Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013223.1 Corchorus olitorius cultivar O-4 contig13256, 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: 33437
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:540 original size:39 final size:39
Alignment explanation
Indices: 497--581 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
487 TAACCACGGC
* * *
497 GCAAAGCCAGACACTTACAAGTCAAAGCTCGAAGGAGAA
1 GCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGAA
* *
536 GCAAAGCCAGACACTTACGAGACAAAACCCGAAGGAGAT
1 GCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGAA
575 GCAAAGC
1 GCAAAGC
582 TCGACTATGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.44, C:0.25, G:0.24, T:0.08
Consensus pattern (39 bp):
GCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGAA
Found at i:567 original size:96 final size:96
Alignment explanation
Indices: 462--639 Score: 223
Period size: 96 Copynumber: 1.9 Consensus size: 96
452 AATTACAAGT
* * *
462 CAAAGCCCGAAGGAGAACCAAAGC-CTAACCACGGCGCAAAGCCAGACACTTACAAGTCAAAGCT
1 CAAAACCCGAAGGAGAACCAAAGCTC-AACCACGGCGCAAAGCCAGACACTTACAAGCCAAAGCC
526 CGAAGGAGAAGCAAAGCCAGACACTTACGAGA
65 CGAAGGAGAAGCAAAGCCAGACACTTACGAGA
** * * * * * *
558 CAAAACCCGAAGGAGATGCAAAGCTCGACTATGGTGCAAAGCCAGACAGTTACAAGCCAAGGCCC
1 CAAAACCCGAAGGAGAACCAAAGCTCAACCACGGCGCAAAGCCAGACACTTACAAGCCAAAGCCC
* *
623 GAAGGAGATGTAAAGCC
66 GAAGGAGAAGCAAAGCC
640 TAACTATGGT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
96 67 0.99
97 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.25, T:0.09
Consensus pattern (96 bp):
CAAAACCCGAAGGAGAACCAAAGCTCAACCACGGCGCAAAGCCAGACACTTACAAGCCAAAGCCC
GAAGGAGAAGCAAAGCCAGACACTTACGAGA
Found at i:580 original size:57 final size:56
Alignment explanation
Indices: 519--727 Score: 145
Period size: 57 Copynumber: 3.7 Consensus size: 56
509 ACTTACAAGT
*
519 CAAAGCTCGA-AGGAGAAGCAAAGCCAGACACTTACGAGACAAAACCCGAAGGAGATG
1 CAAAGCTCGACAGG-G-AGCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGATG
* * * * **
576 CAAAGCTCGACTATGGTGCAAAGCCAGACAGTTACAAGCCAAGGCCCGAAGGAGATG
1 CAAAGCTCGAC-AGGGAGCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGATG
* * * * * * * * *
633 TAAAGC-CTAACTATGGTGCAAAGTCAGACACTTACAAGGCAAAACTCGAAGTAGACG
1 CAAAGCTC-GAC-AGGGAGCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGATG
* * * * *
690 TAACGGCT-AACTAGGGTGCAGAGCCAGACACTTACAAG
1 CAA-AGCTCGAC-AGGGAGCAAAGCCAGACACTTACAAG
728 CGAAAGTCAG
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
56 1 0.01
57 120 0.95
58 3 0.02
59 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (56 bp):
CAAAGCTCGACAGGGAGCAAAGCCAGACACTTACAAGACAAAACCCGAAGGAGATG
Found at i:972 original size:48 final size:48
Alignment explanation
Indices: 898--1081 Score: 181
Period size: 48 Copynumber: 3.6 Consensus size: 48
888 CAGCTGACAC
* *
898 TTACAAGCCAAAGTCTGAAGAGAAGCCTACTACTTATGAAACCAAAGA
1 TTACAAGCCAAAGTCAGAAGAAAAGCCTACTACTTATGAAACCAAAGA
946 TTACAAGCCAAAGTCAGAAGAAAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGA
1 TTACAAGCCAAAGTCAGAAGAAAAGCCT-------A--CT---ACTTATGAAACCAAAGA
* * * *
1006 TTACAAGGCAAAGTCAGAGGAAAAGCCTACCACTTATGAGACCAAAGA
1 TTACAAGCCAAAGTCAGAAGAAAAGCCTACTACTTATGAAACCAAAGA
*
1054 TTACAAGCCAGAA-TCAGAGGAAAAGCCT
1 TTACAAGCCA-AAGTCAGAAGAAAAGCCT
1082 GAAGAGAAGC
Statistics
Matches: 116, Mismatches: 7, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
48 66 0.57
49 2 0.02
51 1 0.01
53 1 0.01
55 1 0.01
57 2 0.02
60 43 0.37
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (48 bp):
TTACAAGCCAAAGTCAGAAGAAAAGCCTACTACTTATGAAACCAAAGA
Found at i:976 original size:60 final size:60
Alignment explanation
Indices: 907--1140 Score: 296
Period size: 60 Copynumber: 4.1 Consensus size: 60
897 CTTACAAGCC
* *
907 AAAGTCTGAAGAGAAGCCTACTACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
* *
967 AAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGATTACAAGGCAAAGTC---AG-
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
* *
1023 --AG---G-A-A-AAGCCTACCACTTATGAGACCAAAGATTACAAGCCAGAA-TCAGAGGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCA-AAGTCAGAAGA
* *
1075 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTATAAGTCAAAGTCAGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
1135 AAAGCC
1 AAAGCC
1141 CGGTTATGAA
Statistics
Matches: 149, Mismatches: 11, Indels: 28
0.79 0.06 0.15
Matches are distributed among these distances:
48 36 0.24
49 3 0.02
50 1 0.01
51 2 0.01
54 4 0.03
57 3 0.02
58 1 0.01
59 3 0.02
60 96 0.64
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.15
Consensus pattern (60 bp):
AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
Found at i:1032 original size:108 final size:108
Alignment explanation
Indices: 898--1140 Score: 380
Period size: 108 Copynumber: 2.2 Consensus size: 108
888 CAGCTGACAC
* * *
898 TTACAAGCCAAAGTCTGAAGAGAAGCCTACTACTTATGAAACCAAAGATTACAAGCCA-AAGTCA
1 TTACAAGCCAAAGTCAGAAGAAAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAGAA-TCA
962 GAAGAAAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGA
65 GAAGAAAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGA
* * *
1006 TTACAAGGCAAAGTCAGAGGAAAAGCCTACCACTTATGAGACCAAAGATTACAAGCCAGAATCAG
1 TTACAAGCCAAAGTCAGAAGAAAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAGAATCAG
* *
1071 AGGAAAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGA
66 AAGAAAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGA
* *
1114 TTATAAGTCAAAGTCAGAAGAAAAGCC
1 TTACAAGCCAAAGTCAGAAGAAAAGCC
1141 CGGTTATGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
108 121 0.98
109 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (108 bp):
TTACAAGCCAAAGTCAGAAGAAAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAGAATCAG
AAGAAAAGCCTGAACAGAAGCCTACCACTTATGAAACCAAAGA
Found at i:2552 original size:2 final size:2
Alignment explanation
Indices: 2547--2572 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2537 TTATCTACAC
2547 TA TA 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
2573 AATAAGTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8351 original size:2 final size:2
Alignment explanation
Indices: 8344--8368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8334 TGGAGACTAG
8344 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 T
8369 GAATTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25638 original size:19 final size:20
Alignment explanation
Indices: 25614--25651 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
25604 TTTATCCTCT
25614 AATGGGTAG-TTTTATTTTA
1 AATGGGTAGTTTTTATTTTA
25633 AATGGGTAGTTTTTATTTT
1 AATGGGTAGTTTTTATTTT
25652 GTTTTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
AATGGGTAGTTTTTATTTTA
Found at i:26934 original size:331 final size:329
Alignment explanation
Indices: 26010--27152 Score: 1316
Period size: 331 Copynumber: 3.5 Consensus size: 329
26000 CCTTTGTTAT
* * * * *
26010 CAAAATTTGTGATGGTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCAAAAGAATT
1 CAAAAATTGTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AATT
* * * *
26075 T-TCCTAAATTTTTTGCCACGATACTCATAAAAAATATATAATTCAACACTAAAAAGATTGAAAG
64 TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAG
* * * * *
26139 GTTTTTCACGCTTCTAATATCAG-TTTTCCTATTTTTTCCGAATTAATTTCTAGTTAAATTGAAA
129 GCTTTTCACGCTTCTAATATC-GTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAA
*
26203 CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGA
193 CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGA
* * * * *
26268 TATAGATATTTCAATGA-TACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGACCTCG--TG-
258 TATAGATATTTCAATGAGT-CTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAGC
*
26329 TTTTTA-C
322 GTTTTAGC
* * *
26336 TCAAAAATTGTGATGATTAGTATACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAATATT
1 -CAAAAATTGTGATG-TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
*** * * * *
26401 TCTCCTCAATTTCCAGCCACCATATTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAT
64 TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAG
* * * *
26466 ACTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGA
129 GCTTTTCACGCTTCTAATATCG--TTTTTCT-TATTTTTTCTGAATTAATTTCTAATTAAATCGA
* * *
26531 AACCA-GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGATTTCGTTAGAT
191 AA-CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
** * *
26595 AAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCGAAACTGAGTCGGGGCCCCAGAA
255 GGATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCC-GAA
*
26660 CGCGTTTTAGC
319 AGCGTTTTAGC
** ** * *
26671 CAAAAACCGTGATAGTTAGTACGTGATTTCTGCTAAAATTTTGTAAAAATTGACCCGAAAGAATT
1 CAAAAATTGTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AATT
* * *
26736 T-TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACAAAAAATATTGAAAG
64 TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAG
* * * * *
26800 GCTATTCATGCTTCTAATATCGTTTTTCTTATTTTTTCTGAATTAATTCCTAATTGAATCGAAAT
129 GCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * * *
26865 ATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGCTAGATGGAT
194 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGAT
* * * **
26930 ATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTTCAAAACTGAGCCGGGGCTCTGGAAAGCG
259 ATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC-CCCGAAAGCG
*
26995 TTTTTAGT
323 -TTTTAGC
* * * * * * * *
27003 CAAAAATTGTGATGTAACATACACGATTTCAGCTAAAGTGTTAC-AAAATTGACCTGAGAAATTT
1 CAAAAATTGTGATGTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT
* * * * ** * *
27067 CTCCTCAATTTTGGGTCACAATACTAATAAAAAATATATAACTCAATGCCAAAAAGACTGAAGGG
65 CTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAGG
*
27132 CTTTTCATGCTTCTAATATCG
130 CTTTTCACGCTTCTAATATCG
27153 CCTTTCCTAC
Statistics
Matches: 684, Mismatches: 112, Indels: 36
0.82 0.13 0.04
Matches are distributed among these distances:
326 6 0.01
327 121 0.18
329 4 0.01
330 144 0.21
331 235 0.34
332 42 0.06
333 1 0.00
334 125 0.18
335 6 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (329 bp):
CAAAAATTGTGATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTC
TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAGGC
TTTTCACGCTTCTAATATCGTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAT
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGATAT
AGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAGCGTTT
TAGC
Found at i:28473 original size:22 final size:22
Alignment explanation
Indices: 28445--28518 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
28435 TTTATGAAAT
*
28445 TTTTGATAACTACCCTATTAAA
1 TTTTGATAACTACCCTATAAAA
* *
28467 TTTTGATAACTACCATATGAAA
1 TTTTGATAACTACCCTATAAAA
*
28489 TTTTGATAATTA-CCTATAAAA
1 TTTTGATAACTACCCTATAAAA
*
28510 TTGTGATAA
1 TTTTGATAA
28519 ATTCCATAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
TTTTGATAACTACCCTATAAAA
Found at i:28517 original size:43 final size:44
Alignment explanation
Indices: 28437--28541 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
28427 TGAATATTTT
* * *
28437 TATGAAATTTTTGATAACTACCCTATTAAATTTTGATAACTACCA
1 TATGAAA-TTTTGATAACTACCCTATAAAATTGTGATAAATACCA
* *
28482 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCA
* *
28525 TAAGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
28542 CTAACAATCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 34 0.65
44 11 0.21
45 7 0.13
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCA
Found at i:32367 original size:131 final size:131
Alignment explanation
Indices: 32159--32423 Score: 530
Period size: 131 Copynumber: 2.0 Consensus size: 131
32149 ACGAGAAGAT
32159 ATTATTGAAAGACATAAGAAATGAGTACAATAATATCTTGAACATTGTACATTCTCTTTCTTTAC
1 ATTATTGAAAGACATAAGAAATGAGTACAATAATATCTTGAACATTGTACATTCTCTTTCTTTAC
32224 AATCAACGAGAAGATATATATTATTGAAAGTTCAGTACAATAATTTTCTTATATGGTCTTTTGAA
66 AATCAACGAGAAGATATATATTATTGAAAGTTCAGTACAATAATTTTCTTATATGGTCTTTTGAA
32289 C
131 C
32290 ATTATTGAAAGACATAAGAAATGAGTACAATAATATCTTGAACATTGTACATTCTCTTTCTTTAC
1 ATTATTGAAAGACATAAGAAATGAGTACAATAATATCTTGAACATTGTACATTCTCTTTCTTTAC
32355 AATCAACGAGAAGATATATATTATTGAAAGTTCAGTACAATAATTTTCTTATATGGTCTTTTGAA
66 AATCAACGAGAAGATATATATTATTGAAAGTTCAGTACAATAATTTTCTTATATGGTCTTTTGAA
32420 C
131 C
32421 ATT
1 ATT
32424 GTACTGAATT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 134 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (131 bp):
ATTATTGAAAGACATAAGAAATGAGTACAATAATATCTTGAACATTGTACATTCTCTTTCTTTAC
AATCAACGAGAAGATATATATTATTGAAAGTTCAGTACAATAATTTTCTTATATGGTCTTTTGAA
C
Done.