Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009672.1 Corchorus capsularis cultivar CVL-1 contig09693, 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: 6029
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Found at i:2797 original size:14 final size:14
Alignment explanation
Indices: 2780--2855 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
2770 ACTTTATTGA
2780 TTACTATTTTACTC
1 TTACTATTTTACTC
* *
2794 TTACCATTTTGCTC
1 TTACTATTTTACTC
*
2808 TTACTGA--TTACTA
1 TTACT-ATTTTACTC
* * *
2821 TT-TTACTCTTACTGA
1 TTACTA-TTTTACT-C
2836 TTACTATTTTACTC
1 TTACTATTTTACTC
2850 TTACTA
1 TTACTA
2856 ATTACCATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 27 0.57
15 10 0.21
16 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (14 bp):
TTACTATTTTACTC
Found at i:2823 original size:21 final size:21
Alignment explanation
Indices: 2794--2872 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
2784 TATTTTACTC
*
2794 TTACCATTTTGCTCTTACTGA
1 TTACCATTTTACTCTTACTGA
*
2815 TTACTATTTTACTCTTACTGA
1 TTACCATTTTACTCTTACTGA
* *
2836 TTACTATTTTACTCTTACTAA
1 TTACCATTTTACTCTTACTGA
*
2857 TTACCATTTTGCTCTT
1 TTACCATTTTACTCTT
2873 TTTAACTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (21 bp):
TTACCATTTTACTCTTACTGA
Found at i:2952 original size:40 final size:40
Alignment explanation
Indices: 2897--2984 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
2887 TAAATACCAT
**
2897 CTTTTGAC-CTTAATTACTGATATACTGACT-ACTTCTTTTA
1 CTTTT-ACTCTTAATTACCAATATACTG-CTCACTTCTTTTA
* *
2937 CTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTA
1 CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
2977 CTTTTACT
1 CTTTTACT
2985 ACATTCTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.50
Consensus pattern (40 bp):
CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
Found at i:3009 original size:72 final size:73
Alignment explanation
Indices: 2919--3089 Score: 204
Period size: 72 Copynumber: 2.4 Consensus size: 73
2909 ATTACTGATA
* * * *
2919 TACTGACTA-CTTCTTTTACTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTA
1 TACTGAATACCTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTA
2983 CTACATTC
66 CTACATTC
* * * * * *
2991 TACT-AATATCTTCTTTTACCTTGATTCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTA
1 TACTGAATACCTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTA
*
3055 CTCCATTC
66 CTACATTC
* *
3063 TGCTGATTACCTT-TTTTACTTTTACTC
1 TACTGAATACCTTCTTTTACTTTTACTC
3090 AATTCTATTG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
71 3 0.04
72 72 0.89
73 6 0.07
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (73 bp):
TACTGAATACCTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTA
CTACATTC
Found at i:3131 original size:96 final size:95
Alignment explanation
Indices: 3026--3203 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 95
3016 TCTTAATTAC
* * *
3026 CCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTGCTGATTACCTT-TTTTACTTTTACTC
1 CCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTA-CTTCTCTTACTTTCACTC
**
3090 AATTCTATTGATTACTTATTTTACTTTTTGT
65 AATTCTACAGATTACTTATTTTACTTTTTGT
* * *
3121 CCATTCTACTGATTATTTCTTTTACTTTTACTCCATTTTACTGATTACTTCCTCTTACTTTCACT
1 CCATT-TACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTACTT-CTCTTACTTTCACT
*
3186 CCATTCTACAGATTACTT
64 CAATTCTACAGATTACTT
3204 CCTCTTTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
95 8 0.11
96 37 0.52
97 26 0.37
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (95 bp):
CCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTACTTCTCTTACTTTCACTCA
ATTCTACAGATTACTTATTTTACTTTTTGT
Found at i:3209 original size:33 final size:32
Alignment explanation
Indices: 3022--3204 Score: 219
Period size: 32 Copynumber: 5.8 Consensus size: 32
3012 TGATTCTTAA
*
3022 TTAC-CCATT-TACTGATTACTTCTTTTACTC
1 TTACTCCATTCTACTGATTACTTCTTTTACTT
*
3052 TTACTCCATTCTGCTGATTACCTT-TTTTACTT
1 TTACTCCATTCTACTGATTA-CTTCTTTTACTT
* * *
3084 TTACTCAATTCTATTGATTACTTATTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTT
** *
3116 TTTGTCCATTCTACTGATTATTTCTTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTT
* *
3148 TTACTCCATTTTACTGATTACTTCCTCTTACTT
1 TTACTCCATTCTACTGATTACTT-CTTTTACTT
* *
3181 TCACTCCATTCTACAGATTACTTC
1 TTACTCCATTCTACTGATTACTTC
3205 CTCTTTTACT
Statistics
Matches: 129, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.03
31 8 0.06
32 86 0.67
33 31 0.24
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (32 bp):
TTACTCCATTCTACTGATTACTTCTTTTACTT
Done.