Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017501.1 Corchorus olitorius cultivar O-4 contig17534, 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: 16090
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:446 original size:31 final size:31
Alignment explanation
Indices: 408--469 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
398 TATGTTAGAA
*
408 AAATAAGGATATAATAGGCATTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
* *
439 AAATAAGGGTACAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
470 TTACAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (31 bp):
AAATAAGGATACAATAGGCATTTCAAAAGTT
Found at i:1063 original size:246 final size:243
Alignment explanation
Indices: 625--1107 Score: 849
Period size: 246 Copynumber: 2.0 Consensus size: 243
615 TTGTGTGAGA
* *
625 TCCCAAGTTCGAATCCTGGGATGGGTAGGGTGGGATTATGGGAAAGGATATAACTACCTCCTATT
1 TCCCAAGTTCGAATCCTGGGATGGGTAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATT
690 GTGTAGTCTATTTCAATACCATGTTCATGAATAACAAAAAAAAACAATTCATTAACCTATAGAAA
66 GTGTAGTCTATTTCAATACCATGTTCATGAATAACAAAAAAAAACAATTCATTAACCTATAGAAA
*
755 AAATTAAATTTGACTAGAATAATTTAATAACAAGTACTTAATATTTTTATATAACTTAAAACAAA
131 AAATTAAATTTGACTAGAATAATTTAATAACAAGTACTTAAAATTTTTATATAACTTAAAACAAA
*
820 ATATTATTAAGTACCTTACATTTCTAACAGCCTTTTTAAACTGTAAGG
196 ATATTAATAAGTACCTTACATTTCTAACAGCCTTTTTAAACTGTAAGG
** * *
868 TCCCAAGTTCGAATTTTGGGATGGGTAGGTTGGGATTATGGGAAAGGAGAGAACTAGCTCCTATT
1 TCCCAAGTTCGAATCCTGGGATGGGTAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATT
*
933 GTGTAGTTTATTTCAATACCATGTTCATGAATAACAAAGAAAAAAAACAATTCATTAACCTATAG
66 GTGTAGTCTATTTCAATACCATGTTCATGAATAAC--A-AAAAAAAACAATTCATTAACCTATAG
*
998 AAAAAATTAAATTTGACTAGAATAATTTAATTACAAGTACTTAAAATTTTTATATAACTTAAAAC
128 AAAAAATTAAATTTGACTAGAATAATTTAATAACAAGTACTTAAAATTTTTATATAACTTAAAAC
1063 AAAATATTAATAAGTACCTTACATTTCTAACAGCCTTTTTAAACT
193 AAAATATTAATAAGTACCTTACATTTCTAACAGCCTTTTTAAACT
1108 AATCCTTCTC
Statistics
Matches: 227, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
243 93 0.41
245 1 0.00
246 133 0.59
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (243 bp):
TCCCAAGTTCGAATCCTGGGATGGGTAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATT
GTGTAGTCTATTTCAATACCATGTTCATGAATAACAAAAAAAAACAATTCATTAACCTATAGAAA
AAATTAAATTTGACTAGAATAATTTAATAACAAGTACTTAAAATTTTTATATAACTTAAAACAAA
ATATTAATAAGTACCTTACATTTCTAACAGCCTTTTTAAACTGTAAGG
Found at i:1725 original size:17 final size:17
Alignment explanation
Indices: 1703--1735 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1693 TTTTATGGAT
1703 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
1720 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
1736 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:2708 original size:77 final size:78
Alignment explanation
Indices: 2622--2789 Score: 236
Period size: 77 Copynumber: 2.2 Consensus size: 78
2612 TTTTTTTAAT
* *
2622 TAAAATAGTAAAATGG-AAAACTAAAATAGTTGTAAGGATATTAGATTTAATTAAA-AAAAATAG
1 TAAAATAGTAAAATGGTAAAA-TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAG
2685 AG-TATTTAGTTGAG
65 AGCT-TTTAGTTGAG
* * *
2699 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAATATGGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
2764 GCTTTTAGTTGAG
66 GCTTTTAGTTGAG
2777 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
2790 GTTTAAACAA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
77 47 0.57
78 32 0.39
79 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
GCTTTTAGTTGAG
Found at i:3328 original size:23 final size:22
Alignment explanation
Indices: 3264--3342 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
3254 GAAATCGATT
* *
3264 CGAGACTAAATCCGAACCCGATC
1 CGAGACCAAAT-CGAACCCAATC
* *
3287 CGACACCAAATCGGGACCCAATC
1 CGAGACCAAATC-GAACCCAATC
*
3310 CGAGACCGAACTCGAACCCAA-C
1 CGAGACC-AAATCGAACCCAATC
3332 CTGAGACCAAA
1 C-GAGACCAAA
3343 CCTGAAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 5 0.11
23 36 0.80
24 4 0.09
ACGTcount: A:0.37, C:0.37, G:0.18, T:0.09
Consensus pattern (22 bp):
CGAGACCAAATCGAACCCAATC
Found at i:8383 original size:16 final size:16
Alignment explanation
Indices: 8356--8405 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 16
8346 CTTTTTTTTG
8356 TTTAA-AAAATATAT-
1 TTTAATAAAATATATA
8370 TTT-ATAAAATATATA
1 TTTAATAAAATATATA
8385 TTTAA-AAAA-ATATA
1 TTTAATAAAATATATA
8399 TTTAATA
1 TTTAATA
8406 CATTGTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.03
14 22 0.69
15 8 0.25
16 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAATAAAATATATA
Found at i:8684 original size:63 final size:63
Alignment explanation
Indices: 8540--8665 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
8530 ATTTGATTCA
* * * *
8540 ATGGTAAGGTGCATGTTTCCTAAACCGTGGGGTTTCAGGTTCAATTCCTACTGTATTCATTGC
1 ATGGTAAGGTGCATGTTCCCTAAACCATGGGGTCTCAGGTTCAATTCCCACTGTATTCATTGC
*
8603 ATGGTAAGGTGCATGTTCCCTAGACCATGGGGTCTCAGGTTCAATTCCCACTGTATTCATTGC
1 ATGGTAAGGTGCATGTTCCCTAAACCATGGGGTCTCAGGTTCAATTCCCACTGTATTCATTGC
8666 GTGTGGGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (63 bp):
ATGGTAAGGTGCATGTTCCCTAAACCATGGGGTCTCAGGTTCAATTCCCACTGTATTCATTGC
Found at i:8712 original size:25 final size:25
Alignment explanation
Indices: 8684--8734 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
8674 TTTTGTGTTC
8684 CAAGAAGGAACCTTATGTGAAGAAG
1 CAAGAAGGAACCTTATGTGAAGAAG
8709 CAAGAAGGAACCTTATGTGAAGAAG
1 CAAGAAGGAACCTTATGTGAAGAAG
8734 C
1 C
8735 TTGCTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (25 bp):
CAAGAAGGAACCTTATGTGAAGAAG
Found at i:9005 original size:174 final size:174
Alignment explanation
Indices: 8709--9044 Score: 582
Period size: 174 Copynumber: 1.9 Consensus size: 174
8699 TGTGAAGAAG
* *
8709 CAAGAAGGAACCTTATGTGAAGAAGCTTGCTTAATTATGAAGATCAAAAATTTCGACAGTGTTCG
1 CAAGAAGGAACCTTATGTCAAGAAGCTTGCTTAATTATGAAGATCAAAAATTTCGACAGTGTTCA
*
8774 TTTTTCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTAACAAGACTCGAACC
66 TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTAACAAGACTCGAACC
*
8839 CGAGATCATTCATGCTTAAGGGGAACAAGTGGGTTTTTGTGTTC
131 CGAGATCATTCATACTTAAGGGGAACAAGTGGGTTTTTGTGTTC
* **
8883 CAAGAAGGAACCTTATGTCAAGAAGCTTGCTTAATTATGAAGATCAAAACTTTCGATGGTGTTCA
1 CAAGAAGGAACCTTATGTCAAGAAGCTTGCTTAATTATGAAGATCAAAAATTTCGACAGTGTTCA
* * *
8948 TTTTGCTCCACTATGGGGGTAAAGCTCTCTCAATAATAGTTTTCTCCATTCACAAGACTCGAACC
66 TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTAACAAGACTCGAACC
9013 CGAGATCATTCATACTTAAGGGGAACAAGTGG
131 CGAGATCATTCATACTTAAGGGGAACAAGTGG
9045 CAAATTACTT
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 152 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (174 bp):
CAAGAAGGAACCTTATGTCAAGAAGCTTGCTTAATTATGAAGATCAAAAATTTCGACAGTGTTCA
TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTAACAAGACTCGAACC
CGAGATCATTCATACTTAAGGGGAACAAGTGGGTTTTTGTGTTC
Found at i:9315 original size:204 final size:205
Alignment explanation
Indices: 8948--9354 Score: 640
Period size: 204 Copynumber: 2.0 Consensus size: 205
8938 ATGGTGTTCA
* *
8948 TTTTGCTCCACTATGGGGGTAAAGCTCTCTCAATAATAGTTTTCTCCATTCACAAGACTCGAACC
1 TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTCACAAGACTCGAACC
**
9013 CGAGATCATTCATACTTAAGGGGAACAAGTGGCAAATTACTTGAACCAACCACTTGTGGGTGACA
66 C-AGATCATTCATACTTAAGGGGAACAAGTGGCAAACCACTTGAACCAACCACTTGTGGGTGACA
* * * *
9078 GTGTTCATTTTAGTCACACGAAAAGGGAAGCTAATATTTATCCTCATAGTTTAGCTAAATTTGAT
130 GTATTCATTTTAGTCACACGAAAAAGAAAGCTAATATTTATCCTCATAATTTAGCTAAATTTGAT
9143 TATAATATTCG
195 TATAATATTCG
* * *
9154 TTTTGCTCCATTAT-GGGGTAAAACTCTCCCAATAATAGTTTTCTTCATTTACAAGACTCGAACC
1 TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTCACAAGACTCGAACC
*
9218 C-GATCATTCATACTTAAGGGGAACAAGTGGCAAAACCACTTGAACCAACCACTTGTTGGT-AGC
66 CAGATCATTCATACTTAAGGGGAACAAGTGGC-AAACCACTTGAACCAACCACTTGTGGGTGA-C
* *
9281 GGTATTCATTTTGGTCACACGAAAAAGAAAGCTAATATTTATCCTCATAATTTAGCTAAATTTGA
129 AGTATTCATTTTAGTCACACGAAAAAGAAAGCTAATATTTATCCTCATAATTTAGCTAAATTTGA
9346 TTATAATAT
194 TTATAATAT
9355 GTTTACTAGC
Statistics
Matches: 185, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
203 31 0.17
204 94 0.51
205 47 0.25
206 13 0.07
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (205 bp):
TTTTGCTCCACTATGGGGGTAAAACTCTCCCAATAATAGTTTTCTCCATTCACAAGACTCGAACC
CAGATCATTCATACTTAAGGGGAACAAGTGGCAAACCACTTGAACCAACCACTTGTGGGTGACAG
TATTCATTTTAGTCACACGAAAAAGAAAGCTAATATTTATCCTCATAATTTAGCTAAATTTGATT
ATAATATTCG
Found at i:10331 original size:34 final size:34
Alignment explanation
Indices: 10269--10333 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
10259 ATCCATCATT
**
10269 AGTTATTGGGAGTTTGGTATTATCAAAAAAAAAA
1 AGTTATTGGGAGTTTGGTAAGATCAAAAAAAAAA
*
10303 AGTTATTGGGAGTTTGGTGAAGA-GAAAAAAA
1 AGTTATTGGGAGTTTGGT-AAGATCAAAAAAA
10334 CAATAGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.29
Consensus pattern (34 bp):
AGTTATTGGGAGTTTGGTAAGATCAAAAAAAAAA
Found at i:13215 original size:29 final size:30
Alignment explanation
Indices: 13157--13235 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
13147 CTTAAATACC
*
13157 AAAA-AAATCCCTTAGCTTTTTCATTTGGGA
1 AAAATAAATCCCTTAGCTTTTT-ATTGGGGA
*
13187 AAAATAAATCCCTTATCTTTTT-TTGGGGA
1 AAAATAAATCCCTTAGCTTTTTATTGGGGA
* *
13216 CAAATAAATCCCTTTGCTTT
1 AAAATAAATCCCTTAGCTTT
13236 CAAAAGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.53
30 4 0.09
31 16 0.37
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
AAAATAAATCCCTTAGCTTTTTATTGGGGA
Done.