Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019017.1 Corchorus olitorius cultivar O-4 contig19050, 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: 4499
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:590 original size:21 final size:21
Alignment explanation
Indices: 561--600 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
551 CCACTAATAA
*
561 TAATTATTATAATAATAAGTT
1 TAATAATTATAATAATAAGTT
*
582 TAATAATTATAATATTAAG
1 TAATAATTATAATAATAAG
601 ATGTTTAACG
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:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TAATAATTATAATAATAAGTT
Found at i:599 original size:15 final size:16
Alignment explanation
Indices: 555--599 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
545 TACATACCAC
*
555 TAATAATAATTATT-A
1 TAATAATAAGTATTAA
570 TAATAATAAGT-TTAA
1 TAATAATAAGTATTAA
*
585 TAATTATAA-TATTAA
1 TAATAATAAGTATTAA
600 GATGTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATAATAAGTATTAA
Found at i:606 original size:24 final size:24
Alignment explanation
Indices: 558--608 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
548 ATACCACTAA
* *
558 TAATAATTATTATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
582 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
606 TAA
1 TAA
609 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:889 original size:2 final size:2
Alignment explanation
Indices: 877--957 Score: 90
Period size: 2 Copynumber: 40.0 Consensus size: 2
867 AGTTTAGACT
* * * * *
877 TA TA TA GTA TA TA GA TA TA GA TA TA GA TA TA GA TA TA TA TA AA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
920 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
958 AAACCATAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
2 62 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3123 original size:105 final size:104
Alignment explanation
Indices: 2953--3162 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 104
2943 ACTATCTTAC
* * *
2953 TACTATATAAAATCACGAACTCAAAAATTTTAATTGGGAAATTTCTAAAATACCTTTAGTGTTAT
1 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATA-CTTTAGTATTAT
*
3018 AGTATAATAATTTTTTAATTAATATTCTTATTAGTTATTA
65 AGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
*
3058 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAAT-TTTCTCAGTATTA
1 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATACTT-T-AGTATTA
*
3122 TAGTATAATAATTTTTTAATTAATATTCTTTTTAGTCATTA
64 TAGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
3163 AATTTTTTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
103 2 0.02
104 1 0.01
105 94 0.97
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (104 bp):
TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATACTTTAGTATTATA
GTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
Found at i:3586 original size:120 final size:118
Alignment explanation
Indices: 3375--3724 Score: 536
Period size: 120 Copynumber: 3.0 Consensus size: 118
3365 TGGAAGAATA
* *
3375 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTC-ATTTTTCCATTTCAAACCA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCC-TCAAATTTTCCACTTCAAACCA
*
3439 ACTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAAGGC
65 ACTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC
3493 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCTCAAGTCCTCAAATTTTCCACTTCAAACC
1 TCCACCACAACCATGAATATTGTTTTGAGGAA-TT-TCAAGTCCTCAAATTTTCCACTTCAAACC
*
3558 AACTCTTCC-ATAAAAAATAGTATAAATTACTCCTTAATTCTTAGGT-TCCAAACGC
64 AACTCTTCCAAT-AAAAATAGTATAAATTACTCCTTAATTCTTAGATCT-CAAACGC
*
3613 TCCACCACAACCATGAATATTGTTTTGAGG-----CAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTCAAATTTTCCACTTCAAACCAA
* *
3673 CTCTTCCAATAAAAATAGTATAAATTACTCCCTAATTCTTAGATCCCAAACG
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACG
3725 TGTTAACAAT
Statistics
Matches: 217, Mismatches: 8, Indels: 19
0.89 0.03 0.08
Matches are distributed among these distances:
113 74 0.34
114 2 0.01
118 32 0.15
119 7 0.03
120 102 0.47
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.33
Consensus pattern (118 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTCAAATTTTCCACTTCAAACCAA
CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC
Done.