Statistics
Matches: 185, Mismatches: 26, Indels: 43
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.01
19 2 0.01
20 7 0.04
21 36 0.19
22 97 0.52
23 25 0.14
24 16 0.09
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:5390 original size:40 final size:40
Alignment explanation
Indices: 5340--5420 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
5330 CAGGGTAAAG
*
5340 AGTAAAAGAGTATTCAGACAAGAGTAATCGGTAAAGAAAA
1 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
*
5380 AGTAAAAGAGTATTCAGACAAGAGTAATTAGTAAAGAAAA
1 AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
5420 A
1 A
5421 TGGTAAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (40 bp):
AGTAAAAGAGTATTCAGACAAGAGTAATCAGTAAAGAAAA
Found at i:5517 original size:35 final size:34
Alignment explanation
Indices: 5430--5530 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 34
5420 ATGGTAAAGA
*
5430 GTAAAGAGTAAAGTAAGAGTAATCAGCAAAGTAAAATG
1 GTAAAGAGTAAAG--A-A-TAATCAGCAAAGAAAAATG
* *
5468 GTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAATG
1 GTAAAGAGT-AAAGAATAATCAGCAAAG-AAAAATG
*
5504 GTAAAGAGTAAAGAGTAATCAGCAAAG
1 GTAAAGAGTAAAGAATAATCAGCAAAG
5531 GAAATGGCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
35 27 0.49
36 15 0.27
37 1 0.02
38 8 0.15
39 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (34 bp):
GTAAAGAGTAAAGAATAATCAGCAAAGAAAAATG
Found at i:5642 original size:7 final size:7
Alignment explanation
Indices: 5618--5718 Score: 61
Period size: 7 Copynumber: 15.1 Consensus size: 7
5608 AAGAGTTATC
5618 AGTAAAG
1 AGTAAAG
*
5625 A-AAAAG
1 AGTAAAG
*
5631 GGTAAAG
1 AGTAAAG
5638 AGTAAAG
1 AGTAAAG
5645 AGTAAAG
1 AGTAAAG
5652 AG--AAG
1 AGTAAAG
**
5657 AGTAATC
1 AGTAAAG
5664 AGTAAAG
1 AGTAAAG
**
5671 AAAAAATG
1 AGTAAA-G
5679 -GTAAAG
1 AGTAAAG
* *
5685 GGTAAAT
1 AGTAAAG
5692 AGT--AG
1 AGTAAAG
5697 AGTAAAG
1 AGTAAAG
**
5704 AGTAATC
1 AGTAAAG
5711 AGTAAAG
1 AGTAAAG
5718 A
1 A
5719 AAAAATGGGG
Statistics
Matches: 68, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
5 9 0.13
6 5 0.07
7 53 0.78
8 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:5659 original size:19 final size:19
Alignment explanation
Indices: 5635--5708 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
5625 AAAAAGGGTA
5635 AAGAGTAAAGAGTAAAGAG
1 AAGAGTAAAGAGTAAAGAG
** *
5654 AAGAGTAATCAGTAAAGAA
1 AAGAGTAAAGAGTAAAGAG
* * *
5673 AAAATGGTAAAGGGTAAATAG
1 AAGA--GTAAAGAGTAAAGAG
*
5694 TAGAGTAAAGAGTAA
1 AAGAGTAAAGAGTAA
5709 TCAGTAAAGA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 29 0.71
21 12 0.29
ACGTcount: A:0.55, C:0.01, G:0.27, T:0.16
Consensus pattern (19 bp):
AAGAGTAAAGAGTAAAGAG
Found at i:5705 original size:47 final size:46
Alignment explanation
Indices: 5607--5726 Score: 170
Period size: 47 Copynumber: 2.6 Consensus size: 46
5597 GTAAAAAGTA
* *
5607 AAAGAGTTATCAGTAAAG-AAAAAGGGTAAAGAGTAAAGAGTAAAG
1 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAG
* * *
5652 AGAAGAGTAATCAGTAAAGAAAAAATGGTAAAGGGTAAATAGTAGAG
1 A-AAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAG
5699 TAAAGAGTAATCAGTAAAGAAAAAATGG
1 -AAAGAGTAATCAGTAAAGAAAAAATGG
5727 GGAAGAGTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.01
46 16 0.24
47 49 0.73
48 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.17
Consensus pattern (46 bp):
AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAAAG
Found at i:5726 original size:129 final size:128
Alignment explanation
Indices: 5399--5722 Score: 371
Period size: 129 Copynumber: 2.5 Consensus size: 128
5389 GTATTCAGAC
* * *
5399 AAGAGTAATTAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAGAGTAATCAGCAAAGTAA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAATAGTAGAGTAAGAGTAATCAGCAAAGTAA
*
5464 AATGGTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCAGCA
66 AATGGTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAAGGGTAAAGAGTAAAGAGTAA-CAGCA
* * *
5528 AAGGAAATGGCAATCAGTAAAGAAAAA--GTAAAAGAGT--AT--TCAGA-CAAGAGTAATTAGC
1 AA-G--A--GTAATCAGTAAAGAAAAATGGT-AAAGAGTAAATAGT-AGAGTAAGAGTAATCAGC
* *
5586 AAAGTAAAATGGTAAAAAGTAAAAGAGTTATCAGTAAAG-AAAAAGGGTAAAGAGTAAAGAGTAA
59 AAAGTAAAATGGTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAAGGGTAAAGAGTAAAGAGTAA
5650 -AG-A
124 CAGCA
* *
5653 GAAGAGTAATCAGTAAAGAAAAAATGGTAAAGGGTAAATAGTAGAGTAAAGAGTAATCAGTAAAG
1 -AAGAGTAATCAGTAAAG-AAAAATGGTAAAGAGTAAATAGTAGAGT-AAGAGTAATCAGCAAAG
*
5718 AAAAA
63 TAAAA
5723 ATGGGGAAGA
Statistics
Matches: 163, Mismatches: 15, Indels: 35
0.77 0.07 0.16
Matches are distributed among these distances:
121 12 0.07
122 5 0.03
123 7 0.04
124 2 0.01
125 4 0.02
126 7 0.04
127 1 0.01
128 43 0.26
129 52 0.32
130 3 0.02
131 1 0.01
132 3 0.02
133 7 0.04
134 16 0.10
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (128 bp):
AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAATAGTAGAGTAAGAGTAATCAGCAAAGTAA
AATGGTAAAAAGTAAAAGAATAATCAGTAAAGAAAAAAGGGTAAAGAGTAAAGAGTAACAGCA
Found at i:5820 original size:36 final size:34
Alignment explanation
Indices: 5695--5822 Score: 132
Period size: 35 Copynumber: 3.6 Consensus size: 34
5685 GGTAAATAGT
**
5695 AGAGTAAAGAGTAATCAGTAAAGAAAAAATGGGGA
1 AGAGTAAAGAGTAATCAGTAAAG-AAAAATGGTAA
* * * *
5730 AGAGTGAAG-GGAAGTCAGTAAAGAAGAATGGTGA
1 AGAGTAAAGAGTAA-TCAGTAAAGAAAAATGGTAA
5764 AGAGTAAAGAGTAATCCAGTAAAGAAAAAATGGTAA
1 AGAGTAAAGAGTAAT-CAGTAAAG-AAAAATGGTAA
* *
5800 AGAGTAAAATATTAATCAGTAAA
1 AGAGT-AAAGAGTAATCAGTAAA
5823 AAGTAATGGC
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
34 21 0.27
35 28 0.36
36 21 0.27
37 8 0.10
ACGTcount: A:0.52, C:0.04, G:0.27, T:0.17
Consensus pattern (34 bp):
AGAGTAAAGAGTAATCAGTAAAGAAAAATGGTAA
Found at i:5885 original size:21 final size:20
Alignment explanation
Indices: 5861--5912 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
5851 TGGTAACTAG
5861 TAATCAGTACAA-AGTAAAGAA
1 TAATCAGTA-AATAGTAAAG-A
*
5882 TAATCAGTGAAATAGTAATGA
1 TAATCAGT-AAATAGTAAAGA
5903 TAATCAGTAA
1 TAATCAGTAA
5913 TTTAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 19 0.68
22 7 0.25
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (20 bp):
TAATCAGTAAATAGTAAAGA
Found at i:15733 original size:15 final size:15
Alignment explanation
Indices: 15715--15752 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
15705 TTGGTGATTC
15715 GCACCATT-TTGGTTT
1 GCACCATTGTT-GTTT
15730 GCACCATTGTTGTTT
1 GCACCATTGTTGTTT
*
15745 GCGCCATT
1 GCACCATT
15753 CACCCTAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (15 bp):
GCACCATTGTTGTTT
Found at i:19613 original size:21 final size:18
Alignment explanation
Indices: 19587--19627 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
19577 GCTTGAAGAC
19587 CATTGAAGATCAATTGGACAG
1 CATTGAAG-TC-ATTGGA-AG
19608 CATTGAAGTCATTGGAAG
1 CATTGAAGTCATTGGAAG
19626 CA
1 CA
19628 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 2 0.10
21 8 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (18 bp):
CATTGAAGTCATTGGAAG
Found at i:27738 original size:21 final size:18
Alignment explanation
Indices: 27712--27752 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
27702 GCTTGAAGAC
27712 CATTGAAGATCAATTGGAGAG
1 CATTGAAG-TC-ATTGGA-AG
27733 CATTGAAGTCATTGGAAG
1 CATTGAAGTCATTGGAAG
27751 CA
1 CA
27753 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 2 0.10
21 8 0.40
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (18 bp):
CATTGAAGTCATTGGAAG
Found at i:35996 original size:24 final size:24
Alignment explanation
Indices: 35940--35996 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
35930 CTATGAAAGG
* *
35940 GAGCAACAAAAGAAGAAAAAGAGT
1 GAGCAACAGAAGAAGAAAAAGAAT
*
35964 GAGCAACAGCAGAAGAAAAAGAAT
1 GAGCAACAGAAGAAGAAAAAGAAT
35988 GAGCAACAG
1 GAGCAACAG
35997 GAAAAGGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.58, C:0.12, G:0.26, T:0.04
Consensus pattern (24 bp):
GAGCAACAGAAGAAGAAAAAGAAT
Found at i:53107 original size:3 final size:3
Alignment explanation
Indices: 53094--53129 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
53084 TATATAAATA
53094 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53130 AGTTGTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56023 original size:21 final size:22
Alignment explanation
Indices: 55987--56032 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
55977 TTTAAATTTG
*
55987 CTGTCAGAATTATGTTTAATGA
1 CTGTCAGAACTATGTTTAATGA
*
56009 CTGTCAG-ACTATGTTTAATTA
1 CTGTCAGAACTATGTTTAATGA
56030 CTG
1 CTG
56033 CTTTAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (22 bp):
CTGTCAGAACTATGTTTAATGA
Found at i:63345 original size:11 final size:11
Alignment explanation
Indices: 63331--63368 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
63321 ATTCATAACA
63331 AATTTATAATT
1 AATTTATAATT
63342 AATTTATAATT
1 AATTTATAATT
63353 -ATTTGATAATT
1 AATTT-ATAATT
*
63364 TATTT
1 AATTT
63369 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:63744 original size:31 final size:31
Alignment explanation
Indices: 63706--63764 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
63696 GGCAAATGGG
*
63706 CGAGTTCGGGCGGGTTCGGGTTCGGGTACTT
1 CGAGTTCGGGCAGGTTCGGGTTCGGGTACTT
* **
63737 CGAGTTCGGGTATTTTCGGGTTCGGGTA
1 CGAGTTCGGGCAGGTTCGGGTTCGGGTA
63765 TTTTTGGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.08, C:0.17, G:0.42, T:0.32
Consensus pattern (31 bp):
CGAGTTCGGGCAGGTTCGGGTTCGGGTACTT
Found at i:63759 original size:16 final size:16
Alignment explanation
Indices: 63720--63809 Score: 85
Period size: 16 Copynumber: 5.7 Consensus size: 16
63710 TTCGGGCGGG
*
63720 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
*
63735 TTCGAGTTCGGGTATT
1 TTCGGGTTCGGGTATT
63751 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* ** * *
63767 TTTGGACTCGAGTTTT
1 TTCGGGTTCGGGTATT
63783 TTCGGGTTCGGGT-TAT
1 TTCGGGTTCGGGTAT-T
*
63799 GTCGGGTTCGG
1 TTCGGGTTCGG
63810 ACTCGGATTG
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
15 14 0.23
16 46 0.77
ACGTcount: A:0.08, C:0.14, G:0.37, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:64448 original size:3 final size:3
Alignment explanation
Indices: 64440--64477 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
64430 GTGATAAAGA
64440 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
64478 ATATATAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.