Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016104.1 Corchorus olitorius cultivar O-4 contig16137, 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: 71715
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:21096 original size:2 final size:2
Alignment explanation
Indices: 21089--21118 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21079 GAGAAACCCA
21089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21119 GCGGCAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25814 original size:2 final size:2
Alignment explanation
Indices: 25809--25834 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25799 TATATAATTC
25809 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25835 TAATGAATAA
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):
AT
Found at i:26791 original size:19 final size:18
Alignment explanation
Indices: 26767--26809 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
26757 AGGGGAATTT
26767 AATAATAATTACTTTGAA-A
1 AATAATAATTA-TTT-AATA
*
26786 AATAATTATTATTTAATA
1 AATAATAATTATTTAATA
26804 AATAAT
1 AATAAT
26810 TAATAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 10 0.45
19 10 0.45
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
AATAATAATTATTTAATA
Found at i:26808 original size:18 final size:18
Alignment explanation
Indices: 26763--26811 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
26753 TTCAAGGGGA
26763 ATTTAAT-AATAATTACT
1 ATTTAATAAATAATTACT
* *
26780 -TTGAA-AAATAATTATT
1 ATTTAATAAATAATTACT
26796 ATTTAATAAATAATTA
1 ATTTAATAAATAATTA
26812 ATAATTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTAATAAATAATTACT
Found at i:28689 original size:49 final size:48
Alignment explanation
Indices: 28588--28729 Score: 148
Period size: 49 Copynumber: 3.0 Consensus size: 48
28578 GAGCGTGCCA
* * * * *
28588 ATCAATTTTGTCAAAAAATTGATAAAATGTGC-AGTGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTCAAAAATAAAAG
28635 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAG-CAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTCAAAAATAAAAG
* * *
28684 TTCAATTTTGTAATAAAAATCGAGAAAAAGTGC-AGT-AAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTCAAAAA-TAAA
28730 GGATTGTTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
47 19 0.23
48 21 0.26
49 39 0.48
50 2 0.02
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTCAAAAATAAAAG
Found at i:32076 original size:4 final size:4
Alignment explanation
Indices: 32062--32095 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
32052 TTTTATTATG
* *
32062 TATA AATA TATA TATA TATA TATA TATA TCTA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TA
32096 CCTTACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:32076 original size:6 final size:6
Alignment explanation
Indices: 32062--32095 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
32052 TTTTATTATG
* *
32062 TATAAA TATATA TATATA TATATA TATATC TATA
1 TATATA TATATA TATATA TATATA TATATA TATA
32096 CCTTACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:35586 original size:434 final size:431
Alignment explanation
Indices: 34692--35618 Score: 1148
Period size: 434 Copynumber: 2.1 Consensus size: 431
34682 CCTTTTTACA
*** * * * *
34692 AATCGATTTAACGCTTTTTGTATTTTTTTTTCTATTTTTCTGATTAAGATAATTCAGGTGTCTAT
1 AATCGATTTAACGCTTTAACTATTTTTTTTTCTATTTGTCCGATTAAGATAATTCAGATGTCGAT
* * * * * ** **
34757 TCAAAGGTAATTTCATGATTTACAACTTTTATGAAAGACTTAAAAGCCAATTTTTATGTTTCAAT
66 TAAAAGGTAATTTCATGATCTACAACTTTCATAAAAAACGCAAAAGCCAATTTTTACATTTCAAT
* * **
34822 TCAAAAAAACGCTTTCGAAATTTGGTGATTTTGATTGCCGATCTATTTAATATGATATAATTTTC
131 TCAAAAAAACGCTTCCCAAATTTGGTGATTTTGATTGCCGATCTATTTAATACCATATAATTTTC
* * *
34887 AATCAACATGTCCGATTAATTATTCTCAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTT
196 AATCAACATGTCCGATTAATAATTCTCAAGTGTCAGTTAAAAGCTTATTGCATGATCTACGACTT
** * * * *
34952 TCATGAAGGACCCGAAAGCTAAATTTGATCTATGAGTTTCATTAAGTGTTCGAAAGGGAATTTTT
261 TCATGAAGGACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTT
* * * * **
35017 ATGTTTTAAGATGTCCATCATCAAACATTTTATTATTTGGATTATTTATGAAATGGTCCTCATTT
326 ATGTTTGAAGATCTCCATCAACAAACATTTTATTATTTGGATTATTTATCAAATGACCCTCATTT
*
35082 TTACTACTTTATACTACTTAGCTCTTTACTAATTCTATCTT
391 TTACTACTTTATACTACTTAGCTCTTTACAAATTCTATCTT
* *
35123 AATCGATTCAACGC-TTAAGCTTATTTTTTTTTCTATTTGTCCGATTAA-ACTGATTCAGATGTC
1 AATCGATTTAACGCTTTAA-C-TATTTTTTTTTCTATTTGTCCGATTAAGA-TAATTCAGATGTC
*
35186 GATTAAAAGGTAATTTCATGATCTCCAACTTTCATAAAAAACGCAAAAGCCAATTTTTACATTTC
63 GATTAAAAGGTAATTTCATGATCTACAACTTTCATAAAAAACGCAAAAGCCAATTTTTACATTTC
* * * * *
35251 AATTCAAAGAAAAATGCTTCCCAAATTTGGTGGTTTTGATTGTCGGTGTATTTAATACCATATAA
128 AATTC-AA-AAAAACGCTTCCCAAATTTGGTGATTTTGATTGCCGATCTATTTAATACCATATAA
* * *
35316 TTTT-AGATCCACATGTCCGATTAAAGTAATT-T-AAGTGTCGGTTAAAAGCTTATTGCGTGATC
191 TTTTCA-ATCAACATGTCCGATT-AA-TAATTCTCAAGTGTCAGTTAAAAGCTTATTGCATGATC
* *
35378 TACGACTTTCATGAAGTACTCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGA
253 TACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGA
* * *
35443 GAATTTTTTATGTTTGAAGATCTCTATCAACAAACATTTTCTTATTTGTATTATTTATCAAATGA
318 GAA-TTTTTATGTTTGAAGATCTCCATCAACAAACATTTTATTATTTGGATTATTTATCAAATGA
*
35508 CCCTCATACTTTT-CTACTTTATACTACTTAG-TCCTTTACAAATTCTTTCTT
382 CCCTCAT--TTTTACTACTTTATACTACTTAGCT-CTTTACAAATTCTATCTT
* * * *
35559 ACTTGATTTAACGCTTTAACTTTTTTTTCTTTGTTCTATTTGTCCAATTAAGATAATTCA
1 AATCGATTTAACGCTTTAAC--TATTTT-TTT-TTCTATTTGTCCGATTAAGATAATTCA
35619 TGAAGCACTC
Statistics
Matches: 420, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
430 2 0.00
431 14 0.03
432 95 0.23
433 3 0.01
434 152 0.36
435 63 0.15
436 50 0.12
437 14 0.03
438 3 0.01
439 23 0.05
440 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (431 bp):
AATCGATTTAACGCTTTAACTATTTTTTTTTCTATTTGTCCGATTAAGATAATTCAGATGTCGAT
TAAAAGGTAATTTCATGATCTACAACTTTCATAAAAAACGCAAAAGCCAATTTTTACATTTCAAT
TCAAAAAAACGCTTCCCAAATTTGGTGATTTTGATTGCCGATCTATTTAATACCATATAATTTTC
AATCAACATGTCCGATTAATAATTCTCAAGTGTCAGTTAAAAGCTTATTGCATGATCTACGACTT
TCATGAAGGACCCGAAAGCTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTT
ATGTTTGAAGATCTCCATCAACAAACATTTTATTATTTGGATTATTTATCAAATGACCCTCATTT
TTACTACTTTATACTACTTAGCTCTTTACAAATTCTATCTT
Found at i:46745 original size:78 final size:78
Alignment explanation
Indices: 46522--46862 Score: 409
Period size: 78 Copynumber: 4.4 Consensus size: 78
46512 AACCGTTTAG
* * *
46522 AATCATTACAAGTCAATACTTTTCAATCATAATTTGTAACATAATACGACAATGAAACCGTTTAC
1 AATCATTACAAATCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTAC
*
46587 AGTTAATGGTTTA
66 AGTTAATGGTTAA
* * * *
46600 AATCATTACAAATCAATACTTTTCAATCAT-TTTTGTAACATAATACGACAATGAAAGCATTTAC
1 AATCATTACAAATCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTAC
*
46664 AGTTAGTGGTTAA
66 AGTTAATGGTTAA
* * * *
46677 AATCGTTATAAGTCAATAATTTTCAATCATGATTTATAACATAATACGACAATGAAACCGTTTAC
1 AATCATTACAAATCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTAC
* *
46742 AGTTATTCGTTAA
66 AGTTAATGGTTAA
* * * * *
46755 AATCGTTATAAATCAATAATATTCAATCATGATTTTGTAACATAATGCGACAATGAAACCGTTAA
1 AATCATTACAAATCAATAATTTTCAATCATGA-TTTGTAACATAATACGACAATGAAACCGTTTA
* *
46820 CCG-TAATCGTTAA
65 CAGTTAATGGTTAA
* * *
46833 AA-CTGTTGAAAAATAAATAATTTTCAATCA
1 AATC-ATT-ACAAATCAATAATTTTCAATCA
46863 GGTTACTTCA
Statistics
Matches: 233, Mismatches: 26, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
77 69 0.30
78 114 0.49
79 50 0.21
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (78 bp):
AATCATTACAAATCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTAC
AGTTAATGGTTAA
Found at i:63879 original size:15 final size:15
Alignment explanation
Indices: 63859--63888 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
63849 TTGTCTTCAC
63859 TTGAAGAAGAAGAAG
1 TTGAAGAAGAAGAAG
63874 TTGAAGAAGAAGAAG
1 TTGAAGAAGAAGAAG
63889 AGGAAGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (15 bp):
TTGAAGAAGAAGAAG
Found at i:63894 original size:15 final size:15
Alignment explanation
Indices: 63861--63895 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
63851 GTCTTCACTT
**
63861 GAAGAAGAAGAAGTT
1 GAAGAAGAAGAAGAG
63876 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
63891 GAAGA
1 GAAGA
63896 GGAGGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:65398 original size:21 final size:21
Alignment explanation
Indices: 65373--65412 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
65363 TGTACGTTTC
65373 AAATTTTAATATGTGAAAAAA
1 AAATTTTAATATGTGAAAAAA
65394 AAATTTTAATATGTGAAAA
1 AAATTTTAATATGTGAAAA
65413 TGATTGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (21 bp):
AAATTTTAATATGTGAAAAAA
Found at i:66649 original size:66 final size:67
Alignment explanation
Indices: 66568--66701 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 67
66558 TAATTAACAC
* *
66568 TTCTCTTTTTTATATAGTGTTGTAGATATAGATATATCAAATAAACTTCAATGCAGTTTCCTTTA
1 TTCTCTTTTTTATATAGTGTTATAGATATAGATATATCAAATAAACTTCAATACAGTTTCCTTTA
66633 TA
66 TA
*
66635 TTCTC-TTTTTATATAGTGTTATAGATATAGATATATCAAATAAACTTTAATACAGTTTCCTTTA
1 TTCTCTTTTTTATATAGTGTTATAGATATAGATATATCAAATAAACTTCAATACAGTTTCCTTTA
66699 TA
66 TA
66701 T
1 T
66702 ATATGCACCA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 59 0.92
67 5 0.08
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (67 bp):
TTCTCTTTTTTATATAGTGTTATAGATATAGATATATCAAATAAACTTCAATACAGTTTCCTTTA
TA
Found at i:67896 original size:18 final size:20
Alignment explanation
Indices: 67873--67919 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
67863 TATATATGTA
*
67873 CATAATAACT-CA-TTACTT
1 CATAATAACTAAATTTACTT
67891 CATAAT-A-TAAATTTACTT
1 CATAATAACTAAATTTACTT
67909 CATAATAACTA
1 CATAATAACTA
67920 CAAAAACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 2 0.08
18 18 0.75
19 1 0.04
20 2 0.08
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (20 bp):
CATAATAACTAAATTTACTT
Found at i:69532 original size:15 final size:16
Alignment explanation
Indices: 69514--69550 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
69504 AAAAGCTTGG
69514 TTTGAAATAAGTGC-T
1 TTTGAAATAAGTGCTT
69529 TTTG-AA-AAGTGCTT
1 TTTGAAATAAGTGCTT
69543 TTTGAAAT
1 TTTGAAAT
69551 TGCAGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.32
14 7 0.37
15 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (16 bp):
TTTGAAATAAGTGCTT
Found at i:69711 original size:19 final size:19
Alignment explanation
Indices: 69684--69725 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
69674 TTTAATGTCT
*
69684 AAAAGCATTTTTGAAACGC
1 AAAAACATTTTTGAAACGC
*
69703 AAAAACATTTTTGAAACGT
1 AAAAACATTTTTGAAACGC
69722 AAAA
1 AAAA
69726 GCACCTAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (19 bp):
AAAAACATTTTTGAAACGC
Found at i:71061 original size:16 final size:16
Alignment explanation
Indices: 71040--71072 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
71030 TTTTGACTTT
71040 TGCCATCAGGCCATTA
1 TGCCATCAGGCCATTA
71056 TGCCATCAGGCCATTA
1 TGCCATCAGGCCATTA
71072 T
1 T
71073 CTTGAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (16 bp):
TGCCATCAGGCCATTA
Done.