Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019380.1 Corchorus olitorius cultivar O-4 contig19413, 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: 14414
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:2185 original size:15 final size:15
Alignment explanation
Indices: 2165--2196 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2155 GCCGAATGAT
2165 TTGTATTTTAATTTC
1 TTGTATTTTAATTTC
2180 TTGTATTTTAATTTC
1 TTGTATTTTAATTTC
2195 TT
1 TT
2197 CTAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TTGTATTTTAATTTC
Found at i:2487 original size:24 final size:24
Alignment explanation
Indices: 2438--2505 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
2428 TAATTCTTCC
*
2438 AAATATTCTCTCTAAATTTTCATTA
1 AAATATTCTCTCT-ATTTTTCATTA
*
2463 AAATATTCTCTCTATTTTTCTTTA
1 AAATATTCTCTCTATTTTTCATTA
2487 AAATA-TCTTCTCTATTTTT
1 AAATATTC-TCTCTATTTTT
2506 AATTGCTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.05
24 25 0.62
25 13 0.32
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATATTCTCTCTATTTTTCATTA
Found at i:3528 original size:17 final size:18
Alignment explanation
Indices: 3506--3539 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3496 ACACTAAAAA
3506 TAATAATAAT-ACAAATC
1 TAATAATAATAACAAATC
3523 TAATAATAATAACAAAT
1 TAATAATAATAACAAAT
3540 AGTCAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
TAATAATAATAACAAATC
Found at i:5181 original size:16 final size:15
Alignment explanation
Indices: 5162--5211 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
5152 ATATAAAAAC
5162 AAATTAATAAATATTA
1 AAATTAATAAA-ATTA
**
5178 AAATTAATTTAATTA
1 AAATTAATAAAATTA
*
5193 AAATAAAATAAAATTA
1 AAAT-TAATAAAATTA
5209 AAA
1 AAA
5212 AAAAAACTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTAATAAAATTA
Found at i:9740 original size:566 final size:562
Alignment explanation
Indices: 8665--9783 Score: 1444
Period size: 566 Copynumber: 2.0 Consensus size: 562
8655 ATGGGTCCAC
* ** *
8665 AAATTTTGGCTCTGATACTTCTTTATTTATCCATGTTCTTGATTTCACAATAATAAAATTTTCAG
1 AAATTTTGGCTCTGATACTCCTTTATTTATCCATACTCATGATTTCACAATAATAAAATTTTCAG
8730 TTTATTTATATAATCTACTTGCCACAAGAAAAAAATCCAAGTTTAAAATTAACTCAACTATGTTT
66 TTTATTTATATAATCTACTTGCCACAAGAAAAAAATCCAAGTTTAAAATTAACTCAACTATGTTT
* * * *
8795 TTTTAAATCAACATATCTGCTTATGCCTTAGATTTATATAATAATTAAATTTTGGTCCACATCTA
131 TTTTAAATCAACATATATGCTCATGCCTTAGATTTATATAATAACTAAATTTTGGTCCACATCCA
* * * *
8860 GAAGATTTATATCGGCATCACACTATTATGATTGATTCTAACATTTTTTCAATAGCTTTGCAACG
196 CAAGATTTATATCGGCATAACACTATTATGATTGATTCAAACATCTTTTCAATAGCTTTGCAACG
* * ** * *
8925 TTTATTGGCAAATTGGGGTGGTGTAACATCCATATTAAAGTTATTGATAAATTAACAAAGCTGTA
261 ATTATAGGCAAATTGGGGTGGTGTAACATCCATATTAAAGGGATGGATAAATTAAAAAAGCTGTA
* * * * * *
8990 AATAGGATATGTGAATAATATAAATATATTTTATTTCTTGAAAATCGAAACATATCCCTTCAACA
326 AATAAGAAATGAGAATAATATAAATATATTTCATTTCATCAAAATCGAAACATATCCCTTCAACA
* * * * * *
9055 TCAAATTGCTCTGGTAAATTTTCTGTCCAACTTCTGCAATAGTTATAATTTTGTGCCATTAACAA
391 TCAAATTGCCCTAGTAAACTTTCTCTCCAACCTCTGCAATACTTATAATTTTGTGCCATTAACAA
9120 CTAGTCAGCGTATTAGGATCAATTTAATCATGGCCAGTGTCTTAAGTGTATACCACATTTTGTTA
456 CTAGTCAGCGTATTAGGATCAATTTAATCATGGCCAGTGTCTTAAGTGTATACCACATTTTGTTA
* * *
9185 TAGCTAATTGGGGTGATGCAACACACATTTTTATGGGTTTAT
521 TAGATAATTGGGGTGATGCAACAAACATATTTATGGGTTTAT
* * * * *
9227 AAATTTT-GCTCTGATTCTCCTTTATTTATTCATACTCATGATTTCACAATAATACATTTTTTAG
1 AAATTTTGGCTCTGATACTCCTTTATTTATCCATACTCATGATTTCACAATAATAAAATTTTCAG
* * * * *
9291 TTTATTTGTATAATTTACTTGCCACAAGAAAAAAAAATCTAAGTTATTTAAAATTTACTCGACTA
66 TTTATTTATATAATCTACTTGCCACAAG--AAAAAAATCCAAG---TTTAAAATTAACTCAACTA
* * * * *
9356 T-TTTCTTTTAAATCAACATATATGCTCATGCCTTCGTTTTATATAATAACTATATTTTTGTCTA
126 TGTTT-TTTTAAATCAACATATATGCTCATGCCTTAGATTTATATAATAACTAAATTTTGGTCCA
*
9420 C-TACCACAAGATTTATATCGGCATAACACTATTATGATTTATTCCAAAC-TCTTTTCAATAGCT
190 CAT-CCACAAGATTTATATCGGCATAACACTATTATGATTGATT-CAAACATCTTTTCAATAGCT
* *
9483 TTGCAACGATTATAGGCAAATTGGGGTGGTGTAACATGCATATT-AAGGGA-GGAATATATTAAA
253 TTGCAACGATTATAGGCAAATTGGGGTGGTGTAACATCCATATTAAAGGGATGG-ATAAATTAAA
* *
9546 AAAGCTGTAAATAAGAAATGAGAATAATGTAAATGA-ATTTCATTTCATCAAAATTGAAACATAT
317 AAAGCTGTAAATAAGAAATGAGAATAATATAAAT-ATATTTCATTTCATCAAAATCGAAACATAT
* * * * *
9610 CTCTTCAATATCAACTTGCCCTATTAACCTTTCTCTCCAACCTCTGCAATTACTGT-TAATTTTG
381 CCCTTCAACATCAAATTGCCCTAGTAAACTTTCTCTCCAACCTCTGCAA-TACT-TATAATTTTG
* * * * * * ** *
9674 TGTCATTGACAACTGGTCATCGTATTAGTATCAATTTGATCATGGCTGGTGTCTTAGGTGTATAC
444 TGCCATTAACAACTAGTCAGCGTATTAGGATCAATTTAATCATGGCCAGTGTCTTAAGTGTATAC
* * *
9739 CACGTTTTGTTGTAGATAATTGGGGTGGTGCAACAAACATATTTA
509 CACATTTTGTTATAGATAATTGGGGTGATGCAACAAACATATTTA
9784 AAGAAATAAG
Statistics
Matches: 475, Mismatches: 70, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
561 74 0.16
562 7 0.01
563 12 0.03
564 1 0.00
565 109 0.23
566 267 0.56
567 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (562 bp):
AAATTTTGGCTCTGATACTCCTTTATTTATCCATACTCATGATTTCACAATAATAAAATTTTCAG
TTTATTTATATAATCTACTTGCCACAAGAAAAAAATCCAAGTTTAAAATTAACTCAACTATGTTT
TTTTAAATCAACATATATGCTCATGCCTTAGATTTATATAATAACTAAATTTTGGTCCACATCCA
CAAGATTTATATCGGCATAACACTATTATGATTGATTCAAACATCTTTTCAATAGCTTTGCAACG
ATTATAGGCAAATTGGGGTGGTGTAACATCCATATTAAAGGGATGGATAAATTAAAAAAGCTGTA
AATAAGAAATGAGAATAATATAAATATATTTCATTTCATCAAAATCGAAACATATCCCTTCAACA
TCAAATTGCCCTAGTAAACTTTCTCTCCAACCTCTGCAATACTTATAATTTTGTGCCATTAACAA
CTAGTCAGCGTATTAGGATCAATTTAATCATGGCCAGTGTCTTAAGTGTATACCACATTTTGTTA
TAGATAATTGGGGTGATGCAACAAACATATTTATGGGTTTAT
Found at i:14380 original size:2 final size:2
Alignment explanation
Indices: 14373--14414 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14363 AGGAAGAATT
14373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.