Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005016.1 Corchorus capsularis cultivar CVL-1 contig05034, 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: 3004
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Found at i:2673 original size:35 final size:35
Alignment explanation
Indices: 2634--2775 Score: 164
Period size: 35 Copynumber: 4.0 Consensus size: 35
2624 TTACTGATTG
*
2634 CCATTTCTT-TTTACTGATTAATATTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
* *
2669 CCATTTTTTTTCTTTACTGATTACTCTTTACTCTTTA
1 CCA--TTTCTTCTTTACTGATTACTTTTTACTCTTTA
* * * *
2706 CCATTT-TTCTTTACTAATTTCTCTATAACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
2741 CCATTTC-TCTTTACTGATTACTTTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
2775 C
1 C
2776 TGATTATCAT
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
34 25 0.28
35 34 0.38
37 19 0.21
38 12 0.13
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (35 bp):
CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
Found at i:2699 original size:7 final size:7
Alignment explanation
Indices: 2679--2811 Score: 55
Period size: 7 Copynumber: 19.1 Consensus size: 7
2669 CCATTTTTTT
2679 TCTTTAC
1 TCTTTAC
**
2686 TGATTAC
1 TCTTTAC
2693 TCTTTAC
1 TCTTTAC
2700 TCTTTAC
1 TCTTTAC
*
2707 -CATTT-T
1 TC-TTTAC
2713 TCTTTAC
1 TCTTTAC
*
2720 TAATTT-C
1 T-CTTTAC
*
2727 TCTATAAC
1 TCT-TTAC
2735 TCTTTAC
1 TCTTTAC
2742 -CATTT-C
1 TC-TTTAC
2748 TCTTTAC
1 TCTTTAC
**
2755 TGATTAC
1 TCTTTAC
*
2762 TTTTTAC
1 TCTTTAC
2769 TCTTTAC
1 TCTTTAC
**
2776 TGATTA-
1 TCTTTAC
*
2782 TCATTAC
1 TCTTTAC
*
2789 TTTTTAC
1 TCTTTAC
2796 -CATTTTAC
1 TC--TTTAC
2804 TCTTTAC
1 TCTTTAC
2811 T
1 T
2812 GATTGCCTTT
Statistics
Matches: 92, Mismatches: 21, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
6 15 0.16
7 64 0.70
8 12 0.13
9 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (7 bp):
TCTTTAC
Found at i:2806 original size:69 final size:71
Alignment explanation
Indices: 2656--2810 Score: 167
Period size: 69 Copynumber: 2.2 Consensus size: 71
2646 ACTGATTAAT
* * *
2656 ATTTTACTCTTTACCATTTTTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTACT
1 ATTTTACTCTTTACCA--TTTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTATCATTACT
2721 AATTTCTC
64 AATTTCTC
* * * *
2729 -TATAACTCTTTACCA-TTTCTCTTTACTGATTACTTTTTACTCTTTACTGA-TTATCATTACT-
1 ATTTTACTCTTTACCATTTTCTCTTTACTGATTACTCTTTACTCTTTAC-CATTTATCATTACTA
*
2790 TTTTAC-C
65 ATTT-CTC
2797 ATTTTACTCTTTAC
1 ATTTTACTCTTTAC
2811 TGATTGCCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
68 4 0.06
69 51 0.74
70 1 0.01
72 13 0.19
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (71 bp):
ATTTTACTCTTTACCATTTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTATCATTACTAA
TTTCTC
Found at i:2909 original size:26 final size:26
Alignment explanation
Indices: 2892--2991 Score: 148
Period size: 26 Copynumber: 3.8 Consensus size: 26
2882 CTATTACGCT
*
2892 TTTCTTACTCTTTTTACTGAATATTG
1 TTTCTTACTCTTTTTACTGAATACTG
*
2918 TTTCTTACTCTTTTTACTG-ATGACTCTT
1 TTTCTTACTCTTTTTACTGAAT-A--CTG
2946 TTTCTTACTCTTTTTACTGAATACTG
1 TTTCTTACTCTTTTTACTGAATACTG
2972 TTTCTTACTCTTTTTACTGA
1 TTTCTTACTCTTTTTACTGA
2992 TGGCTCTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
25 2 0.03
26 42 0.63
28 21 0.31
29 2 0.03
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (26 bp):
TTTCTTACTCTTTTTACTGAATACTG
Found at i:2945 original size:16 final size:15
Alignment explanation
Indices: 2923--2980 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
2913 TATTGTTTCT
2923 TACTCTTTTTACTGA
1 TACTCTTTTTACTGA
2938 TGACTCTTTTT-CT--
1 T-ACTCTTTTTACTGA
2951 TACTCTTTTTACTGAA
1 TACTCTTTTTACTG-A
*
2967 TACTGTTTCTTACT
1 TACTCTTT-TTACT
2981 CTTTTTACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.25
13 3 0.08
15 3 0.08
16 16 0.44
17 5 0.14
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (15 bp):
TACTCTTTTTACTGA
Found at i:2956 original size:54 final size:54
Alignment explanation
Indices: 2891--3001 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
2881 ACTATTACGC
*
2891 TTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACTCT
1 TTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTTACTGATGACTCT
*
2945 TTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTTACTGATGGCTCT
1 TTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTTACTGATGACTCT
2999 TTT
1 TTT
3002 CTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (54 bp):
TTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTTACTGATGACTCT
Done.