Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005641.1 Corchorus capsularis cultivar CVL-1 contig05659, 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: 10200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1126 original size:154 final size:152
Alignment explanation
Indices: 950--1479 Score: 572
Period size: 155 Copynumber: 3.4 Consensus size: 152
940 GACTTAAGAC
* * * *
950 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGGGGTGAGAAACC-ACTTCACCATGATA
1 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTTCACCATCA-A
* *
1014 -GGAGTTCGGTTTTACTTAGAATTTTTTCCATAAGT-TTGTGGAGATAATCTAAGTCTCTTGGCC
65 GGGAGCTCGGTTTTACTTAGAATTTTTTCCAT-AGTCTTATGGAGATAATCTAAGTCTCTTGG--
* * * **
1077 AAGTTTCACCTAAAACAGACTTAGAAT
127 AA-ATTCAGCTCATTCAGACTTAGAAT
* * * ** * * *
1104 GAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATCTGAGGTGTGAAGTC-GGTTCACTACCAAG
1 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTTCACCATCAAG
* *
1168 GGAAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATGGAAAGAATCTAA-TCCTACTGGTG
66 GG-AGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGT-CT-CT--TG
* *
1232 GAAAATCAGCTCATTTAGACTTAGAAT
126 GAAATTCAGCTCATTCAGACTTAGAAT
* **
1259 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGTG-GAAACCTAGTTCACCATCAAG
1 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTTCACCATCAAG
* * *
1323 GAGAGCTCGGTTTTACTTA-ATATTTTTTTCATAGTCTTATGTG-GATATTCTAAGTCCCTTGGA
66 G-GAGCTCGGTTTTACTTAGA-ATTTTTTCCATAGTCTTATG-GAGATAATCTAAGTCTCTTGG-
1386 AAAAATTCAGCTCATTCAGACTTAGAAT
127 --AAATTCAGCTCATTCAGACTTAGAAT
* * *
1414 GAAAAACTTATGCTAGTTTCTCATTTAAAGACAATTTGGGGTGTGAAACCTAGTTCACCATGAAG
1 GAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTTCACCATCAAG
1479 G
66 G
1480 AGGGCTCGAA
Statistics
Matches: 313, Mismatches: 47, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
152 3 0.01
153 1 0.00
154 63 0.20
155 215 0.69
156 28 0.09
158 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (152 bp):
GAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTTCACCATCAAG
GGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGTCTCTTGGAAAT
TCAGCTCATTCAGACTTAGAAT
Found at i:5805 original size:156 final size:156
Alignment explanation
Indices: 5525--5805 Score: 352
Period size: 156 Copynumber: 1.8 Consensus size: 156
5515 TAGTGGAAAA
5525 TCAGCTCATTCAGACTCAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGT
1 TCAGCTCATTCAGACTCAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGT
**** ** ** *
5590 GGAAACCTAGTTCAACATCAAGGAGAGCTCTGTTTTACTTAGAATTTTTTCCATAGTCTTATGTG
66 GGAAACCTAGTTCAACATCAAGGAGAGCTCTGAACAACCAAGAATTTTTAACACAGTCTTATGTG
5655 TATATTCTATGTCCCTTGGAAAAATT
131 TATATTCTATGTCCCTTGGAAAAATT
* * **
5681 TCAGCTCATTCATACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAA-TTTGGGGT
1 TCAGCTCATTCAGACTCAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGT
* * * * *
5745 GTGAAACCTAGTTCACCATGAAGGGGGGCTC-GAAACAACCCAAG-ATTTTTAACACGGTCTT
66 G-GAAACCTAGTTCAACATCAAGGAGAGCTCTG-AACAA-CCAAGAATTTTTAACACAGTCTT
5806 TGGATGATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
155 8 0.08
156 93 0.89
157 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (156 bp):
TCAGCTCATTCAGACTCAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGT
GGAAACCTAGTTCAACATCAAGGAGAGCTCTGAACAACCAAGAATTTTTAACACAGTCTTATGTG
TATATTCTATGTCCCTTGGAAAAATT
Found at i:6318 original size:21 final size:21
Alignment explanation
Indices: 6284--6324 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6274 GAAGAGTTTG
*
6284 CCTTCTTCAACAAGTAAAACA
1 CCTTCCTCAACAAGTAAAACA
*
6305 CCTTCCTCAGCAAGTAAAAC
1 CCTTCCTCAACAAGTAAAAC
6325 CCGCCAGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.22
Consensus pattern (21 bp):
CCTTCCTCAACAAGTAAAACA
Found at i:6510 original size:18 final size:19
Alignment explanation
Indices: 6461--6511 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
6451 TCCGCTCCTT
6461 TTTCTCTTGTTCTTCACGA
1 TTTCTCTTGTTCTTCACGA
* *
6480 GTTCTTACTTGTTCTTCA-TA
1 TTTC-T-CTTGTTCTTCACGA
6500 TTTCTCTTGTTC
1 TTTCTCTTGTTC
6512 AATCTTGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 5 0.19
21 11 0.41
ACGTcount: A:0.10, C:0.24, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTCTCTTGTTCTTCACGA
Found at i:7979 original size:351 final size:342
Alignment explanation
Indices: 7309--8229 Score: 1205
Period size: 351 Copynumber: 2.6 Consensus size: 342
7299 TAAAAAAAAA
* *
7309 AGTAAATTTAATCATAATAGATAAAATTATAATAATAATATAAATTTTATTGAATAAATGATAA-
1 AGTAAATTTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAAT
*
7373 -T----T-TTAAAATTATAACAATGTGGATTT-AGCTGAATAAAACATAATTTTACTTTATAATA
66 TTAGAATGTTAAAATTATAACAATGTGGATTTGA-CTGAATAAAACATAATTTTAGTTTATAATA
* * *
7431 TTTTTGCGTCATTT-GGGTTAACTTCTCAGGTCATTCGGGTTACGAGTTTGTCGAGTCTGTATAT
130 TTATTGCGT-ATTTCGGGTTAACTTCTCGGGTCATTCGGGTTAC-A---AGTCG-GTCTG-ATAT
* * *
7495 GATAGGCTTGGAACGTTTACTTTTAT-TGGTCAAATAATAATTATTATTTATTTATTATGTAAAA
188 GACAGGTTTGGAACGTTTACTTTT-TCTGGTCAAATAATAATTATTATTTATTCATTATGTAAAA
* * * *
7559 AAATAAATTATTAATTATAAAGTTATCATAAATTATTCATATAACTTATTTAGTATTTATCCATA
252 AAACAAATTACTAATTATAAACTTATCATAAATTATTCATATAACTGATTTAGTATTTATCCATA
*
7624 TAATTATTATTCATATGATGAAGTTT
317 TAATTATTATTCATATAATGAAGTTT
* *
7650 AGTAAATTTAATTATAATAGGTAAAATTATAACAATAATATAAATTTTATTGGATAAATGATAAT
1 AGTAAATTTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAAT
* * *
7715 TTAGAATGGTTAAAATTATAACAATGTTGATTTGAATGAATAACACATAATTTTAGTTTATAATA
66 TTAGAAT-GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATA
* * * * *
7780 TTCTTGGGTATTTCGGGTTAACTTCTCGGGTTATTCAGATTACAAGTCAGGTCTAGATATGACAG
130 TTATTGCGTATTTCGGGTTAACTTCTCGGGTCATTCGGGTTACAAGTC-GGTCT-GATATGACAG
7845 GTTTGGAACGTTTACTTTTTCTGGTCAAATAATAATTAATATTTATATTTATTCATTATGTAAAA
193 GTTTGGAACGTTTACTTTTTCTGGTCAAATAATAA-T--TA--T-TATTTATTCATTATGTAAAA
* * *
7910 TAACAAATTACTAATTATAAACTTATTATAAATTATTCATATAACTGATTTAGTATTTATTCATA
252 AAACAAATTACTAATTATAAACTTATCATAAATTATTCATATAACTGATTTAGTATTTATCCATA
*
7975 TAATTATTGTTCATATAATGAAGTTT
317 TAATTATTATTCATATAATGAAGTTT
* *
8001 AGTAAATTTAATCATAATAGGTAAAATTATGACAATAACATAAATTTTATTGAATAAATGATAAT
1 AGTAAATTTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAAT
8066 TTAGAATAGTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATA
66 TTAGAAT-GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATA
** * * * *
8131 TTATTGTTTCTCTCGGGATAACTTCTCGAGTCATTCGGGTTACAAGTTTGTCGGGTCTGGATATG
130 TTATTGCGTATTTCGGGTTAACTTCTCGGGTCATTCGGGTTACAA----GTC-GGTCT-GATATG
* *
8196 ACGGGTTTGGATCGTTTACTTTTTCTGGTCAAAT
189 ACAGGTTTGGAACGTTTACTTTTTCTGGTCAAAT
8230 TGGGTTCAAC
Statistics
Matches: 508, Mismatches: 49, Indels: 32
0.86 0.08 0.05
Matches are distributed among these distances:
341 60 0.12
343 1 0.00
344 1 0.00
345 47 0.09
346 3 0.01
347 1 0.00
348 7 0.01
349 82 0.16
350 2 0.00
351 258 0.51
355 46 0.09
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (342 bp):
AGTAAATTTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAAT
TTAGAATGTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATAT
TATTGCGTATTTCGGGTTAACTTCTCGGGTCATTCGGGTTACAAGTCGGTCTGATATGACAGGTT
TGGAACGTTTACTTTTTCTGGTCAAATAATAATTATTATTTATTCATTATGTAAAAAAACAAATT
ACTAATTATAAACTTATCATAAATTATTCATATAACTGATTTAGTATTTATCCATATAATTATTA
TTCATATAATGAAGTTT
Done.