Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010003.1 Corchorus olitorius cultivar O-4 contig10035, 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: 11647
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:637 original size:24 final size:24
Alignment explanation
Indices: 610--683 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
600 GAAGCTACGA
*
610 ATGCAGCTTCAATTGCAGCTGCGG
1 ATGCAGCTTCAATTGCAGCTGCAG
* * * *
634 ATGCATCTGC-ATATGAATCTGCAG
1 ATGCAGCTTCAAT-TGCAGCTGCAG
658 ATGCAGCTTCAATTGCAGCTGCAG
1 ATGCAGCTTCAATTGCAGCTGCAG
682 AT
1 AT
684 TCATATGCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (24 bp):
ATGCAGCTTCAATTGCAGCTGCAG
Found at i:674 original size:12 final size:12
Alignment explanation
Indices: 659--836 Score: 77
Period size: 12 Copynumber: 14.8 Consensus size: 12
649 AATCTGCAGA
*
659 TGCAGCTTCAAT
1 TGCAGCTGCAAT
671 TGCAGCTGCAGAT
1 TGCAGCTGCA-AT
** *
684 T-CATATGCAAA
1 TGCAGCTGCAAT
*
695 TGCAGCTTCAAT
1 TGCAGCTGCAAT
707 TGCAGCTGCAGA-
1 TGCAGCTGCA-AT
*
719 TGCATCTGCAGAT
1 TGCAGCTGCA-AT
**
732 T-CATATGCAGA-
1 TGCAGCTGCA-AT
*
743 TGCAGCTTCAAT
1 TGCAGCTGCAAT
755 TGCAGCTGCAGAT
1 TGCAGCTGCA-AT
**
768 T-CATATGCAGA-
1 TGCAGCTGCA-AT
779 TGCAGCTGCAGA-
1 TGCAGCTGCA-AT
*
791 TGCAACTGCAGAT
1 TGCAGCTGCA-AT
**
804 T-CATATGCAGA-
1 TGCAGCTGCA-AT
*
815 TGCAGCTTCAAT
1 TGCAGCTGCAAT
827 TGCAGCTGCA
1 TGCAGCTGCA
837 GATGCATCTG
Statistics
Matches: 129, Mismatches: 26, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
11 7 0.05
12 113 0.88
13 9 0.07
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (12 bp):
TGCAGCTGCAAT
Found at i:680 original size:36 final size:36
Alignment explanation
Indices: 635--851 Score: 211
Period size: 36 Copynumber: 5.7 Consensus size: 36
625 CAGCTGCGGA
* * * *
635 TGCATCTGCATATGAATCTGCAGATGCAGCTTCAAT
1 TGCAGCTGCAGATGCATATGCAGATGCAGCTTCAAT
* *
671 TGCAGCTGCAGATTCATATGCAAATGCAGCTTCAAT
1 TGCAGCTGCAGATGCATATGCAGATGCAGCTTCAAT
707 TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAAT
1 TGCAGCTGC--A-G-A--T---G---CATATGCAGATGCAGCTTCAAT
* *
755 TGCAGCTGCAGATTCATATGCAGATGCAGCTGCAGA-
1 TGCAGCTGCAGATGCATATGCAGATGCAGCTTCA-AT
* *
791 TGCAACTGCAGATTCATATGCAGATGCAGCTTCAAT
1 TGCAGCTGCAGATGCATATGCAGATGCAGCTTCAAT
*
827 TGCAGCTGCAGATGCATCTGCAGAT
1 TGCAGCTGCAGATGCATATGCAGAT
852 TCATATGCAG
Statistics
Matches: 152, Mismatches: 15, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.01
36 112 0.74
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
42 2 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 30 0.20
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (36 bp):
TGCAGCTGCAGATGCATATGCAGATGCAGCTTCAAT
Found at i:711 original size:48 final size:48
Alignment explanation
Indices: 611--761 Score: 180
Period size: 48 Copynumber: 3.1 Consensus size: 48
601 AAGCTACGAA
* * * * * * *
611 TGCAGCTTCAATTGCAGCTGCGGATGCATCTGCATATGAATCTGCAGA-
1 TGCAGCTTCAATTGCAGCTGCAGATTCATATGCAAATGCAGCTTCA-AT
659 TGCAGCTTCAATTGCAGCTGCAGATTCATATGCAAATGCAGCTTCAAT
1 TGCAGCTTCAATTGCAGCTGCAGATTCATATGCAAATGCAGCTTCAAT
* * *
707 TGCAGCTGCAGA-TGCATCTGCAGATTCATATGCAGATGCAGCTTCAAT
1 TGCAGCTTCA-ATTGCAGCTGCAGATTCATATGCAAATGCAGCTTCAAT
755 TGCAGCT
1 TGCAGCT
762 GCAGATTCAT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 89 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
TGCAGCTTCAATTGCAGCTGCAGATTCATATGCAAATGCAGCTTCAAT
Found at i:745 original size:84 final size:84
Alignment explanation
Indices: 609--848 Score: 324
Period size: 84 Copynumber: 3.0 Consensus size: 84
599 AGAAGCTACG
* * ** *
609 AATGCAGCTTCAATTGCAGCTGCGGATGCATCTGCATATGAATCTGCAGATGCAGCTTCAATTGC
1 AATGCAGCTTCAATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGC
674 AGCTGCAGATTCATATGCA
66 AGCTGCAGATTCATATGCA
693 AATGCAGCTTCAATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGC
1 AATGCAGCTTCAATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGC
758 AGCTGCAGATTC--AT---
66 AGCTGCAGATTCATATGCA
*
772 -ATGCAG-----A-TGCAGCTGCAGATGCAACTGCAGATTCATATGCAGATGCAGCTTCAATTGC
1 AATGCAGCTTCAATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGC
* *
830 AGCTGCAGATGCATCTGCA
66 AGCTGCAGATTCATATGCA
849 GATTCATATG
Statistics
Matches: 143, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
72 61 0.43
73 1 0.01
74 1 0.01
78 6 0.04
82 2 0.01
84 72 0.50
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (84 bp):
AATGCAGCTTCAATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGC
AGCTGCAGATTCATATGCA
Found at i:762 original size:48 final size:48
Alignment explanation
Indices: 671--872 Score: 185
Period size: 48 Copynumber: 4.2 Consensus size: 48
661 CAGCTTCAAT
* * * * *
671 TGCAGCTGCAGATTCATATGCAAATGCAGCTTCA-ATTGCAGCTGCAGA
1 TGCATCTGCAGATTCAGATGCAGATGCAGCTGCAGATT-CAGATGCAGA
* * *
719 TGCATCTGCAGATTCATATGCAGATGCAGCTTCA-ATTGCAGCTGCAGA
1 TGCATCTGCAGATTCAGATGCAGATGCAGCTGCAGATT-CAGATGCAGA
* * * * * *
767 TTCATATGCAGATGCAGCTGCAGATGCAACTGCAGATTCATATGCAGA
1 TGCATCTGCAGATTCAGATGCAGATGCAGCTGCAGATTCAGATGCAGA
* * * * *
815 TGCAGCTTCA-ATTGCAGCTGCAGATGCATCTGCAGATTCATATGCAGA
1 TGCATCTGCAGATT-CAGATGCAGATGCAGCTGCAGATTCAGATGCAGA
863 TGCATCTGCA
1 TGCATCTGCA
873 TCAACCTCAC
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
47 2 0.02
48 128 0.96
49 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (48 bp):
TGCATCTGCAGATTCAGATGCAGATGCAGCTGCAGATTCAGATGCAGA
Found at i:849 original size:72 final size:72
Alignment explanation
Indices: 707--872 Score: 278
Period size: 72 Copynumber: 2.3 Consensus size: 72
697 CAGCTTCAAT
*
707 TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGCAGCTGCAGATTCAT
1 TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGCAGCTGCAGATGCAT
772 ATGCAGA
66 ATGCAGA
*
779 TGCAGCTGCAGATGCAACTGCAGATTCATATGCAGATGCAGCTTCAATTGCAGCTGCAGATGCAT
1 TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGCAGCTGCAGATGCAT
*
844 CTGCAGA
66 ATGCAGA
* **
851 TTCATATGCAGATGCATCTGCA
1 TGCAGCTGCAGATGCATCTGCA
873 TCAACCTCAC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 87 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (72 bp):
TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGATGCAGCTTCAATTGCAGCTGCAGATGCAT
ATGCAGA
Found at i:860 original size:18 final size:18
Alignment explanation
Indices: 653--849 Score: 135
Period size: 18 Copynumber: 11.3 Consensus size: 18
643 CATATGAATC
* *
653 TGCAGATGCAGCTTCA-A
1 TGCAGCTGCAGATTCATA
670 TTGCAGCTGCAGATTCATA
1 -TGCAGCTGCAGATTCATA
** *
689 TGCAAATGCAGCTTCA-A
1 TGCAGCTGCAGATTCATA
706 TTGCAGCTGCAG------A
1 -TGCAGCTGCAGATTCATA
*
719 TGCATCTGCAGATTCATA
1 TGCAGCTGCAGATTCATA
* *
737 TGCAGATGCAGCTTCA-A
1 TGCAGCTGCAGATTCATA
754 TTGCAGCTGCAGATTCATA
1 -TGCAGCTGCAGATTCATA
* * * *
773 TGCAGATGCAGCTGCAGA
1 TGCAGCTGCAGATTCATA
*
791 TGCAACTGCAGATTCATA
1 TGCAGCTGCAGATTCATA
* *
809 TGCAGATGCAGCTTCA-A
1 TGCAGCTGCAGATTCATA
* *
826 TTGCAGCTGCAGATGCATC
1 -TGCAGCTGCAGATTCATA
845 TGCAG
1 TGCAG
850 ATTCATATGC
Statistics
Matches: 138, Mismatches: 29, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
12 10 0.07
13 1 0.01
17 3 0.02
18 122 0.88
19 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
TGCAGCTGCAGATTCATA
Found at i:872 original size:36 final size:36
Alignment explanation
Indices: 707--872 Score: 210
Period size: 36 Copynumber: 4.6 Consensus size: 36
697 CAGCTTCAAT
*
707 TGCAGCTGCAGATGCATCTGCAGATTCATATGCAGA
1 TGCAGCTGCAGATGCAGCTGCAGATTCATATGCAGA
*
743 TGCAGCTTCA-ATTGCAGCTGCAGATTCATATGCAGA
1 TGCAGCTGCAGA-TGCAGCTGCAGATTCATATGCAGA
*
779 TGCAGCTGCAGATGCAACTGCAGATTCATATGCAGA
1 TGCAGCTGCAGATGCAGCTGCAGATTCATATGCAGA
* * *
815 TGCAGCTTCA-ATTGCAGCTGCAGATGCATCTGCAGA
1 TGCAGCTGCAGA-TGCAGCTGCAGATTCATATGCAGA
* ** *
851 TTCATATGCAGATGCATCTGCA
1 TGCAGCTGCAGATGCAGCTGCA
873 TCAACCTCAC
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
35 2 0.02
36 109 0.96
37 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (36 bp):
TGCAGCTGCAGATGCAGCTGCAGATTCATATGCAGA
Found at i:2839 original size:1 final size:1
Alignment explanation
Indices: 2835--2864 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2825 AATTTTTTAA
2835 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2865 AAAATACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6421 original size:2 final size:2
Alignment explanation
Indices: 6406--6532 Score: 77
Period size: 2 Copynumber: 69.5 Consensus size: 2
6396 ATTATTTTGT
6406 TA TA TA T- TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
6444 TA TA T- TA CT- TG TA TA T- TG TA TA T- TA TA TA CT- TG T- TG TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
6482 TA T- TA T- TGG TA TA T- TA TA TA T- TA TA -A TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6520 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
6533 TACTTGTTTT
Statistics
Matches: 103, Mismatches: 4, Indels: 36
0.72 0.03 0.25
Matches are distributed among these distances:
1 15 0.15
2 85 0.83
3 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6471 original size:36 final size:35
Alignment explanation
Indices: 6406--6522 Score: 119
Period size: 36 Copynumber: 3.2 Consensus size: 35
6396 ATTATTTTGT
* *
6406 TATATATTATTATATAATATATATATATATATATAA
1 TATATATTATTGTATATTATATAT-TATATATATAA
* **
6442 TATATATTACTTGTATATTGTATATTATATACT-TGT
1 TATATATTA-TTGTATATTATATATTATATA-TATAA
*
6478 TGTATATTATTGGTATATTATATATTATAATATATATA
1 TATATATTATT-GTATATTATATATTAT-ATATATA-A
6516 TATATAT
1 TATATAT
6523 ATATATATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
35 2 0.03
36 40 0.62
37 17 0.26
38 6 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (35 bp):
TATATATTATTGTATATTATATATTATATATATAA
Found at i:7110 original size:18 final size:18
Alignment explanation
Indices: 7077--7118 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
7067 TAATAAATTA
7077 ATTTAATATTGAA-TTTT
1 ATTTAATATTGAATTTTT
7094 ATTTATATATT-ATATTTTT
1 ATTTA-ATATTGA-ATTTTT
7113 ATTTAA
1 ATTTAA
7119 AAGTTACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTAATATTGAATTTTT
Done.