Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011575.1 Corchorus olitorius cultivar O-4 contig11608, 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: 4706
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:2578 original size:154 final size:155
Alignment explanation
Indices: 2294--4706 Score: 3579
Period size: 154 Copynumber: 15.6 Consensus size: 155
2284 CGACCGATCA
* *
2294 TGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
** *
2358 TTGCCAAATCGAAGACGATTCAAAACGGAACTAAAGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
2423 TCCAAATGAGTTAAGAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* ** * *
2448 TGGTCTAATCTCATGAAAATGATTATAGTTAGGCCATAACCAACT-TAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
2512 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
2577 TCCAAATGAGCTAAAAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
*
2602 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* * *
2666 TTGCCAAATCGAAGACGATTCAAAACGTCACAAAAGGGCCTCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
** * *
2731 TTTAAATGAGCTAAAAACATCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* * *
2756 TGGACTAATCTCACCAAAATGATTATAGTTAGTCCCTAAA-AAATGGAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* ** *
2820 TTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
2885 TCCAAATGAGCTAAAAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* *
2910 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGACGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* * *
2974 TTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGA
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
3039 TCCAAATGAGCTAAGAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* *
3064 TGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* * *
3128 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGGCCAAAATGACAAGTGA
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
3193 TCCAAATGAGCTAAGAACTTTACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* *
3218 TGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
3282 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
3347 TCCAAACGAGCTAAAAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* * * *
3372 TGGACGAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAACTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* *
3436 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCTATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
3501 TCCAAATGAGCTAAAAACTTCGCAG
131 TCCAAATGAGCTAAGAACTTCACAG
* *
3526 TGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA-AAATGGAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
*
3590 TTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
66 TTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
3654 TTCCAAATGAGCTAAGAACTTCACAG
130 TTCCAAATGAGCTAAGAACTTCACAG
* * *
3680 TGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT--TAAGAAAAGCTTTCAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
*
3743 TTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
3808 TCCAAATGAGCCAAGTGTTCCAATTGAGCTAAAAACATCACAG
131 TCCAAATGAG-C------T--AA--GAACT----TCA-CA--G
* * * *
3851 TAGACTAATCTCACCAAAATGATTACAGTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* *
3915 TTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGA
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
3980 TCCAAATGAGCTAAGAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
*
4005 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
** *
4069 TTGCCAAATCGAAGACGATTCAAAACGGAACTAAAGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
** * * *
4134 TTTAAATTAGCTAAAAACATCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* *
4159 TGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA-AAATGGAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
* ** * *
4223 TTGCTAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCCGATAGGCACAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
4288 TCCAAATGAGCTAAGAACTTCACAG
131 TCCAAATGAGCTAAGAACTTCACAG
* * *
4313 TGGACCAATCTCACCAAATTGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
*
4377 TTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
4442 TGCAAATGAGCTAAGAACTTCATAG
131 TCCAAATGAGCTAAGAACTTCACAG
* * * *
4467 TGGATTAATCTCACCAAAATGATTATAGTTAGTCCACAAA-AAATGGAAAGAAAAGCTTTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
**
4531 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
66 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
4596 TGCAAATGAGCTAAGAACTTCATAG
131 TCCAAATGAGCTAAGAACTTCACAG
* * * *
4621 TGGACTAATCTCATCAAAATGATTATAGTTAGGCCATTAATAACAT--AAAGGAAAA-CTTTGTG
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAC-TGGAAA-GAAAAGCTTTGAG
* *
4683 GTTTACCAAATCGAAGAAGATTCA
64 GTTTGCCAAATCGAAGACGATTCA
Statistics
Matches: 2064, Mismatches: 160, Indels: 70
0.90 0.07 0.03
Matches are distributed among these distances:
152 1 0.00
153 98 0.05
154 1795 0.87
155 18 0.01
156 3 0.00
157 2 0.00
160 1 0.00
161 4 0.00
162 2 0.00
163 2 0.00
164 4 0.00
165 1 0.00
168 2 0.00
169 2 0.00
170 1 0.00
171 41 0.02
172 87 0.04
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (155 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCTTTGAGGT
TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAGAACTTCACAG
Found at i:3824 original size:18 final size:18
Alignment explanation
Indices: 3801--3836 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3791 CCCAAAATAA
3801 CAAGTGTTCCAAATGAGC
1 CAAGTGTTCCAAATGAGC
*
3819 CAAGTGTTCCAATTGAGC
1 CAAGTGTTCCAAATGAGC
3837 TAAAAACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (18 bp):
CAAGTGTTCCAAATGAGC
Found at i:3962 original size:172 final size:171
Alignment explanation
Indices: 3648--3990 Score: 544
Period size: 172 Copynumber: 2.0 Consensus size: 171
3638 CCCAAAATAA
* * * * *
3648 CAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACATCACAGTAGACTAATCTCACCAAAATGATTACAGTTAGG
* *
3713 CCATAAACAACTTAAGAAAAGCTTTCAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAAT
66 CCATAAACAACTAAAGAAAAGCATTCAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAAT
*
3778 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
131 GGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGC
* *
3819 CAAGTGTTCCAATTGAGCTAAAAACATCACAGTAGACTAATCTCACCAAAATGATTACAGTTAGT
1 CAAGTGTTCCAAATGAGCTAAAAACATCACAGTAGACTAATCTCACCAAAATGATTACAGTTAGG
* * *
3884 CCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTA
66 CCATAAACAACT--AAAGAAAAGCATTCAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTA
3948 ATGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGC
129 ATGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGC
3991 TAAGAACTTC
Statistics
Matches: 157, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
170 1 0.01
171 68 0.43
172 88 0.56
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (171 bp):
CAAGTGTTCCAAATGAGCTAAAAACATCACAGTAGACTAATCTCACCAAAATGATTACAGTTAGG
CCATAAACAACTAAAGAAAAGCATTCAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAAT
GGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGC
Done.