Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014020.1 Corchorus olitorius cultivar O-4 contig14053, 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: 53957
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1771 original size:21 final size:21
Alignment explanation
Indices: 1738--1854 Score: 164
Period size: 21 Copynumber: 5.6 Consensus size: 21
1728 CTTAGGCAAT
* *
1738 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
* *
1759 TCTAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
1780 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
1801 TCCAATGAACTTTGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
1822 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
1843 TCCAATGAACTT
1 TCCAATGAACTT
1855 CTAGCATCTT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 3 0.03
21 83 0.97
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:8277 original size:21 final size:21
Alignment explanation
Indices: 8253--8369 Score: 173
Period size: 21 Copynumber: 5.6 Consensus size: 21
8243 CTTAGGCAAT
* *
8253 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
8274 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
8295 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
8316 TCCAATGAACTTTGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
8337 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
8358 TCCAATGAACTT
1 TCCAATGAACTT
8370 CTAGCATCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 3 0.03
21 85 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:10682 original size:20 final size:21
Alignment explanation
Indices: 10654--10697 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
10644 GTGACACTGC
* *
10654 CCACCTGGGTTCTCAA-GCAA
1 CCACATGGGTGCTCAAGGCAA
10674 CCACATGGGTGCTCAAGGCAA
1 CCACATGGGTGCTCAAGGCAA
10695 CCA
1 CCA
10698 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGGCAA
Found at i:17339 original size:15 final size:16
Alignment explanation
Indices: 17315--17354 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
17305 AGAGGTTGAA
*
17315 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
17330 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
17346 AGAAAACAA
1 AGAAAACAA
17355 AACAAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:22882 original size:21 final size:21
Alignment explanation
Indices: 22858--22903 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
22848 CTAAGATGCA
*
22858 TAAAAA-AATAAATCTTAAATC
1 TAAAAACAAGAAAT-TTAAATC
22879 TAAAAACAAGAAATTTAAATC
1 TAAAAACAAGAAATTTAAATC
22900 TAAA
1 TAAA
22904 CCTAAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAACAAGAAATTTAAATC
Found at i:33519 original size:107 final size:108
Alignment explanation
Indices: 33258--33548 Score: 379
Period size: 107 Copynumber: 2.6 Consensus size: 108
33248 AATGGCTTAC
*
33258 GGACTATGACTTAAGGGCACAATGATGAATTAATCAGTTAAGGGTGGGAACACATGATCGAGTTG
1 GGACTATGA-TTAAGGGCACAATGATGAATTAATCAATTAAGGGTGGGAACACATGATCGAGTT-
*
33323 GGCCGGGTTGATTACAGACTATGACTTAAGGGCACAATGATGAATTGA
64 -G--GGGTGGATTACAGACTATGACTTAAGGGCACAATGATGAATTGA
* *
33371 GGATTATGGATTAAGGGCACAATGATGAATCAATCAATTAAGGGTGGGAACACATGATCGAGTTG
1 GGACTAT-GATTAAGGGCACAATGATGAATTAATCAATTAAGGGTGGGAACACATGATCGAGTTG
* * *
33436 GGGTGGCTTCCAGACTATGACTTAA-GTCA-AATGATGAATTGA
65 GGGTGGATTACAGACTATGACTTAAGGGCACAATGATGAATTGA
* * * * ***
33478 GGACTATGATTTATGGGAACCATAATGAATTAATCAATTAAGGGTGGGAATGTATGATCGAGTTG
1 GGACTATGA-TTAAGGGCACAATGATGAATTAATCAATTAAGGGTGGGAACACATGATCGAGTTG
33543 GGGTGG
65 GGGTGG
33549 GCACCATCTA
Statistics
Matches: 160, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
106 2 0.01
107 72 0.45
108 3 0.02
109 22 0.14
111 1 0.01
113 58 0.36
114 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (108 bp):
GGACTATGATTAAGGGCACAATGATGAATTAATCAATTAAGGGTGGGAACACATGATCGAGTTGG
GGTGGATTACAGACTATGACTTAAGGGCACAATGATGAATTGA
Found at i:33728 original size:30 final size:31
Alignment explanation
Indices: 33669--33729 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
33659 ATATTAGAGC
33669 ACAAAATTATCCACTAACCTACTCCAAATTG
1 ACAAAATTATCCACTAACCTACTCCAAATTG
*
33700 ACAAAATT-TCCCACTAGCCTAC-CCAAATTG
1 ACAAAATTAT-CCACTAACCTACTCCAAATTG
33730 GCAATGTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.25
Consensus pattern (31 bp):
ACAAAATTATCCACTAACCTACTCCAAATTG
Found at i:37973 original size:19 final size:19
Alignment explanation
Indices: 37949--38006 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
37939 ATTACAGACT
37949 ATGAATTAAGGGCACAATG
1 ATGAATTAAGGGCACAATG
*
37968 ATGAATTGA-GG-AC--T-
1 ATGAATTAAGGGCACAATG
* *
37982 ATGGATTAAGGTCACAATG
1 ATGAATTAAGGGCACAATG
38001 ATGAAT
1 ATGAAT
38007 CAATCAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 2 0.07
17 2 0.07
18 3 0.10
19 13 0.45
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (19 bp):
ATGAATTAAGGGCACAATG
Found at i:40975 original size:74 final size:77
Alignment explanation
Indices: 40806--40962 Score: 221
Period size: 78 Copynumber: 2.1 Consensus size: 77
40796 GTATCTTTAA
* * *
40806 AATAAAATCAACAATTTTCATTTGGGGCTAAATTTAGTGACATTAGTTTTATATTTTAATATTTC
1 AATAAAATTAA-AATTTTAATTTGGGGCTAAACTTAGTGACATTAGTTTTATATTTT-ATATTTC
**
40871 TAAAATTCTATAAC
64 TAAAACCCTATAAC
*
40885 AATAAAATTAAAATTTTAATTTGGGGTTAAACTTAGTGA-ATTAGTTTTATA-TTT-TATTTCTA
1 AATAAAATTAAAATTTTAATTTGGGGCTAAACTTAGTGACATTAGTTTTATATTTTATATTTCTA
40947 AAACCCTATAAC
66 AAACCCTATAAC
40959 AATA
1 AATA
40963 TGTTATTAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
74 22 0.31
76 3 0.04
77 12 0.17
78 25 0.35
79 10 0.14
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (77 bp):
AATAAAATTAAAATTTTAATTTGGGGCTAAACTTAGTGACATTAGTTTTATATTTTATATTTCTA
AAACCCTATAAC
Found at i:44303 original size:6 final size:6
Alignment explanation
Indices: 44294--44361 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
44284 AAAAAAATAA
* * *
44294 AAAAGG AAAAGG AAAA-G AAAAGG -AAAGA AAAAGG AAAAAG AAAATG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
* *
44340 AAAACG AAAAGA AAAAGG AAAA
1 AAAAGG AAAAGG AAAAGG AAAA
44362 AAAAAAAGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
5 9 0.17
6 43 0.83
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (6 bp):
AAAAGG
Found at i:44366 original size:11 final size:11
Alignment explanation
Indices: 44300--44343 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
44290 ATAAAAAAGG
*
44300 AAAAGGAAAAG
1 AAAAGGAAAAA
*
44311 AAAAGGAAAGA
1 AAAAGGAAAAA
44322 AAAAGGAAAAA
1 AAAAGGAAAAA
*
44333 GAAAATGAAAA
1 -AAAAGGAAAA
44344 CGAAAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
AAAAGGAAAAA
Found at i:44366 original size:17 final size:16
Alignment explanation
Indices: 44292--44375 Score: 62
Period size: 18 Copynumber: 5.1 Consensus size: 16
44282 GAAAAAAAAT
*
44292 AAAAAAGGAAAAGGAA
1 AAAAAAAGAAAAGGAA
* * *
44308 AAGAAAAGGAAAGAAA
1 AAAAAAAGAAAAGGAA
*
44324 AAGGAAAAAGAAAATGAA
1 AA--AAAAAGAAAAGGAA
*
44342 AACGAAAAGAAAAAGGAA
1 AA-AAAAAG-AAAAGGAA
*
44360 AAAAAAA-AAGAGGAA
1 AAAAAAAGAAAAGGAA
44375 A
1 A
44376 TAAGAAAATA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
15 8 0.15
16 14 0.27
17 9 0.17
18 21 0.40
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.01
Consensus pattern (16 bp):
AAAAAAAGAAAAGGAA
Found at i:46414 original size:25 final size:24
Alignment explanation
Indices: 46378--46424 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
46368 TCCTTCTATT
46378 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
46401 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
46425 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:50894 original size:16 final size:15
Alignment explanation
Indices: 50873--50914 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
50863 TTACTTTGTT
*
50873 TTGTTTTTTAGTATAA
1 TTGTTTTCT-GTATAA
*
50889 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTATAA
50904 TTGTTTTCTGT
1 TTGTTTTCTGT
50915 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:50904 original size:15 final size:15
Alignment explanation
Indices: 50886--50914 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50876 TTTTTTAGTA
50886 TAATTGTTTTCTGTT
1 TAATTGTTTTCTGTT
50901 TAATTGTTTTCTGT
1 TAATTGTTTTCTGT
50915 CAACCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (15 bp):
TAATTGTTTTCTGTT
Done.