Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006207.1 Corchorus olitorius cultivar O-4 contig06232, 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, 853
Length: 1423
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Found at i:512 original size:6 final size:6
Alignment explanation
Indices: 503--560 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
493 TAGTAATATC
*
503 TTACTA TTACT- TT--TA TTATTA TTACTA TTACTA TTACTA TTACT-
1 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA
547 TTACTA TATACTA T
1 TTACTA T-TACTA T
561 ATAAAACGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 7 0.15
6 30 0.65
7 6 0.13
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (6 bp):
TTACTA
Found at i:529 original size:21 final size:22
Alignment explanation
Indices: 502--560 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
492 ATAGTAATAT
* *
502 CTTACTATTACTTTTATTATTA
1 CTTACTATTACTATTACTATTA
524 -TTACTATTACTATTACTATTA
1 CTTACTATTACTATTACTATTA
545 CTTTACTATATACTAT
1 C-TTACTAT-TACTAT
561 ATAAAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 19 0.59
23 7 0.22
24 6 0.19
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (22 bp):
CTTACTATTACTATTACTATTA
Found at i:601 original size:23 final size:22
Alignment explanation
Indices: 575--650 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 22
565 AACGAATTCA
575 AAAATCTTAATTAGTCAATTACT
1 AAAATCTTAATTAGTCAATTA-T
* *
598 AAAATACCCTTAA-TA-TTATAGTAT
1 AAAAT---CTTAATTAGTCA-ATTAT
622 AAAAATCTTAATTAGTCAATTATT
1 -AAAATCTTAATTAGTCAATTA-T
646 AAAAT
1 AAAAT
651 ACCCTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
22 5 0.12
23 15 0.37
24 6 0.15
25 10 0.24
26 5 0.12
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATCTTAATTAGTCAATTAT
Found at i:610 original size:26 final size:25
Alignment explanation
Indices: 580--659 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 25
570 ATTCAAAAAT
580 CTTAATTAGTCAATTACTAAAATACC
1 CTTAATTAGTCAATTA-TAAAATACC
* * *
606 CTTAA-TA-TTATAGTATAAAA-A-T
1 CTTAATTAGTCA-ATTATAAAATACC
628 CTTAATTAGTCAATTATTAAAATACC
1 CTTAATTAGTCAATTA-TAAAATACC
654 CTTAAT
1 CTTAAT
660 ATTATAGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 5 0.12
23 6 0.14
24 14 0.33
25 6 0.14
26 11 0.26
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (25 bp):
CTTAATTAGTCAATTATAAAATACC
Found at i:627 original size:48 final size:48
Alignment explanation
Indices: 574--671 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
564 AAACGAATTC
574 AAAAATCTTAATTAGTCAATTACTAAAATACCCTTAATATTATAGTAT
1 AAAAATCTTAATTAGTCAATTACTAAAATACCCTTAATATTATAGTAT
*
622 AAAAATCTTAATTAGTCAATTATTAAAATACCCTTAATATTATAGTAT
1 AAAAATCTTAATTAGTCAATTACTAAAATACCCTTAATATTATAGTAT
670 AA
1 AA
672 TAATTTTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (48 bp):
AAAAATCTTAATTAGTCAATTACTAAAATACCCTTAATATTATAGTAT
Found at i:1022 original size:14 final size:17
Alignment explanation
Indices: 983--1017 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
973 ATTATAAGTA
*
983 TTAATTTTAACTTTTTT
1 TTAATATTAACTTTTTT
1000 TTAATATTAACTTTTTT
1 TTAATATTAACTTTTTT
1017 T
1 T
1018 AATTATGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATATTAACTTTTTT
Found at i:1078 original size:14 final size:14
Alignment explanation
Indices: 1059--1085 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1049 ATTTTAATTA
1059 ATAATTTATTTTTC
1 ATAATTTATTTTTC
1073 ATAATTTATTTTT
1 ATAATTTATTTTT
1086 TATTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATAATTTATTTTTC
Found at i:1083 original size:18 final size:18
Alignment explanation
Indices: 1062--1118 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1052 TTAATTAATA
1062 ATTTATTT-TTCATAATTT
1 ATTTATTTATT-ATAATTT
*
1080 ATTT-TTTATTTATAATAT
1 ATTTATTTA-TTATAATTT
1098 ATTTATTTATT-TAATTT
1 ATTTATTTATTATAATTT
1115 ATTT
1 ATTT
1119 CAGATTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 12 0.35
18 16 0.47
19 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTATTTATTATAATTT
Done.