Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023284.1 Corchorus olitorius cultivar O-4 contig23317, 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: 49054
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:590 original size:11 final size:11
Alignment explanation
Indices: 574--598 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
564 AGAAAATTGT
574 TTGTTTTTGGA
1 TTGTTTTTGGA
585 TTGTTTTTGGA
1 TTGTTTTTGGA
596 TTG
1 TTG
599 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:6306 original size:2 final size:2
Alignment explanation
Indices: 6299--6325 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6289 ACAGTTTAAT
6299 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6326 TACATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7923 original size:27 final size:27
Alignment explanation
Indices: 7893--7951 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
7883 GTGGAGCCAT
*
7893 TAGTGACACCAATCTTGGTCAATAAAG
1 TAGTGACACCAATCTTGGACAATAAAG
7920 TAGTGACACCAATCTTGGACAATAAAG
1 TAGTGACACCAATCTTGGACAATAAAG
7947 T-GTGA
1 TAGTGA
7952 AATCTGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (27 bp):
TAGTGACACCAATCTTGGACAATAAAG
Found at i:13200 original size:27 final size:27
Alignment explanation
Indices: 13170--13267 Score: 187
Period size: 27 Copynumber: 3.6 Consensus size: 27
13160 AAGGGTCACC
13170 CAGGGGCATTTTGGTCATTCGCATGTT
1 CAGGGGCATTTTGGTCATTCGCATGTT
13197 CAGGGGCATTTTGGTCATTCGCATGTT
1 CAGGGGCATTTTGGTCATTCGCATGTT
*
13224 CAGGGTCATTTTGGTCATTCGCATGTT
1 CAGGGGCATTTTGGTCATTCGCATGTT
13251 CAGGGGCATTTTGGTCA
1 CAGGGGCATTTTGGTCA
13268 ATTTTACACT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.37
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTCGCATGTT
Found at i:13311 original size:54 final size:53
Alignment explanation
Indices: 13173--13326 Score: 177
Period size: 54 Copynumber: 2.9 Consensus size: 53
13163 GGTCACCCAG
** * *
13173 GGGCATTTTGGTCATTCGCATGTTCAGGGGCATTTTGGTCA-TTCGCATGTTCA
1 GGGCATTTTGGTCATTCGCATGTTCAGGGGCATTTTGGTCATTTTACA-GCTAA
13226 GGGTCATTTTGGTCATTCGCATGTTCAGGGGCATTTTGGTCAATTTTACA-CTAA
1 GGG-CATTTTGGTCATTCGCATGTTCAGGGGCATTTTGGTC-ATTTTACAGCTAA
* * * **
13280 GGGCATTTTGGTGATTTGCATATTCAGGGGGCACGTTGGTCATTTTA
1 GGGCATTTTGGTCATTCGCATGTTCA-GGGGCATTTTGGTCATTTTA
13327 AGTCAACTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
53 29 0.33
54 54 0.61
55 1 0.01
56 4 0.05
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (53 bp):
GGGCATTTTGGTCATTCGCATGTTCAGGGGCATTTTGGTCATTTTACAGCTAA
Found at i:17281 original size:27 final size:27
Alignment explanation
Indices: 17248--17304 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
17238 TTAGTATTAC
17248 TTCGCCAAGTTTAGGTTAATATTAGGG
1 TTCGCCAAGTTTAGGTTAATATTAGGG
17275 TTCGCCAAGTTTAGGTTAATATTAGGG
1 TTCGCCAAGTTTAGGTTAATATTAGGG
17302 TTC
1 TTC
17305 AGCAGGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (27 bp):
TTCGCCAAGTTTAGGTTAATATTAGGG
Found at i:20588 original size:11 final size:11
Alignment explanation
Indices: 20572--20619 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
20562 GAAGTTCGTG
20572 TTTGAAGACCA
1 TTTGAAGACCA
**
20583 TTTGAAGATAA
1 TTTGAAGACCA
20594 TTTGAAGA-C-
1 TTTGAAGACCA
20603 -TTGAAGACCA
1 TTTGAAGACCA
20613 -TTGAAGA
1 TTTGAAGA
20620 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:22018 original size:15 final size:15
Alignment explanation
Indices: 21988--22029 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
21978 TTACTTTGCT
21988 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
22004 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
22019 TTGTTTTCTGT
1 TTGTTTTCTGT
22030 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:29934 original size:25 final size:25
Alignment explanation
Indices: 29906--29956 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29896 TTATATATAG
29906 CATGACTCTCTTGAGACGATACATA
1 CATGACTCTCTTGAGACGATACATA
29931 CATGACTCTCTTGAGACGATACATA
1 CATGACTCTCTTGAGACGATACATA
29956 C
1 C
29957 CCTATCAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (25 bp):
CATGACTCTCTTGAGACGATACATA
Found at i:34806 original size:22 final size:21
Alignment explanation
Indices: 34780--34829 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
34770 AAATTTATGA
*
34780 AGAGAGATAGTGAGTGGGAGG
1 AGAGAGAGAGTGAGTGGGAGG
* * *
34801 AGGAGAAAGAGTTAGTGGGGGG
1 A-GAGAGAGAGTGAGTGGGAGG
34823 AGAGAGA
1 AGAGAGA
34830 AGAAGGGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (21 bp):
AGAGAGAGAGTGAGTGGGAGG
Found at i:42918 original size:15 final size:16
Alignment explanation
Indices: 42877--42918 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
42867 GAATCCAAAC
42877 GACCCGAACCCGAAAAT
1 GACCCGAA-CCGAAAAT
**
42894 GACCTAAACC-AAAAT
1 GACCCGAACCGAAAAT
42909 GACCCGAACC
1 GACCCGAACC
42919 CGATCAACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 13 0.62
16 2 0.10
17 6 0.29
ACGTcount: A:0.43, C:0.36, G:0.14, T:0.07
Consensus pattern (16 bp):
GACCCGAACCGAAAAT
Found at i:42918 original size:32 final size:32
Alignment explanation
Indices: 42851--42921 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
42841 TTGGGTACCT
* *
42851 GAACCCG-AAATTACCTGAATCCAAACGACCC
1 GAACCCGAAAATGACCTGAAACCAAACGACCC
*
42882 GAACCCGAAAATGACCT-AAACCAAAATGACCC
1 GAACCCGAAAATGACCTGAAACC-AAACGACCC
42914 GAACCCGA
1 GAACCCGA
42922 TCAACCCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
32 24 0.69
ACGTcount: A:0.42, C:0.34, G:0.14, T:0.10
Consensus pattern (32 bp):
GAACCCGAAAATGACCTGAAACCAAACGACCC
Found at i:43346 original size:28 final size:26
Alignment explanation
Indices: 43314--43366 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
43304 TTTGAAAAGG
43314 TAAATAAAATGCATTATAAGTTATATTA
1 TAAATAAAATGCATTA-AA-TTATATTA
*
43342 TAAATAAAATGGATTAAATTATATT
1 TAAATAAAATGCATTAAATTATATT
43367 GTGTTGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 2 0.08
28 15 0.62
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAATAAAATGCATTAAATTATATTA
Found at i:46732 original size:241 final size:241
Alignment explanation
Indices: 46295--46766 Score: 599
Period size: 241 Copynumber: 2.0 Consensus size: 241
46285 CAAAAGGTTA
* * * *
46295 TTAACTAAAGGTTTTAATCACTTGTTTAAACCTTAAGTTTTAGGTTACTTAACCCCAATTTCAAA
1 TTAACTAAAGGTTATAATCACTTATTTAAACCTGAAGTTTTAGGTCACTTAACCCCAATTTCAAA
* * * * *
46360 TTCGATTAAGGATTCACTTAAATCTTAATGAACTATGAAAAATTCACAACTTTTATTAACTATAG
66 TTCAATTAAGAATTCACTTAAATCTTAATGAACTATGAAAAATTCAAAACTTTTATAAACTAAAG
* * * *
46425 GTTATAATCACTTAATTTAACCTAAAGTTTTATGGTTACTTAACCTTGATTTCAAATTCGATTAA
131 GTTATAATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTGATTTCAAATTCAATTAA
* *
46490 GGATTCACTTGAATCTTAATAAATTGTGAAAATTACTAAACTTTTG
196 GGATTCACTTAAATCTTAATAAATTATGAAAATTACTAAACTTTTG
* * *** *
46536 TTAACTATAGGTTATAATTACTTATTTAAACCTGAAGTTTTAAGGTCACTTAACCTTGATTTCCA
1 TTAACTAAAGGTTATAATCACTTATTTAAACCTGAAGTTTT-AGGTCACTTAACCCCAATTTCAA
* * * * *
46601 ATTCAATTAAGAATTCATTTAAATGTTAATGAATTATG-AAACTTACCAAAAGTTTT-TAAACTA
65 ATTCAATTAAGAATTCACTTAAATCTTAATGAACTATGAAAAATT--CAAAACTTTTATAAACTA
* * *
46664 AAGGTTTTAATTACTTAATTAAACCTAAAG-TTTAAGGTCACTTAACCTTGATTTCCAATTCAAT
128 AAGGTTATAATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTGATTTCAAATTCAAT
* * * *
46728 TAAGGGTTCATTTAAATCTTAATGAATTATGAAACTTAC
193 TAAGGATTCACTTAAATCTTAATAAATTATGAAAATTAC
46767 CAAATGTCAC
Statistics
Matches: 195, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
241 104 0.53
242 83 0.43
243 8 0.04
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (241 bp):
TTAACTAAAGGTTATAATCACTTATTTAAACCTGAAGTTTTAGGTCACTTAACCCCAATTTCAAA
TTCAATTAAGAATTCACTTAAATCTTAATGAACTATGAAAAATTCAAAACTTTTATAAACTAAAG
GTTATAATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTGATTTCAAATTCAATTAA
GGATTCACTTAAATCTTAATAAATTATGAAAATTACTAAACTTTTG
Found at i:46739 original size:120 final size:122
Alignment explanation
Indices: 46270--46770 Score: 566
Period size: 121 Copynumber: 4.1 Consensus size: 122
46260 TCATTTAAGG
* ** * ** *
46270 ATTATGAAAGCTTCCCAAAA-GGTTATTAACTAAAGGTTTTAATCACTTGTTTAAACCTTAAGTT
1 ATTATGAAA-CTTACCAAAACTTTTATTAACTAAAGGTTATAATCACTTAATTAAACCTAAAGTT
* *** *
46334 TT-AGGTTACTTAACCCCAATTTCAAATTCGATTAAGGATTCACTTAAATCTTAATGA
65 TTAAGGTCACTTAACCTTGATTTCAAATTCAATTAAGGATTCACTTAAATCTTAATGA
* * * * *
46391 ACTATGAAAAATT--CACAACTTTTATTAACTATAGGTTATAATCACTTAATTTAACCTAAAGTT
1 ATTATG-AAACTTACCAAAACTTTTATTAACTAAAGGTTATAATCACTTAATTAAACCTAAAGTT
* * * * *
46454 TTATGGTTACTTAACCTTGATTTCAAATTCGATTAAGGATTCACTTGAATCTTAATAA
65 TTAAGGTCACTTAACCTTGATTTCAAATTCAATTAAGGATTCACTTAAATCTTAATGA
* * * * * * * *
46512 ATTGTGAAAATTA-CTAAACTTTTGTTAACTATAGGTTATAATTACTTATTTAAACCTGAAGTTT
1 ATTATGAAACTTACCAAAACTTTTATTAACTAAAGGTTATAATCACTTAATTAAACCTAAAGTTT
* * * *
46576 TAAGGTCACTTAACCTTGATTTCCAATTCAATTAAGAATTCATTTAAATGTTAATGA
66 TAAGGTCACTTAACCTTGATTTCAAATTCAATTAAGGATTCACTTAAATCTTAATGA
* * * *
46633 ATTATGAAACTTACCAAAAGTTTT-TAAACTAAAGGTTTTAATTACTTAATTAAACCTAAAG-TT
1 ATTATGAAACTTACCAAAACTTTTATTAACTAAAGGTTATAATCACTTAATTAAACCTAAAGTTT
* * *
46696 TAAGGTCACTTAACCTTGATTTCCAATTCAATTAAGGGTTCATTTAAATCTTAATGA
66 TAAGGTCACTTAACCTTGATTTCAAATTCAATTAAGGATTCACTTAAATCTTAATGA
46753 ATTATGAAACTTACCAAA
1 ATTATGAAACTTACCAAA
46771 TGTCACGCCC
Statistics
Matches: 328, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
119 4 0.01
120 118 0.36
121 195 0.59
122 11 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (122 bp):
ATTATGAAACTTACCAAAACTTTTATTAACTAAAGGTTATAATCACTTAATTAAACCTAAAGTTT
TAAGGTCACTTAACCTTGATTTCAAATTCAATTAAGGATTCACTTAAATCTTAATGA
Done.