Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018043.1 Corchorus olitorius cultivar O-4 contig18076, 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: 35175
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1800 original size:18 final size:19
Alignment explanation
Indices: 1772--1809 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1762 GTTTAATAGG
1772 ATTTTTAAGTGTAAGAATA
1 ATTTTTAAGTGTAAGAATA
1791 ATTTTT-AGTGTAAGAATA
1 ATTTTTAAGTGTAAGAATA
1809 A
1 A
1810 ACGACAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTTAAGTGTAAGAATA
Found at i:3491 original size:20 final size:20
Alignment explanation
Indices: 3468--3506 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3458 AAGCTTTGTA
3468 GTATATGGTTATAGTTAAGC
1 GTATATGGTTATAGTTAAGC
*
3488 GTATATGGTTATGGTTAAG
1 GTATATGGTTATAGTTAAG
3507 TGTTCCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (20 bp):
GTATATGGTTATAGTTAAGC
Found at i:4869 original size:13 final size:13
Alignment explanation
Indices: 4853--4899 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
4843 GAAAAAAAAG
4853 AGAAAAATAGAAA
1 AGAAAAATAGAAA
4866 AGAAAAATAGAAA
1 AGAAAAATAGAAA
* *
4879 GGAAAAGAAAGAAA
1 AGAAAA-ATAGAAA
4893 AGAAAAA
1 AGAAAAA
4900 GGAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (13 bp):
AGAAAAATAGAAA
Found at i:4891 original size:14 final size:13
Alignment explanation
Indices: 4844--4899 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
4834 CAAAAGGGAG
*
4844 AAAAAA-AAGAGA
1 AAAAAAGAAAAGA
*
4856 AAAATAGAAAAGA
1 AAAAAAGAAAAGA
* *
4869 AAAATAGAAAGGA
1 AAAAAAGAAAAGA
4882 AAAGAAAGAAAAGA
1 AAA-AAAGAAAAGA
4896 AAAA
1 AAAA
4900 GGAAGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 5 0.14
13 21 0.57
14 11 0.30
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:4916 original size:15 final size:16
Alignment explanation
Indices: 4876--4918 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4866 AGAAAAATAG
* *
4876 AAAGGAAAA-GAAAGA
1 AAAGAAAAAGGAAGGA
4891 AAAGAAAAAGGAAGGA
1 AAAGAAAAAGGAAGGA
4907 AAA-AAAAAGGAA
1 AAAGAAAAAGGAA
4919 AATAAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGGAAGGA
Found at i:15759 original size:229 final size:229
Alignment explanation
Indices: 15358--15817 Score: 875
Period size: 229 Copynumber: 2.0 Consensus size: 229
15348 TTGTATAAAT
*
15358 TATGGAGAACAAGAGTTATTAAAGCTTTCCTATATGAGTTCGACGTGATTTGACTCGAGATTAAT
1 TATGGAGAACAAGAGTTATTAAAGCTTTCCTATATGAATTCGACGTGATTTGACTCGAGATTAAT
*
15423 CCAAACTTATATTAGAAGGATTGGTTTTAAAAAATTTACAAGGAAATTACCAAGAATCATGGGTT
66 CCAAACTTATATTAGAAGGATTAGTTTTAAAAAATTTACAAGGAAATTACCAAGAATCATGGGTT
15488 GACCCCATCTCAAAGAAATATAGTAACCCAATGTCTTAATCACTCTAATTAGACTTTACAAAGAG
131 GACCCCATCTCAAAGAAATATAGTAACCCAATGTCTTAATCACTCTAATTAGACTTTACAAAGAG
15553 CAGAAGAAATAAAGGGGAGTTTGCCCCCAACAAA
196 CAGAAGAAATAAAGGGGAGTTTGCCCCCAACAAA
*
15587 TATGGAGAACAAGAGTTATTAAAGTTTTCCTATATGAATTCGACGTGATTTGACTCGAGATTAAT
1 TATGGAGAACAAGAGTTATTAAAGCTTTCCTATATGAATTCGACGTGATTTGACTCGAGATTAAT
**
15652 CCGGACTTATATTAGAAGGATTAGTTTTAAAAAATTTACAAGGAAATTACCAAGAATCATGGGTT
66 CCAAACTTATATTAGAAGGATTAGTTTTAAAAAATTTACAAGGAAATTACCAAGAATCATGGGTT
15717 GACCCCATCTCAAAGAAATATAGTAACCCAATGTCTTAATCACTCTAATTAGACTTTACAAAGAG
131 GACCCCATCTCAAAGAAATATAGTAACCCAATGTCTTAATCACTCTAATTAGACTTTACAAAGAG
15782 CAGAAGAAATAAAGGGGAGTTTGCCCCCAACAAA
196 CAGAAGAAATAAAGGGGAGTTTGCCCCCAACAAA
15816 TA
1 TA
15818 CAGCTGGTTA
Statistics
Matches: 226, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 226 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (229 bp):
TATGGAGAACAAGAGTTATTAAAGCTTTCCTATATGAATTCGACGTGATTTGACTCGAGATTAAT
CCAAACTTATATTAGAAGGATTAGTTTTAAAAAATTTACAAGGAAATTACCAAGAATCATGGGTT
GACCCCATCTCAAAGAAATATAGTAACCCAATGTCTTAATCACTCTAATTAGACTTTACAAAGAG
CAGAAGAAATAAAGGGGAGTTTGCCCCCAACAAA
Found at i:20415 original size:15 final size:15
Alignment explanation
Indices: 20386--20434 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
20376 TGGTACGAAG
*
20386 GAAATGGGAAGGAAA
1 GAAAGGGGAAGGAAA
20401 GAAGAGGGG-AGGAAA
1 GAA-AGGGGAAGGAAA
*
20416 GAAAGGGGAAGGAAG
1 GAAAGGGGAAGGAAA
20431 GAAA
1 GAAA
20435 AGGGTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (15 bp):
GAAAGGGGAAGGAAA
Found at i:21043 original size:2 final size:2
Alignment explanation
Indices: 21036--21077 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21026 TAAATTACCA
21036 AT AT AT AT 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 AT AT AT AT
21078 TGTAACAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26601 original size:26 final size:26
Alignment explanation
Indices: 26565--26617 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
26555 TCCTGCCTAG
*
26565 TGAGGAATGGTCATTAATATAACTAA
1 TGAGAAATGGTCATTAATATAACTAA
26591 TGAGAAATGGTCATTAATATAACTAA
1 TGAGAAATGGTCATTAATATAACTAA
26617 T
1 T
26618 ATGATTAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (26 bp):
TGAGAAATGGTCATTAATATAACTAA
Found at i:26941 original size:26 final size:26
Alignment explanation
Indices: 26873--26943 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
26863 AAGTGGACTT
* *
26873 AAAATGACCAACATGCCCCTGAATGTG
1 AAAATGACCAAAATG-CCCTGAATGTA
* ** * *
26900 CAAATGACCAGGATGCCCTTAGTGTA
1 AAAATGACCAAAATGCCCTGAATGTA
26926 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
26944 CTAGGTGACC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTGAATGTA
Found at i:28360 original size:14 final size:14
Alignment explanation
Indices: 28341--28368 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28331 TTTAATATAT
28341 GTTATATATATTTC
1 GTTATATATATTTC
28355 GTTATATATATTTC
1 GTTATATATATTTC
28369 CTTTTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
GTTATATATATTTC
Found at i:29323 original size:4 final size:4
Alignment explanation
Indices: 29316--29362 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
29306 TATATATATA
29316 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
29363 AGCTGTTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:30264 original size:2 final size:2
Alignment explanation
Indices: 30257--30285 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30247 ATGTTATCAA
30257 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 A
30286 GAGTAATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30987 original size:41 final size:44
Alignment explanation
Indices: 30942--31028 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 44
30932 TTGAAGCTAA
*
30942 AAACTATTTAA-AAA-AC-ACATAAAATTCATAAACAGTTAAAC
1 AAACTATTTAAGAAACACTACAAAAAATTCATAAACAGTTAAAC
30983 AAACTATTTAAGAAACACATTACAAAAAATTCATAAACAGTTAAAC
1 AAACTATTTAAGAAACAC--TACAAAAAATTCATAAACAGTTAAAC
31029 GTTTTGCCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 11 0.28
42 3 0.08
43 2 0.05
46 24 0.60
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.24
Consensus pattern (44 bp):
AAACTATTTAAGAAACACTACAAAAAATTCATAAACAGTTAAAC
Found at i:32273 original size:62 final size:62
Alignment explanation
Indices: 32197--32327 Score: 262
Period size: 62 Copynumber: 2.1 Consensus size: 62
32187 CAATAATGAA
32197 TTTTTTTTTTGTAGAAAATGCATTATACGTTTCATGTTCAAATAGGAATGATTATAGTCTTT
1 TTTTTTTTTTGTAGAAAATGCATTATACGTTTCATGTTCAAATAGGAATGATTATAGTCTTT
32259 TTTTTTTTTTGTAGAAAATGCATTATACGTTTCATGTTCAAATAGGAATGATTATAGTCTTT
1 TTTTTTTTTTGTAGAAAATGCATTATACGTTTCATGTTCAAATAGGAATGATTATAGTCTTT
32321 TTTTTTT
1 TTTTTTT
32328 AAAAAAGAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 69 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (62 bp):
TTTTTTTTTTGTAGAAAATGCATTATACGTTTCATGTTCAAATAGGAATGATTATAGTCTTT
Done.