Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011560.1 Corchorus capsularis cultivar CVL-1 contig11581, 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: 8517
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
*
1 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 TTAAAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294 original size:23 final size:24
Alignment explanation
Indices: 1268--1315 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1258 TAAGGATGAG
1268 AAATAATTTATGAAT-AATTT-TTA
1 AAATAA-TTATGAATAAATTTCTTA
*
1291 AAATAATTATTAATAAATTTCTTA
1 AAATAATTATGAATAAATTTCTTA
1315 A
1 A
1316 CAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 11 0.50
24 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATAATTATGAATAAATTTCTTA
Found at i:5311 original size:98 final size:98
Alignment explanation
Indices: 5202--5390 Score: 360
Period size: 98 Copynumber: 1.9 Consensus size: 98
5192 AGTTTTAATG
*
5202 TAAAACCTACATTATTTTTTGTAATGTTACCTTGATTTGTTAAATTATGCAGTAAAGCAAAATTT
1 TAAAACCTACATTATTTTTTGTAATGTAACCTTGATTTGTTAAATTATGCAGTAAAGCAAAATTT
5267 CCAAGGAAGAGCAATTACTAATTTTAATGTAAA
66 CCAAGGAAGAGCAATTACTAATTTTAATGTAAA
5300 TAAAACCTACATTATTTTTTGTAATGTAACCTTGATTTGTTAAATTATGCAGTAAAGCAAAATTT
1 TAAAACCTACATTATTTTTTGTAATGTAACCTTGATTTGTTAAATTATGCAGTAAAGCAAAATTT
*
5365 CCAAGGAAGAGCGATTACTAATTTTA
66 CCAAGGAAGAGCAATTACTAATTTTA
5391 GGTAACATTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (98 bp):
TAAAACCTACATTATTTTTTGTAATGTAACCTTGATTTGTTAAATTATGCAGTAAAGCAAAATTT
CCAAGGAAGAGCAATTACTAATTTTAATGTAAA
Found at i:6011 original size:202 final size:197
Alignment explanation
Indices: 5527--6483 Score: 1060
Period size: 200 Copynumber: 4.9 Consensus size: 197
5517 ATATTATATT
* * *
5527 GTCAGTGGAGTTTAGCAGCCTGCACGTGCGGGGTTTAAGGGTTGATATATGT-CCCATTAGGGAA
1 GTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGTTTAAGGGTTGACATGTGTACCC-TTAGGGAA
* * *
5591 TATGTATTAATATTAAATATTTAATTAATTTTGAAATGTGATATGTG------TC---ACCCGCT
64 TATGTATTAATATTAAATATTT-ATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCT
* * *
5647 TAT-GACGTCTAAAATTTACGCTGACAATGTATTGTATAATAATCCTATAA-AAAAATTATACAA
128 TATGGA-GTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAA
5710 TACACC
192 TACACC
* * * *
5716 TTTAGTGGAGTTTAGCAGACTGCAAGTGCTGGGTTTAAGAGTTGACATGTGTA-CCTTAGGGAAT
1 GTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGTTTAAGGGTTGACATGTGTACCCTTAGGGAAT
* *
5780 ATATATTAATATTAAATA--T-TTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGTTTA
65 ATGTATTAATATTAAATATTTATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTA
* * *
5842 TGGAGTCCAAAATTCACACTGACAGTGTATTGTATAATAATCCCTATAAGAAAATTTATATAATA
130 TGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAAT-CCTATAAGAAAAATTATACAATA
5907 CACC
194 CACC
*
5911 GTCAGTGGAGTTTAGCAGACTGCACGTGCGGGATTTAACTTTAAGGGTTGACATATGTACCCTTA
1 GTCAGTGGAGTTTAGCAGACTGCACGTGCGGG-------TTTAAGGGTTGACATGTGTACCCTTA
*
5976 GGGAATATGTATTAATA-TAAA-ATTT-TTAATTATGAAATGGGGTATGTGTCAACTTCTTAACC
59 GGGAATATGTATTAATATTAAATATTTATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACC
* * * * * *
6038 CGTTTATGAAGAT-CAAAATTTGCATTGACAGTGTATTATATAATAATTCTATAAGAAAAATTAT
124 CGCTTATGGAG-TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTAT
6102 ACAATAC-CC
188 ACAATACACC
* * * * * * * * *
6111 GTTAGTAGATTTTAGCAGACTGAACGTGCAAGATTTAAGAGTTGACATGTGTCCCCTTTGGGAAT
1 GTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGTTTAAGGGTTGACATGTGTACCCTTAGGGAAT
* * *
6176 ATGTATTAATATTAAATATTTAATTAATTATGAAAT-AGGGTATGTGTCAACTTTTTAACCCACG
65 ATGTATTAATATTAAATATTT-ATTAATTATGAAATGA-GGTATGTGTCAACTTCTTAACCCGCT
* * *
6240 TATGGAATCCAAAATTTACACTGACAGTGTATTGTATAATAATCATATAAAAAAAATTATACAAT
128 TATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAAT
*
6305 ACACT
193 ACACC
* * * * ** * * *
6310 ATCAATGGAGTTTAGCAGATTGCACACATG-GGGTTTTTGGGGTTTACATGTATCCCCTTAGGGA
1 GTCAGTGGAGTTTAGCAGACTG--CACGTGCGGG-TTTAAGGGTTGACATGTGTACCCTTAGGGA
* * *
6374 ATATGTATTAATATTAAATATTTAATTAATCATGAAATGGGGTATGTGTCAATTTCTTAACCCGC
63 ATATGTATTAATATTAAATATTT-ATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGC
*
6439 TTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAAGTAAT
127 TTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA-TAAT
6484 TTTTATTATA
Statistics
Matches: 649, Mismatches: 82, Indels: 62
0.82 0.10 0.08
Matches are distributed among these distances:
184 20 0.03
186 1 0.00
188 26 0.04
189 46 0.07
190 2 0.00
193 42 0.06
194 51 0.08
195 47 0.07
196 4 0.01
197 1 0.00
198 92 0.14
199 18 0.03
200 148 0.23
201 52 0.08
202 98 0.15
203 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (197 bp):
GTCAGTGGAGTTTAGCAGACTGCACGTGCGGGTTTAAGGGTTGACATGTGTACCCTTAGGGAATA
TGTATTAATATTAAATATTTATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTAT
GGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATACA
CC
Found at i:7141 original size:32 final size:32
Alignment explanation
Indices: 7102--7162 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
7092 ACATGTGTCC
7102 TTATTAATATTAAAAAATCTTATATATATGTA
1 TTATTAATATTAAAAAATCTTATATATATGTA
7134 TTATTAATATTAAAAAATCTTATATATAT
1 TTATTAATATTAAAAAATCTTATATATAT
7163 ATTATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (32 bp):
TTATTAATATTAAAAAATCTTATATATATGTA
Found at i:7482 original size:14 final size:15
Alignment explanation
Indices: 7463--7497 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
7453 CCATATTATC
7463 ATATAATAA-TAATT
1 ATATAATAATTAATT
*
7477 ATATAATAATTGATT
1 ATATAATAATTAATT
7492 ATATAA
1 ATATAA
7498 ATCAAGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATATAATAATTAATT
Found at i:8402 original size:2 final size:2
Alignment explanation
Indices: 8395--8420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8385 TGATTAAAAG
8395 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
8421 ATTTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.