Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015840.1 Corchorus capsularis cultivar CVL-1 contig15861, 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: 5589
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Found at i:3241 original size:78 final size:77
Alignment explanation
Indices: 3159--3397 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
3149 TTTTTTTAAC
* *
3159 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATTTTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
3224 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
3237 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
3302 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
3315 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
3373 TTTTTAGTTGAG
66 TTTTTAGTTGAG
3385 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
3398 ACCTAAACAA
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 87 0.56
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:3356 original size:70 final size:70
Alignment explanation
Indices: 3243--3397 Score: 240
Period size: 70 Copynumber: 2.2 Consensus size: 70
3233 TGAGTAAAAT
* * * * *
3243 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
3308 AGTTG
66 AGTTG
*
3313 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
3378 AGTTG
66 AGTTG
3383 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
3398 ACCTAAACAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
70 76 0.97
71 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:4051 original size:26 final size:26
Alignment explanation
Indices: 4018--4082 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
4008 ATTTTCAACC
4018 AAATCAATTAATTAATT-AAATACAAA
1 AAATCAATTAATTAATTCAAATA-AAA
* *
4044 AAATCAATTAATTAATTCCAATTAAAC
1 AAATCAATTAATTAATT-CAAATAAAA
4071 AAATCAATTAAT
1 AAATCAATTAAT
4083 CGCCCCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 17 0.49
27 14 0.40
28 4 0.11
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATCAATTAATTAATTCAAATAAAA
Found at i:5506 original size:190 final size:191
Alignment explanation
Indices: 5052--5589 Score: 704
Period size: 193 Copynumber: 2.8 Consensus size: 191
5042 AAACAAAAAG
* * *
5052 CCGCTTATGGAGTCCAAAATTTACACTTA-ATGTGTATTGTATAATAATCCTATAAGAAAAATTC
1 CCGCTTATGGAGTCCAAAATTTACACTGACA-GTTTATTGTATAATAATCCTATAAGAAAAATTA
* * * * * *
5116 TACTATACACCGTCAATCGAATTTAGCAGACTGCACATGCGGGGTTTAAGGGTTTACATGTGTCT
65 TACTAT--ACCGT-AATGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTAACATGTGTCC
* * *
5181 CATTAAGGAATATGTATTAATATTAAATATTTTGATTATGAAATGAGATATGTGTCAACTTCTTA
127 CCTTAAGGAATATGTATTAATATTAAATATTTTAATTATGAAATGAGATA--TCTCAACTTCTTA
5246 AC
190 AC
* * * *
5248 CCGCTTATGGAATTCAAAATTTACACTGACAATTTATTGTATAATAATCCTATAAGAAAAAGTAT
1 CCGCTTATGGAGTCCAAAATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTAT
* * * *
5313 ACTAT-GCGTAAGTGGAGTTTAGCAGACTGCACGTACAGGGCTTAAGGGTTAATATGTGTCCCCT
66 ACTATACCGTAA-TGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTAACATGTGTCCCCT
* *
5377 TAAGGAATATGTATTAATATTAAATATTTTAATTATGAAATTAGGTA-CTCAACTTCTTAAC
130 TAAGGAATATGTATTAATATTAAATATTTTAATTATGAAATGAGATATCTCAACTTCTTAAC
* *
5438 TCGCTTATGGAGTCCAAAATTTATACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTAT
1 CCGCTTATGGAGTCCAAAATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTAT
* * *
5503 ACTATACACCATAAATGGAGTTTAGCAGACTGCACGTGCAGGGTTTGAGGGTTGACATGTGTCCC
66 ACTAT--ACCGT-AATGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTAACATGTGTCCC
*
5568 CATTAGGGAATATGTATTAATA
128 C-TTAAGGAATATGTATTAATA
Statistics
Matches: 299, Mismatches: 36, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
190 77 0.26
192 2 0.01
193 137 0.46
194 21 0.07
196 61 0.20
197 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (191 bp):
CCGCTTATGGAGTCCAAAATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTAT
ACTATACCGTAATGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTAACATGTGTCCCCTT
AAGGAATATGTATTAATATTAAATATTTTAATTATGAAATGAGATATCTCAACTTCTTAAC
Done.