Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013108.1 Corchorus olitorius cultivar O-4 contig13141, 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: 18036
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:5417 original size:77 final size:78
Alignment explanation
Indices: 5285--5442 Score: 196
Period size: 77 Copynumber: 2.0 Consensus size: 78
5275 CTTCATCATA
* * * *
5285 GACAGGATTTCTACGAACATGTTCAGGTCTTTCAATAGGGCCACCACGAGGCATCTCCACCCCTG
1 GACAGGATTTCTACAAACATGTACAGGTCTTTCAATAGGACCACCACGAGCCATCTCCACCCCTG
5350 -CTTTCT-ATTGTC
66 TCTTT-TGATTGTC
* * * * *
5362 GACAGGATTTCTGCAAACA-GATACAGGTTTTTCAATAGGACTACCATGAGCCATCTCCACCCTT
1 GACAGGATTTCTACAAACATG-TACAGGTCTTTCAATAGGACCACCACGAGCCATCTCCACCCCT
5426 GTCTTTTGATTGTC
65 GTCTTTTGATTGTC
5440 GAC
1 GAC
5443 TTGTCTCCTG
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
76 1 0.01
77 55 0.80
78 13 0.19
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (78 bp):
GACAGGATTTCTACAAACATGTACAGGTCTTTCAATAGGACCACCACGAGCCATCTCCACCCCTG
TCTTTTGATTGTC
Found at i:5875 original size:25 final size:26
Alignment explanation
Indices: 5836--5891 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
5826 AGTACTAAAC
*
5836 AAAATAAAATACTAAAGTCTAATAAT
1 AAAATAAAATACTAAAATCTAATAAT
* * *
5862 AAAATAAAGT-CTAAAATGTAATTAT
1 AAAATAAAATACTAAAATCTAATAAT
5887 AAAAT
1 AAAAT
5892 CCAACCAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
AAAATAAAATACTAAAATCTAATAAT
Found at i:9659 original size:18 final size:18
Alignment explanation
Indices: 9636--9672 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9626 TACATTTTGT
*
9636 ACAAGCCTTGTGGTATTG
1 ACAAGCCTTATGGTATTG
9654 ACAAGCCTTATGGTATTG
1 ACAAGCCTTATGGTATTG
9672 A
1 A
9673 AACCACATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (18 bp):
ACAAGCCTTATGGTATTG
Found at i:10902 original size:2 final size:2
Alignment explanation
Indices: 10895--10919 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10885 TCAGATAAAT
10895 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10920 GTATCGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11204 original size:115 final size:116
Alignment explanation
Indices: 10998--11221 Score: 344
Period size: 115 Copynumber: 1.9 Consensus size: 116
10988 AGAAGTCTCA
* *
10998 TTACAATCAGATTTCTCTCTATATTCACAAACAATCCAATAAAAAATCACAAATACAAACTACGT
1 TTACAATCAGATATCTCTCTATATGCACAAACAATCCAATAAAAAATCACAAATACAAACTACGT
* *
11063 CCCATGGTCGAACATACCGTGAAACTTTAGGTGAAATTCATTTTGAATCGC
66 CCCATGATCGAACATACCGTGAAACTTTAGGTCAAATTCATTTTGAATCGC
* * *
11114 TTACAATTAGATATCTCTCTATATGCTCAAACAATCCAAT-AAAAATCACAAATACAAACTATGT
1 TTACAATCAGATATCTCTCTATATGCACAAACAATCCAATAAAAAATCACAAATACAAACTACGT
* *
11178 -CCACTGATCGGACATACCTTGAAACTTTAGGTCAAATTCATTTT
66 CCCA-TGATCGAACATACCGTGAAACTTTAGGTCAAATTCATTTT
11222 CCGATCATGT
Statistics
Matches: 98, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
114 3 0.03
115 59 0.60
116 36 0.37
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (116 bp):
TTACAATCAGATATCTCTCTATATGCACAAACAATCCAATAAAAAATCACAAATACAAACTACGT
CCCATGATCGAACATACCGTGAAACTTTAGGTCAAATTCATTTTGAATCGC
Found at i:11855 original size:23 final size:22
Alignment explanation
Indices: 11829--11871 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11819 TTTAATACAA
11829 TTTTTAAAGTAAATAAAAAATAG
1 TTTTTAAAG-AAATAAAAAATAG
* *
11852 TTTTTGAAGGAATAAAAAAT
1 TTTTTAAAGAAATAAAAAAT
11872 GGTTGGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
TTTTTAAAGAAATAAAAAATAG
Found at i:12217 original size:22 final size:22
Alignment explanation
Indices: 12177--12218 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12167 AAATGAAACG
*
12177 AGAGAGAACGAGAAAGAAAATT
1 AGAGAGAAAGAGAAAGAAAATT
* *
12199 AGAGAGAAAGCGAAGGAAAA
1 AGAGAGAAAGAGAAAGAAAA
12219 CGAGAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.31, T:0.05
Consensus pattern (22 bp):
AGAGAGAAAGAGAAAGAAAATT
Done.