Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006418.1 Corchorus capsularis cultivar CVL-1 contig06439, 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: 7570
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Found at i:2554 original size:15 final size:16
Alignment explanation
Indices: 2530--2564 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2520 CTCTTGTTGA
*
2530 TTACCTTTTTACT-TT
1 TTACCATTTTACTCTT
2545 TTACCATTTTACTCTT
1 TTACCATTTTACTCTT
2561 TTAC
1 TTAC
2565 TGATTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (16 bp):
TTACCATTTTACTCTT
Found at i:2571 original size:15 final size:15
Alignment explanation
Indices: 2553--2609 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2543 TTTTACCATT
2553 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
2568 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
2581 CTCCTTTTTTTACTGA
1 TTAC-TCTTTTACTGA
2597 TTACTCTTTTACT
1 TTACTCTTTTACT
2610 TCTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
13 2 0.06
14 8 0.25
15 20 0.62
16 2 0.06
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:2737 original size:35 final size:35
Alignment explanation
Indices: 2661--2746 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
2651 CTCTCACTAG
*
2661 TTACTGTTTTACTCTTAATGACTACCTTTTATAGA
1 TTACTATTTTACTCTTAATGACTACCTTTTATAGA
* * ** *
2696 TCACTATTTTACTCTTAATGGCTGTCTTTTGCT-GA
1 TTACTATTTTACTCTTAATGACTACCTTTT-ATAGA
*
2731 TTACTATTTTATTCTT
1 TTACTATTTTACTCTT
2747 TACTGATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.52
Consensus pattern (35 bp):
TTACTATTTTACTCTTAATGACTACCTTTTATAGA
Found at i:2956 original size:31 final size:32
Alignment explanation
Indices: 2906--2969 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
2896 TACTGATTTG
2906 CTGATTACTATTTTTACCTTGAC-TCTTAATTA
1 CTGATTAC-ATTTTTACCTTGACTTCTTAATTA
2938 CTGATTA-ATTTCTTACCTTGACTTCTTAATTA
1 CTGATTACATTT-TTACCTTGACTTCTTAATTA
2970 TCAATTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 4 0.13
31 10 0.33
32 16 0.53
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (32 bp):
CTGATTACATTTTTACCTTGACTTCTTAATTA
Found at i:3055 original size:45 final size:46
Alignment explanation
Indices: 3004--3112 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 46
2994 TACTTGATTG
* * * *
3004 CTGATTTACTGATTACTATTACCTTGACTTTTGATTAA-T-TTTTTA
1 CTGATTTACTGATTACCATCACCTTAAC-TTCGATTAACTCTTTTTA
*
3049 CTGATTTACTGATTACCATCACTTTAACTTCGATTAACCTCTTTTTA
1 CTGATTTACTGATTACCATCACCTTAACTTCGATTAA-CTCTTTTTA
*
3096 CTGATTTACCGATTACC
1 CTGATTTACTGATTACC
3113 CCTTTTTACT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 8 0.15
45 24 0.44
46 1 0.02
47 22 0.40
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (46 bp):
CTGATTTACTGATTACCATCACCTTAACTTCGATTAACTCTTTTTA
Found at i:3805 original size:51 final size:49
Alignment explanation
Indices: 3733--4229 Score: 312
Period size: 51 Copynumber: 9.9 Consensus size: 49
3723 AACTAATCAG
* * * *
3733 TTTATTTACTAATGGT-C-TAAAAAGTTTAAACTTCTAATTCAAAGGTGACAT
1 TTTATTTACTAAT--TACTTAAAAA-TTCAAACTT-TTATTCAAAGATGAAAT
* * * *
3784 TTTATTTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGC
1 TTTATTTACTAATTACTTAAAAATTCAAACTTTTATTCAAAGATGAAA-T
* * * ** * *
3834 TTTATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAAACTTTTATTCAAAGATGA-AAT
* * * *
3885 TTTATTTACCAATTACTTAGAAA-TCTAAATCTTTTATTCAAAGGTTAAAT
1 TTTATTTACTAATTACTTAAAAATTC-AAA-CTTTTATTCAAAGATGAAAT
* * * * *
3935 CTTTATTTACTAATCATTCTAAAAAATTCAATCTTTTACTCAAAGATGACAT
1 -TTTATTTACTAAT--TACTTAAAAATTCAAACTTTTATTCAAAGATGAAAT
* * *
3987 TTTACTTT-CCAATTACTTAGAAA-TCTAAATCTTTTATTCAAAGGTGAAAT
1 TTTA-TTTACTAATTACTTAAAAATTC-AAA-CTTTTATTCAAAGATGAAAT
* * * *
4037 CTTTATTTACTAATTATTCTAAAAATTCAATCTTTTACTCAAAGATGACATT
1 -TTTATTTACTAATTACT-TAAAAATTCAAACTTTTATTCAAAGATGA-AAT
* * * * *
4089 TTTACTT-CCAATTACTTAGAAA-TCTAAATCTTTTATTCAAAGGTTAAAT
1 TTTATTTACTAATTACTTAAAAATTC-AAA-CTTTTATTCAAAGATGAAAT
* * * * *
4138 CTTTA-TTACTAATCATTCTAAAAATTCAATCTTTTACTCAAAGATGACATT
1 -TTTATTTACTAATTACT-TAAAAATTCAAACTTTTATTCAAAGATGA-AAT
* * *
4189 TTTACTTT-CCAATTA-TTTAAAATTCAATCTTTTATTCAAAG
1 TTTA-TTTACTAATTACTTAAAAATTCAAACTTTTATTCAAAG
4230 GTTATCTTTT
Statistics
Matches: 345, Mismatches: 73, Indels: 58
0.72 0.15 0.12
Matches are distributed among these distances:
48 4 0.01
49 58 0.17
50 102 0.30
51 135 0.39
52 33 0.10
53 11 0.03
54 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (49 bp):
TTTATTTACTAATTACTTAAAAATTCAAACTTTTATTCAAAGATGAAAT
Found at i:3940 original size:102 final size:101
Alignment explanation
Indices: 3771--4233 Score: 695
Period size: 101 Copynumber: 4.6 Consensus size: 101
3761 AACTTCTAAT
* * * * * * *
3771 TCAAAGGTGACA-TTTTATTTACTAATTACTTAAAAAT-TCAATCTTTCATTCAAAGATTAAAGC
1 TCAAAGATGACATTTTTATTT-CCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATC
* *
3834 TTTATTTACTAATCACTCTAAAGATTCAATCTTTTAC
65 TTTATTTACTAATCATTCTAAAAATTCAATCTTTTAC
* *
3871 CCAAAGACGACATTTTTATTTACCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATC
1 TCAAAGATGACATTTTTATTT-CCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATC
3936 TTTATTTACTAATCATTCTAAAAAATTCAATCTTTTAC
65 TTTATTTACTAATCATTCT-AAAAATTCAATCTTTTAC
*
3974 TCAAAGATGACA-TTTTACTTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTGAAATC
1 TCAAAGATGACATTTTTA-TTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATC
*
4038 TTTATTTACTAATTATTCTAAAAATTCAATCTTTTAC
65 TTTATTTACTAATCATTCTAAAAATTCAATCTTTTAC
*
4075 TCAAAGATGACATTTTTACTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATCT
1 TCAAAGATGACATTTTTATTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATCT
4140 TTA-TTACTAATCATTCTAAAAATTCAATCTTTTAC
66 TTATTTACTAATCATTCTAAAAATTCAATCTTTTAC
* *
4175 TCAAAGATGACATTTTTACTTTCCAATTATTTA-AAAT-TCAATCTTTTATTCAAAGGTTA
1 TCAAAGATGACATTTTTA-TTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTA
4234 TCTTTTAACC
Statistics
Matches: 336, Mismatches: 21, Indels: 13
0.91 0.06 0.04
Matches are distributed among these distances:
99 21 0.06
100 62 0.18
101 113 0.34
102 110 0.33
103 30 0.09
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.42
Consensus pattern (101 bp):
TCAAAGATGACATTTTTATTTCCAATTACTTAGAAATCTAAATCTTTTATTCAAAGGTTAAATCT
TTATTTACTAATCATTCTAAAAATTCAATCTTTTAC
Found at i:6965 original size:27 final size:28
Alignment explanation
Indices: 6935--7004 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
6925 AGGTGAACCT
*
6935 AAAAATGACTAAAATGCCCCT-GAGTAC
1 AAAAATGACCAAAATGCCCCTAGAGTAC
* * *
6962 AAAAATGGCCAAAATGCCCCTAGGGTGC
1 AAAAATGACCAAAATGCCCCTAGAGTAC
6990 AAAAATGACCAAAAT
1 AAAAATGACCAAAAT
7005 ACCCTTGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTAGAGTAC
Done.