Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013357.1 Corchorus olitorius cultivar O-4 contig13390, 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: 23145
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1716 original size:27 final size:27
Alignment explanation
Indices: 1686--1816 Score: 217
Period size: 27 Copynumber: 4.9 Consensus size: 27
1676 TGACCCACAA
1686 AGCAATGATCCTGAATAGGATTCAGAG
1 AGCAATGATCCTGAATAGGATTCAGAG
*
1713 AGCAATGATCCTGAATAGGGTTCAGAG
1 AGCAATGATCCTGAATAGGATTCAGAG
* *
1740 AGCAATGATCCTGAATAGGATTGAGAT
1 AGCAATGATCCTGAATAGGATTCAGAG
* *
1767 AGCAATGATCCTGAATAGGATTGAGAT
1 AGCAATGATCCTGAATAGGATTCAGAG
1794 AGCAATGATCCTGAATAGGATTC
1 AGCAATGATCCTGAATAGGATTC
1817 TAAAATGACA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (27 bp):
AGCAATGATCCTGAATAGGATTCAGAG
Found at i:1880 original size:27 final size:28
Alignment explanation
Indices: 1850--1912 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1840 TCCTAAATAG
* * *
1850 GATCCTGAAATTGG-TTGATAAAGCATT
1 GATCCTGAAATAGGATTGAGAAAGCAAT
*
1877 GATCCTG-AATAGGATTGAGATAGCAAT
1 GATCCTGAAATAGGATTGAGAAAGCAAT
1904 GATCCTGAA
1 GATCCTGAA
1913 TAAGATTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 5 0.17
27 24 0.80
28 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (28 bp):
GATCCTGAAATAGGATTGAGAAAGCAAT
Found at i:1884 original size:104 final size:107
Alignment explanation
Indices: 1758--1999 Score: 337
Period size: 107 Copynumber: 2.3 Consensus size: 107
1748 TCCTGAATAG
* * *
1758 GATTGAGATAGCAATGATCCTGAATAGGATTGAGATAGCAATGATCCTGAATAGGATT-CT-AAA
1 GATTGATAAAGCAATGATCCTGAATAGGATTGAGATAGCAATGATCCTGAATAAGATTCCTGAAA
*
1821 ATGACA-GATAAAGCAATGATCCTAAATAGGATCCTGAAATT
66 ATGACATGATAAAGCAATGATCCTAAATAGGATCCTGAAACT
* *
1862 GGTTGATAAAGCATTGATCCTGAATAGGATTGAGATAGCAATGATCCTGAATAAGATTCCTGAAA
1 GATTGATAAAGCAATGATCCTGAATAGGATTGAGATAGCAATGATCCTGAATAAGATTCCTGAAA
* * * * *
1927 TTGATATGATAAGGCAATGATCCTGAATAGGATTCTGAAACT
66 ATGACATGATAAAGCAATGATCCTAAATAGGATCCTGAAACT
* * *
1969 GATTGATAAAGTAATGATCCTAAAAAGGATT
1 GATTGATAAAGCAATGATCCTGAATAGGATT
2000 AAAACACATA
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
104 53 0.45
105 2 0.02
106 7 0.06
107 57 0.48
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (107 bp):
GATTGATAAAGCAATGATCCTGAATAGGATTGAGATAGCAATGATCCTGAATAAGATTCCTGAAA
ATGACATGATAAAGCAATGATCCTAAATAGGATCCTGAAACT
Found at i:1946 original size:41 final size:39
Alignment explanation
Indices: 1889--1989 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 39
1879 TCCTGAATAG
* * *
1889 GATTGAGATAGCAATGATCCTGAATAAGATTCCTGAAATT
1 GATTGATAAAGCAATGATCCTGAATAAGATT-CTGAAACT
* *
1929 GATATGATAAGGCAATGATCCTGAATAGGATTCTGAAACT
1 GAT-TGATAAAGCAATGATCCTGAATAAGATTCTGAAACT
*
1969 GATTGATAAAGTAATGATCCT
1 GATTGATAAAGCAATGATCCT
1990 AAAAAGGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 16 0.30
40 13 0.25
41 24 0.45
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (39 bp):
GATTGATAAAGCAATGATCCTGAATAAGATTCTGAAACT
Found at i:1948 original size:68 final size:66
Alignment explanation
Indices: 1832--1960 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 66
1822 TGACAGATAA
* * *
1832 AGCAATGATCCTAAATAGGATCCTGAAATTGGTTGATAAAGCATTGATCCTGAATAGGATTGAGA
1 AGCAATGATCCTAAATAAGATCCTGAAATTGATTGATAAAGCAATGATCCTGAATAGGATTGAGA
1897 T
66 T
* *
1898 AGCAATGATCCTGAATAAGATTCCTGAAATTGATATGATAAGGCAATGATCCTGAATAGGATT
1 AGCAATGATCCTAAATAAGA-TCCTGAAATTGAT-TGATAAAGCAATGATCCTGAATAGGATT
1961 CTGAAACTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 18 0.32
67 12 0.21
68 26 0.46
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (66 bp):
AGCAATGATCCTAAATAAGATCCTGAAATTGATTGATAAAGCAATGATCCTGAATAGGATTGAGA
T
Found at i:1987 original size:39 final size:41
Alignment explanation
Indices: 1898--1999 Score: 136
Period size: 39 Copynumber: 2.5 Consensus size: 41
1888 GGATTGAGAT
* *
1898 AGCAATGATCCTGAATAAGATTCCTGAAATTGATATGATAA
1 AGCAATGATCCTGAATAGGATTCCTGAAACTGATATGATAA
*
1939 GGCAATGATCCTGAATAGGATT-CTGAAACTGAT-TGATAA
1 AGCAATGATCCTGAATAGGATTCCTGAAACTGATATGATAA
* * *
1978 AGTAATGATCCTAAAAAGGATT
1 AGCAATGATCCTGAATAGGATT
2000 AAAACACATA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 24 0.44
40 10 0.19
41 20 0.37
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCAATGATCCTGAATAGGATTCCTGAAACTGATATGATAA
Found at i:2371 original size:145 final size:145
Alignment explanation
Indices: 2182--2931 Score: 1229
Period size: 145 Copynumber: 5.2 Consensus size: 145
2172 AGAATTAATA
*
2182 CCCGGAGGTCTTACAAATGCAAACTCGACCCTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
*
2247 CTTTGATTAAAAACTTGATGAAATGAGATGATACACGGAGGATTTATCAGAATTAATACCCGGAG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAG
*
2312 GTTTCTGGAATTGTG
131 GTTTCTGAAATTGTG
**
2327 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAATAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
* *
2392 CTTTGATTAACAAA-TTGATGAAAAGA-AGTGATACCCAGAGGATTTATCAGAATTAATACCCGG
66 CTTTGATTAA-AAACTTGATGAAATGAGA-TGATACCCGGAGGATTTATCAGAATTAATACCCGG
2455 AGGTTTCTGAAATTGTG
129 AGGTTTCTGAAATTGTG
* * *
2472 CCCGGAGGTCTTATAAATGCAAACTCGACCTTGAGCAATGTTTTTATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
* *
2537 CTTTGATTAAAAACTTGATGAAATGAGATGATACCTGGAGGATTTATCAGAATTAGTACCC-GAG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAG
2601 GTTTCTGAAATTGTG
131 GTTTCTGAAATTGTG
* *
2616 CCCAGAGGTCTTACAAATGCAAACTCGACCTTGAGTAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
* * * *
2681 CTTTGATTAACAACTTGATGAAAAGA-AGTGATACCCGAAGGATTTATCAGAATTAATACCTGGA
66 CTTTGATTAAAAACTTGATGAAATGAGA-TGATACCCGGAGGATTTATCAGAATTAATACCCGGA
2745 GGTTTCTGAAATTGTG
130 GGTTTCTGAAATTGTG
2761 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
* ** *
2826 CTTCGATTAAAAACTTGATGAAATGAGATGATACCCAAAGGATTTATCAGAATTAATACTCGGAG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAG
*
2891 GATTCTGAAATTGTG
131 GTTTCTGAAATTGTG
*
2906 CCCGAAGGTCTTACAAATGCAAACTC
1 CCCGGAGGTCTTACAAATGCAAACTC
2932 TGAGTAGAGA
Statistics
Matches: 561, Mismatches: 37, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
143 1 0.00
144 135 0.24
145 420 0.75
146 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (145 bp):
CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
CTTTGATTAAAAACTTGATGAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAG
GTTTCTGAAATTGTG
Found at i:2710 original size:289 final size:287
Alignment explanation
Indices: 2182--2931 Score: 1286
Period size: 289 Copynumber: 2.6 Consensus size: 287
2172 AGAATTAATA
*
2182 CCCGGAGGTCTTACAAATGCAAACTCGACCCTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
2247 CTTTGATTAAAAACTTGATGAAATGAGATGATACACGGAGGATTTATCAGAATTAATACCCGGAG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATAC-CGGAGGATTTATCAGAATTAATACCC-GAG
*
2312 GTTTCTGGAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAATAAGGTTTTGATTTT
129 GTTTCTGAAATTGTGCCC-GAGGTCTTACAAATGCAAACTCGACCTTGAATAAGGTTTTGATTTT
2377 GAAACTTAAACGCAACTTTGATTAACAAATTGATGAAAAGAAGTGATACCC-AGAGGATTTATCA
193 GAAACTTAAACGCAACTTTGATTAACAAATTGATGAAAAGAAGTGATACCCGA-AGGATTTATCA
2441 GAATTAATACCCGGAGGTTTCTGAAATTGTG
257 GAATTAATACCCGGAGGTTTCTGAAATTGTG
* * *
2472 CCCGGAGGTCTTATAAATGCAAACTCGACCTTGAGCAATGTTTTTATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
*
2537 CTTTGATTAAAAACTTGATGAAATGAGATGATACCTGGAGGATTTATCAGAATTAGTACCCGAGG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATACC-GGAGGATTTATCAGAATTAATACCCGAGG
*
2602 TTTCTGAAATTGTGCCCAGAGGTCTTACAAATGCAAACTCGACCTTGAGTAAGGTTTTGATTTTG
130 TTTCTGAAATTGTGCCC-GAGGTCTTACAAATGCAAACTCGACCTTGAATAAGGTTTTGATTTTG
*
2667 AAACTTAAACGCAACTTTGATTAACAACTTGATGAAAAGAAGTGATACCCGAAGGATTTATCAGA
194 AAACTTAAACGCAACTTTGATTAACAAATTGATGAAAAGAAGTGATACCCGAAGGATTTATCAGA
*
2732 ATTAATACCTGGAGGTTTCTGAAATTGTG
259 ATTAATACCCGGAGGTTTCTGAAATTGTG
2761 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
1 CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
* ** *
2826 CTTCGATTAAAAACTTGATGAAATGAGATGATACCCAAAGGATTTATCAGAATTAATACTCGGAG
66 CTTTGATTAAAAACTTGATGAAATGAGATGATA-CCGGAGGATTTATCAGAATTAATAC-CCGAG
*
2891 GATTCTGAAATTGTGCCCGAAGGTCTTACAAATGCAAACTC
129 GTTTCTGAAATTGTGCCCG-AGGTCTTACAAATGCAAACTC
2932 TGAGTAGAGA
Statistics
Matches: 436, Mismatches: 19, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
289 272 0.62
290 164 0.38
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (287 bp):
CCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAA
CTTTGATTAAAAACTTGATGAAATGAGATGATACCGGAGGATTTATCAGAATTAATACCCGAGGT
TTCTGAAATTGTGCCCGAGGTCTTACAAATGCAAACTCGACCTTGAATAAGGTTTTGATTTTGAA
ACTTAAACGCAACTTTGATTAACAAATTGATGAAAAGAAGTGATACCCGAAGGATTTATCAGAAT
TAATACCCGGAGGTTTCTGAAATTGTG
Found at i:3914 original size:5 final size:5
Alignment explanation
Indices: 3904--3948 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
3894 AGCTTTATTC
* * *
3904 CCTTT CCTTT CCTTT CCTTT CCTTT TCTTT TCTTT CCTTT TCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
3949 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
CCTTT
Found at i:3959 original size:15 final size:15
Alignment explanation
Indices: 3905--3949 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3895 GCTTTATTCC
* *
3905 CTTTCCTTTCCTTTC
1 CTTTCCTTTTCTTTT
3920 CTTTCCTTTTCTTTT
1 CTTTCCTTTTCTTTT
3935 CTTTCCTTTTCTTTT
1 CTTTCCTTTTCTTTT
3950 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
CTTTCCTTTTCTTTT
Found at i:11776 original size:23 final size:23
Alignment explanation
Indices: 11741--11785 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11731 CTCTTCTTTA
11741 TTTTTGGCTTTTTCTTT-TGTATT
1 TTTTTGGCTTTTT-TTTCTGTATT
11764 TTTTTGG-TATTTTTTTCTGTAT
1 TTTTTGGCT-TTTTTTTCTGTAT
11786 ACTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (23 bp):
TTTTTGGCTTTTTTTTCTGTATT
Found at i:21217 original size:1 final size:1
Alignment explanation
Indices: 21213--21242 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
21203 CATACTATAG
21213 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21243 GGTGGAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.