Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006983.1 Corchorus capsularis cultivar CVL-1 contig07004, 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: 11931
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1442 original size:2 final size:2
Alignment explanation
Indices: 1435--1468 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1425 AAAGATAAAG
1435 AT AT AT AT 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 AT AT AT AT
1469 TAAAAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10637 original size:22 final size:21
Alignment explanation
Indices: 10609--10735 Score: 114
Period size: 22 Copynumber: 6.0 Consensus size: 21
10599 TGTCTCTATG
10609 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
10631 TGGTTATTATAATTTCAT-GA
1 TGGTTATCAAAATTTCATAGA
* *
10651 -GGTTATCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
10672 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATA-GA
** *
10694 AAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
10716 TGGTTACCAAAATTTTATAG
1 TGGTTATCAAAATTTCATAG
10736 GATCATGTTA
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
19 14 0.17
20 3 0.04
21 1 0.01
22 64 0.77
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:10676 original size:41 final size:43
Alignment explanation
Indices: 10610--10730 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
10600 GTCTCTATGT
* ** *
10610 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTC-ATG-A
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAATGAA
*
10651 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCA-ATGAA
*
10695 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTT
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTT
10731 TATAGGATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.03
41 29 0.42
43 3 0.04
44 35 0.51
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAATGAA
Found at i:10774 original size:22 final size:22
Alignment explanation
Indices: 10608--10789 Score: 102
Period size: 22 Copynumber: 8.3 Consensus size: 22
10598 TTGTCTCTAT
* *
10608 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* *
10630 ATGGTTATTATAATTTCAT---
1 GTGGTTATTAAAATTTCATAGG
* * * *
10649 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
** *
10671 GTGGTTACCAAAATTTCATATG
1 GTGGTTATTAAAATTTCATAGG
*** * *
10693 AAAGTTATCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCATAGG
** *
10715 GTGGTTACCAAAATTTTATAGG
1 GTGGTTATTAAAATTTCATAGG
* *
10737 ATCATGTTATTAAAATTT-ATTAGG
1 GT--GGTTATTAAAATTTCA-TAGG
* *
10761 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
10783 GTGGTTA
1 GTGGTTA
10790 ATTATCACAA
Statistics
Matches: 120, Mismatches: 33, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
19 14 0.12
22 88 0.73
23 2 0.02
24 16 0.13
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:10961 original size:22 final size:22
Alignment explanation
Indices: 10826--11125 Score: 106
Period size: 22 Copynumber: 13.5 Consensus size: 22
10816 TCAACGAAAT
* *
10826 TTATCAAAATGTCATA-GCGAGG
1 TTATCAAAATTTCATATG-AAGG
**
10848 TTAT-AAGAATTTCATA-GTCTGG
1 TTATCAA-AATTTCATATG-AAGG
*
10870 TTAACAAAATTTCATTATG-AGG
1 TTATCAAAATTTCA-TATGAAGG
* ** *
10892 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATATGAAGG
* *
10914 TTATCAAAATTTTATAGTG-TGG
1 TTATCAAAATTTCATA-TGAAGG
10936 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGAAGG
* *
10958 TTAT-AAAAGTCTCAATTCCATAAAGAG
1 TTATCAAAA-TTTC-A-T--ATGAAG-G
* *
10985 -TACCAAAATTTGATA-GAAGG
1 TTATCAAAATTTCATATGAAGG
* *
11005 TTATC-AAATATCATA-GAGTGG
1 TTATCAAAATTTCATATGA-AGG
* * *
11026 TTATCGAAATTTCATAAAGATCAGA
1 TTATCAAAATTTCAT-ATGA--AGG
* *
11051 TTATC-AAATTT-ATAGGAAGA
1 TTATCAAAATTTCATATGAAGG
**
11071 TTATCAAAATTTCATAGTG-TTG
1 TTATCAAAATTTCATA-TGAAGG
* **
11093 TTATCAAAATTTCAAAACAAGG
1 TTATCAAAATTTCATATGAAGG
11115 TTATCAAAATT
1 TTATCAAAATT
11126 ATATAATGTG
Statistics
Matches: 212, Mismatches: 40, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
20 19 0.09
21 30 0.14
22 120 0.57
23 11 0.05
24 11 0.05
25 7 0.03
26 9 0.04
27 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATATGAAGG
Found at i:11013 original size:20 final size:21
Alignment explanation
Indices: 10990--11087 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 21
10980 AAGAGTACCA
* *
10990 AAATTTGATAGA-AGGTTATC
1 AAATTTCATAGACAGATTATC
* ** *
11010 AAATATCATAGAGTGGTTATC
1 AAATTTCATAGACAGATTATC
11031 GAAATTTCATAAAGATCAGATTATC
1 -AAATTTCAT--AGA-CAGATTATC
11056 AAATTT-ATAGGA-AGATTATC
1 AAATTTCATA-GACAGATTATC
11076 AAAATTTCATAG
1 -AAATTTCATAG
11088 TGTTGTTATC
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
20 18 0.29
21 15 0.24
22 13 0.21
23 2 0.03
24 9 0.14
25 6 0.10
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (21 bp):
AAATTTCATAGACAGATTATC
Found at i:11167 original size:66 final size:66
Alignment explanation
Indices: 11069--11219 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 66
11059 TTTATAGGAA
* ** * * *
11069 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAACAAGGTTATCAAAATTAT-ATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAA-AAGGTTATC-AAATTATCAAAA
11132 TGT
64 TGT
* * * *
11135 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAAAGGTTATCAAATTATCAAAATG
11200 T
66 T
11201 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
11220 TGGTATTTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
65 7 0.10
66 61 0.86
67 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAAAGGTTATCAAATTATCAAAATG
T
Found at i:11188 original size:22 final size:22
Alignment explanation
Indices: 11092--11192 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
11082 TCATAGTGTT
* *
11092 GTTATCAAAATTTCA-AAACAAG
1 GTTATCAAAATTTTATAAA-GAG
* * *
11114 GTTATCAAAATTATATAATGTG
1 GTTATCAAAATTTTATAAAGAG
* * * * *
11136 ATTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTTATAAAGAG
* *
11158 GTCAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTTATAAAGAG
11180 GTTATC-AAATTTT
1 GTTATCAAAATTTT
11193 CAAAATGTGA
Statistics
Matches: 57, Mismatches: 21, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
21 7 0.12
22 48 0.84
23 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTTATAAAGAG
Found at i:11325 original size:20 final size:20
Alignment explanation
Indices: 11300--11373 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
11290 TTATGGAGTA
*
11300 ATCAAAATTTCAGAGATGAT
1 ATCAAAATTTCAGAGAGGAT
*
11320 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
* *
11340 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCAGA-G-AGGAT
11362 ATCAAAATTTCA
1 ATCAAAATTTCA
11374 TAGTTTAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 30 0.64
21 1 0.02
22 16 0.34
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:11367 original size:22 final size:21
Alignment explanation
Indices: 11300--11790 Score: 209
Period size: 22 Copynumber: 22.7 Consensus size: 21
11290 TTATGGAGTA
* * *
11300 ATCAAAATTTCAGA-GATGAT
1 ATCAAAATTTCATATGAGGTT
** *
11320 ATCAAAATTTCA-GGGAGGAT
1 ATCAAAATTTCATATGAGGTT
11340 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATG-AGGTT
*
11362 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA--TGAGGTT
* *
11384 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGA-GGTT
* *
11406 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATG-AGGT-T
11428 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
**
11450 ATCAAAAAATCATAGTGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
*
11472 ATCAAAA-TT--TGT-A-GTT
1 ATCAAAATTTCATATGAGGTT
* * *
11488 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATG-AGGTT
* *
11510 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-TGAGG-TT
* *
11533 ATCAAAATGTT-ATAGGAAGATTT
1 ATCAAAAT-TTCATATG-AG-GTT
* **
11556 ATCTAAATTTCATGGCGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
* * *
11578 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATA-TGAGGTT
* * * *
11600 ATCAATATTTCAGAGTGTGATT
1 ATCAAAATTTCATA-TGAGGTT
11622 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAT-GAGGTT
* * * *
11644 TTTAAATTTTCATAATGTGGTT
1 ATCAAAATTTCAT-ATGAGGTT
** *
11666 ATCAATGTATCATATGGAGGTT
1 ATCAAAATTTCATAT-GAGGTT
* * *
11688 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TG-AGGTT
*
11711 ATCAAAATTTCAT-TGGGAAGTT
1 ATCAAAATTTCATAT--GAGGTT
11733 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATA-TGAGGT-T
* * *
11756 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
*
11777 AACAAAATTTCATA
1 ATCAAAATTTCATA
11791 AGAAGGTTCA
Statistics
Matches: 362, Mismatches: 69, Indels: 78
0.71 0.14 0.15
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 30 0.08
21 13 0.04
22 244 0.67
23 54 0.15
24 6 0.02
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (21 bp):
ATCAAAATTTCATATGAGGTT
Found at i:11476 original size:44 final size:44
Alignment explanation
Indices: 11319--11790 Score: 273
Period size: 44 Copynumber: 10.8 Consensus size: 44
11309 TCAGAGATGA
* *
11319 TATCAAAATTTC--AGGGAGGATATCAAAATTTCATA-TGAAGGT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGTG-AGGT
* * *
11361 TATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATA-AGAGGGT
1 TATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAGTGA-GGT
* *
11405 TATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGTGAGGT
**
11449 TATCAAAAAATCATAGTGAGGTTATCAAAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGTGAGGT
* * * * *
11487 TATCAAGATTTCATAAG-AAAGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATAGTGAGG-T
* * * *
11532 TATCAAAATGTT-ATAG-GAAGATTTATCTAAATTTCATGGCGAGGT
1 TATCAAAAT-TTCATAGTG-AG-GTTATCAAAATTTCATAGTGAGGT
* * * * * * *
11577 TATCACAATTTCATAGTGTGATTATCAATATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGTGAGGT
* * * * *
11621 TA-CTAACAA-TTCATA-TGGAGGTTTTTAAATTTTCATAATGTGGT
1 TATC-AA-AATTTCATAGT-GAGGTTATCAAAATTTCATAGTGAGGT
** * * * *
11665 TATCAATGTATCATA-TGGAGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGT-GAGGTTATCAAAATTTCATAGTG-AGGT
* * * *
11710 TATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGTGAGGT
* * * *
11754 CT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 -TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
11791 AGAAGGTTCA
Statistics
Matches: 331, Mismatches: 70, Indels: 56
0.72 0.15 0.12
Matches are distributed among these distances:
38 24 0.07
39 5 0.02
40 2 0.01
41 2 0.01
42 14 0.04
43 9 0.03
44 184 0.56
45 70 0.21
46 21 0.06
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGTGAGGT
Found at i:11877 original size:22 final size:22
Alignment explanation
Indices: 11319--11881 Score: 204
Period size: 22 Copynumber: 25.7 Consensus size: 22
11309 TCAGAGATGA
* *
11319 TATCAAAATTTC--AGGGAGGA
1 TATCAAAATTTCATAGGAAGGT
*
11339 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGAAGGT
**
11361 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-GAAGGT
* * *
11383 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGAAGGT
* *
11405 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAGGT
*
11426 AGATCAAAATTTCATAGTG-AGGT
1 -TATCAAAATTTCATAG-GAAGGT
**
11449 TATCAAAAAATCATAGTG-AGGT
1 TATCAAAATTTCATAG-GAAGGT
*
11471 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAAGGT
* * *
11487 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAGGAAGGT
* *
11509 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGG-T
*
11532 TATCAAAATGTT-ATAGGAAGATT
1 TATCAAAAT-TTCATAGGAAG-GT
* *
11555 TATCTAAATTTCAT-GGCGAGGT
1 TATCAAAATTTCATAGG-AAGGT
* * *
11577 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
* * * *
11599 TATCAATATTTCAGAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
11621 TA-CTAACAA-TTCATATGG-AGGT
1 TATC-AA-AATTTCATA-GGAAGGT
* * * * *
11643 TTTTAAATTTTCATAATG-TGGT
1 TATCAAAATTTCAT-AGGAAGGT
** *
11665 TATCAATGTATCATATGG-AGGT
1 TATCAAAATTTCATA-GGAAGGT
* * **
11687 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GAAGGT
*
11710 TATCAAAATTTCATTGGGAA-GT
1 TATCAAAATTTCA-TAGGAAGGT
*
11732 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-GGAAGGT
* * *
11754 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAGGAAGGT
* *
11776 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAGGAAGGT
** * **
11798 TCAAAAAAAAATTTTA-AAAAAGGT
1 T---ATCAAAATTTCATAGGAAGGT
* * * * **
11822 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGT
*
11844 TATTAAAAATTTCATAGGAAGGT
1 TA-TCAAAATTTCATAGGAAGGT
11867 TATCAAAATTTCATA
1 TATCAAAATTTCATA
11882 ATGGGATCAT
Statistics
Matches: 406, Mismatches: 96, Indels: 80
0.70 0.16 0.14
Matches are distributed among these distances:
16 10 0.02
17 3 0.01
19 2 0.00
20 12 0.03
21 20 0.05
22 265 0.65
23 70 0.17
24 14 0.03
25 10 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Done.