Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013619.1 Corchorus olitorius cultivar O-4 contig13652, 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: 27545
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Found at i:1004 original size:24 final size:23
Alignment explanation
Indices: 971--1016 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
961 ACGTTTGCAC
*
971 AAATAGCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
995 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
1017 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:1245 original size:102 final size:103
Alignment explanation
Indices: 1138--1344 Score: 371
Period size: 103 Copynumber: 2.0 Consensus size: 103
1128 ATTTTAATAT
* * *
1138 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTT-AAAGTTTTATTTGATA
1 AATAATATATTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTTAACTTGATA
1202 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
*
1240 AATAATATATTTAATTTAATTGATAAATAAAATTACATATTGAACCTTAAAAGTTTAACTTGATA
1 AATAATATATTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTTAACTTGATA
1305 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
1343 AA
1 AA
1345 ATTAAAAAGG
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 46 0.46
103 54 0.54
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (103 bp):
AATAATATATTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTTAACTTGATA
AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
Found at i:1409 original size:2 final size:2
Alignment explanation
Indices: 1397--1432 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
1387 AGTTTAGACT
1397 TA TA TA GTA 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 TA T
1433 GGTTAGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3570 original size:11 final size:11
Alignment explanation
Indices: 3551--3587 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
3541 GTCAAAAAGA
3551 TTTTT-TTTAT
1 TTTTTATTTAT
3561 TTTTTATTTAT
1 TTTTTATTTAT
3572 TTTTTATTTAT
1 TTTTTATTTAT
3583 TTTTT
1 TTTTT
3588 GCAATGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:5539 original size:21 final size:20
Alignment explanation
Indices: 5514--5573 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
5504 GGGATTGGAG
*
5514 TATTTATTTATCTTGTTACT
1 TATTTATTTATATTGTTACT
* * *
5534 TAATTT-TATTATTTTCTTGCT
1 T-ATTTAT-TTATATTGTTACT
5555 TATTTATTT-TATTGTTACT
1 TATTTATTTATATTGTTACT
5574 CTTTTCACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.23
20 8 0.26
21 16 0.52
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (20 bp):
TATTTATTTATATTGTTACT
Found at i:5551 original size:24 final size:25
Alignment explanation
Indices: 5517--5567 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5507 ATTGGAGTAT
5517 TTATTTATCTTG-TTACTTAATTTTA
1 TTATTTATCTTGCTTA-TTAATTTTA
*
5542 TTATTT-TCTTGCTTATTTATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
5566 TT
1 TT
5568 GTTACTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGCTTATTAATTTTA
Found at i:10501 original size:26 final size:26
Alignment explanation
Indices: 10472--10539 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
10462 TACTTCTTGA
10472 TTACTGATTACTATTTTTTACTCTTT
1 TTACTGATTACTATTTTTTACTCTTT
*
10498 TTACTGATTACCATTTTTTACTCTTT
1 TTACTGATTACTATTTTTTACTCTTT
*
10524 TTGCTGATTACTATTT
1 TTACTGATTACTATTT
10540 CTCTCTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (26 bp):
TTACTGATTACTATTTTTTACTCTTT
Found at i:10587 original size:21 final size:21
Alignment explanation
Indices: 10522--10588 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
10512 TTTTTACTCT
*
10522 TTTTGCTGATTACTATTTCTC-
1 TTTTGCTGATTACTATTAC-CA
* * * *
10543 TCTTGCTGACTACTCTTACTA
1 TTTTGCTGATTACTATTACCA
*
10564 TTTTGCTGGTTACTATTACCA
1 TTTTGCTGATTACTATTACCA
10585 TTTT
1 TTTT
10589 TACTCTTTAC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.21, G:0.10, T:0.52
Consensus pattern (21 bp):
TTTTGCTGATTACTATTACCA
Found at i:10595 original size:36 final size:35
Alignment explanation
Indices: 10553--10667 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 35
10543 TCTTGCTGAC
10553 TACTCTTACTATTTTGCTGGTTACTATTACCATTTT
1 TACTCTTACT-TTTTGCTGGTTACTATTACCATTTT
* ** * *
10589 TACTCTTTACTCTTTGCTCATTGCTATTACCA-TCT
1 TACTC-TTACTTTTTGCTGGTTACTATTACCATTTT
* *
10624 TACTGTTTACTCTTTTAC-GGATTACTATTACTC-TTTT
1 TACT-CTTACT-TTTTGCTGG-TTACTATTAC-CATTTT
10661 TACTCTT
1 TACTCTT
10668 TACTCTTTAC
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
35 11 0.18
36 37 0.62
37 12 0.20
ACGTcount: A:0.18, C:0.23, G:0.07, T:0.52
Consensus pattern (35 bp):
TACTCTTACTTTTTGCTGGTTACTATTACCATTTT
Found at i:10677 original size:36 final size:35
Alignment explanation
Indices: 10573--10710 Score: 143
Period size: 36 Copynumber: 3.9 Consensus size: 35
10563 ATTTTGCTGG
* *
10573 TTACTATTACCATTTTTACTCTTTACTCTTTGCTCA
1 TTACTATTACC-TTTTTACTCTTTACTCTTTACTGA
* * * * *
10609 TTGCTATTACCATCTTACTGTTTACTCTTTTACGGA
1 TTACTATTACCTTTTTACTCTTTACTC-TTTACTGA
10645 TTACTATTACTCTTTTTACTCTTTACTCTTTACTGA
1 TTACTATTAC-CTTTTTACTCTTTACTCTTTACTGA
* * *
10681 CTATTATTA-CTCCTTTACTCTTTACTCTTT
1 TTACTATTACCT-TTTTACTCTTTACTCTTT
10711 GCCATTGCCA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
34 2 0.02
35 30 0.36
36 38 0.45
37 14 0.17
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (35 bp):
TTACTATTACCTTTTTACTCTTTACTCTTTACTGA
Found at i:10689 original size:72 final size:72
Alignment explanation
Indices: 10573--10710 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
10563 ATTTTGCTGG
* * * *
10573 TTACTATTACCATTTTTACTCTTTACTCTTTGCTCATTGCTATTAC-CATCTTACTGTTTACTCT
1 TTACTATTACCATTTTTACTCTTTACTCTTTACTCACTACTATTACTCAT-TTACTCTTTACTCT
10637 TTTACGGA
65 TTTACGGA
* * *
10645 TTACTATTACTC-TTTTTACTCTTTACTCTTTACTGACTATTATTACTCCTTTACTCTTTACTCT
1 TTACTATTAC-CATTTTTACTCTTTACTCTTTACTCACTACTATTACTCATTTACTCTTTACTCT
10709 TT
65 TT
10711 GCCATTGCCA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 54 0.95
73 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (72 bp):
TTACTATTACCATTTTTACTCTTTACTCTTTACTCACTACTATTACTCATTTACTCTTTACTCTT
TTACGGA
Found at i:10860 original size:32 final size:32
Alignment explanation
Indices: 10812--10964 Score: 173
Period size: 32 Copynumber: 4.7 Consensus size: 32
10802 TTATCCTTAG
** *
10812 TTACTAACCACCATTTTA-CTCTTTAAATTTGA
1 TTACTAATTACCATTTTACCT-TTTGAATTTGA
* *
10844 TTGCTAATTACTATTTTACCTTTTGAATTTGA
1 TTACTAATTACCATTTTACCTTTTGAATTTGA
* * * *
10876 TTGCTAACTACTATTTTACCCTTTTGAACTTGA
1 TTACTAATTACCATTTTA-CCTTTTGAATTTGA
*
10909 TTACTAATTACCATTTTACCATTTGAATTTGA
1 TTACTAATTACCATTTTACCTTTTGAATTTGA
*
10941 TTACTAGTTACCATTTTACTCTTT
1 TTACTAATTACCATTTTAC-CTTT
10965 ACTGACTGAC
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
32 71 0.68
33 33 0.32
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (32 bp):
TTACTAATTACCATTTTACCTTTTGAATTTGA
Found at i:10957 original size:65 final size:65
Alignment explanation
Indices: 10812--10964 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 65
10802 TTATCCTTAG
* * * * *
10812 TTACTAACCACCATTTTACTC-TTTAAATTTGATTGCTAATTACTATTTTACCTTTTGAATTTGA
1 TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
* * * *
10876 TTGCTAACTACTATTTTACCCTTTTGAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
1 TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
**
10941 TTACTAGTTACCATTTTACTCTTT
1 TTACTAACTACCATTTTACTCTTT
10965 ACTGACTGAC
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 17 0.23
65 57 0.77
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (65 bp):
TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
Found at i:11984 original size:51 final size:51
Alignment explanation
Indices: 11882--11986 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 51
11872 ATCTAATCAT
* ** * * *
11882 CAAGACTCTACCTTTATTTCCCCAAGACTCAATTTTTATCGTCAAACTTGC
1 CAAGACTCAACCTTTATCACCCAAAGACTCAATTTTTATCCTCAAAATTGC
*
11933 CAAGACTCAACCTTTATCACCCAAAGATTCAATTTTTATCACT-AAAATTGC
1 CAAGACTCAACCTTTATCACCCAAAGACTCAATTTTTATC-CTCAAAATTGC
11984 CAA
1 CAA
11987 CTTTTAGACT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (51 bp):
CAAGACTCAACCTTTATCACCCAAAGACTCAATTTTTATCCTCAAAATTGC
Found at i:17826 original size:290 final size:290
Alignment explanation
Indices: 17299--17881 Score: 1112
Period size: 290 Copynumber: 2.0 Consensus size: 290
17289 ACCGACTGGA
17299 TTGATAGAGAATTTAGAGATGATGTCAGATTCAAGAATCTTCTGATGTTTTCTGATGACGAGATG
1 TTGATAGAGAATTTAGAGATGATGTCAGATTCAAGAATCTTCTGATGTTTTCTGATGACGAGATG
17364 GAGGGTGGCGGGTGTTTTCTGATTGAGACTGCAATATCCTACCCTCTTCTGCAAGTTTTTCTATA
66 GAGGGTGGCGGGTGTTTTCTGATTGAGACTGCAATATCCTACCCTCTTCTGCAAGTTTTTCTATA
*
17429 TGAGCATTATTCTGGTTTTGTTGTTCCCTTTAATTCTCTGAGGGAGATTGATACTCGGCATTCTT
131 TGAGCATTATTCTGGTTTTGCTGTTCCCTTTAATTCTCTGAGGGAGATTGATACTCGGCATTCTT
17494 GTGGATGGAGTGGTGATGGCGGCTTCAGCTTTGGAGGTTACCCCCACATCTGTGGTTGGATCAGC
196 GTGGATGGAGTGGTGATGGCGGCTTCAGCTTTGGAGGTTACCCCCACATCTGTGGTTGGATCAGC
*
17559 AAAAAGGTCCCTGCTACTGAGTATACCCGC
261 AAAAAGGTCCCTGCTACTGAGTATACCCAC
* *
17589 TTGATATAGAATTTAGAGATGATGTCGGATTCAAGAATCTTCTGATGTTTTCTGATGACGAGATG
1 TTGATAGAGAATTTAGAGATGATGTCAGATTCAAGAATCTTCTGATGTTTTCTGATGACGAGATG
*
17654 GAGGGTGGCGGGTGTTTTCTGATTGAGACTGCAGTATCCTACCCTCTTCTGCAAGTTTTTCTATA
66 GAGGGTGGCGGGTGTTTTCTGATTGAGACTGCAATATCCTACCCTCTTCTGCAAGTTTTTCTATA
17719 TGAGCATTATTCTGGTTTTGCTGTTCCCTTTAATTCTCTGAGGGAGATTGATACTCGGCATTCTT
131 TGAGCATTATTCTGGTTTTGCTGTTCCCTTTAATTCTCTGAGGGAGATTGATACTCGGCATTCTT
*
17784 GTGGATGGAGTGGTGATGGCGGCTTCAGCTTTGGAGGTTACCCCCGCATCTGTGGTTGGATCAGC
196 GTGGATGGAGTGGTGATGGCGGCTTCAGCTTTGGAGGTTACCCCCACATCTGTGGTTGGATCAGC
17849 AAAAAGGTCCCTGCTACTGAGTATACCCAC
261 AAAAAGGTCCCTGCTACTGAGTATACCCAC
17879 TTG
1 TTG
17882 TACACTGTAT
Statistics
Matches: 287, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
290 287 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (290 bp):
TTGATAGAGAATTTAGAGATGATGTCAGATTCAAGAATCTTCTGATGTTTTCTGATGACGAGATG
GAGGGTGGCGGGTGTTTTCTGATTGAGACTGCAATATCCTACCCTCTTCTGCAAGTTTTTCTATA
TGAGCATTATTCTGGTTTTGCTGTTCCCTTTAATTCTCTGAGGGAGATTGATACTCGGCATTCTT
GTGGATGGAGTGGTGATGGCGGCTTCAGCTTTGGAGGTTACCCCCACATCTGTGGTTGGATCAGC
AAAAAGGTCCCTGCTACTGAGTATACCCAC
Done.