Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010584.1 Corchorus capsularis cultivar CVL-1 contig10605, 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: 101952
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:1434 original size:14 final size:14
Alignment explanation
Indices: 1415--1443 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1405 TTAGAACTTC
1415 ACTTATGAGTTATG
1 ACTTATGAGTTATG
1429 ACTTATGAGTTATG
1 ACTTATGAGTTATG
1443 A
1 A
1444 TTAAACAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (14 bp):
ACTTATGAGTTATG
Found at i:19472 original size:28 final size:25
Alignment explanation
Indices: 19440--19571 Score: 131
Period size: 25 Copynumber: 5.2 Consensus size: 25
19430 TTGGGTTATA
*
19440 TAGTTGCATATTCAGTAGGGTGCAGATG
1 TAGTTGCATATTCAGTA-GG-GC-CATG
* *
19468 TAGTTGCATATTCTGTAGGGCCCTG
1 TAGTTGCATATTCAGTAGGGCCATG
* **
19493 TAGTTGCATATTTAGT-GGGTTTATG
1 TAGTTGCATATTCAGTAGGG-CCATG
*
19518 TAGTTGCATATTCTGTAGGGCCATG
1 TAGTTGCATATTCAGTAGGGCCATG
* **
19543 TAGTTGCATATTCAATAGTACCATG
1 TAGTTGCATATTCAGTAGGGCCATG
19568 TAGT
1 TAGT
19572 AGGTCATGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.03
25 60 0.70
26 5 0.06
27 2 0.02
28 16 0.19
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.38
Consensus pattern (25 bp):
TAGTTGCATATTCAGTAGGGCCATG
Found at i:23306 original size:2 final size:2
Alignment explanation
Indices: 23299--23335 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
23289 TATAAAATAG
23299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23336 CTTTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45113 original size:4 final size:4
Alignment explanation
Indices: 45104--45141 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
45094 AACAATGATT
*
45104 TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
45142 TGGAAACCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:59287 original size:45 final size:46
Alignment explanation
Indices: 59204--59293 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
59194 ATTACTTCTT
*
59204 CAGCTCATCATTAATCCTAGGGTAGAGATCTTTTAGTAATTCCACC
1 CAGCTCATCATTAATCCTAGGGTAGAGATCTTTCAGTAATTCCACC
* *
59250 CAGCTCATCATTAATTC-GGGGTAGAGATCTTTCAGTAATTCCAC
1 CAGCTCATCATTAATCCTAGGGTAGAGATCTTTCAGTAATTCCAC
59294 TACTCTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 25 0.61
46 16 0.39
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (46 bp):
CAGCTCATCATTAATCCTAGGGTAGAGATCTTTCAGTAATTCCACC
Found at i:59890 original size:650 final size:635
Alignment explanation
Indices: 58836--60123 Score: 2204
Period size: 650 Copynumber: 2.0 Consensus size: 635
58826 TTAATACTAA
* * *
58836 CAAGTTGATTTACCCGCACTGCGTTACGAGTGTTTTTTTGTTAAAATCGTGATTCAGCACCATGC
1 CAAGTTGATTTACCCGCACTGCGCTACGAGCGTTCTTTTGTTAAAATCGTGATTCAGCACCATGC
*
58901 ATATATTAAAAGATTTTTTCCGTAAATATATAAGAATTTCTTGATCATATGATACTTAAAAAGTA
66 ATATATTAAAAGATTTTCTCCGTAAATATATAAGAATTTCTTGATCATATGATACTTAAAAAGTA
*
58966 AGATTCCATTGTTTTAAACATATATGAGTCAAACATGATCTGTAGAAAATAATTTTTAAGTTCAG
131 AGATTCCATTGTTTTAAACATATATGAGTCAAACATGATCTGTAGAAAATAATTTTTAAGTTCAA
59031 ATTAGTACAAATACGCTTTGACGTGTTTATTGGGATTGTTCTATTTCCTTTTTTAAGATACAGTT
196 ATTAGTACAAATACGCTTTGACGTGTTTATTGGGATTGTTCTATTTCCTTTTTTAAGATACAGTT
*
59096 TTTTGTAAAAATGACCTAAAAGTTTAGATATTTAATCTCCTTAAGAATAAAAAGTTAGGACATTT
261 TTTTGTAAAAATGACCTAAAAGTTTAGATATTTAATCCCCTTAAGAATAAAAAGTTAGGACATTT
* * *
59161 ACGTAATCTGTCAAGTAGGTAAAGACGAAAAAGATTACTTCTTCAGCTCATCATTAATCCTAGGG
326 AAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAGCTCATCATTAATCCTAGGG
59226 TAGAGATCTTTTAGTAATTCCACCCAGCTCATCATTAATTCGGGGTAGAGATCTTTCAGTAATTC
391 TAGAGATCTTTTAGTAATTCCACCCAGCTCATCATTAATTCGGGGTAGAGATCTTTCAGTAATTC
59291 CACTACTCTATTAAAGTCATTTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCTA-AAA
456 CACTACTCTATTAAAGTCATTTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAAA
*
59355 TC-AAAAGTTAGGGCATTTAAGTAATCGGTCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCTCG
521 -CAAAAAGTTAGGGCATTTAAGTAATCGGTCAAATGGGAAAAGACGAAAAAAATTAGTTCTCTCG
59419 CTCCTCATTAATCCG-GGGTAGGGATCTTTTAGTAATTTCCATATGTTTATT
585 CTCCTCATTAAT-CGAGGGTAGGGATCTTTTAGTAATTTCCATATGTTTATT
* * *
59470 CAAGTTGATTTGCCCGCGCTGGCGCTACGAGCGTTCTTTTGTTAGAATCGTGATTCAGCACCATG
1 CAAGTTGATTTACCCGCACT-GCGCTACGAGCGTTCTTTTGTTAAAATCGTGATTCAGCACCATG
59535 CATATATTAAAAGATTTTCTCCGTAAATATATAAGAATTTCTTGATCATATGATACTTAAAAAGT
65 CATATATTAAAAGATTTTCTCCGTAAATATATAAGAATTTCTTGATCATATGATACTTAAAAAGT
59600 AAGATTCCATTGTTTTAAACATATATGAGTCAAACATGATCTGTAGAAAATAATTTTTAAGTTCA
130 AAGATTCCATTGTTTTAAACATATATGAGTCAAACATGATCTGTAGAAAATAATTTTTAAGTTCA
59665 AATTAGTACAAAGACTTTTTGGCACACAGTGCTTTGACGTGTTTATTGGGATTGTTCTATTTCCT
195 AATTAGTAC-AA-A-----T-----AC---GCTTTGACGTGTTTATTGGGATTGTTCTATTTCCT
59730 TTTTTAAGATACAGTTTTTTGTAAAAATGACCTAAAAGTTTAGATATTTAATCCCCTTAAGAATA
245 TTTTTAAGATACAGTTTTTTGTAAAAATGACCTAAAAGTTTAGATATTTAATCCCCTTAAGAATA
* *
59795 AAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGTAAAGGCGAAAAAGATTAGTTCTCCAGCTC
310 AAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAGCTC
* * *
59860 ATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTCATCATTAATTCGGGGTAGG
375 ATCATTAATCCTAGGGTAGAGATCTTTTAGTAATTCCACCCAGCTCATCATTAATTCGGGGTAGA
*
59925 GATCTTTTAGTAATTCCACTACTCTATTAAAGTCATTTGAGAAATGACCAAAAAGTCTAGTTATT
440 GATCTTTCAGTAATTCCACTACTCTATTAAAGTCATTTGAGAAATGACCAAAAAGTCTAGTTATT
*
59990 TAATCACTTCTAGAAACAAAAAGTTAGGGCATTTAAGTAATCGGTCAAATGGGAAAAGACGAAAA
505 TAATCACCTCTAGAAACAAAAAGTTAGGGCATTTAAGTAATCGGTCAAATGGGAAAAGACGAAAA
*
60055 AAATTAGTTCTCTCGCTCCTCATTAATCGAGGGTAGGGATCTTTTAGTAGTTTCCATATGTTTAT
570 AAATTAGTTCTCTCGCTCCTCATTAATCGAGGGTAGGGATCTTTTAGTAATTTCCATATGTTTAT
60120 T
635 T
60121 CAA
1 CAA
60124 ATAATATGTA
Statistics
Matches: 614, Mismatches: 21, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
634 18 0.03
635 177 0.29
636 2 0.00
637 1 0.00
642 1 0.00
647 2 0.00
650 299 0.49
651 114 0.19
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (635 bp):
CAAGTTGATTTACCCGCACTGCGCTACGAGCGTTCTTTTGTTAAAATCGTGATTCAGCACCATGC
ATATATTAAAAGATTTTCTCCGTAAATATATAAGAATTTCTTGATCATATGATACTTAAAAAGTA
AGATTCCATTGTTTTAAACATATATGAGTCAAACATGATCTGTAGAAAATAATTTTTAAGTTCAA
ATTAGTACAAATACGCTTTGACGTGTTTATTGGGATTGTTCTATTTCCTTTTTTAAGATACAGTT
TTTTGTAAAAATGACCTAAAAGTTTAGATATTTAATCCCCTTAAGAATAAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAGCTCATCATTAATCCTAGGG
TAGAGATCTTTTAGTAATTCCACCCAGCTCATCATTAATTCGGGGTAGAGATCTTTCAGTAATTC
CACTACTCTATTAAAGTCATTTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAAA
CAAAAAGTTAGGGCATTTAAGTAATCGGTCAAATGGGAAAAGACGAAAAAAATTAGTTCTCTCGC
TCCTCATTAATCGAGGGTAGGGATCTTTTAGTAATTTCCATATGTTTATT
Found at i:59932 original size:45 final size:46
Alignment explanation
Indices: 59853--59943 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 46
59843 GATTAGTTCT
59853 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
*
59899 CCAGCTCATCATTAATTC-GGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
59944 TACTCTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 27 0.61
46 17 0.39
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (46 bp):
CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:65582 original size:25 final size:26
Alignment explanation
Indices: 65539--65589 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
65529 TCACGGCTTT
*
65539 TTCTCTCTCTCAATCTCTCACACAATA
1 TTCTCTCTCACAA-CTCTCACACAATA
65566 TTCTCTCTCACAA-TCTCACACAAT
1 TTCTCTCTCACAACTCTCACACAAT
65590 CTCTCACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
27 12 0.52
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.35
Consensus pattern (26 bp):
TTCTCTCTCACAACTCTCACACAATA
Found at i:73569 original size:2 final size:2
Alignment explanation
Indices: 73562--73592 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73552 ATTACTGATT
73562 TA TA 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 T
73593 GATTCCCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85011 original size:35 final size:37
Alignment explanation
Indices: 84944--85013 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
84934 GGTTCTTCAT
*
84944 ACTTTCCCCATTAAATATAACATTAATCCTAGGATTA
1 ACTTTCCACATTAAATATAACATTAATCCTAGGATTA
*
84981 ACTTTCCACATT-AAT-TAACATTAATTCTAGGAT
1 ACTTTCCACATTAAATATAACATTAATCCTAGGAT
85014 AAGACATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
36 3 0.10
37 11 0.35
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (37 bp):
ACTTTCCACATTAAATATAACATTAATCCTAGGATTA
Found at i:87595 original size:50 final size:49
Alignment explanation
Indices: 87520--87643 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 49
87510 GCTCATTCTA
* * *
87520 GGTTAAATAAATCTCAGGTTCGAGAGCTTGTGTACGCAGCCGCCTCTCCC
1 GGTTAAGTAAATCTCAGGTTCGAGAGCTTGCGTACGCAGCC-ACTCTCCC
*
87570 GGTTAAGTAAATCTCAGGTTCGAGAGCTTGCGTACGCGGCCACTCTCCC
1 GGTTAAGTAAATCTCAGGTTCGAGAGCTTGCGTACGCAGCCACTCTCCC
* * *
87619 AGTTAAGCAAATCTCAGATTCGAGA
1 GGTTAAGTAAATCTCAGGTTCGAGA
87644 CGTCGAAACC
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 29 0.43
50 38 0.57
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (49 bp):
GGTTAAGTAAATCTCAGGTTCGAGAGCTTGCGTACGCAGCCACTCTCCC
Found at i:94391 original size:3 final size:3
Alignment explanation
Indices: 94383--94426 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
94373 TTTTAAAATT
94383 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
94427 GATCATCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:101919 original size:2 final size:2
Alignment explanation
Indices: 101912--101944 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
101902 TGGAATAACT
101912 TA TA TA 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
101945 GATTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.