Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007837.1 Corchorus capsularis cultivar CVL-1 contig07858, 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: 8801
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 19--50 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9 AGAGATAATG
19 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51 TTGATTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:772 original size:15 final size:15
Alignment explanation
Indices: 738--798 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
728 TTTATTTATT
* *
738 TATATATAATAAAAA
1 TATATATAATATATA
*
753 CATATATAATATATA
1 TATATATAATATATA
* *
768 TATATATTATATTTTA
1 TATATATAATA-TATA
* *
784 AATATATATTATATA
1 TATATATAATATATA
799 AAAATATCTA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATATAATATATA
Found at i:778 original size:20 final size:20
Alignment explanation
Indices: 755--799 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
745 AATAAAAACA
*
755 TATATAATATATATATATAT
1 TATATAATATAAATATATAT
*
775 TATAT--TTTAAATATATAT
1 TATATAATATAAATATATAT
793 TATATAA
1 TATATAA
800 AAATATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.76
20 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATAATATAAATATATAT
Found at i:2884 original size:3 final size:3
Alignment explanation
Indices: 2876--2907 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2866 AGGTAATTGT
2876 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2908 TTATCTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3728 original size:1 final size:1
Alignment explanation
Indices: 3722--3746 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3712 AACTGAATGT
3722 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3747 CAAGATAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4261 original size:42 final size:40
Alignment explanation
Indices: 4197--4293 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 40
4187 TATTAACCAT
* *
4197 ATTATCCATATATATTTAAGAGATAATTATGTTGATTATA-TA
1 ATTAACCATAT-TATTCAAGAGATAATTATG--GATTATATTA
* *
4239 ATTACCCATATTATTCATAGAGATAATTATGGATTATATTT
1 ATTAACCATATTATTCA-AGAGATAATTATGGATTATATTA
4280 ATTAACCATATTAT
1 ATTAACCATATTAT
4294 CTACAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 7 0.14
41 19 0.39
42 23 0.47
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (40 bp):
ATTAACCATATTATTCAAGAGATAATTATGGATTATATTA
Found at i:7247 original size:11 final size:11
Alignment explanation
Indices: 7233--7297 Score: 55
Period size: 11 Copynumber: 5.8 Consensus size: 11
7223 TCACAAAAAA
7233 AAAAAAAAAGC
1 AAAAAAAAAGC
7244 AAAACAAAAA-C
1 AAAA-AAAAAGC
* *
7255 AACACAAAA-C
1 AAAAAAAAAGC
7265 AAAAACAAAAGC
1 AAAAA-AAAAGC
7277 AAAAACAAAAAG-
1 -AAAA-AAAAAGC
7289 AAAAAAAAA
1 AAAAAAAAA
7298 ACATATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
10 13 0.29
11 16 0.36
12 6 0.13
13 9 0.20
14 1 0.02
ACGTcount: A:0.82, C:0.14, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:7269 original size:33 final size:34
Alignment explanation
Indices: 7224--7287 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
7214 CAAGTTCAGT
7224 CACAAAAAAAAAAAAAAAGC-AAAACAAAAACAA
1 CACAAAAAAAAAAAAAAAGCAAAAACAAAAACAA
* *
7257 CACAAAACAAAAACAAAAGCAAAAACAAAAA
1 CACAAAAAAAAAAAAAAAGCAAAAACAAAAA
7288 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (34 bp):
CACAAAAAAAAAAAAAAAGCAAAAACAAAAACAA
Found at i:7351 original size:39 final size:40
Alignment explanation
Indices: 7308--7384 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
7298 ACATATGTTT
7308 ACATATACAACAACAATGGCCTATGTC-ACCATATATACA
1 ACATATACAACAACAATGGCCTATGTCGACCATATATACA
*
7347 ACATATACAACAACAATGGCCTATGTCGCCCATATATA
1 ACATATACAACAACAATGGCCTATGTCGACCATATATA
7385 TTAAATGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (40 bp):
ACATATACAACAACAATGGCCTATGTCGACCATATATACA
Found at i:7429 original size:35 final size:35
Alignment explanation
Indices: 7390--7475 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
7380 ATATATTAAA
7390 TGGCCTATGTCGCCACATATCATGTACTATTACCT
1 TGGCCTATGTCGCCACATATCATGTACTATTACCT
*
7425 TGGCCTATGTCCCCACATATCATGTACTATTACCT
1 TGGCCTATGTCGCCACATATCATGTACTATTACCT
*
7460 TGGCCTATGACGCCAC
1 TGGCCTATGTCGCCAC
7476 TCCATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (35 bp):
TGGCCTATGTCGCCACATATCATGTACTATTACCT
Found at i:7523 original size:29 final size:29
Alignment explanation
Indices: 7460--7569 Score: 121
Period size: 29 Copynumber: 3.7 Consensus size: 29
7450 ACTATTACCT
* *
7460 TGGCCTATGACGCCACTCCATATATACAAAAA
1 TGGCCTATGATGCCAC-ACATATAT--AAAAA
*
7492 TGGCCTATGATGCCACACATATATAACAA
1 TGGCCTATGATGCCACACATATATAAAAA
* *
7521 TGGCCTATGATGCCACATATATATAATAA
1 TGGCCTATGATGCCACACATATATAAAAA
* * *
7550 TGGCTTATGTTGCCAAACAT
1 TGGCCTATGATGCCACACAT
7570 TTAAGTCTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
29 47 0.68
31 7 0.10
32 15 0.22
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCTATGATGCCACACATATATAAAAA
Found at i:7753 original size:89 final size:89
Alignment explanation
Indices: 7660--7863 Score: 245
Period size: 95 Copynumber: 2.2 Consensus size: 89
7650 AGGCAAGCTC
7660 AATATCTAAATGCTCCCTCCAAGTAGTAG-AA-TCTTTTCTCCTTGTAGAGGTTGAAAGCACTCT
1 AATATCTAAATGCTCCCTCCAAGTAGTAGAAATTCTTTTCTCCTTGTAGAGGTTGAAAGCACT-T
* *
7723 TATTTGCCGCTAATCAAAGCGACCTT
65 TACTTGCAGCT-ATCAAAGCGACCTT
* * * *
7749 AATATCTATATACTCTCTCCAAGTAGTAGAATAATTTTTTTTTCTCCTTGTAGAGGTTGAAAGCA
1 AATATCTAAATGCTCCCTCCAAGTAGTAG-A-AA--TTCTTTTCTCCTTGTAGAGGTTGAAAGCA
*
7814 CTTTCCTTGCAGCTATCAAAGCGACCTT
62 CTTTACTTGCAGCTATCAAAGCGACCTT
7842 -ATCATCTAAATG-TCTCCTCCAA
1 AAT-ATCTAAATGCTC-CCTCCAA
7864 AATGAACTTC
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
89 26 0.27
92 6 0.06
93 27 0.28
94 9 0.09
95 29 0.30
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (89 bp):
AATATCTAAATGCTCCCTCCAAGTAGTAGAAATTCTTTTCTCCTTGTAGAGGTTGAAAGCACTTT
ACTTGCAGCTATCAAAGCGACCTT
Done.