Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012894.1 Corchorus olitorius cultivar O-4 contig12927, 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: 39959
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Found at i:5348 original size:163 final size:163
Alignment explanation
Indices: 5078--5407 Score: 633
Period size: 163 Copynumber: 2.0 Consensus size: 163
5068 ACCCTTAACC
5078 AAACTAATTTAAGGATAATTCTTCCCATAGTTGAGGATAATTCTTCTGTCATCATTTCAAGCAAA
1 AAACTAATTTAAGGATAATTCTTCCCATAGTTGAGGATAATTCTTCTGTCATCATTTCAAGCAAA
*
5143 AAGGAAGATATTGCAGTCATATGAGAAAACACTATATGTAAGCATCTCAATAACTCATCGTCCAT
66 AAGGAACATATTGCAGTCATATGAGAAAACACTATATGTAAGCATCTCAATAACTCATCGTCCAT
*
5208 TCTGATTGAAGTAATTCAACACTTTGCATGGAT
131 TCTGATTGAAGTAATTCAACACTTTGCATGAAT
*
5241 AAACTAATTTAAGGATAATTCTTCCCATAGTTGAGGATAATTCTTCTGTCATCATTTCCAGCAAA
1 AAACTAATTTAAGGATAATTCTTCCCATAGTTGAGGATAATTCTTCTGTCATCATTTCAAGCAAA
5306 AAGGAACATATTGCAGTCATATGAGAAAACACTATATGTAAGCATCTCAATAACTCATCGTCCAT
66 AAGGAACATATTGCAGTCATATGAGAAAACACTATATGTAAGCATCTCAATAACTCATCGTCCAT
5371 TCTGATTGAAGTAATTCAACACTTTGCATGAAT
131 TCTGATTGAAGTAATTCAACACTTTGCATGAAT
5404 AAAC
1 AAAC
5408 ATTTCTTTCA
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (163 bp):
AAACTAATTTAAGGATAATTCTTCCCATAGTTGAGGATAATTCTTCTGTCATCATTTCAAGCAAA
AAGGAACATATTGCAGTCATATGAGAAAACACTATATGTAAGCATCTCAATAACTCATCGTCCAT
TCTGATTGAAGTAATTCAACACTTTGCATGAAT
Found at i:6593 original size:22 final size:22
Alignment explanation
Indices: 6565--6611 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
6555 CAACGAAAAG
6565 GAAACCCAGTTGCCTACAAATA
1 GAAACCCAGTTGCCTACAAATA
6587 GAAACCCAGTTGCCTACAAATA
1 GAAACCCAGTTGCCTACAAATA
6609 GAA
1 GAA
6612 CACCACAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (22 bp):
GAAACCCAGTTGCCTACAAATA
Found at i:7019 original size:23 final size:23
Alignment explanation
Indices: 6977--7025 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6967 CTAAATTTCT
* * *
6977 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
*
7000 AAGTTTAAACAATCAACTCTGTA
1 AAGTTTAAACAATCAACTCTATA
7023 AAG
1 AAG
7026 CTAAATTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Found at i:11814 original size:13 final size:13
Alignment explanation
Indices: 11796--11850 Score: 76
Period size: 13 Copynumber: 4.2 Consensus size: 13
11786 GCATATATTT
11796 TTAATAATAATTA
1 TTAATAATAATTA
11809 TTAATAATAATTA
1 TTAATAATAATTA
*
11822 TTAAT-ATATTTA
1 TTAATAATAATTA
*
11834 TTACTAAATAATTA
1 TTAAT-AATAATTA
11848 TTA
1 TTA
11851 TTTATTTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.27
13 18 0.49
14 9 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATAATAATTA
Found at i:11843 original size:26 final size:25
Alignment explanation
Indices: 11796--11858 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
11786 GCATATATTT
*
11796 TTAATAATAATTATTAATAATAATTA
1 TTAAT-ATATTTATTAATAATAATTA
*
11822 TTAATATATTTATTACTAAATAATTA
1 TTAATATATTTATTAAT-AATAATTA
*
11848 TT-ATTTATTTA
1 TTAATATATTTA
11859 GTAAATTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATATATTTATTAATAATAATTA
Found at i:12614 original size:9 final size:8
Alignment explanation
Indices: 12597--12621 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12587 CCTCAATATC
12597 TTCTTTTT
1 TTCTTTTT
12605 TTCTTTTT
1 TTCTTTTT
12613 TTCTTTTT
1 TTCTTTTT
12621 T
1 T
12622 ACATGAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:18183 original size:437 final size:432
Alignment explanation
Indices: 17250--18388 Score: 1259
Period size: 437 Copynumber: 2.6 Consensus size: 432
17240 AAAATTGCAA
* * * * * * * *
17250 AAGCATTTTTTAGAATTGAAATATAAAAATTAGCTTTTTGAGTCTTTCATGAAGGTTGTAGATTA
1 AAGCATTTTTTTGAATTGAAACATAAAAATTGGC-TTTTCAGTCATTCATGAAAGTTATAGATAA
* * * ** * * * * * *
17315 TAAAATTACATTTTAATAAACACCTGAATTACCTTAATTGGATAAATAG---AAAAAAAAATGAA
65 TGAAATTACCTTGTAATAGGCACATGAATCAACTTAATCGGACAAATAGAACAAAAAAAAATAAA
* * * ** *
17377 G-T---TC-TAAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAACATAAAATAGAAAAGTAT
130 GCTGAAGCGTTAA-CGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTAT
* * * * ** * *
17437 GAGAGTGATTTGGTAACTAATTTAAATAAGAAAATATTTGTTAATGGAGACCTTGAAACATAAAA
194 GAGGGTCATTTGATAAATAATCCAAATAAGAAAATACTTGTTAATGGAGATCTTGAAACAT-AAA
* * *
17502 AATTCCTTTTGAACCCCTCATGAAACTCGTAGATCAAATTAACTTTCAGGTTCTTCATGAAAGTC
258 AATTCCTTTTGAATCCCTCAAGAAACTCGTAGATCAAATTAACTTTCAGGTACTTCATGAAAGTC
* * * *
17567 GTAGATCATATAGTAACCTTTAACCGACACTTGAATAACTTTAATCGGACATGTGTATCGAAAAT
323 GTAGATCATATAATAACCTTTAACCAACAATTGAATAAATTTAATCGGACATGTGTATCGAAAAT
* * ** *
17632 TATATGGTATTAAATAGACCAACAATCGAAATGACCAAATTTATG
388 CATATGGTATTAAATACACCAACAATCGAAACCACCAAATTTAGG
* * * *
17677 AAGCATTTTTTTGAATTGAAACCTAAAAATTTGCTTTTCAGTCATTCATGAAAGTTGTAGATCAT
1 AAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTCAGTCATTCATGAAAGTTATAGATAAT
*
17742 GAAATTACCTTTTAATAGAG-ACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAA
66 GAAATTACCTTGTAATAG-GCACATGAATCAACTTAATCGGACAAATAGAAC----AA-AAAAAA
*
17806 ATAAAGCTTACA-CGTT-A-GATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAA
125 ATAAAGCTGA-AGCGTTAACGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAA
17868 AGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATACTTGTTAATGGAGATCTTGAAACA
189 AGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATACTTGTTAATGGAGATCTTGAAACA
* *
17933 TAAAAATTCCCTTTTGAATCCTTCAAGAAACTCGTAGATCAAATTTAGCTTTC-GAGTACTTCAT
254 TAAAAATT-CCTTTTGAATCCCTCAAGAAACTCGTAGATCAAA-TTAACTTTCAG-GTACTTCAT
* * * *
17997 GAAAGTCATTA-ATTATGTAATAACCTTTTACCAACAATTGAATAAATTTAATCGGACATGTGTA
316 GAAAGTC-GTAGATCATATAATAACCTTTAACCAACAATTGAATAAATTTAATCGGACATGTGTA
* * *
18061 TCGAAAATCATATGGTATTAAATACA-CAAGCAATTGAACCCACCAAATTTGGG
380 TCGAAAATCATATGGTATTAAATACACCAA-CAATCGAAACCACCAAATTTAGG
* * *
18114 AAGCATTTTGTTT-AATTGAAACATAAAAATTGGCTTTTGAGTCCTTTATGAAAGTTATAGATAA
1 AAGCATTTT-TTTGAATTGAAACATAAAAATTGGCTTTTCAGTCATTCATGAAAGTTATAGATAA
* * * *
18178 TGAAATTACCTTGTAATAGGCACCTGAATCACCTTAATTGGACAAATAGAACAAAAAAAATTAAA
65 TGAAATTACCTTGTAATAGGCACATGAATCAACTTAATCGGACAAATAGAACAAAAAAAAATAAA
* * ** * * *
18243 GCTGAAGCGTTGAATCGATTAAAATATAATTAATAAAGGACTAAGTTGTAAAAAGTAGAGAAAAT
130 GCTGAAGCGTT-AA-CGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGA-AAAGT
* * * * *
18308 ATGAGGGTCATTTGATAAATAATCCAATTAAGAAAAT-GTTCGTTGATAGAGATCTTGAAATATA
192 ATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATACTT-GTTAATGGAGATCTTGAAACATA
18372 AAAATTTCCTTTTGAAT
256 AAAA-TTCCTTTTGAAT
18389 TCATGAAAGT
Statistics
Matches: 605, Mismatches: 77, Indels: 50
0.83 0.11 0.07
Matches are distributed among these distances:
426 65 0.11
427 30 0.05
431 1 0.00
432 18 0.03
433 4 0.01
434 12 0.02
435 8 0.01
436 174 0.29
437 283 0.47
438 9 0.01
439 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (432 bp):
AAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTCAGTCATTCATGAAAGTTATAGATAAT
GAAATTACCTTGTAATAGGCACATGAATCAACTTAATCGGACAAATAGAACAAAAAAAAATAAAG
CTGAAGCGTTAACGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATGA
GGGTCATTTGATAAATAATCCAAATAAGAAAATACTTGTTAATGGAGATCTTGAAACATAAAAAT
TCCTTTTGAATCCCTCAAGAAACTCGTAGATCAAATTAACTTTCAGGTACTTCATGAAAGTCGTA
GATCATATAATAACCTTTAACCAACAATTGAATAAATTTAATCGGACATGTGTATCGAAAATCAT
ATGGTATTAAATACACCAACAATCGAAACCACCAAATTTAGG
Found at i:21045 original size:31 final size:31
Alignment explanation
Indices: 21007--21071 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
20997 AATTGCAATC
21007 ACAAATCAAGGTTCGAGGTTCGTTGCGGTCA
1 ACAAATCAAGGTTCGAGGTTCGTTGCGGTCA
21038 ACAAATCAAGGTTCGAGGTTCGTTGCGGTCA
1 ACAAATCAAGGTTCGAGGTTCGTTGCGGTCA
21069 ACA
1 ACA
21072 TATGCAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (31 bp):
ACAAATCAAGGTTCGAGGTTCGTTGCGGTCA
Found at i:29992 original size:60 final size:59
Alignment explanation
Indices: 29859--29994 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
29849 AACATTTAGC
* ** *
29859 AAAATGTTCAAATAAAAGTCCGATCTTTTAATTTGACCAAATAAGTGCATAATGTATCG
1 AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGACCAAATAAGTGCATAACGTATCG
* * * *
29918 AAAATGCTCAAATAAGGGTCTGGTCTTTTAATTTGGCCGAATAAGTGTC-TAACGTTATCG
1 AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGACCAAATAAGTG-CATAACG-TATCG
29978 AAAATGCTCAAATAAGG
1 AAAATGCTCAAATAAGG
29995 ACCTGACGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 44 0.66
60 23 0.34
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (59 bp):
AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGACCAAATAAGTGCATAACGTATCG
Found at i:32123 original size:14 final size:14
Alignment explanation
Indices: 32104--32133 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
32094 ACAAAAGAAA
*
32104 AAAATAGATATTAG
1 AAAATAGAAATTAG
32118 AAAATAGAAATTAG
1 AAAATAGAAATTAG
32132 AA
1 AA
32134 TAAATAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
AAAATAGAAATTAG
Done.