Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020282.1 Corchorus olitorius cultivar O-4 contig20315, 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: 79384
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1090 original size:24 final size:23
Alignment explanation
Indices: 1053--1098 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1043 CATGCCAAAT
*
1053 ATAAAAATAAAAAAAATAATTTA
1 ATAAAAAAAAAAAAAATAATTTA
1076 ATAAAAAAAATAAAAAATAATTT
1 ATAAAAAAAA-AAAAAATAATTT
1099 CTTATAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAAAAAAAAAAAAATAATTTA
Found at i:6468 original size:10 final size:10
Alignment explanation
Indices: 6439--6470 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
6429 CTGTTGGACA
6439 ACCGAAACCG
1 ACCGAAACCG
6449 ACCGACAACCG
1 ACCGA-AACCG
6460 ACCGAAACCG
1 ACCGAAACCG
6470 A
1 A
6471 TTTCAGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.41, C:0.41, G:0.19, T:0.00
Consensus pattern (10 bp):
ACCGAAACCG
Found at i:6819 original size:2 final size:2
Alignment explanation
Indices: 6812--6838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6802 AGTAATTAAT
6812 TA 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 TA T
6839 CTTTACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20923 original size:81 final size:81
Alignment explanation
Indices: 20828--20979 Score: 259
Period size: 81 Copynumber: 1.9 Consensus size: 81
20818 ACCCTAGTCT
* * * *
20828 ACTCAAACAAGTAGTAGTAAGCACATATAAATTAGTATAGAGATAGATTTATCGAATCAAATATA
1 ACTCAAACAAGTAGTAGTAAGCACACATAAATAAGCATAGAAATAGATTTATCGAATCAAATATA
20893 GTTTGACTCAAACCTA
66 GTTTGACTCAAACCTA
*
20909 ACTCAAACAAGTAGTAGTAAGCACACATGAATAAGCATAGAAATAGATTTATCGAATCAAATATA
1 ACTCAAACAAGTAGTAGTAAGCACACATAAATAAGCATAGAAATAGATTTATCGAATCAAATATA
20974 GTTTGA
66 GTTTGA
20980 TTCATAGTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (81 bp):
ACTCAAACAAGTAGTAGTAAGCACACATAAATAAGCATAGAAATAGATTTATCGAATCAAATATA
GTTTGACTCAAACCTA
Found at i:21060 original size:20 final size:20
Alignment explanation
Indices: 21037--21079 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
21027 CCTATTCTTG
*
21037 TCCCTTATTATTTGTCACCT
1 TCCCTTATTATCTGTCACCT
21057 TCCCTTATTATCTGTCACCT
1 TCCCTTATTATCTGTCACCT
21077 TCC
1 TCC
21080 AACGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.05, T:0.47
Consensus pattern (20 bp):
TCCCTTATTATCTGTCACCT
Found at i:22978 original size:24 final size:26
Alignment explanation
Indices: 22942--22997 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
22932 ATGAGTACCA
22942 ACCAAAGGCATACCGT-AA-ACACCC
1 ACCAAAGGCATACCGTGAACACACCC
* *
22966 ATCAAAGGTATACCGTGAACACACCC
1 ACCAAAGGCATACCGTGAACACACCC
22992 ACCAAA
1 ACCAAA
22998 TATTATACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 14 0.52
25 2 0.07
26 11 0.41
ACGTcount: A:0.43, C:0.34, G:0.12, T:0.11
Consensus pattern (26 bp):
ACCAAAGGCATACCGTGAACACACCC
Found at i:60392 original size:36 final size:36
Alignment explanation
Indices: 60346--60429 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
60336 AACTAATTTC
*
60346 CCAAATCCTAATTGAATTGGGTCAATCAATTTCCCT
1 CCAAATCCTAATTGAATTAGGTCAATCAATTTCCCT
* *
60382 CCGAATCCTAATTGATTTAGGTCAATCAATTTCCCT
1 CCAAATCCTAATTGAATTAGGTCAATCAATTTCCCT
60418 CCAAATCCTAAT
1 CCAAATCCTAAT
60430 CCTAATCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (36 bp):
CCAAATCCTAATTGAATTAGGTCAATCAATTTCCCT
Found at i:60934 original size:24 final size:24
Alignment explanation
Indices: 60904--60949 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
60894 TCAAACGGGG
*
60904 AAAGGAATTTATGAAGCGTGAAGA
1 AAAGGAACTTATGAAGCGTGAAGA
*
60928 AAAGGAACTTATGAAGCTTGAA
1 AAAGGAACTTATGAAGCGTGAA
60950 TGGCAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.22
Consensus pattern (24 bp):
AAAGGAACTTATGAAGCGTGAAGA
Found at i:62278 original size:18 final size:18
Alignment explanation
Indices: 62255--62301 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
62245 AGAGGTTTTG
62255 GCAGAGGTAATTTTGATC
1 GCAGAGGTAATTTTGATC
* *
62273 GCAGAGGCAACTTTGATC
1 GCAGAGGTAATTTTGATC
* *
62291 GAAAAGGTAAT
1 GCAGAGGTAAT
62302 ACTGATCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (18 bp):
GCAGAGGTAATTTTGATC
Found at i:69219 original size:30 final size:31
Alignment explanation
Indices: 69195--69252 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
69185 TGTGAATTTC
*
69195 ATTGGGCCTC-TTTGAGTGTGTGTGAAGCAT
1 ATTGGGCCACTTTTGAGTGTGTGTGAAGCAT
*
69225 ATTGGGCCACTTTTTAGTGTGTGTGAAG
1 ATTGGGCCACTTTTGAGTGTGTGTGAAG
69253 TATGTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (31 bp):
ATTGGGCCACTTTTGAGTGTGTGTGAAGCAT
Found at i:70662 original size:31 final size:31
Alignment explanation
Indices: 70624--70685 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
70614 TTCAAGCTTG
70624 ACAAAGAACAACAAATACAGATCTGAAAGGA
1 ACAAAGAACAACAAATACAGATCTGAAAGGA
70655 ACAAAGAACAACAAATACAGATCTGAAAGGA
1 ACAAAGAACAACAAATACAGATCTGAAAGGA
70686 GATATATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (31 bp):
ACAAAGAACAACAAATACAGATCTGAAAGGA
Found at i:77978 original size:95 final size:95
Alignment explanation
Indices: 77844--78034 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
77834 GGCTAGAGTT
77844 TCTCATTACTTAATTAAGTTCTATTTGAAAATATTACTACTACTACTAATAGAAGGAATATAGCC
1 TCTCATTACTTAATTAAGTTCTATTTGAAAATATTACTACTACTACTAATAGAAGGAATATAGCC
77909 AACATAGGTGAGATTTATTTAAACTTGAAA
66 AACATAGGTGAGATTTATTTAAACTTGAAA
77939 TCTCATTACTTAATTAAGTTCTATTTGAAAATATTACTACTACTACTAATAGAAGGAATATAGCC
1 TCTCATTACTTAATTAAGTTCTATTTGAAAATATTACTACTACTACTAATAGAAGGAATATAGCC
78004 AACATAGGTGAGATTTATTTAAACTTGAAA
66 AACATAGGTGAGATTTATTTAAACTTGAAA
78034 T
1 T
78035 AAAGATTTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (95 bp):
TCTCATTACTTAATTAAGTTCTATTTGAAAATATTACTACTACTACTAATAGAAGGAATATAGCC
AACATAGGTGAGATTTATTTAAACTTGAAA
Done.