Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016350.1 Corchorus olitorius cultivar O-4 contig16383, 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: 5632
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:680 original size:330 final size:329
Alignment explanation
Indices: 34--1265 Score: 1482
Period size: 330 Copynumber: 3.7 Consensus size: 329
24 AAATTTGATA
* * * *
34 GAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTT
1 GAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
* * *
99 TTGGCTAAAAACGCATTCCGGGGCCCGACTAAGTTTTGCATGATTTTT-GTGTCGAGACTCCTTG
66 TTGGCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTG
* * * *
163 AAATATTTATATTCATCTTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCA
131 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTG-AGTTAAGGATTTGTTTTTACGAGCA
* * * *
228 TCTGAATCTTGTTTCAATTTAATTAGAAACTAATCCAGAAAAATATGAAAAACGATATTAAAAGC
195 TCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGC
* * * * * * *
293 GTGAAAAAGGCTTTCAATTTTTTTGGCGTTGAATTGTATATTTTGTATGAGTATTTTAACTAGAA
260 GT-CAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAGTATTTTAACCAGAA
358 ATCAAG
324 ATCAAG
*
364 GAAAAATCTTTCGAGTAAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
1 GAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
* * * * *
429 TCGGCTAAAACCGCGTTTCGGGGCCCGGCAT-AGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
66 TTGGCTAAAAACGCATTCCGGGGCCCGAC-TCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
* * *
493 GAAATATCTATATTCATGTAACCAAATCTTAGCCACATTAGAGTTAAGGATTTGTGTTTACGAGC
130 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GAGTTAAGGATTTGTTTTTACGAGC
** *
558 ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAATAGGAAAAACGATATTAGAAA
194 ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTA-AAA
* * * * * *
623 -CGTCAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATAATTATTTTAGCCAAA
258 GCGTCAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAGTATTTTAACCAGA
**
687 AATTTAG
323 AATCAAG
* * * * * * **
694 GAAATAAT-TTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCATAGTT
1 GAAA-AATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTT
* * * * *
758 TTTGGCTAAAAAAGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCT-TCAAGACTCT
65 TTTGGCTAAAAACGCATTCCGGGG-CCCGACTCAGTTTTGCATGATTTTTGG-TGCCAAGACTCC
* * * *
822 TTG----A--GATATTCATCTAATCAAATCTCAGCCACATTGAGTTTAAGGATTTGTTTTTATGT
128 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAG-TTAAGGATTTGTTTTTACGA
* * *
881 GCTTCTGAAT-TTATTTTCGATTTAATAAAAAATTAATTCAGAAAAAGTATGAAAAACGATATTA
192 GCATCTGAATCTT-GTTTCGATTTAATTAAAAATTAATTCAGAAAAA-TATGAAAAACGATATTA
** * * * *
945 AAAGCG-CGAAAAGTACTCCAATCCTTTTGACGTTGAATTATATATTTTCTATGAGTATTTTTAC
255 AAAGCGTC-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAGTATTTTAAC
*
1009 CAGAAATCGAG
319 CAGAAATCAAG
* * *
1020 GAAAAGTCTTTCGGGTCAATATTTGCAAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTT
1 GAAAAATCTTTCGAGTCAATTTTTGC-AAAATTTTAGCCGAAATCATGTACTAACCATCACGGTT
* * * *
1085 TTTGGCTAAAATCGCATTCCGGGACCCGACTCAGTTTTGCAGGATTTTTTGTGCCAAGACTCCTT
65 TTTGGCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
* * * * *
1150 AAAATATCTATATTCATCTAACCAAATCTCAACCACGTTAAATTTAAGGATTTGTTTTTACGAGC
130 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GAGTTAAGGATTTGTTTTTACGAGC
* * * *
1215 ATCTGAATCTTGTTTCGCTTTAATTAGAAATTAATTCAAAAAAATACGAAA
194 ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAA
1266 CAAAATTTTG
Statistics
Matches: 758, Mismatches: 120, Indels: 47
0.82 0.13 0.05
Matches are distributed among these distances:
324 5 0.01
325 89 0.12
326 123 0.16
327 53 0.07
330 227 0.30
331 171 0.23
332 87 0.11
333 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (329 bp):
GAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
TTGGCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTG
AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAGTTAAGGATTTGTTTTTACGAGCAT
CTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG
TCAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAGTATTTTAACCAGAAAT
CAAG
Found at i:4790 original size:33 final size:32
Alignment explanation
Indices: 4675--4792 Score: 96
Period size: 33 Copynumber: 3.6 Consensus size: 32
4665 AAATGGTCGG
** *
4675 TGCCGCCCTTGGTGGGC-GCGTGGCCATGGGGA
1 TGCCGCCCTCAGTGGGCGGCGT-ACCATGGGGA
* * * **
4707 TGCTGCCCCCGGTGGGCGGCGTAGCCATGGTCA
1 TGCCGCCCTCAGTGGGCGGCGTA-CCATGGGGA
* *
4740 TGCCGCCC-AAGGAGGGCGGCGTCACCATGGGGA
1 TGCCGCCCTCA-GTGGGCGGCGT-ACCATGGGGA
4773 TGCCGCCCTCAGTGGGCGGC
1 TGCCGCCCTCAGTGGGCGGC
4793 ATGATCTTGG
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
32 14 0.21
33 51 0.76
34 2 0.03
ACGTcount: A:0.10, C:0.32, G:0.42, T:0.15
Consensus pattern (32 bp):
TGCCGCCCTCAGTGGGCGGCGTACCATGGGGA
Found at i:5459 original size:27 final size:26
Alignment explanation
Indices: 5429--5496 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 26
5419 AGCACCAGCG
5429 GCAGCCTC-CCTCTTCCTATACATCCGA
1 GCAGCCTCACCTC--CCTATACATCCGA
5456 GCAGCCTCAGCCTCCCTATACATCCGA
1 GCAGCCTCA-CCTCCCTATACATCCGA
5483 GCAGCCTCAGCCTC
1 GCAGCCTCA-CCTC
5497 TTTATCCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 35 0.90
29 4 0.10
ACGTcount: A:0.19, C:0.46, G:0.15, T:0.21
Consensus pattern (26 bp):
GCAGCCTCACCTCCCTATACATCCGA
Found at i:5505 original size:33 final size:27
Alignment explanation
Indices: 5443--5496 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5433 CCTCCCTCTT
5443 CCTATACATCCGAGCAGCCTCAGCCTC
1 CCTATACATCCGAGCAGCCTCAGCCTC
5470 CCTATACATCCGAGCAGCCTCAGCCTC
1 CCTATACATCCGAGCAGCCTCAGCCTC
5497 TTTATCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.44, G:0.15, T:0.19
Consensus pattern (27 bp):
CCTATACATCCGAGCAGCCTCAGCCTC
Done.