Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014502.1 Corchorus olitorius cultivar O-4 contig14535, 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: 57754
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:5979 original size:15 final size:15
Alignment explanation
Indices: 5960--5995 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5950 GTATAAACAC
5960 AATATATATATATAT
1 AATATATATATATAT
* *
5975 GATATGTATATATAT
1 AATATATATATATAT
5990 AATATA
1 AATATA
5996 CACTAACATA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:6647 original size:129 final size:129
Alignment explanation
Indices: 6514--6763 Score: 385
Period size: 129 Copynumber: 1.9 Consensus size: 129
6504 TTGTTTAGAC
* * *
6514 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATATAATATCCTTATAACTA
* *
6579 TTTAATTTTTACCATTTTACTATTTTAATTGAAAAAGCTT-ATATATTAGAATTTTTTAATATAT
66 TTTAATTTTTACCATTTTACTAATTTAATTGAAAAA-CTTAATATATTAAAATTTTTTAATATAT
* * * *
6643 TTTTATAATTTTGCTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATATAATATCCTTATAACTA
*
6708 TTTTATTTTTACCATTTTACTAATTTAATTGAAAAACTTAGATATATTAAAATTTT
66 TTTAATTTTTACCATTTTACTAATTTAATTGAAAAACTTA-ATATATTAAAATTTT
6764 AAAAATATAT
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
128 3 0.03
129 92 0.84
130 14 0.13
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (129 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATATAATATCCTTATAACTA
TTTAATTTTTACCATTTTACTAATTTAATTGAAAAACTTAATATATTAAAATTTTTTAATATAT
Found at i:9390 original size:21 final size:22
Alignment explanation
Indices: 9366--9406 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9356 GTGTATAATA
*
9366 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
9387 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
9407 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:10249 original size:18 final size:19
Alignment explanation
Indices: 10215--10251 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
10205 GTTAAATTTC
10215 ATTATATGAACAATAAATA
1 ATTATATGAACAATAAATA
*
10234 ATTATAT-AAGAATAAATA
1 ATTATATGAACAATAAATA
10252 CTAAATCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATATGAACAATAAATA
Found at i:21410 original size:13 final size:13
Alignment explanation
Indices: 21392--21430 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
21382 TGAAAAATAG
21392 TAAAATGGTAAAA
1 TAAAATGGTAAAA
** *
21405 TAAAATTTTAAAT
1 TAAAATGGTAAAA
21418 TAAAATGGTAAAA
1 TAAAATGGTAAAA
21431 AATTAATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (13 bp):
TAAAATGGTAAAA
Found at i:21464 original size:146 final size:148
Alignment explanation
Indices: 21283--21556 Score: 383
Period size: 146 Copynumber: 1.9 Consensus size: 148
21273 TGACAAAAAT
* * * *
21283 AAAATAATTATAAAAACATTGAATTTAATTAAATGAATATAGAGTTTTCAGTAGAATAAAACTAT
1 AAAATAATTATAAAAACATTAAATTTAATTAAATGAAAATAAAGTTTTCAGTAAAATAAAACTAT
21348 ATATTAAA-AAATTATAATATAACCAAGTTTTTAATGAAAAATAGTAAAATGGT-AAAATAAAAT
66 ATATTAAATAAATTATAATATAACCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAAAT
21411 TTTAAATTAAAATGGTAA
131 TTTAAATTAAAATGGTAA
* * *
21429 AAAATTAATTA-AAAAATATTAAATTTAATTAAATGAAAATAAAGTTTTTAGTAAAATAAAACTG
1 AAAA-TAATTATAAAAACATTAAATTTAATTAAATGAAAATAAAGTTTTCAGTAAAATAAAACTA
* *** * * * *
21493 TATGTTAAATTTTTTTTAATATATCCTAGTTTTTAATGAAAAATAGTGAAATGGTAAAAATAAA
65 TATATTAAATAAATTATAATATAACCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAA
21557 GTAATTATAA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
146 58 0.53
147 44 0.40
148 8 0.07
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (148 bp):
AAAATAATTATAAAAACATTAAATTTAATTAAATGAAAATAAAGTTTTCAGTAAAATAAAACTAT
ATATTAAATAAATTATAATATAACCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAAAT
TTTAAATTAAAATGGTAA
Found at i:29588 original size:146 final size:141
Alignment explanation
Indices: 29300--29602 Score: 371
Period size: 146 Copynumber: 2.1 Consensus size: 141
29290 AAACCGTGCG
* **
29300 CACATTATTTTCAAATCTAATGACTTGCTTTTAAAAATGTATTACGACATACACGCATTTTTTCA
1 CACATTATTTTCAAATCTAATGACTTGCTTTTAAAAATGCATTACGACATACAAACATTTTTTCA
* * * ** *
29365 TATTGTAACTATATTTTAAAACCTTGACTTTTTTTAATTATAAAATATTATTAATTAACAATCTC
66 CATTATAACTATATTTTAAAACCTTGACTTTTTTAAAACATAAAAGATTATTAATTAACAATCTC
29430 ATTTTCGAGCA
131 ATTTTCGAGCA
* **
29441 CACATTATTTTCAAATCTAATGATTTGCTTTTAAAAAATGCATTTGGACATACAAACATTTTTTT
1 CACATTATTTTCAAATCTAATGACTTGCTTTT-AAAAATGCATTACGACATACAAACA----TTT
*
29506 TTTCACATTATAACTATATTTTAAAGCC-T-A-TTTTTTAAAACATAAAAGATTATTAATATTTA
61 TTTCACATTATAACTATATTTTAAAACCTTGACTTTTTTAAAACATAAAAGATTATT-A-A-TTA
*
29568 ACGATCTCATTTTC-ACGCA
123 ACAATCTCATTTTCGA-GCA
29587 CACATTATTTTCAAAT
1 CACATTATTTTCAAAT
29603 ATACCTATGT
Statistics
Matches: 139, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
141 31 0.22
142 20 0.14
143 20 0.14
144 2 0.01
145 3 0.02
146 63 0.45
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (141 bp):
CACATTATTTTCAAATCTAATGACTTGCTTTTAAAAATGCATTACGACATACAAACATTTTTTCA
CATTATAACTATATTTTAAAACCTTGACTTTTTTAAAACATAAAAGATTATTAATTAACAATCTC
ATTTTCGAGCA
Found at i:31111 original size:89 final size:89
Alignment explanation
Indices: 30988--31281 Score: 498
Period size: 89 Copynumber: 3.3 Consensus size: 89
30978 CCTGTTGGCT
* * * *
30988 GTTTATGGCTATACCAATGCCCCCCGCTGTTGGTATACATTCTACAGCAACGGAACCCGTGGGTA
1 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGGAAGCCGTAGGTA
* *
31053 TATCTCAAATCATACTATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* *
31077 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGGAAGCCGTAGGTA
31142 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* *
31166 GTTTGTGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACAGAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGGAAGCCGTAGGTA
31231 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
31255 GTTTATGGCTATACCAACGCCCCCCGC
1 GTTTATGGCTATACCAACGCCCCCCGC
31282 CGTTTGTAAA
Statistics
Matches: 192, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 192 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (89 bp):
GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGGAAGCCGTAGGTA
TATCTCCAATCATACCATTTTTTG
Found at i:31465 original size:40 final size:40
Alignment explanation
Indices: 31420--31496 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
31410 GTCATTCACA
*
31420 TTAAAAAT-ATAATCCAAAACAATTTGCTCTAATCCACACG
1 TTAAAAATGA-AATCAAAAACAATTTGCTCTAATCCACACG
* *
31460 TTAAAAATGAAATTAAAAACAATTTGTTCTAATCCAC
1 TTAAAAATGAAATCAAAAACAATTTGCTCTAATCCAC
31497 TCATGTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (40 bp):
TTAAAAATGAAATCAAAAACAATTTGCTCTAATCCACACG
Found at i:36428 original size:15 final size:15
Alignment explanation
Indices: 36408--36436 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36398 AACTGTTGAT
36408 GAGACTCTTCTTGTC
1 GAGACTCTTCTTGTC
36423 GAGACTCTTCTTGT
1 GAGACTCTTCTTGT
36437 GGAGGCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (15 bp):
GAGACTCTTCTTGTC
Found at i:46182 original size:39 final size:39
Alignment explanation
Indices: 46128--46207 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
46118 TCACATTTTG
46128 ACCACAACACTTCCAGTATAAGTTAGATGCGAGAAATTA
1 ACCACAACACTTCCAGTATAAGTTAGATGCGAGAAATTA
*
46167 ACCACAACACTTCCAGTATGAGTTAGATGCGAGAAATTA
1 ACCACAACACTTCCAGTATAAGTTAGATGCGAGAAATTA
46206 AC
1 AC
46208 AAAGAGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (39 bp):
ACCACAACACTTCCAGTATAAGTTAGATGCGAGAAATTA
Found at i:47403 original size:20 final size:19
Alignment explanation
Indices: 47363--47400 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47353 TTTCTAACAA
*
47363 AAAATAGCCACGTGGCATT
1 AAAATAGCCACGTGGAATT
47382 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
47401 TAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:52874 original size:22 final size:22
Alignment explanation
Indices: 52846--52890 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52836 AGAGTGTAAA
52846 TGGAACAATGATACTCGAACTT
1 TGGAACAATGATACTCGAACTT
52868 TGGAACAATGATACTCGAACTT
1 TGGAACAATGATACTCGAACTT
52890 T
1 T
52891 AGAGTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
TGGAACAATGATACTCGAACTT
Found at i:53012 original size:22 final size:23
Alignment explanation
Indices: 52949--53018 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
52939 ATGGTAAGTG
52949 CACATTATGAAATTTTGATAACCTT
1 CACATTATGAAATTTTGATAA-C-T
* *
52974 C-CATAAAATAAAATTTTGATAA-T
1 CACAT--TATGAAATTTTGATAACT
52997 CACATTATGAAATTTTGATAAC
1 CACATTATGAAATTTTGATAAC
53019 CATACAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
22 14 0.38
23 2 0.05
24 6 0.16
25 1 0.03
26 14 0.38
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (23 bp):
CACATTATGAAATTTTGATAACT
Done.