Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007307.1 Corchorus capsularis cultivar CVL-1 contig07328, 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: 28541
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2896 original size:51 final size:52
Alignment explanation
Indices: 2836--2935 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
2826 ATCTTTAATT
*
2836 AGAGAATGTGCAAATACA-TTGACTTT-CCTATTTATAAATTGAAATACAAAA
1 AGAGAATGTGCAAATACATTTG-CTTTCCCTATTTACAAATTGAAATACAAAA
*
2887 AGAGAATGTGCAAATACATTTGGTTTCCCTATTTACAAATTGAAATACA
1 AGAGAATGTGCAAATACATTTGCTTTCCCTATTTACAAATTGAAATACA
2936 GAAATCAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 21 0.47
52 24 0.53
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (52 bp):
AGAGAATGTGCAAATACATTTGCTTTCCCTATTTACAAATTGAAATACAAAA
Found at i:7393 original size:21 final size:21
Alignment explanation
Indices: 7369--7408 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7359 CGAAATTATT
7369 AAATAATAATAATTATTTCGA
1 AAATAATAATAATTATTTCGA
* *
7390 AAATAATTATTATTATTTC
1 AAATAATAATAATTATTTC
7409 CCCATATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
AAATAATAATAATTATTTCGA
Found at i:14012 original size:21 final size:21
Alignment explanation
Indices: 13974--14014 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13964 CCTTGGCTTA
*
13974 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
13995 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
14015 GCCTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:16019 original size:53 final size:53
Alignment explanation
Indices: 15956--16116 Score: 148
Period size: 53 Copynumber: 3.2 Consensus size: 53
15946 TGGTCAAAAG
15956 AAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATA
1 AAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATA
* * ** * * **
16009 AAAAGAAATTA---GCAATATG--T-T---TAA-TTTTAGATTTA-ATCCAA-A
1 AAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCA-ATTTAGGTGTAATA
16051 GAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATA
1 -AAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATA
16105 AAAAGAAATTAG
1 AAAAGAAATTAG
16117 CAATATGTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 28
0.64 0.13 0.23
Matches are distributed among these distances:
42 1 0.01
43 16 0.21
44 7 0.09
46 7 0.09
47 1 0.01
48 2 0.03
49 1 0.01
50 7 0.09
52 7 0.09
53 28 0.36
54 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (53 bp):
AAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATA
Found at i:16116 original size:96 final size:96
Alignment explanation
Indices: 15952--16140 Score: 378
Period size: 96 Copynumber: 2.0 Consensus size: 96
15942 TTTTTGGTCA
15952 AAAGAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATAAAAAGAAA
1 AAAGAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATAAAAAGAAA
16017 TTAGCAATATGTTTAATTTTAGATTTAATCC
66 TTAGCAATATGTTTAATTTTAGATTTAATCC
16048 AAAGAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATAAAAAGAAA
1 AAAGAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATAAAAAGAAA
16113 TTAGCAATATGTTTAATTTTAGATTTAA
66 TTAGCAATATGTTTAATTTTAGATTTAA
16141 GATTCTTAGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (96 bp):
AAAGAAAAGAAATTAGGTGTAATATGACTATGAAGAACCATCAATTTAGGTGTAATAAAAAGAAA
TTAGCAATATGTTTAATTTTAGATTTAATCC
Found at i:21279 original size:2 final size:2
Alignment explanation
Indices: 21261--21309 Score: 80
Period size: 2 Copynumber: 23.5 Consensus size: 2
21251 CTCTTTATCT
21261 TA TA TCA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21305 TA TA T
1 TA TA T
21310 TTAAAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 41 0.91
3 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22703 original size:2 final size:2
Alignment explanation
Indices: 22691--22725 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
22681 TCAATCAATC
22691 AT AT CAT AT 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
22726 TAAAACTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22816 original size:10 final size:11
Alignment explanation
Indices: 22801--22829 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
22791 AATTACTTTG
22801 ATCAATTA-AA
1 ATCAATTACAA
22811 ATCAATTACAA
1 ATCAATTACAA
22822 ATCAATTA
1 ATCAATTA
22830 TTACAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (11 bp):
ATCAATTACAA
Found at i:24183 original size:24 final size:25
Alignment explanation
Indices: 24147--24199 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
24137 AATTCAACTA
24147 ATGTATCGATATGATTATTA-AAAC
1 ATGTATCGATATGATTATTATAAAC
* *
24171 ATGTATCGGTATGATTATTATTAAC
1 ATGTATCGATATGATTATTATAAAC
24196 ATGT
1 ATGT
24200 CTTCTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.42
Consensus pattern (25 bp):
ATGTATCGATATGATTATTATAAAC
Found at i:24856 original size:16 final size:16
Alignment explanation
Indices: 24835--24865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24825 TTGAAAAATA
24835 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
24851 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
24866 AATATGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:26192 original size:400 final size:394
Alignment explanation
Indices: 25452--26192 Score: 1160
Period size: 400 Copynumber: 1.9 Consensus size: 394
25442 ATTTCATAAT
*
25452 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAATCCTACA
1 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAATCCCACA
* * * *
25517 TGTGCAGTTTGCTAAAATCCACTGACGGGTATTTGTATAATTTTTCTTATAGAATTATTATATAA
66 CGTGCAGTCTGCTAAAATCCACTGACGGGTATTTGTATAAATTTTCTTATAGAATTATTATACAA
* *
25582 TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAATACACACCCCATTTCA
131 TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACACAACCCATTTCA
*
25647 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
196 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
* *** *
25712 CCCGCACGTGCAGTCTGCTAAACTCCACTGATGGTGTATTATATAAATTTTCTTATAAGATTATT
261 CCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTATAAGATAATT
*
25777 ATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAACGGGTTAAGAAGTTGACATATCCCAT
326 ATACAATAAACTGTCAGTGTAAATTTTGGACTCCAAAAACGGGTTAAGAAGTTGACATATCCCAT
25842 TTCA
391 TTCA
* * *
25846 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAA--T----
* * * *
25911 CCCGCACGTGCAGTCTGCTAAACTCCATTGACGGTGTA-TTGTATAAATTTTCTTATAGGATTAT
60 CCCACACGTGCAGTCTGCTAAAATCCACTGACGG-GTATTTGTATAAATTTTCTTATAGAATTAT
* *
25975 TATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATC
124 TATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACACAACC
26040 CATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAA
189 CATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAA
* * * * *
26105 GTTAAACCCCGCACATGCAGTCTGCTAAACTCTACTGACAATGTATTGTATAATTTTTCTTATAG
254 CTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTATAA
26170 GATAATTATACAATAAACTGTCA
319 GATAATTATACAATAAACTGTCA
26193 AATTAAATTT
Statistics
Matches: 312, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
394 55 0.18
396 1 0.00
400 253 0.81
401 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (394 bp):
TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAATCCCACA
CGTGCAGTCTGCTAAAATCCACTGACGGGTATTTGTATAAATTTTCTTATAGAATTATTATACAA
TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACACAACCCATTTCA
TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
CCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTATAAGATAATT
ATACAATAAACTGTCAGTGTAAATTTTGGACTCCAAAAACGGGTTAAGAAGTTGACATATCCCAT
TTCA
Found at i:26213 original size:201 final size:201
Alignment explanation
Indices: 25452--26192 Score: 1115
Period size: 201 Copynumber: 3.7 Consensus size: 201
25442 ATTTCATAAT
* *
25452 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAA--T----
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
** * * * * *
25511 CCTACATGTGCAGTTTGCTAAAATCCACTGACGG-GTATTTGTATAATTTTTCTTATAGAATTAT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-TTGTATAAATTTTCTTATAGGATTAT
* * * **
25575 TATATAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAATACACACCC
130 TATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATC
25640 CATTTCA
195 CATTTCA
* *
25647 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
* * *
25712 CCCGCACGTGCAGTCTGCTAAACTCCACTGATGGTGTATTATATAAATTTTCTTATAAGATTATT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
* * *
25777 ATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAACGGGTTAAGAAGTT--GACAT-ATCC
131 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAAT-C
25839 CATTTCA
195 CATTTCA
*
25846 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
*
25911 CCCGCACGTGCAGTCTGCTAAACTCCATTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
25976 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATCC
131 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATCC
26041 ATTTCA
196 ATTTCA
26047 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
* * ** * *
26112 CCCGCACATGCAGTCTGCTAAACTCTACTGACAATGTATTGTATAATTTTTCTTATAGGATAATT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
*
26177 ATACAATAAACTGTCA
131 ATACAATACACTGTCA
26193 AATTAAATTT
Statistics
Matches: 498, Mismatches: 37, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
195 55 0.11
197 1 0.00
199 187 0.38
201 250 0.50
202 5 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (201 bp):
TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATCC
ATTTCA
Found at i:26272 original size:21 final size:21
Alignment explanation
Indices: 26248--26296 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
26238 CTTGTGAAGA
*
26248 TTTTTAGT-AACCTTATTAATC
1 TTTTTAATAAACCTTATT-ATC
*
26269 TTTTTAATAAACCTTATTATT
1 TTTTTAATAAACCTTATTATC
26290 TTTTTAA
1 TTTTTAA
26297 AAAAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTTAATAAACCTTATTATC
Found at i:26406 original size:22 final size:23
Alignment explanation
Indices: 26377--26430 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
26367 GATTGCTAAG
*
26377 TTTATTAGCAACGTTACTAAA-TT
1 TTTATTAGCAACCTTAC-AAACTT
*
26400 TTT-TTAGTAACCTTACAAACTT
1 TTTATTAGCAACCTTACAAACTT
26422 TTTATTAGC
1 TTTATTAGC
26431 TTGTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.46
Consensus pattern (23 bp):
TTTATTAGCAACCTTACAAACTT
Done.