Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007427.1 Corchorus capsularis cultivar CVL-1 contig07448, 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: 16583
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Found at i:2669 original size:29 final size:28
Alignment explanation
Indices: 2604--2683 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
2594 TTTTATCATT
*
2604 TTTACTCTTTTCTTACTCT-TTTTACTA
1 TTTACACTTTTCTTACTCTCTTTTACTA
* *
2631 TTTACTCTTTTCTTACTCTCTTTTATTGA
1 TTTACACTTTTCTTACTCTCTTTTACT-A
2660 -TTACCACTTTT-TTACTCTTCTTTT
1 TTTA-CACTTTTCTTACTC-TCTTTT
2684 TTTCTTATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 19 0.40
28 15 0.32
29 13 0.28
ACGTcount: A:0.14, C:0.23, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTACACTTTTCTTACTCTCTTTTACTA
Found at i:2747 original size:22 final size:22
Alignment explanation
Indices: 2686--2972 Score: 224
Period size: 22 Copynumber: 13.8 Consensus size: 22
2676 CTTCTTTTTT
*
2686 TCTTATACTGACTACCATTTTAC
1 TCTT-TACTGATTACCATTTTAC
*
2709 TCTTTGAATTTGATTACCATTTTAC
1 TCTTT--A-CTGATTACCATTTTAC
*
2734 TCTTTACTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
* *
2756 TC-TTACTAATTACCATTTTGC
1 TCTTTACTGATTACCATTTTAC
* *
2777 TC-TTACTGATTACTATTTTAT
1 TCTTTACTGATTACCATTTTAC
*
2798 TC-TAACTGATTACC-TTTTA-
1 TCTTTACTGATTACCATTTTAC
*
2817 ------CTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
2833 TCTTTACTGATTACC-TTCTTAC
1 TCTTTACTGATTACCATT-TTAC
* * *
2855 TTTTTACTGATTACTATTTCAC
1 TCTTTACTGATTACCATTTTAC
*
2877 TCTTTACTGATTACCATTTTGC
1 TCTTTACTGATTACCATTTTAC
2899 TC-TTACTGATTACC-TTTTA-
1 TCTTTACTGATTACCATTTTAC
**
2918 -C--TA---ATTAGTATTTTAC
1 TCTTTACTGATTACCATTTTAC
2934 TCTTTACTGATTACC-TTCTTAC
1 TCTTTACTGATTACCATT-TTAC
2956 T-TTTACTGATTACCATT
1 TCTTTACTGATTACCATT
2973 ACTTTTTACC
Statistics
Matches: 214, Mismatches: 27, Indels: 47
0.74 0.09 0.16
Matches are distributed among these distances:
14 12 0.06
15 10 0.05
17 3 0.01
18 1 0.00
19 2 0.01
20 9 0.04
21 74 0.35
22 76 0.36
23 7 0.03
24 1 0.00
25 19 0.09
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.51
Consensus pattern (22 bp):
TCTTTACTGATTACCATTTTAC
Found at i:2818 original size:35 final size:37
Alignment explanation
Indices: 2737--2855 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 37
2727 ATTTTACTCT
*
2737 TTACTGATTACTATTTTACTCTT-ACTAATTACCATTTTGCTC
1 TTACTGATTACTATTTTACTCTTAACTGATTACC----T--TC
*
2779 TTACTGATTACTATTTTATTC-TAACTGATTACCTT-
1 TTACTGATTACTATTTTACTCTTAACTGATTACCTTC
*
2814 TTACTGATTACTATTTTACTCTTTACTGATTACCTTC
1 TTACTGATTACTATTTTACTCTTAACTGATTACCTTC
2851 TTACT
1 TTACT
2856 TTTTACTGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
35 20 0.29
36 14 0.20
37 5 0.07
38 1 0.01
41 1 0.01
42 29 0.41
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (37 bp):
TTACTGATTACTATTTTACTCTTAACTGATTACCTTC
Found at i:2919 original size:101 final size:99
Alignment explanation
Indices: 2719--2972 Score: 357
Period size: 101 Copynumber: 2.5 Consensus size: 99
2709 TCTTTGAATT
* * * * **
2719 TGATTACCATTTTACTCTTTACTGATTA-CTATTTTACTCTTACTAATTACCATTTTGCTCTTAC
1 TGATTACTATTTTACTCTTTACTGATTACCT-TCTTACTTTTACTGATTACCATTTCACTCTTAC
* *
2783 TGATTACTATTTTATTCTAACTGATTACCTTTTAC
65 TGATTACCATTTTACTCTAACTGATTACCTTTTAC
*
2818 TGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTCACTCTTTA
1 TGATTACTATTTTACTCTTTACTGATTACCTTCTTAC-TTTTACTGATTACCATTTCACTC-TTA
* *
2883 CTGATTACCATTTTGCTCTTACTGATTACCTTTTAC
64 CTGATTACCATTTTACTCTAACTGATTACCTTTTAC
* *
2919 TAATTAGTATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCATT
1 TGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCATT
2973 ACTTTTTACC
Statistics
Matches: 138, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
99 32 0.23
100 36 0.26
101 70 0.51
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (99 bp):
TGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCATTTCACTCTTACT
GATTACCATTTTACTCTAACTGATTACCTTTTAC
Found at i:2930 original size:57 final size:57
Alignment explanation
Indices: 2851--3006 Score: 190
Period size: 57 Copynumber: 2.8 Consensus size: 57
2841 GATTACCTTC
* * * *
2851 TTACTTTTTACTGATTACTATTTCACTCTTTACTGATTACCATT-TTGCTCTTACTGA
1 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACC-TTCTTACTCTTACTGA
* *
2908 TTACCTTTTACTAATTAGTATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGA
1 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTCTTACTGA
* ** * *
2965 TTACC-ATTACTTTTTACCATTTTACTCTTTACTGATTGCCTT
1 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTT
3007 TTCACATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
56 33 0.38
57 53 0.62
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (57 bp):
TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTCTTACTGA
Found at i:2968 original size:28 final size:28
Alignment explanation
Indices: 2927--3026 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
2917 ACTAATTAGT
*
2927 ATTTTACTCTTTACTGATTACCTTCTTAC
1 ATTTTACTCATTACTGATTACCTT-TTAC
* * *
2956 -TTTTACTGATTAC-CATTACTTTTTACC
1 ATTTTACTCATTACTGATTACCTTTTA-C
* *
2983 ATTTTACTCTTTACTGATTGCCTTTTCAC
1 ATTTTACTCATTACTGATTACCTTTT-AC
*
3012 ATTTTTACTGATTAC
1 A-TTTTACTCATTAC
3027 AATTTGACTT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.05
27 8 0.15
28 22 0.40
29 10 0.18
30 12 0.22
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTTTACTCATTACTGATTACCTTTTAC
Found at i:3221 original size:40 final size:41
Alignment explanation
Indices: 3177--3262 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
3167 TAAATACCAT
**
3177 CTTTTAAC-CTTAATTACTGATATACTGACT-ACTTCTTTTA
1 CTTTTAACTCTTAATTACCAATATACTG-CTCACTTCTTTTA
* *
3217 CTTTT-ACTCTTAATTACCAATTTACTGCTCCCTTCTTTTA
1 CTTTTAACTCTTAATTACCAATATACTGCTCACTTCTTTTA
3257 CTTTTA
1 CTTTTA
3263 CTCCATTCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.50
Consensus pattern (41 bp):
CTTTTAACTCTTAATTACCAATATACTGCTCACTTCTTTTA
Found at i:3289 original size:32 final size:32
Alignment explanation
Indices: 3250--3506 Score: 86
Period size: 32 Copynumber: 7.8 Consensus size: 32
3240 ACTGCTCCCT
3250 TCTTTTACTTTTACTCCATTCTACTAATATCC
1 TCTTTTACTTTTACTCCATTCTACTAATATCC
* * *
3282 TCTTTTACCTTGATTCTTAATTACCCATT-TACTGAT-TACT
1 TCTTTTA-C----TT-TT-ACT--CCATTCTACTAATAT-CC
* * *
3322 TCTTTCACTCTTACTCCATTCTACTGAT-TACC
1 TCTTTTACTTTTACTCCATTCTACTAATAT-CC
* * * * *
3354 TTTTTTACTTTTACTCAATTCTATTGAT-TACT
1 TCTTTTACTTTTACTCCATTCTACTAATAT-CC
* * *
3386 TATTTTACTTTTAC-CCTATTCTACTGATTAT-T
1 TCTTTTACTTTTACTCC-ATTCTACT-AATATCC
* * *
3418 TATTTTACTTTTACTCCATTTTACTGATTACTTCC
1 TCTTTTACTTTTACTCCATTCTACT-AATA--TCC
*
3453 TC--TTACTTTTACTCCATT-TACTGATTACTTCC
1 TCTTTTACTTTTACTCCATTCTACT-AATA--TCC
*
3485 TC--TTACTTTCACTCCATTCTAC
1 TCTTTTACTTTTACTCCATTCTAC
3507 GGATTACTTC
Statistics
Matches: 184, Mismatches: 22, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
31 6 0.03
32 121 0.66
33 25 0.14
34 4 0.02
35 2 0.01
37 2 0.01
38 2 0.01
39 4 0.02
40 13 0.07
41 5 0.03
ACGTcount: A:0.21, C:0.25, G:0.03, T:0.51
Consensus pattern (32 bp):
TCTTTTACTTTTACTCCATTCTACTAATATCC
Found at i:3361 original size:72 final size:72
Alignment explanation
Indices: 3210--3346 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
3200 ACTGACTACT
* * * * * * *
3210 TCTTTTACTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTACTCCATTCTACT
1 TCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTCACTCTTACTCCATTCTACT
3275 AATATCC
66 AATATCC
* *
3282 TCTTTTACCTTGATTCTTAATTACCCATTTACTGATTACTTCTTTCACTCTTACTCCATTCTACT
1 TCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTCACTCTTACTCCATTCTACT
3347 GATTACCTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (72 bp):
TCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTCACTCTTACTCCATTCTACT
AATATCC
Found at i:3407 original size:64 final size:64
Alignment explanation
Indices: 3302--3516 Score: 251
Period size: 64 Copynumber: 3.4 Consensus size: 64
3292 TGATTCTTAA
* *
3302 TTAC-CCATT-TACTGATTACTTCTTTCACTCTTACTCCATTCTACTGATTACCTT-TTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTA-CTTCTTTTACTT
* * * * *
3364 TTACTCAATTCTATTGATTACTTATTTTACTTTTAC-CCTATTCTACTGATTATTTATTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCC-ATTCTACTGATTACTTCTTTTACTT
* * *
3428 TTACTCCATTTTACTGATTACTTCCTCTTACTTTTACTCCATT-TACTGATTACTTCCTCTTACT
1 TTACTCCATTCTACTGATTACTT-CTTTTACTTTTACTCCATTCTACTGATTACTT-CTTTTACT
3492 T
64 T
* *
3493 TCACTCCATTCTACGGATTACTTC
1 TTACTCCATTCTACTGATTACTTC
3517 CTCTTTTACT
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
62 4 0.03
63 8 0.06
64 74 0.57
65 41 0.32
66 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (64 bp):
TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTT
Found at i:3458 original size:17 final size:17
Alignment explanation
Indices: 3438--3491 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
3428 TTACTCCATT
3438 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
*
3455 TTACT-TTTAC-TCCAT-
1 TTACTGATTACTTCC-TC
3470 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
3487 TTACT
1 TTACT
3492 TTCACTCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 8 0.26
16 10 0.32
17 13 0.42
ACGTcount: A:0.19, C:0.28, G:0.04, T:0.50
Consensus pattern (17 bp):
TTACTGATTACTTCCTC
Found at i:8163 original size:3 final size:3
Alignment explanation
Indices: 8155--8197 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
8145 TTTTATAAAC
8155 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8198 TCGGTATCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9004 original size:22 final size:22
Alignment explanation
Indices: 8979--9027 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
8969 GAAGAAATAA
8979 GCAATGC-AGCAAAAAAAAAAAT
1 GCAATGCTAGC-AAAAAAAAAAT
* *
9001 GCAATTCTGGCAAAAAAAAAAT
1 GCAATGCTAGCAAAAAAAAAAT
9023 GCAAT
1 GCAAT
9028 TCCATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
GCAATGCTAGCAAAAAAAAAAT
Found at i:9037 original size:21 final size:22
Alignment explanation
Indices: 8985--9037 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
8975 ATAAGCAATG
8985 CAGCAAAAAAAAAAATGCAATTC
1 CAGC-AAAAAAAAAATGCAATTC
**
9008 TGGCAAAAAAAAAATGCAATTC
1 CAGCAAAAAAAAAATGCAATTC
*
9030 CATCAAAA
1 CAGCAAAA
9038 CAAGCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.15
Consensus pattern (22 bp):
CAGCAAAAAAAAAATGCAATTC
Done.