Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007017.1 Corchorus capsularis cultivar CVL-1 contig07038, 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: 30296
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:6098 original size:54 final size:54
Alignment explanation
Indices: 6040--6147 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
6030 CGCTTTTCCT
6040 TTCCTATTTTCTTTTTACCTTCAAAACTCTTCAGATGATATAAATTTTATTTAA
1 TTCCTATTTTCTTTTTACCTTCAAAACTCTTCAGATGATATAAATTTTATTTAA
* * *
6094 TTCCTATTTTCTTTTTTCCTTCAAATCTCTTCAGATGGTATAAATTTTATTTAA
1 TTCCTATTTTCTTTTTACCTTCAAAACTCTTCAGATGATATAAATTTTATTTAA
6148 GGAAAAATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (54 bp):
TTCCTATTTTCTTTTTACCTTCAAAACTCTTCAGATGATATAAATTTTATTTAA
Found at i:6502 original size:11 final size:11
Alignment explanation
Indices: 6479--6518 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6469 AAAAATTGAC
*
6479 AACACAACAAA
1 AACAAAACAAA
*
6490 AACAAAACGAA
1 AACAAAACAAA
*
6501 AACGAAACAAA
1 AACAAAACAAA
6512 AACAAAA
1 AACAAAA
6519 AACAGAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.75, C:0.20, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAACAAA
Found at i:9205 original size:6 final size:6
Alignment explanation
Indices: 9194--9236 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
9184 CAGGCTGCAC
9194 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT C
9237 TAGCTAACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:9296 original size:38 final size:38
Alignment explanation
Indices: 9242--9348 Score: 180
Period size: 38 Copynumber: 2.8 Consensus size: 38
9232 CAATCTAGCT
9242 AACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTACC
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
*
9279 AACAGTTTAACCTCCTGAGGCACGGGTCCACTCTTACC
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
* *
9317 ATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACT
9349 ATGCACAGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 5 0.08
38 60 0.92
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (38 bp):
AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
Found at i:13901 original size:14 final size:14
Alignment explanation
Indices: 13878--13919 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
13868 AAAGTCTAAA
*
13878 ATTATCTTTTAATT
1 ATTATTTTTTAATT
13892 ATTATTTTTT-ATT
1 ATTATTTTTTAATT
*
13905 ATTACTTTTATAATT
1 ATTA-TTTTTTAATT
13920 GAATTTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 14 0.58
15 3 0.12
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTTTTAATT
Found at i:16268 original size:14 final size:14
Alignment explanation
Indices: 16249--16276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16239 AATTCTTACA
16249 AAGATAACTGACAG
1 AAGATAACTGACAG
16263 AAGATAACTGACAG
1 AAGATAACTGACAG
16277 GAGGAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
AAGATAACTGACAG
Found at i:20440 original size:18 final size:18
Alignment explanation
Indices: 20413--20453 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20403 AACAGGCAGA
20413 AAACAAGACCAAAAGGTC
1 AAACAAGACCAAAAGGTC
* *
20431 AAACAGGACCAACAGGTC
1 AAACAAGACCAAAAGGTC
*
20449 GAACA
1 AAACA
20454 TGCAGAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.24, G:0.20, T:0.05
Consensus pattern (18 bp):
AAACAAGACCAAAAGGTC
Found at i:20529 original size:47 final size:46
Alignment explanation
Indices: 20360--20514 Score: 166
Period size: 47 Copynumber: 3.3 Consensus size: 46
20350 TCAAATGAAG
* * ** *
20360 GGCAGAAAACATGACAGAAAGGTCAAAGAGGACCTAGAGGTCAAACA
1 GGCAGAAAACAGGACA-AAAGGTCAAACAGGACAAACAGGTCAAACA
* * *
20407 GGCAGAAAACAAGACCAAAAGGTCAAACAGGACCAACAGGTCGAACA
1 GGCAGAAAACAGGA-CAAAAGGTCAAACAGGACAAACAGGTCAAACA
* * * * *
20454 TGCAGAAAACGGGACCAAAGGTCAAACAGGACTAAATAGGTCAAATA
1 GGCAGAAAACAGGACAAAAGGTCAAACAGGAC-AAACAGGTCAAACA
20501 GGCAGAAAACAGGA
1 GGCAGAAAACAGGA
20515 TCGAATGGTC
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
46 17 0.19
47 72 0.79
48 2 0.02
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.08
Consensus pattern (46 bp):
GGCAGAAAACAGGACAAAAGGTCAAACAGGACAAACAGGTCAAACA
Found at i:20567 original size:28 final size:24
Alignment explanation
Indices: 20503--20573 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 24
20493 GTCAAATAGG
* *
20503 CAGAAAACAGGATCGAATGGTCAA
1 CAGAAAACAGGACCGAAAGGTCAA
*
20527 CAGAAAACGGGACCGAAAGGTCAACAGA
1 CAGAAAACAGGACCGAAAGGT---CA-A
20555 CAGAAAACAGGACCGAAAG
1 CAGAAAACAGGACCGAAAG
20574 ATTAAACAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.46
27 2 0.05
28 19 0.49
ACGTcount: A:0.48, C:0.20, G:0.27, T:0.06
Consensus pattern (24 bp):
CAGAAAACAGGACCGAAAGGTCAA
Found at i:21189 original size:17 final size:17
Alignment explanation
Indices: 21169--21203 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21159 TAAAAAAACT
21169 AAAATTC-AGCAAAAAAA
1 AAAATTCTA-CAAAAAAA
21186 AAAATTCTACAAAAAAA
1 AAAATTCTACAAAAAAA
21203 A
1 A
21204 GAACAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATTCTACAAAAAAA
Found at i:22634 original size:12 final size:13
Alignment explanation
Indices: 22617--22645 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
22607 CAAAAAAATG
22617 AAAAATAAAT-TA
1 AAAAATAAATATA
22629 AAAAATAAATATA
1 AAAAATAAATATA
22642 AAAA
1 AAAA
22646 GATGAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAAATATA
Found at i:22702 original size:66 final size:65
Alignment explanation
Indices: 22567--22703 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 65
22557 GAGAAAGGAG
* *
22567 AGAA-AAATATAAACGTGAATTTCAAAAAATATTTTTTGGCCAAAAAAATGAAAAATAAATTAAA
1 AGAATAAATATAAAAGTGAATTTCAAAAAATATTTTTTGGCCAAAAAAATGAAAAATAAATAAAA
* * *
22631 A-AATAAATATAAAAAGATGAATTTCAAAAAATATTTTTTGGCCAAAAAATTTAAAAA-ATATAA
1 AGAATAAATAT-AAAAG-TGAATTTCAAAAAATATTTTTTGGCCAAAAAAATGAAAAATAAATAA
22694 AA
64 AA
22696 AGAATAAA
1 AGAATAAA
22704 AATATTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
63 2 0.03
64 7 0.11
65 11 0.17
66 44 0.69
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (65 bp):
AGAATAAATATAAAAGTGAATTTCAAAAAATATTTTTTGGCCAAAAAAATGAAAAATAAATAAAA
Found at i:22722 original size:17 final size:18
Alignment explanation
Indices: 22682--22723 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
22672 CCAAAAAATT
22682 TAAAAAATATAAAAAGAA
1 TAAAAAATATAAAAAGAA
**
22700 T-AAAAATATTTAAA-AA
1 TAAAAAATATAAAAAGAA
22716 TAAAAAAT
1 TAAAAAAT
22724 GCCACGTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 17 0.81
18 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
TAAAAAATATAAAAAGAA
Found at i:22833 original size:31 final size:30
Alignment explanation
Indices: 22794--22865 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
22784 TAGAAATGTT
22794 ACCAAATTGAGCCA-ATTTGGAAAGGTTTGGC
1 ACCAAATTGAGCCAGATTT--AAAGGTTTGGC
** *
22825 ACTGAATTGAG-CAGGTTTAAAGGTTTGGC
1 ACCAAATTGAGCCAGATTTAAAGGTTTGGC
22854 ACCAAATTGAGC
1 ACCAAATTGAGC
22866 ATCTGGCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 20 0.59
30 2 0.06
31 12 0.35
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (30 bp):
ACCAAATTGAGCCAGATTTAAAGGTTTGGC
Done.