Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024591.1 Corchorus olitorius cultivar O-4 contig24624, 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: 25120
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2031 original size:20 final size:20
Alignment explanation
Indices: 2006--2046 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1996 GGATGGTCAC
*
2006 TCTTTTGAGGCTCCCTGCTT
1 TCTTTTGAAGCTCCCTGCTT
2026 TCTTTTGAAGCTCCCTGCTT
1 TCTTTTGAAGCTCCCTGCTT
2046 T
1 T
2047 GTGGAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.29, G:0.17, T:0.46
Consensus pattern (20 bp):
TCTTTTGAAGCTCCCTGCTT
Found at i:2182 original size:29 final size:29
Alignment explanation
Indices: 2145--2202 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2135 GGCGGGGTTC
*
2145 ATTATTTATCGTCCTCTACCTCTGCATCG
1 ATTATTTATCGCCCTCTACCTCTGCATCG
2174 ATTATTTATCGCCCTCTACCTCTGCATCG
1 ATTATTTATCGCCCTCTACCTCTGCATCG
2203 GCATCTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.33, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTATTTATCGCCCTCTACCTCTGCATCG
Found at i:2247 original size:47 final size:47
Alignment explanation
Indices: 2178--2381 Score: 320
Period size: 47 Copynumber: 4.4 Consensus size: 47
2168 GCATCGATTA
*
2178 TTTATCGCCCTCTACCTCTGCATCGGCATCTTGGCGGGGTTGATTTT
1 TTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTT
*
2225 TTTATCGCCCTCTACCTCTGCATCGGCGTCTTGGCGGGGTTGATTTT
1 TTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTT
* * *
2272 TTTATCACCCTCTACCTCTACATCGGCTTCTTGGCGGGGTTGA-TTA
1 TTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTT
* * * *
2318 TTTATCACCCTCAACCTCTGTATCGACTTCTTGGCGGGGTTGATTTT
1 TTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTT
2365 TTTATCGCCCTCTACCT
1 TTTATCGCCCTCTACCT
2382 TTTGCTTCAG
Statistics
Matches: 144, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 41 0.28
47 103 0.72
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.39
Consensus pattern (47 bp):
TTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTT
Found at i:2376 original size:93 final size:94
Alignment explanation
Indices: 2178--2381 Score: 320
Period size: 93 Copynumber: 2.2 Consensus size: 94
2168 GCATCGATTA
* * * *
2178 TTTATCGCCCTCTACCTCTGCATCGGCATCTTGGCGGGGTTGATTTTTTTATCGCCCTCTACCTC
1 TTTATCGCCCTCTACCTCTACATCGGCATCTTGGCGGGGTTGATTTATTTATCACCCTCAACCTC
*
2243 TGCATCGGCGTCTTGGCGGGGTTGATTTT
66 TGCATCGACGTCTTGGCGGGGTTGATTTT
* *
2272 TTTATCACCCTCTACCTCTACATCGGCTTCTTGGCGGGGTTGA-TTATTTATCACCCTCAACCTC
1 TTTATCGCCCTCTACCTCTACATCGGCATCTTGGCGGGGTTGATTTATTTATCACCCTCAACCTC
* *
2336 TGTATCGACTTCTTGGCGGGGTTGATTTT
66 TGCATCGACGTCTTGGCGGGGTTGATTTT
2365 TTTATCGCCCTCTACCT
1 TTTATCGCCCTCTACCT
2382 TTTGCTTCAG
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 60 0.60
94 40 0.40
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.39
Consensus pattern (94 bp):
TTTATCGCCCTCTACCTCTACATCGGCATCTTGGCGGGGTTGATTTATTTATCACCCTCAACCTC
TGCATCGACGTCTTGGCGGGGTTGATTTT
Found at i:5867 original size:70 final size:70
Alignment explanation
Indices: 5787--5940 Score: 247
Period size: 70 Copynumber: 2.2 Consensus size: 70
5777 TGCTTTGCTT
**
5787 GAGAAGAACTTTGCCTTGCCTTGTTTTGAATTTGGAGAGATTGCTGGTGGCTTGGAATGCTCTGT
1 GAGAAGAACTTTGCCTTGCCTTGCCTTGAATTTGGAGAGATTGCTGGTGGCTTGGAATGCTCTGT
5852 TGATG
66 TGATG
* *
5857 GAGAAGAACTTTGCCTTGCCTTGCCTTGAATTTGGAGAGATTGCTGGTGGCTTTGAATGCTTTGT
1 GAGAAGAACTTTGCCTTGCCTTGCCTTGAATTTGGAGAGATTGCTGGTGGCTTGGAATGCTCTGT
*
5922 TGATT
66 TGATG
5927 GAGAATG-ACTTTGC
1 GAGAA-GAACTTTGC
5941 TTCAGATTTG
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
70 77 0.99
71 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (70 bp):
GAGAAGAACTTTGCCTTGCCTTGCCTTGAATTTGGAGAGATTGCTGGTGGCTTGGAATGCTCTGT
TGATG
Found at i:10643 original size:1 final size:1
Alignment explanation
Indices: 10639--10665 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
10629 ATGGTTTTTT
10639 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
10666 CTTTTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11712 original size:20 final size:20
Alignment explanation
Indices: 11648--11712 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
11638 TCAACATAAG
11648 AAACAATAATATATAATGAA
1 AAACAATAATATATAATGAA
* * * * *
11668 AAACTATAGATATCTTATTAG
1 AAACAATA-ATATATAATGAA
11689 AAACAATAATATATAATGAA
1 AAACAATAATATATAATGAA
11709 AAAC
1 AAAC
11713 CATAGATGTC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (20 bp):
AAACAATAATATATAATGAA
Found at i:14603 original size:13 final size:13
Alignment explanation
Indices: 14566--14598 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
14556 AAAACGAAAT
14566 AAAAA-AAAAAAG
1 AAAAAGAAAAAAG
14578 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
14591 AAAGAAGA
1 AAA-AAGA
14599 CAAAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 10 0.53
14 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:15505 original size:89 final size:89
Alignment explanation
Indices: 15350--15529 Score: 310
Period size: 89 Copynumber: 2.0 Consensus size: 89
15340 ATTACTAACT
* *
15350 AATGGTATAGTATAATCTTTATGTAGTTATCCAATATTATTTTAAGTGACAATGATTACTGTACT
1 AATGGTATAGTATAATCTTTATGTAGTTATCCAATATTATTTCAAGTGACAATGATTACTGCACT
15415 GTATCTCAATTCTCAAATGATTTC
66 GTATCTCAATTCTCAAATGATTTC
15439 AATGGTATAGTATAATCTTTATGTAGTTATCC-A-ATTATTTCAAGTGACAAAATGATTACTGCA
1 AATGGTATAGTATAATCTTTATGTAGTTATCCAATATTATTTCAAGTGAC--AATGATTACTGCA
15502 CTGTATCTCAATTCTCAAATGATTTC
64 CTGTATCTCAATTCTCAAATGATTTC
15528 AA
1 AA
15530 GTTTTTTTTT
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
87 14 0.16
88 1 0.01
89 72 0.83
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (89 bp):
AATGGTATAGTATAATCTTTATGTAGTTATCCAATATTATTTCAAGTGACAATGATTACTGCACT
GTATCTCAATTCTCAAATGATTTC
Found at i:17942 original size:2 final size:2
Alignment explanation
Indices: 17931--17968 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17921 ATAGTAAGAC
17931 TA TA -A TA TA TA 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 TA TA TA TA TA TA T
17969 CTTACTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18579 original size:15 final size:15
Alignment explanation
Indices: 18559--18591 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18549 CTAGCCCAAA
18559 AATTAAAACCAATTT
1 AATTAAAACCAATTT
*
18574 AATTAAATCCAATTT
1 AATTAAAACCAATTT
18589 AAT
1 AAT
18592 CAGCCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAAAACCAATTT
Found at i:20307 original size:22 final size:22
Alignment explanation
Indices: 20202--20409 Score: 113
Period size: 22 Copynumber: 9.6 Consensus size: 22
20192 ACAATCAAAC
* *
20202 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
* * * *
20224 TAAAATTTCATAGTATA-GCTAC
1 CAAAATTTCATAG-AAAGGTTAT
20246 CAAAATTTCAT-G--AGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
* * * **
20265 CAACACTTCATTGTGTA-GTTAT
1 CAAAATTTCATAG-AAAGGTTAT
*
20287 CAAAATTTCATACAAAGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
**
20309 CAAAATTTCATAGAAACTTTAT
1 CAAAATTTCATAGAAAGGTTAT
* ** *
20331 CAAAATTTCTTAGGCAGGTTAA
1 CAAAATTTCATAGAAAGGTTAT
* *
20353 CAAAATCTCATACG-AATGTTAT
1 CAAAATTTCATA-GAAAGGTTAT
** * ***
20375 TGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
20397 CAAAATTTCATAG
1 CAAAATTTCATAG
20410 GGAGGGAGGT
Statistics
Matches: 136, Mismatches: 41, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
18 1 0.01
19 12 0.09
20 1 0.01
21 3 0.02
22 116 0.85
23 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGGTTAT
Found at i:20469 original size:42 final size:42
Alignment explanation
Indices: 20388--20472 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
20378 AATTTTATAG
* * *
20388 TGTGGTTATCAAAATTTCATAGGGAGGGAGGTTATCAAAATT
1 TGTGCTTATCAAAATTTCATAGGGAGGGAGATTAACAAAATT
*
20430 TGTGCTTATCAAAATTTCATAGGGAGGTTA-ATTAACAAAATT
1 TGTGCTTATCAAAATTTCATAGGGAGG-GAGATTAACAAAATT
20472 T
1 T
20473 CATATGGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (42 bp):
TGTGCTTATCAAAATTTCATAGGGAGGGAGATTAACAAAATT
Found at i:20677 original size:22 final size:22
Alignment explanation
Indices: 20630--20753 Score: 144
Period size: 22 Copynumber: 5.6 Consensus size: 22
20620 CATAGTATAA
*
20630 TTATCAAAATATT-ATAG-GGGG
1 TTATCAAAAT-TTCATAGTGAGG
*
20651 ATTATCAAAATTTCATACTGAGG
1 -TTATCAAAATTTCATAGTGAGG
*
20674 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
20696 TTATCAAATTTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
** *
20718 TTATTGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
*
20740 TTATCAAATTTTCA
1 TTATCAAAATTTCA
20754 GTTTGGTTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
21 2 0.02
22 82 0.94
23 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:20700 original size:66 final size:67
Alignment explanation
Indices: 20615--20766 Score: 170
Period size: 66 Copynumber: 2.3 Consensus size: 67
20605 TGTTGTTACC
** * *
20615 AATTTCATAGTATAATTATCAAAATATT-ATAG-GGGGATTATCAAAATTTCATACTGAGGTTAT
1 AATTTCATAGTATGGTTATCAAAATATTCATAGTGAGG-TTATCAAAATTTCATAATGAGGTTAT
20678 CAA
65 CAA
* * **
20681 AATTTCATAGTGTGGTTATC-AAATTTTCATAGTGAGGTTATTGAAATTTCATAATGAGGTTATC
1 AATTTCATAGTATGGTTATCAAAATATTCATAGTGAGGTTATCAAAATTTCATAATGAGGTTATC
20745 AA
66 AA
* *
20747 ATTTTC--AGTTTGGTTATCAA
1 AATTTCATAGTATGGTTATCAA
20767 TATTTCTATG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 11 0.15
65 7 0.10
66 52 0.71
67 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (67 bp):
AATTTCATAGTATGGTTATCAAAATATTCATAGTGAGGTTATCAAAATTTCATAATGAGGTTATC
AA
Found at i:24065 original size:7 final size:7
Alignment explanation
Indices: 24053--24114 Score: 90
Period size: 7 Copynumber: 8.7 Consensus size: 7
24043 AAAAAAATAG
24053 ATTACTA
1 ATTACTA
24060 ATTACTA
1 ATTACTA
24067 ATTACTA
1 ATTACTA
*
24074 ATTACAA
1 ATTACTA
24081 ATGTTACTA
1 A--TTACTA
24090 ATTACT-
1 ATTACTA
24096 ATTACTA
1 ATTACTA
24103 ATTACTA
1 ATTACTA
24110 ATTAC
1 ATTAC
24115 AAATGTTACA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
6 6 0.12
7 38 0.76
9 6 0.12
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (7 bp):
ATTACTA
Found at i:24088 original size:23 final size:20
Alignment explanation
Indices: 24053--24114 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 20
24043 AAAAAAATAG
*
24053 ATTACTAATTACTAATTACT
1 ATTACAAATTACTAATTACT
24073 AATTACAAATGTTACTAATTACT
1 -ATTACAAA--TTACTAATTACT
*
24096 ATTACTAATTACTAATTAC
1 ATTACAAATTACTAATTAC
24115 AAATGTTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.30
21 7 0.19
22 7 0.19
23 12 0.32
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTACAAATTACTAATTACT
Found at i:24102 original size:36 final size:37
Alignment explanation
Indices: 24053--24123 Score: 135
Period size: 36 Copynumber: 1.9 Consensus size: 37
24043 AAAAAAATAG
24053 ATTACTAATTACTAATTACTAATTACAAATGTTACTA
1 ATTACTAATTACTAATTACTAATTACAAATGTTACTA
24090 ATTACT-ATTACTAATTACTAATTACAAATGTTAC
1 ATTACTAATTACTAATTACTAATTACAAATGTTAC
24124 ATACTTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 28 0.82
37 6 0.18
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (37 bp):
ATTACTAATTACTAATTACTAATTACAAATGTTACTA
Done.