Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013404.1 Corchorus capsularis cultivar CVL-1 contig13425, 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: 25704
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:196 original size:2 final size:2
Alignment explanation
Indices: 191--221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
181 TTCATATAAA
191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
222 CCTTACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:424 original size:38 final size:39
Alignment explanation
Indices: 381--473 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 39
371 CTCCCATCCC
*
381 AAAATTAAAATAC-CCTTGTCTCTTACATTTTCTTTCTT
1 AAAATTAAAATACTCCTTGTCTCTCACATTTTCTTTCTT
*
419 AAAATTAAAATTCTTTGTGCCTTGTCTCTCACATTTTCTTTCTT
1 AAAATTAAAATAC----T-CCTTGTCTCTCACATTTTCTTTCTT
*
463 AAGATTAAAAT
1 AAAATTAAAAT
474 TCTTTGTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 12 0.26
44 34 0.74
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.46
Consensus pattern (39 bp):
AAAATTAAAATACTCCTTGTCTCTCACATTTTCTTTCTT
Found at i:442 original size:44 final size:44
Alignment explanation
Indices: 394--482 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
384 ATTAAAATAC
*
394 CCTTGTCTCTTACATTTTCTTTCTTAAAATTAAAATTCTTTGTG
1 CCTTGTCTCTCACATTTTCTTTCTTAAAATTAAAATTCTTTGTG
*
438 CCTTGTCTCTCACATTTTCTTTCTTAAGATTAAAATTCTTTGTG
1 CCTTGTCTCTCACATTTTCTTTCTTAAAATTAAAATTCTTTGTG
482 C
1 C
483 AACTATTGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.51
Consensus pattern (44 bp):
CCTTGTCTCTCACATTTTCTTTCTTAAAATTAAAATTCTTTGTG
Found at i:1971 original size:17 final size:17
Alignment explanation
Indices: 1945--1979 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1935 ATTACTATAC
*
1945 AATATGGATGAAATTTT
1 AATATAGATGAAATTTT
1962 AATATAGATGAAATTTT
1 AATATAGATGAAATTTT
1979 A
1 A
1980 TATTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (17 bp):
AATATAGATGAAATTTT
Found at i:4495 original size:19 final size:20
Alignment explanation
Indices: 4468--4505 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4458 TATTATTATT
4468 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
4488 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
4506 AATATCAATA
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:4790 original size:44 final size:44
Alignment explanation
Indices: 4707--4806 Score: 157
Period size: 44 Copynumber: 2.2 Consensus size: 44
4697 GGTTATTATG
*
4707 ATTTCATGAGGAGGTTATCAAAAATTCCATAGTGTGGTTACCAAA
1 ATTTCAT-AGGAAGTTATCAAAAATTCCATAGTGTGGTTACCAAA
*
4752 ATTTCATACGGAAGTTATC-AAAATTTCATAGTGTGGTTACCAAA
1 ATTTCATA-GGAAGTTATCAAAAATTCCATAGTGTGGTTACCAAA
4796 ATTTCATAGGA
1 ATTTCATAGGA
4807 TCAAGTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
43 3 0.06
44 33 0.63
45 16 0.31
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (44 bp):
ATTTCATAGGAAGTTATCAAAAATTCCATAGTGTGGTTACCAAA
Found at i:4835 original size:46 final size:45
Alignment explanation
Indices: 4720--4853 Score: 157
Period size: 46 Copynumber: 3.0 Consensus size: 45
4710 TCATGAGGAG
*
4720 GTTATCAAAAATTCCATAGTGTGGTTACCAAAATTTCATACGG--AA
1 GTTATC-AAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGATAA
4765 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAA
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAT-AA
* * ***
4811 GTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCATAGGAT
1 GTTATCAAAATTTCATAGTG-TGGTTACCAAAATTTCATAGGAT
4854 GGTTAATTAT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
43 2 0.03
44 32 0.41
45 7 0.09
46 38 0.48
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (45 bp):
GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATAA
Found at i:4843 original size:22 final size:22
Alignment explanation
Indices: 4674--4858 Score: 126
Period size: 22 Copynumber: 8.3 Consensus size: 22
4664 TATCTCTATG
* * *
4674 TGGTTATCAAAATTTTATAAGA
1 TGGTTATTAAAATTTCATAGGA
**
4696 TGGTTATTATGATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
* *
4719 -GGTTATCAAAAATTCCATAGTG-
1 TGGTTAT-TAAAATTTCATAG-GA
**
4741 TGGTTACCAAAATTTCATACGGA
1 TGGTTATTAAAATTTCATA-GGA
* *
4764 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
4785 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
* * *
4807 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGA
*
4831 TGGTTATTGAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
4853 TGGTTA
1 TGGTTA
4859 ATTATCACAA
Statistics
Matches: 127, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
21 2 0.02
22 91 0.72
23 17 0.13
24 17 0.13
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:4907 original size:23 final size:22
Alignment explanation
Indices: 4871--4921 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
4861 TATCACAATT
*
4871 TTATAGAAAGGTTATCAAAGAGA
1 TTATAAAAAGGTTAT-AAAGAGA
* * *
4894 TTATAAAAATGTTATAACGAGG
1 TTATAAAAAGGTTATAAAGAGA
4916 TTATAA
1 TTATAA
4922 GAATTTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
TTATAAAAAGGTTATAAAGAGA
Found at i:4961 original size:22 final size:23
Alignment explanation
Indices: 4923--4985 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
4913 AGGTTATAAG
*
4923 AATTTCA-TAGTATGGTTAAC-AA
1 AATTTCATTAGGA-GGTTAACTAA
4945 AATTTCATTAGGAGGTT-ACTAA
1 AATTTCATTAGGAGGTTAACTAA
* **
4967 TATTTCATGGGGAGGTTAA
1 AATTTCATTAGGAGGTTAA
4986 TTATAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.06
22 27 0.79
23 5 0.15
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (23 bp):
AATTTCATTAGGAGGTTAACTAA
Found at i:5151 original size:22 final size:21
Alignment explanation
Indices: 5123--5205 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
5113 AGAAATCAGA
5123 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTG-TG
* * *
5145 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTG-TG
* * *
5167 TTACCAAAATTACATAATGTG
1 TTATCAAAATTTCATAGTGTG
*
5188 ATTATCAGAATTTCATAG
1 -TTATCAAAATTTCATAG
5206 AGGGGTCAAC
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGTGTG
Found at i:5219 original size:44 final size:44
Alignment explanation
Indices: 5127--5221 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
5117 ATCAGATTAT
* * * * *
5127 CAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTAC
1 CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
* * *
5171 CAAAATTACATAATG-TGATTATCAGAATTTCATAGAGGGGTCAA
1 CAAAATTACATAATGTTG-TTATCAAAATTTCAAAGAGAGGTCAA
5215 CAAAATT
1 CAAAATT
5222 TTATAAAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (44 bp):
CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
Found at i:5265 original size:21 final size:22
Alignment explanation
Indices: 5215--5266 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5205 GAGGGGTCAA
*
5215 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTTATAAAAAGATTAT
*
5237 CAAAATTTTATAAAGAGATTAT
1 CAAAATTTTATAAAAAGATTAT
5259 C-AAATTTT
1 CAAAATTTT
5267 CAAAATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (22 bp):
CAAAATTTTATAAAAAGATTAT
Found at i:5461 original size:22 final size:22
Alignment explanation
Indices: 5359--5772 Score: 122
Period size: 22 Copynumber: 19.0 Consensus size: 22
5349 ATATTAAACC
*
5359 AGGGAGGATATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* ** * *
5381 TGTTTA-GTTCTCAAATTTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* *
5403 A-AGAGGGTTATCAAAATTTTAT
1 AGGGA-GGTTATCAAAATTTCAT
* * *
5425 A-GTATGTAGATCAAAATTTCAT
1 AGGGAGGT-TATCAAAATTTCAT
* *
5447 AGGGAGATTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** **
5469 AATGAGGTTATCAAAAAATCAT
1 AGGGAGGTTATCAAAATTTCAT
5491 AGGGAGGTTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* *
5510 ---G-TGTTATCAAGATATTTTAT
1 AGGGAGGTTATCAA-A-ATTTCAT
* * * *
5530 AAGAAAGTTATCAAAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
* *
5552 AGGAAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
* **
5575 AGGAAAATTTATCAAAATTTCAT
1 AGG-GAGGTTATCAAAATTTCAT
** *
5598 AGCCAGG---TCACAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
5617 AGTGTGATTATCAAAATTTCAA
1 AGGGAGGTTATCAAAATTTCAT
* * *
5639 AGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGGTTATC-AA-AATTTCAT
* * * *
5661 ATGGAGGTTTTTAAATTTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * * *
5683 AACGTGGTTATCAACATATCAT
1 AGGGAGGTTATCAAAATTTCAT
* * *
5705 ATGGAGGTTATCAACATCTCAT
1 AGGGAGGTTATCAAAATTTCAT
*
5727 A-GTATTGGTTATCAAAATTTCAT
1 AGGGA--GGTTATCAAAATTTCAT
* * * *
5750 TGAGAAGTGATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
5772 A
1 A
5773 TTAAGGTCTT
Statistics
Matches: 287, Mismatches: 79, Indels: 52
0.69 0.19 0.12
Matches are distributed among these distances:
15 8 0.03
16 2 0.01
17 1 0.00
18 2 0.01
19 15 0.05
20 2 0.01
21 7 0.02
22 183 0.64
23 56 0.20
24 11 0.04
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:5567 original size:23 final size:23
Alignment explanation
Indices: 5513--5599 Score: 113
Period size: 23 Copynumber: 3.7 Consensus size: 23
5503 AAAATTTGTG
*
5513 TTATCAAGATATTTTATAAGAAAG-
1 TTATCAA-A-ATTTTATAGGAAAGT
*
5537 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAAGT
*
5560 TTATCAAAATTTTATAGGAAAAT
1 TTATCAAAATTTTATAGGAAAGT
*
5583 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
5600 CCAGGTCACA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 12 0.21
23 38 0.67
24 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAAGT
Found at i:5763 original size:45 final size:45
Alignment explanation
Indices: 5687--5772 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
5677 TTTCATAACG
* * * *
5687 TGGTTATCAACATATCATATGGAGGTTATCAACATCTCATAGTAT
1 TGGTTATCAAAATATCATATGGAAGTGATCAAAATCTCATAGTAT
* *
5732 TGGTTATCAAAATTTCAT-TGAGAAGTGATCAAAATTTCATA
1 TGGTTATCAAAATATCATATG-GAAGTGATCAAAATCTCATA
5773 TTAAGGTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.06
45 32 0.94
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTGATCAAAATCTCATAGTAT
Found at i:5821 original size:22 final size:21
Alignment explanation
Indices: 5796--5845 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
5786 AATTCCTTCG
*
5796 AAAGGTT-AACAAAATTTCATAA
1 AAAGGTTAAAAAAAATTT-AT-A
5818 AAAGGTTAAAAAAAATTTATA
1 AAAGGTTAAAAAAAATTTATA
5839 AAAGGTT
1 AAAGGTT
5846 CTCGAAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.31
22 9 0.35
23 9 0.35
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (21 bp):
AAAGGTTAAAAAAAATTTATA
Found at i:8683 original size:25 final size:25
Alignment explanation
Indices: 8634--8684 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
8624 TTAGTAGAAT
*
8634 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
8659 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
8685 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:9444 original size:19 final size:17
Alignment explanation
Indices: 9420--9462 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
9410 GTCTAGTTAT
9420 TATATAATATATATATATA
1 TATATAATATATA-AT-TA
* *
9439 TATATATTATCTAATTA
1 TATATAATATATAATTA
9456 TATATAA
1 TATATAA
9463 ACGTGTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATAATATATAATTA
Found at i:10563 original size:29 final size:29
Alignment explanation
Indices: 10519--10575 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10509 CGAACGAAAT
*
10519 CAAAATCAAACAGAAACAGAATACGGGAC
1 CAAAATCAAACAGAAACAGAACACGGGAC
* * *
10548 CAAAGTCAAACGGAAACTGAACACGGGA
1 CAAAATCAAACAGAAACAGAACACGGGA
10576 TCGAACATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.07
Consensus pattern (29 bp):
CAAAATCAAACAGAAACAGAACACGGGAC
Found at i:18224 original size:84 final size:84
Alignment explanation
Indices: 18119--18293 Score: 350
Period size: 84 Copynumber: 2.1 Consensus size: 84
18109 GTTTCAAGGC
18119 AATTGAGTTTCTTTGTAGCAATTTAGCAATGAATTTAGTTAATCTAGGAAAAGCTATAAATTTGA
1 AATTGAGTTTCTTTGTAGCAATTTAGCAATGAATTTAGTTAATCTAGGAAAAGCTATAAATTTGA
18184 GCTTTTATCAAGAAGTTAA
66 GCTTTTATCAAGAAGTTAA
18203 AATTGAGTTTCTTTGTAGCAATTTAGCAATGAATTTAGTTAATCTAGGAAAAGCTATAAATTTGA
1 AATTGAGTTTCTTTGTAGCAATTTAGCAATGAATTTAGTTAATCTAGGAAAAGCTATAAATTTGA
18268 GCTTTTATCAAGAAGTTAA
66 GCTTTTATCAAGAAGTTAA
18287 AATTGAG
1 AATTGAG
18294 CTTCCCGCAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (84 bp):
AATTGAGTTTCTTTGTAGCAATTTAGCAATGAATTTAGTTAATCTAGGAAAAGCTATAAATTTGA
GCTTTTATCAAGAAGTTAA
Found at i:21688 original size:22 final size:23
Alignment explanation
Indices: 21660--21702 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
21650 TAGAAGGAGT
21660 AGGTTTTACT-TTCCTAACAGAA
1 AGGTTTTACTATTCCTAACAGAA
21682 AGGTTTTACTATTCCTAACAG
1 AGGTTTTACTATTCCTAACAG
21703 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTAACAGAA
Done.