Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011230.1 Corchorus olitorius cultivar O-4 contig11263, 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: 56891
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3453 original size:27 final size:27
Alignment explanation
Indices: 3416--3541 Score: 180
Period size: 27 Copynumber: 4.7 Consensus size: 27
3406 AGTGAGCTTA
3416 AAATGACCAAAATGCCCCTGAATGCGT
1 AAATGACCAAAATGCCCCTGAATGCGT
3443 AAATGACCAAAATGCCCCTGAATGCGT
1 AAATGACCAAAATGCCCCTGAATGCGT
*
3470 AAATGACCAAAATGCCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGCGT
* * * * * *
3497 AAATGAGCATAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGAATGCGT
*
3524 AAATGACAAAAATGCCCC
1 AAATGACCAAAATGCCCC
3542 ATAGATGACC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGCGT
Found at i:5093 original size:26 final size:26
Alignment explanation
Indices: 5055--5108 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
5045 TGCCTAATAG
*
5055 CATTCATAGTAGTAATTAGGCATTAA
1 CATTCACAGTAGTAATTAGGCATTAA
*
5081 CATTCACATTAGTAATTAGGCATTAA
1 CATTCACAGTAGTAATTAGGCATTAA
5107 CA
1 CA
5109 GTTTGCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (26 bp):
CATTCACAGTAGTAATTAGGCATTAA
Found at i:6682 original size:17 final size:17
Alignment explanation
Indices: 6662--6715 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
6652 CCTCTCTCTC
6662 TCCATAATCTCTTCCCA
1 TCCATAATCTCTTCCCA
*
6679 TCCATAATCCCTTCCCA
1 TCCATAATCTCTTCCCA
*
6696 TCGATAATCTCTTCCCA
1 TCCATAATCTCTTCCCA
6713 TCC
1 TCC
6716 CCTCTCTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.22, C:0.43, G:0.02, T:0.33
Consensus pattern (17 bp):
TCCATAATCTCTTCCCA
Found at i:9431 original size:41 final size:40
Alignment explanation
Indices: 9383--9505 Score: 147
Period size: 41 Copynumber: 3.0 Consensus size: 40
9373 GGCTCAATCA
* *
9383 GTAATATTTGCTTATTAATTCAATTTTGTCACTGATTTAGG
1 GTAATATTT-ATTATTAATTCAATTTTGTCCCTGATTTAGG
* *
9424 TTAATATTTATTAATTGATTCAATTTTGTCCCTGATTTAGG
1 GTAATATTTATT-ATTAATTCAATTTTGTCCCTGATTTAGG
* * * *
9465 GTAACATTTATTATAAGATGCAATTTTATCCCTGATTTAGG
1 GTAATATTTATTATTA-ATTCAATTTTGTCCCTGATTTAGG
9506 ATTTTACTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.06
41 66 0.94
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (40 bp):
GTAATATTTATTATTAATTCAATTTTGTCCCTGATTTAGG
Found at i:22553 original size:42 final size:42
Alignment explanation
Indices: 22494--22573 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
22484 ATAAATATTC
*
22494 CAAAAAACCTACCCCACTAAATAAAATCTATACCTTACATTT
1 CAAAAAACCTACCCCACTAAACAAAATCTATACCTTACATTT
22536 CAAAAAACCTACCCCACTAAACAAAATCTATACCTTAC
1 CAAAAAACCTACCCCACTAAACAAAATCTATACCTTAC
22574 TATTAAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (42 bp):
CAAAAAACCTACCCCACTAAACAAAATCTATACCTTACATTT
Found at i:23973 original size:439 final size:440
Alignment explanation
Indices: 23115--24094 Score: 1447
Period size: 439 Copynumber: 2.2 Consensus size: 440
23105 TGGGTCCCTC
* *
23115 TCTCAATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCAT-ATACTTTTATGCTTT
1 TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCC-TCAGACTTTTATGCTTT
* * * *
23179 ATGCTATTTAGTCCCTCATAATTTCTGGGTTTGAGGACTGAATGTTTCGTCTTTAATTTTTTATT
65 ATGCTATTTAGTCCCTCATAATTTCTGGGTTGGAGGACTAAACGTTTAGTCTTTAATTTTTTATT
** * * *
23244 TTTTGTTTTGCTTGTTTGATCAAGGTGGTTCAAGTGTCTCTTAAGAGGTAATTTCATGATCTACA
130 TTTTGTTTTGCTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACA
*
23309 ACTTCCATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTT
195 ACTTCCATGAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTT
* * * *
23374 GTGGTCTTGATTGTCGTTCTATTTTATTCATATAATTTTTGTTCCACCTGTCCGATCGAGATCGA
260 ATGGTCTTGATTGTCGGTCTATTTGATTCATATAATTTTTGATCCACCTGT-C-ATC-AGATCGA
**
23439 GGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGTTTCAAAGC
322 GGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAAGC
* *
23504 TGAATTTGATTAATGAGTTTCGTGGAGGGTTCACGAGGGAATTTTTATGTTTGG
387 TGAATTTGATTAATAAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGG
* *
23558 TCTCCATAAACAAATATTTTTTTGCTGGATTATTTATCAAATGATCCTCAGACTTTTATGTTTTA
1 TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCTCAGACTTTTATGCTTTA
* * *
23623 TGTTATTTAGTCCCTCACAATTTCTGGGTTGGATGACTAAACGTTTTAGT-TTTAATTCTTTTAT
66 TGCTATTTAGTCCCTCATAATTTCTGGGTTGGAGGACTAAACG-TTTAGTCTTTAATT-TTTTAT
* *
23687 TTTTATTTTTTGCTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTA
129 TTTT-TGTTTTGCTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTA
23752 CAACTTCCATG-AGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATT
193 CAACTTCCATGAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATT
* *
23816 TTATGGTCTTGATTG-CTGGTCTATTTGATATCGTATAATTTTTGATCCA-CT-T-ATTC-GATT
258 TTATGGTCTTGATTGTC-GGTCTATTTGAT-TCATATAATTTTTGATCCACCTGTCA-TCAGATC
* * *
23876 GAGGTTATTCAAGTGTCGGTTAAAAGTTTATTGTGTGGTCTACGGCTTTCGTTAAGGGCCTCAAA
320 GAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAA
* *
23941 GCTGAATTTGATTGATAAGTTTCGTGGAGGGTTCAAGAGGGGATTTTTATGTTTGG
385 GCTGAATTTGATTAATAAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGG
*
23997 TCTCCATAAACAAATATTATTTTTGTTGGATTATTTATCAAATGATCCTCAGATTTTTATGCTTT
1 TCTCCATAAACAAATATT-TTTTTGTTGGATTATTTATCAAATGATCCTCAGACTTTTATGCTTT
* * * *
24062 AGGCTAATTAATCCCTCATAA-TTATGGGTTGGA
65 ATGCTATTTAGTCCCTCATAATTTCTGGGTTGGA
24095 CCATTTAATG
Statistics
Matches: 486, Mismatches: 43, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
439 144 0.30
440 60 0.12
441 2 0.00
442 1 0.00
443 105 0.22
444 93 0.19
445 81 0.17
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (440 bp):
TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCTCAGACTTTTATGCTTTA
TGCTATTTAGTCCCTCATAATTTCTGGGTTGGAGGACTAAACGTTTAGTCTTTAATTTTTTATTT
TTTGTTTTGCTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA
CTTCCATGAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTA
TGGTCTTGATTGTCGGTCTATTTGATTCATATAATTTTTGATCCACCTGTCATCAGATCGAGGTT
ATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAAGCTGAA
TTTGATTAATAAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGG
Found at i:26897 original size:13 final size:13
Alignment explanation
Indices: 26879--26905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26869 TTCAATACAC
26879 TGTCAGTGGAGTT
1 TGTCAGTGGAGTT
26892 TGTCAGTGGAGTT
1 TGTCAGTGGAGTT
26905 T
1 T
26906 AGAAGACTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.37, T:0.41
Consensus pattern (13 bp):
TGTCAGTGGAGTT
Found at i:29109 original size:30 final size:30
Alignment explanation
Indices: 29070--29136 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
29060 CCAGGATCTT
*
29070 ATCTCTCTCTCAC-ACCCTCATCCCTCCAGA
1 ATCTCTCTCTCACAACCCTC-TCCCTCAAGA
* *
29100 ATTTCTCTCTCACAACTCTCTCCCTCAAGA
1 ATCTCTCTCTCACAACCCTCTCCCTCAAGA
29130 ATCTCTC
1 ATCTCTC
29137 ATGGACACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.21, C:0.45, G:0.03, T:0.31
Consensus pattern (30 bp):
ATCTCTCTCTCACAACCCTCTCCCTCAAGA
Found at i:33450 original size:2 final size:2
Alignment explanation
Indices: 33403--33434 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33393 TAAATATAAT
33403 TA TA TA 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 TA TA TA
33435 ATAAACCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33540 original size:17 final size:16
Alignment explanation
Indices: 33518--33561 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
33508 GGTGAGTAAT
33518 AGCAGCTTCAGCTCAAA
1 AGCAGCTTCA-CTCAAA
33535 AGCAGCTTCTACTCAAA
1 AGCAGCTTC-ACTCAAA
*
33552 AGCAGGTTCA
1 AGCAGCTTCA
33562 ACTTCCAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (16 bp):
AGCAGCTTCACTCAAA
Found at i:37939 original size:21 final size:22
Alignment explanation
Indices: 37906--37946 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
37896 ATATATGGAA
*
37906 AAAATAAATTAATAATTAATGT
1 AAAATAAACTAATAATTAATGT
*
37928 AAAA-AAACTAATTATTAAT
1 AAAATAAACTAATAATTAAT
37947 TAATTAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATAAACTAATAATTAATGT
Found at i:40268 original size:2 final size:2
Alignment explanation
Indices: 40263--40296 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
40253 TATTATTTGA
*
40263 AT AT AT AT AT AT AT AT AT AT AT AT CAT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
40297 CGATAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40738 original size:49 final size:49
Alignment explanation
Indices: 40685--40831 Score: 258
Period size: 49 Copynumber: 3.0 Consensus size: 49
40675 AATTCAAATA
40685 GATTTTTATAATCACAATTCAAATAACAATTCAAATTATTTTTAAGATT
1 GATTTTTATAATCACAATTCAAATAACAATTCAAATTATTTTTAAGATT
* *
40734 GATTTTTATAATCACAATTCAAATAACAGTTCAAATTAATTTTAAGATT
1 GATTTTTATAATCACAATTCAAATAACAATTCAAATTATTTTTAAGATT
* *
40783 GATTTTTATAATCACAATTCAAATAACAATTTAAATTGTTTTTAAGATT
1 GATTTTTATAATCACAATTCAAATAACAATTCAAATTATTTTTAAGATT
40832 TCTCTCTCAT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 92 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (49 bp):
GATTTTTATAATCACAATTCAAATAACAATTCAAATTATTTTTAAGATT
Found at i:41770 original size:31 final size:31
Alignment explanation
Indices: 41735--41799 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
41725 CTATGAACTT
*
41735 TATTTTCCCTAACTTTAAAAGTATTTGTATG
1 TATTTTCCCTAACTTTAAAAGTATGTGTATG
41766 TATTTTCCCTAACTTTAAAAGTATGTGTATG
1 TATTTTCCCTAACTTTAAAAGTATGTGTATG
41797 TAT
1 TAT
41800 AGTGTATTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (31 bp):
TATTTTCCCTAACTTTAAAAGTATGTGTATG
Found at i:45019 original size:19 final size:18
Alignment explanation
Indices: 44982--45020 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
44972 CTCTTGAAAT
*
44982 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
45000 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
45019 AA
1 AA
45021 AAAATCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:53038 original size:15 final size:15
Alignment explanation
Indices: 53016--53059 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
53006 GGGAGGAAGT
53016 GGGAAGGAAAGAAGAG
1 GGGAAGGAAAGAA-AG
53032 GGG-AGGAAAGAAAG
1 GGGAAGGAAAGAAAG
*
53046 GGGAAGGAAGGAAA
1 GGGAAGGAAAGAAA
53060 AAACTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 18 0.69
16 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GGGAAGGAAAGAAAG
Found at i:56095 original size:27 final size:27
Alignment explanation
Indices: 56055--56119 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
56045 AGAAATCTAC
** *
56055 TTGATTTATTTTGGTTATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
56082 TTGATTTAGATTGGTCATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
56109 TTGATTTAGAT
1 TTGATTTAGAT
56120 GACATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.57
Consensus pattern (27 bp):
TTGATTTAGATTGGTCATATTTTGTAA
Found at i:56853 original size:16 final size:16
Alignment explanation
Indices: 56832--56884 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
56822 TATGACTTCC
56832 TTTCCCTTCCTTCCTA
1 TTTCCCTTCCTTCCTA
**
56848 TTTCCCTTCCCTTGTTA
1 TTTCCCTT-CCTTCCTA
* *
56865 TTTCCTTTCCTCCCTA
1 TTTCCCTTCCTTCCTA
56881 TTTC
1 TTTC
56885 TTTCCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.06, C:0.40, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTCCCTTCCTTCCTA
Done.