Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017807.1 Corchorus olitorius cultivar O-4 contig17840, 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: 58017
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2607 original size:64 final size:64
Alignment explanation
Indices: 2512--2637 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
2502 GTCCACTCCT
*
2512 AGCAAAAAGAAAAGGTTAGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATAGCAA
1 AGCAAAAAGAAAACGTTAGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATAGCAA
*
2576 AGCAAAAAGAAAACGTTTGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATAGC
1 AGCAAAAAGAAAACGTTAGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATAGC
2638 CAAGACAGGA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (64 bp):
AGCAAAAAGAAAACGTTAGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATAGCAA
Found at i:9338 original size:152 final size:153
Alignment explanation
Indices: 8971--9391 Score: 695
Period size: 152 Copynumber: 2.8 Consensus size: 153
8961 CCTAAATCCT
*
8971 ATACTGATACGATCAGAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTGTCTCCC
1 ATACTGAGACGATCAGAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTGTCTCCC
9036 AATGAATGCAAAT--AGAGATAAAGAAATTATGATTTTTATCAACCACCTAAACCCTATACTAAG
66 AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAACCCTATACTAAG
* * *
9099 ACGATCTTTTTTTTTTGCCAGAC
131 ACAATCTTTTCTTTTGGCCAGAC
* * *
9122 ATACTGAGACTATCAAAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTATCTCCC
1 ATACTGAGACGATCAGAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTGTCTCCC
*
9187 AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAACCCTATACTGAG
66 AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAACCCTATACTAAG
*
9252 ACAATC-TTTCTTTTGGTCAGAC
131 ACAATCTTTTCTTTTGGCCAGAC
* * * * *
9274 ATACTGAGACGGTCAGAGTTCTGATTCTTTTTGCTTTTTTGGGTTGTAAATTCTAGTTGTCTCCC
1 ATACTGAGACGATCAGAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTGTCTCCC
9339 AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAA
66 AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAA
9392 ATTCTTTTTT
Statistics
Matches: 251, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
151 74 0.29
152 123 0.49
153 54 0.22
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (153 bp):
ATACTGAGACGATCAGAGTGCTGATTCTTTTTGCTTGTTTGGGTTGTAAATTCGAGCTGTCTCCC
AATGAATGCAAATGGAGAGATAAAGAAATTATGATTTTTATCAACCACCTAAACCCTATACTAAG
ACAATCTTTTCTTTTGGCCAGAC
Found at i:15796 original size:21 final size:21
Alignment explanation
Indices: 15746--15790 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15736 GTGACACTGC
*
15746 CCACCTGGGTCCTCAAGCAAA
1 CCACATGGGTCCTCAAGCAAA
* *
15767 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTCCTCAAGCAAA
15788 CCA
1 CCA
15791 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGCAAA
Found at i:18574 original size:21 final size:21
Alignment explanation
Indices: 18535--18583 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
18525 TCAATGCTTT
**
18535 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
18557 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
18578 A-GAAGC
1 AGGAAGC
18584 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:21066 original size:21 final size:21
Alignment explanation
Indices: 21042--21086 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21032 CTTCTATTAC
*
21042 CTTTATTCA-CAAATTCACTCA
1 CTTTAATCATCAAATTCACT-A
*
21063 CTTTAATCATCAATTTCACTA
1 CTTTAATCATCAAATTCACTA
21084 CTT
1 CTT
21087 CATCACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTTAATCATCAAATTCACTA
Found at i:26637 original size:4 final size:4
Alignment explanation
Indices: 26630--26687 Score: 64
Period size: 4 Copynumber: 14.5 Consensus size: 4
26620 GTGTGTCTAA
* *
26630 ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT-T AGTAT GTAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A-TAT ATAT ATAT ATAT
* *
26678 GTAT GTAT AT
1 ATAT ATAT AT
26688 TCTCATATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 2 0.04
4 45 0.94
5 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:26731 original size:2 final size:2
Alignment explanation
Indices: 26719--26752 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
26709 AAATTAATCC
26719 TA TA CTA 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 T
26753 TTTCATAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27849 original size:67 final size:68
Alignment explanation
Indices: 27738--27876 Score: 253
Period size: 67 Copynumber: 2.0 Consensus size: 68
27728 TATGAATAAT
*
27738 CAAAATTTCATTACAATCGATCATGAAGAAAAC-AAAAAATTTGAGACTTCAAGTTTGAGCAAGA
1 CAAAATTTCATTACAATCGATCATGAAGAAAACAAAAAAATTAGAGACTTCAAGTTTGAGCAAGA
27802 ACC
66 ACC
27805 CAAAATTTCATTACAATCGATCATGAAGAAAACAAAAAAATTGAGAGACTTCAAGTTTGAGCAAG
1 CAAAATTTCATTACAATCGATCATGAAGAAAACAAAAAAATT-AGAGACTTCAAGTTTGAGCAAG
27870 AACC
65 AACC
27874 CAA
1 CAA
27877 GTTGGAAACA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 33 0.48
68 8 0.12
69 28 0.41
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (68 bp):
CAAAATTTCATTACAATCGATCATGAAGAAAACAAAAAAATTAGAGACTTCAAGTTTGAGCAAGA
ACC
Found at i:28928 original size:12 final size:13
Alignment explanation
Indices: 28886--28925 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
28876 TCAATTATTT
*
28886 ATTTATTTATTAA
1 ATTTATTTTTTAA
*
28899 ATACTATTTTTTAA
1 AT-TTATTTTTTAA
28913 ATTTATTTTTTAA
1 ATTTATTTTTTAA
28926 TTTTTTCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATTTTTTAA
Found at i:28939 original size:8 final size:8
Alignment explanation
Indices: 28928--28975 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
28918 TTTTTTAATT
28928 TTTTCTGA
1 TTTTCTGA
28936 TTTTCTGA
1 TTTTCTGA
28944 TTTTCTGA
1 TTTTCTGA
28952 TTTT-T-A
1 TTTTCTGA
28958 TTTTCT--
1 TTTTCTGA
28964 TTTTCTGA
1 TTTTCTGA
28972 TTTT
1 TTTT
28976 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.30
7 2 0.05
8 24 0.65
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.71
Consensus pattern (8 bp):
TTTTCTGA
Found at i:32234 original size:32 final size:32
Alignment explanation
Indices: 32187--32247 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
32177 TGTAAAACTT
* *
32187 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCAACCATTATACCCTTATTTTTCTAA
32219 TTGAATCAACCATTATACCCTTATTTTTC
1 TTGAATCAACCATTATACCCTTATTTTTC
32248 AGACATATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (32 bp):
TTGAATCAACCATTATACCCTTATTTTTCTAA
Found at i:53419 original size:34 final size:31
Alignment explanation
Indices: 53288--53524 Score: 240
Period size: 34 Copynumber: 7.6 Consensus size: 31
53278 AAAAATTTAA
*
53288 TTGACACCAGAAGTTGTCATATTAAATTATA
1 TTGACACCAGAAGTTGTCATATTAAATTATC
* *
53319 TTGACACCAGAAGTTGTCATA--GAATTATA
1 TTGACACCAGAAGTTGTCATATTAAATTATC
*
53348 TTGACACCAGAAGTTGTCATA-GAAATTA--
1 TTGACACCAGAAGTTGTCATATTAAATTATC
*
53376 TTGACACCAGAAGTTGTCATATTATATTGTTATC
1 TTGACACCAGAAGTTGTCATATTA-A--ATTATC
*
53410 TTGACACCAGAAGTTGTCATATTATATTGTTATC
1 TTGACACCAGAAGTTGTCATATTA-A--ATTATC
53444 TTGACACCAGAAGTTGTCATGA--AAATTA--
1 TTGACACCAGAAGTTGTCAT-ATTAAATTATC
* *
53472 TTGACACTAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATAT-TAA--ATTATC
*
53506 TTGACACCAAAAGTTGTCA
1 TTGACACCAGAAGTTGTCA
53525 CCTAAGGGTT
Statistics
Matches: 183, Mismatches: 8, Indels: 27
0.84 0.04 0.12
Matches are distributed among these distances:
27 1 0.01
28 40 0.22
29 29 0.16
30 11 0.06
31 21 0.11
32 8 0.04
33 1 0.01
34 71 0.39
35 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (31 bp):
TTGACACCAGAAGTTGTCATATTAAATTATC
Found at i:53476 original size:62 final size:59
Alignment explanation
Indices: 53287--53524 Score: 241
Period size: 62 Copynumber: 3.9 Consensus size: 59
53277 AAAAAATTTA
* * *
53287 ATTGACACCAGAAGTTGTCATATTAAATTATATTGACACCAGAAGTTGTCATAGAATTAT
1 ATTGACACCAGAAGTTGTCATATTAAATTATCTTGACACCAGAAGTTGTCATATAAAT-T
* *
53347 ATTGACACCAGAAGTTGTCATA-GAAATTA--TTGACACCAGAAGTTGTCATATTATATTGTT
1 ATTGACACCAGAAGTTGTCATATTAAATTATCTTGACACCAGAAGTTGTCATA-TA-A--ATT
*
53407 ATCTTGACACCAGAAGTTGTCATATTATATTGTTATCTTGACACCAGAAGTTGTCATGA-AAATT
1 A--TTGACACCAGAAGTTGTCATATTA-A--ATTATCTTGACACCAGAAGTTGTCAT-ATAAATT
* * *
53471 ATTGACACTAGAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCA
1 ATTGACACCAGAAGTTGTCATAT-TAA--ATTATCTTGACACCAGAAGTTGTCA
53525 CCTAAGGGTT
Statistics
Matches: 154, Mismatches: 10, Indels: 26
0.81 0.05 0.14
Matches are distributed among these distances:
57 21 0.14
58 1 0.01
59 7 0.05
60 24 0.16
61 1 0.01
62 68 0.44
63 2 0.01
64 4 0.03
66 4 0.03
67 1 0.01
68 20 0.13
69 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (59 bp):
ATTGACACCAGAAGTTGTCATATTAAATTATCTTGACACCAGAAGTTGTCATATAAATT
Found at i:53478 original size:96 final size:90
Alignment explanation
Indices: 53287--53524 Score: 320
Period size: 96 Copynumber: 2.6 Consensus size: 90
53277 AAAAAATTTA
*
53287 ATTGACACCAGAAGTTGTCATATTAA--ATTATATTGACACCAGAAGTTGTCATAGAATTATATT
1 ATTGACACCAGAAGTTGTCATATTAATTATTATCTTGACACCAGAAGTTGTCATAGAATTATATT
53350 GACACCAGAAGTTGTCATAGAAATT
66 GACACCAGAAGTTGTCATAGAAATT
* *
53375 ATTGACACCAGAAGTTGTCATATTATATTGTTATCTTGACACCAGAAGTTGTCATATTATATTGT
1 ATTGACACCAGAAGTTGTCATATTA-ATTATTATCTTGACACCAGAAGTTGTCATA-GA-A---T
*
53440 TATCTTGACACCAGAAGTTGTCAT-GAAAATT
60 TATATTGACACCAGAAGTTGTCATAG-AAATT
* * *
53471 ATTGACACTAGAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCA
1 ATTGACACCAGAAGTTGTCATAT-TAATTATTATCTTGACACCAGAAGTTGTCA
53525 CCTAAGGGTT
Statistics
Matches: 132, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
88 25 0.19
89 1 0.01
91 25 0.19
92 1 0.01
93 1 0.01
95 1 0.01
96 77 0.58
97 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (90 bp):
ATTGACACCAGAAGTTGTCATATTAATTATTATCTTGACACCAGAAGTTGTCATAGAATTATATT
GACACCAGAAGTTGTCATAGAAATT
Found at i:53702 original size:2 final size:2
Alignment explanation
Indices: 53691--53719 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53681 AGTTTAGACT
53691 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53720 CTAGTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:54814 original size:29 final size:29
Alignment explanation
Indices: 54781--54839 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54771 TTAATCTATG
54781 AGTCAACAAACCCCTTCCCCAACAAACAA
1 AGTCAACAAACCCCTTCCCCAACAAACAA
54810 AGTCAACAAACCCCTTCCCCAACAAACAA
1 AGTCAACAAACCCCTTCCCCAACAAACAA
54839 A
1 A
54840 CCCAGTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.41, G:0.03, T:0.10
Consensus pattern (29 bp):
AGTCAACAAACCCCTTCCCCAACAAACAA
Found at i:55688 original size:58 final size:57
Alignment explanation
Indices: 55594--55705 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
55584 ATTAATCAAA
*
55594 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCGAGCCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGCCT
* * * *
55651 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGATGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAG
55706 GCATGATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 13 0.27
58 36 0.73
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (57 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGCCT
Found at i:57905 original size:164 final size:165
Alignment explanation
Indices: 57616--57945 Score: 592
Period size: 164 Copynumber: 2.0 Consensus size: 165
57606 TTAATTTTTT
*
57616 AAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTATTATTATTATATATAA
1 AAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTATTATTATATATAA
**
57681 AACTATACCAAAAAAAATTAGTTGAGTATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGT
66 AACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGT
57746 CAAACAAAATTTCAAAATTATAAAAGATATTAAAG
131 CAAACAAAATTTCAAAATTATAAAAGATATTAAAG
*
57781 AAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTATTA-TATATATAG
1 AAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTATTATTATATATAA
57845 AACTATACCAAAAAAAAATT-GTTGAACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATG
66 AACTATACC-AAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATG
*
57909 TCAAACAAAATTTTAAAATTATAAAAGATATTAAAG
130 TCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
57945 A
1 A
57946 TCCGATTTAT
Statistics
Matches: 159, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
164 95 0.60
165 64 0.40
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (165 bp):
AAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTATTATTATATATAA
AACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGT
CAAACAAAATTTCAAAATTATAAAAGATATTAAAG
Done.