Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011428.1 Corchorus capsularis cultivar CVL-1 contig11449, 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: 56875
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1868 original size:43 final size:42
Alignment explanation
Indices: 1812--2094 Score: 189
Period size: 43 Copynumber: 6.5 Consensus size: 42
1802 CTGATCATTC
* **
1812 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
* * *
1854 TCTTACTTTTTACTGACTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTACTGATTAC---CT
* * * ** ** *
1902 TCTGCTCCTTTTTTAATGATTACTCTTTTA-T-TTTTTTTTTGCCT
1 T-T--TAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACCT
* * *
1946 TTTGCTTTTTTACTGATTAC-CTTTTACTTCTTACTGATTAGCT
1 TTTAC-TTTTTACTGATTACTATTTTAC-TCTTACTGATTACCT
* * *
1989 CTTTACTCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 -TTTACTTTTTACTGATTA-CTATTTTACTCTTACTGATTACCT
*
2032 TTTACTTCTTACTGATTACTATTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
* *
2073 ATTTACTCTTTACTGACTACTA
1 -TTTACTTTTTACTGATTACTA
2095 CCCTTTTTGA
Statistics
Matches: 187, Mismatches: 37, Indels: 34
0.72 0.14 0.13
Matches are distributed among these distances:
40 6 0.03
41 20 0.11
42 52 0.28
43 57 0.30
44 13 0.07
45 9 0.05
47 6 0.03
48 4 0.02
50 3 0.02
51 17 0.09
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
Found at i:1981 original size:21 final size:20
Alignment explanation
Indices: 1955--2088 Score: 153
Period size: 21 Copynumber: 6.3 Consensus size: 20
1945 TTTTGCTTTT
1955 TTACTGATTACCTTTTACTTC
1 TTACTGATTACCTTTTAC-TC
*
1976 TTACTGATTAGCTCTTTACTC
1 TTACTGATTACCT-TTTACTC
*
1997 TTTACTGATCACCTTTTTACTC
1 -TTACTGATTACC-TTTTACTC
*
2019 TTACTGATTTCCTTTTACTTC
1 TTACTGATTACCTTTTAC-TC
*
2040 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
2061 TTACTGATTA-CTATTTACTC
1 TTACTGATTACCT-TTTACTC
2081 TTTACTGA
1 -TTACTGA
2089 CTACTACCCT
Statistics
Matches: 98, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
19 1 0.01
20 13 0.13
21 55 0.56
22 28 0.29
23 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.51
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:2328 original size:55 final size:53
Alignment explanation
Indices: 2259--2449 Score: 268
Period size: 55 Copynumber: 3.6 Consensus size: 53
2249 ATTACATTTT
* *
2259 TTTTTACTTGATTACTGATTTACTGATTACTCTTACCTTAACTCTGATTAATCTC
1 TTTTTACTTAATTACTGATTTACTGATTACTCTTACCTT--CTTTGATTAATCTC
*
2314 TTTTTACTTAATTACTGA-TTACT-ATTAC-CTT---GTCTTTGATTAATCTC
1 TTTTTACTTAATTACTGATTTACTGATTACTCTTACCTTCTTTGATTAATCTC
*
2361 TTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCTTTGATTAATCTC
1 TTTTTACTTAATTACTGATTTACTGATTACTCTTACC-T-TCTTTGATTAATCTC
2416 TTTTTACTTAATTACTGATTTACTGATTACTCTT
1 TTTTTACTTAATTACTGATTTACTGATTACTCTT
2450 TACTTTGCTC
Statistics
Matches: 122, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
47 31 0.25
48 5 0.04
49 6 0.05
50 2 0.02
52 3 0.02
53 5 0.04
54 5 0.04
55 65 0.53
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (53 bp):
TTTTTACTTAATTACTGATTTACTGATTACTCTTACCTTCTTTGATTAATCTC
Found at i:2342 original size:47 final size:49
Alignment explanation
Indices: 2278--2445 Score: 200
Period size: 47 Copynumber: 3.4 Consensus size: 49
2268 GATTACTGAT
*
2278 TTACTGA-TTACT-CTTACCTTAACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACCTTAACTCTGATTAATCTCTTTTTACTTAA
** *
2325 TTACTGA-TTACT-ATTACCTTGTCTTTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACCTTAACTCTGATTAATCTCTTTTTACTTAA
* *
2372 TTACTGATTTACTGATTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTAC-CTTAAC---TC--TGATTAATCTCTTTTTACTTAA
2427 TTACTGATTTACTGATTAC
1 TTACTGATTTACTGATTAC
2446 TCTTTACTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
47 50 0.48
48 5 0.05
49 5 0.05
50 3 0.03
53 1 0.01
55 41 0.39
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (49 bp):
TTACTGATTTACTGATTACCTTAACTCTGATTAATCTCTTTTTACTTAA
Found at i:2376 original size:102 final size:104
Alignment explanation
Indices: 2259--2445 Score: 315
Period size: 102 Copynumber: 1.8 Consensus size: 104
2249 ATTACATTTT
* *
2259 TTTTTACTTGATTACTGATTTACTGATTACTCTTACCTTAACTCTGATTAATCTCTTTTTACTTA
1 TTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
2324 ATTACTGA-TTACT-ATTACCTTGTCTTTGATTAATCTC
66 ATTACTGATTTACTGATTACCTTGTCTTTGATTAATCTC
** *
2361 TTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTA
1 TTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
2426 ATTACTGATTTACTGATTAC
66 ATTACTGATTTACTGATTAC
2446 TCTTTACTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 68 0.87
103 5 0.06
104 5 0.06
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (104 bp):
TTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
ATTACTGATTTACTGATTACCTTGTCTTTGATTAATCTC
Found at i:2452 original size:7 final size:7
Alignment explanation
Indices: 2442--2566 Score: 61
Period size: 7 Copynumber: 18.7 Consensus size: 7
2432 GATTTACTGA
2442 TTACTCT
1 TTACTCT
2449 TTA--CT
1 TTACTCT
*
2454 TTGCTCT
1 TTACTCT
*
2461 TTACTATT
1 TTACT-CT
2469 TTACT-T
1 TTACTCT
*
2475 TT-TTCT
1 TTACTCT
**
2481 TTACTGA
1 TTACTCT
2488 TTACTCT
1 TTACTCT
2495 TTA--CT
1 TTACTCT
2500 TTACTCT
1 TTACTCT
2507 TTACTCT
1 TTACTCT
2514 TTA-TCAT
1 TTACTC-T
*
2521 TT--TTT
1 TTACTCT
**
2526 TTACTAA
1 TTACTCT
2533 TTACTCT
1 TTACTCT
**
2540 TTACTGA
1 TTACTCT
2547 TTACTCTT
1 TTACTC-T
*
2555 TTACTTT
1 TTACTCT
2562 TTACT
1 TTACT
2567 GATTGCCTTT
Statistics
Matches: 88, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
5 13 0.15
6 9 0.10
7 55 0.62
8 11 0.12
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.60
Consensus pattern (7 bp):
TTACTCT
Found at i:2462 original size:12 final size:12
Alignment explanation
Indices: 2442--2511 Score: 67
Period size: 12 Copynumber: 6.0 Consensus size: 12
2432 GATTTACTGA
2442 TTACTCTTTACT
1 TTACTCTTTACT
*
2454 TTGCTCTTTAC-
1 TTACTCTTTACT
2465 -TA-T-TTTACT
1 TTACTCTTTACT
**
2474 TTTTTCTTTACT
1 TTACTCTTTACT
2486 GATTACTCTTTACT
1 --TTACTCTTTACT
2500 TTACTCTTTACT
1 TTACTCTTTACT
2512 CTTTATCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 5 0.11
9 1 0.02
10 2 0.04
11 1 0.02
12 28 0.60
14 10 0.21
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.60
Consensus pattern (12 bp):
TTACTCTTTACT
Found at i:2473 original size:20 final size:20
Alignment explanation
Indices: 2448--2485 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2438 CTGATTACTC
2448 TTTACTTTGCTCTTTACTAT
1 TTTACTTTGCTCTTTACTAT
**
2468 TTTACTTTTTTCTTTACT
1 TTTACTTTGCTCTTTACT
2486 GATTACTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTACTTTGCTCTTTACTAT
Found at i:2492 original size:46 final size:44
Alignment explanation
Indices: 2434--2566 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 44
2424 TAATTACTGA
*
2434 TTTACTGATTACTCTTTACTTTGCTCTTTACTATTTTACTTTTTT
1 TTTACTGATTACTCTTTACTTTACTCTTTACT-TTTTACTTTTTT
* *
2479 CTTTACTGATTACTCTTTACTTTACTCTTTACTCTTTATCATTTTT
1 -TTTACTGATTACTCTTTACTTTACTCTTTACTTTTTA-CTTTTTT
*
2525 TTTACTAATTACTCTTTACTGATTACTCTTTTACTTTTTACT
1 TTTACTGATTACTCTTTACT--TTACTC-TTTACTTTTTACT
2567 GATTGCCTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
45 23 0.30
46 37 0.48
47 7 0.09
48 10 0.13
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (44 bp):
TTTACTGATTACTCTTTACTTTACTCTTTACTTTTTACTTTTTT
Found at i:2613 original size:36 final size:37
Alignment explanation
Indices: 2544--2614 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
2534 TACTCTTTAC
* * **
2544 TGATTACTCTTTTACTTTTTACTGATTGCCTTTTTGT
1 TGATTACTCTTTTACTTCTTACTGAATAACTTTTTGT
2581 TGATTAC-CTTTTACTTCTTACTGAATAACTTTTT
1 TGATTACTCTTTTACTTCTTACTGAATAACTTTTT
2615 ACTCTTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.18, C:0.17, G:0.08, T:0.56
Consensus pattern (37 bp):
TGATTACTCTTTTACTTCTTACTGAATAACTTTTTGT
Found at i:2620 original size:21 final size:21
Alignment explanation
Indices: 2589--2689 Score: 98
Period size: 22 Copynumber: 4.7 Consensus size: 21
2579 GTTGATTACC
2589 TTTTACTTCTTACTGAATAACT
1 TTTTAC-TCTTACTGAATAACT
* *
2611 TTTTACTCTTTACTGATTACCT
1 TTTTACTC-TTACTGAATAACT
* *
2633 TTTTACTCTTACTG-ATTACC
1 TTTTACTCTTACTGAATAACT
**
2653 TTTTACTTCTTACTG-ATTGCT
1 TTTTAC-TCTTACTGAATAACT
2674 ATTTTACTCTTACTGA
1 -TTTTACTCTTACTGA
2690 TTACTATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.12
21 28 0.42
22 31 0.46
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTTACTCTTACTGAATAACT
Found at i:2660 original size:64 final size:63
Alignment explanation
Indices: 2540--3002 Score: 412
Period size: 64 Copynumber: 7.3 Consensus size: 63
2530 TAATTACTCT
* * *
2540 TTACTGATTACTCTTTTACTTTTTACTGATTGC-CTTTT--T-GT--TGATTACCTTTTACTTC
1 TTACTGATTACT-TTTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
* *
2598 TTACTGAATAACTTTTTACTCTTTACTGATTACCT-TTTTACTCTTACTGATTACCTTTTACTTC
1 TTACTG-ATTACTTTTTACTTTTTACTGATTA-CTATTTTACTCTTACTGATTACCTTTTACTTC
* * * * * *
2662 TTACTGATTGCTATTTTAC-TCTTACTGATTACTA-TTTACTTTTTTGCCGATTACTATTTTAC-
1 TTACTGATTACT-TTTTACTTTTTACTGATTACTATTTTAC--TCTTACTGATTAC-CTTTTACT
2724 TC
62 TC
* * *
2726 TTACTAATTACCTTTTACTTTTTACTGATTGCTATTTTACTCTTACTGATTACCTTCTTACTT-
1 TTACTGATTACTTTTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTT-TTACTTC
* * * *
2789 TCTACTGATTATTATTTTACTTTTTTACTGATTAC-CTTTTACTTCTTACTGATTGCTATTTTAC
1 T-TACTGATTACT-TTTTAC-TTTTTACTGATTACTATTTTAC-TCTTACTGATTAC-CTTTTAC
2853 -TC
61 TTC
* * * * * *
2855 TTACTGATTACTATTTACTTTTTTGCCGATTACTATTATACTCTTACTAATTACCTTTTACTTT
1 TTACTGATTACTTTTTAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
* * * * * *
2919 TTACTGATTACTATTCACTTTTTTGCCGATTACTATTTTACTCTTACTAATTACCTTTTACTTT
1 TTACTGATTACTTTTTAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
*
2983 TTACTGACTACTATTTTACT
1 TTACTGATTACT-TTTTACT
3003 CTTTGAATTT
Statistics
Matches: 336, Mismatches: 43, Indels: 46
0.79 0.10 0.11
Matches are distributed among these distances:
58 23 0.07
59 10 0.03
61 1 0.00
62 10 0.03
63 41 0.12
64 176 0.52
65 43 0.13
66 30 0.09
67 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.54
Consensus pattern (63 bp):
TTACTGATTACTTTTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
Found at i:2690 original size:21 final size:21
Alignment explanation
Indices: 2581--3005 Score: 307
Period size: 21 Copynumber: 19.9 Consensus size: 21
2571 GCCTTTTTGT
*
2581 TGATTAC-CTTTTACTTCTTAC
1 TGATTACTATTTTAC-TCTTAC
*
2602 TGAATAACT-TTTTACTCTTTAC
1 TG-ATTACTATTTTACTC-TTAC
2624 TGATTACCT-TTTTACTCTTAC
1 TGATTA-CTATTTTACTCTTAC
*
2645 TGATTAC-CTTTTACTTCTTAC
1 TGATTACTATTTTAC-TCTTAC
*
2666 TGATTGCTATTTTACTCTTAC
1 TGATTACTATTTTACTCTTAC
* *
2687 TGATTACTA-TTTACTTTTTTGC
1 TGATTACTATTTTAC--TCTTAC
*
2709 CGATTACTATTTTACTCTTAC
1 TGATTACTATTTTACTCTTAC
* * *
2730 TAATTAC-CTTTTACTTTTTAC
1 TGATTACTATTTTAC-TCTTAC
*
2751 TGATTGCTATTTTACTCTTAC
1 TGATTACTATTTTACTCTTAC
* *
2772 TGATTACCT-TCTTACTTTCTAC
1 TGATTA-CTATTTTACTCT-TAC
* *
2794 TGATTATTATTTTACTTTTTTAC
1 TGATTACTATTTTAC--TCTTAC
*
2817 TGATTAC-CTTTTACTTCTTAC
1 TGATTACTATTTTAC-TCTTAC
*
2838 TGATTGCTATTTTACTCTTAC
1 TGATTACTATTTTACTCTTAC
* *
2859 TGATTACTA-TTTACTTTTTTGC
1 TGATTACTATTTTAC--TCTTAC
* *
2881 CGATTACTATTATACTCTTAC
1 TGATTACTATTTTACTCTTAC
* * *
2902 TAATTAC-CTTTTACTTTTTAC
1 TGATTACTATTTTAC-TCTTAC
* * *
2923 TGATTACTA-TTCACTTTTTTGC
1 TGATTACTATTTTAC--TCTTAC
*
2945 CGATTACTATTTTACTCTTAC
1 TGATTACTATTTTACTCTTAC
* * *
2966 TAATTAC-CTTTTACTTTTTAC
1 TGATTACTATTTTAC-TCTTAC
*
2987 TGACTACTATTTTACTCTT
1 TGATTACTATTTTACTCTT
3006 TGAATTTGAT
Statistics
Matches: 321, Mismatches: 56, Indels: 54
0.74 0.13 0.13
Matches are distributed among these distances:
20 34 0.11
21 152 0.47
22 110 0.34
23 22 0.07
24 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.53
Consensus pattern (21 bp):
TGATTACTATTTTACTCTTAC
Found at i:2715 original size:85 final size:84
Alignment explanation
Indices: 2589--2933 Score: 451
Period size: 85 Copynumber: 4.0 Consensus size: 84
2579 GTTGATTACC
* * * * *
2589 TTTTACTTCTTACTGAATAACTTTTTACTCTTTACTGATTACCT-TTTTACTCTTACTGATTACC
1 TTTTAC-TCTTACTG-ATTACTATTTACTTTTTACCGATTA-CTATTTTACTCTTACTAATTACC
2653 TTTTACTTCTTACTGATTGCTA
63 TTTTACTTCTTACTGATTGCTA
*
2675 TTTTACTCTTACTGATTACTATTTACTTTTTTGCCGATTACTATTTTACTCTTACTAATTACCTT
1 TTTTACTCTTACTGATTACTATTTAC-TTTTTACCGATTACTATTTTACTCTTACTAATTACCTT
*
2740 TTACTTTTTACTGATTGCTA
65 TTACTTCTTACTGATTGCTA
* * * * *
2760 TTTTACTCTTACTGATTACCT-TCTTACTTTCTACTGATTATTATTTTACTTTTTTACTGATTAC
1 TTTTACTCTTACTGATTA-CTAT-TTACTTTTTACCGATTACTATTTTAC--TCTTACTAATTAC
2824 CTTTTACTTCTTACTGATTGCTA
62 CTTTTACTTCTTACTGATTGCTA
* *
2847 TTTTACTCTTACTGATTACTATTTACTTTTTTGCCGATTACTATTATACTCTTACTAATTACCTT
1 TTTTACTCTTACTGATTACTATTTAC-TTTTTACCGATTACTATTTTACTCTTACTAATTACCTT
* *
2912 TTACTTTTTACTGATTACTA
65 TTACTTCTTACTGATTGCTA
2932 TT
1 TT
2934 CACTTTTTTG
Statistics
Matches: 228, Mismatches: 23, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
84 12 0.05
85 129 0.57
86 18 0.08
87 69 0.30
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (84 bp):
TTTTACTCTTACTGATTACTATTTACTTTTTACCGATTACTATTTTACTCTTACTAATTACCTTT
TACTTCTTACTGATTGCTA
Found at i:2731 original size:14 final size:14
Alignment explanation
Indices: 2712--2772 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2702 TTTTTGCCGA
2712 TTACTATTTTACTC
1 TTACTATTTTACTC
* *
2726 TTACTA-ATTACCTT
1 TTACTATTTTA-CTC
*
2740 TTACT-TTTTACTGA
1 TTACTATTTTACT-C
*
2754 TTGCTATTTTACTC
1 TTACTATTTTACTC
2768 TTACT
1 TTACT
2773 GATTACCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
13 5 0.14
14 24 0.67
15 7 0.19
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (14 bp):
TTACTATTTTACTC
Found at i:2838 original size:236 final size:235
Alignment explanation
Indices: 2581--3005 Score: 635
Period size: 236 Copynumber: 1.8 Consensus size: 235
2571 GCCTTTTTGT
*
2581 TGATTACCTTTTACTTCTTACTGAATAACT-TTTTACTCTTTACTGATTACCTTTTTAC-TCTTA
1 TGATTACCTTTTACTTCTTACTG-ATAACTATTTTACTC-TTACTGATTA-CTATTTACTTCTTA
* * * *
2644 CTGATTACCT-TT-TACTTCTTACTGATTGCTATTTTAC-TCTTACTGATTACTATTTACTTTTT
63 CCGATTA-CTATTATAC-TCTTACTAATTAC-ATTTTACTTCTTACTGATTACTATTCACTTTTT
* *
2706 TGCCGATTACTATTTTACTCTTACTAATTACCTTTTACTTTTTACTGATTGCTATTTTACTCTTA
125 TGCCGATTACTATTTTACTCTTACTAATTACCTTTTACTTTTTACTGACTACTATTTTACTCTTA
2771 CTGATTACCTTCTTACTTTCTACTGATTATTATTTTACTTTTTTAC
190 CTGATTACCTTCTTACTTTCTACTGATTATTATTTTACTTTTTTAC
** * *
2817 TGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTTTGCC
1 TGATTACCTTTTACTTCTTACTGATAACTATTTTACTCTTACTGATTACTATTTAC-TTCTTACC
* *
2882 GATTACTATTATACTCTTACTAATTACCTTTTACTTTTTACTGATTACTATTCACTTTTTTGCCG
65 GATTACTATTATACTCTTACTAATTACATTTTACTTCTTACTGATTACTATTCACTTTTTTGCCG
2947 ATTACTATTTTACTCTTACTAATTACCTTTTACTTTTTACTGACTACTATTTTACTCTT
130 ATTACTATTTTACTCTTACTAATTACCTTTTACTTTTTACTGACTACTATTTTACTCTT
3006 TGAATTTGAT
Statistics
Matches: 170, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
234 7 0.04
235 22 0.13
236 138 0.81
237 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.53
Consensus pattern (235 bp):
TGATTACCTTTTACTTCTTACTGATAACTATTTTACTCTTACTGATTACTATTTACTTCTTACCG
ATTACTATTATACTCTTACTAATTACATTTTACTTCTTACTGATTACTATTCACTTTTTTGCCGA
TTACTATTTTACTCTTACTAATTACCTTTTACTTTTTACTGACTACTATTTTACTCTTACTGATT
ACCTTCTTACTTTCTACTGATTATTATTTTACTTTTTTAC
Found at i:2846 original size:172 final size:171
Alignment explanation
Indices: 2581--2933 Score: 570
Period size: 172 Copynumber: 2.1 Consensus size: 171
2571 GCCTTTTTGT
* *
2581 TGATTAC-CTTTTACTTCTTACTGAATAACTTTTTACTCTTTACTGATTACCTTTTTACTCTTAC
1 TGATTACTATTTTACTTCTTACTGAATAACTTCTTACTCTTTACTGATTACCTTTTTACTCTTAC
2645 TGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTTTGCC
66 TGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTTTGCC
*
2710 GATTACTATTTTACTCTTACTAATTACCTTTTACTTTTTAC
131 GATTACTATTATACTCTTACTAATTACCTTTTACTTTTTAC
* * * * *
2751 TGATTGCTATTTTAC-TCTTACTGATTACCTTCTTACT-TTCTACTGATTA-TTATTTTACTTTT
1 TGATTACTATTTTACTTCTTACTGAATAACTTCTTACTCTT-TACTGATTACCT-TTTTAC--TC
2813 TTACTGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTT
62 TTACTGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTT
2878 TGCCGATTACTATTATACTCTTACTAATTACCTTTTACTTTTTAC
127 TGCCGATTACTATTATACTCTTACTAATTACCTTTTACTTTTTAC
2923 TGATTACTATT
1 TGATTACTATT
2934 CACTTTTTTG
Statistics
Matches: 169, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
169 3 0.02
170 40 0.24
171 6 0.04
172 120 0.71
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.54
Consensus pattern (171 bp):
TGATTACTATTTTACTTCTTACTGAATAACTTCTTACTCTTTACTGATTACCTTTTTACTCTTAC
TGATTACCTTTTACTTCTTACTGATTGCTATTTTACTCTTACTGATTACTATTTACTTTTTTGCC
GATTACTATTATACTCTTACTAATTACCTTTTACTTTTTAC
Found at i:2967 original size:14 final size:14
Alignment explanation
Indices: 2948--3005 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
2938 TTTTTGCCGA
2948 TTACTATTTTACTC
1 TTACTATTTTACTC
* *
2962 TTACTA-ATTACCTT
1 TTACTATTTTA-CTC
2976 TTACT-TTTTACTGAC
1 TTACTATTTTACT--C
2991 -TACTATTTTACTC
1 TTACTATTTTACTC
3004 TT
1 TT
3006 TGAATTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 6 0.18
14 21 0.62
15 7 0.21
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.55
Consensus pattern (14 bp):
TTACTATTTTACTC
Found at i:2987 original size:85 final size:83
Alignment explanation
Indices: 2589--2980 Score: 391
Period size: 85 Copynumber: 4.6 Consensus size: 83
2579 GTTGATTACC
* *
2589 TTTTACTTCTTACTGAATAACT-TTTTACTCTTTACTGATTACCTTTTTACTCTTACTGATTACC
1 TTTTAC-TCTTACTG-ATTACTATTTTACT-TTTACTGATTACC-TTTTACTCTTACTAATTACC
2653 TTTTACTTCTTACTGATTGCTA
62 TTTTACTTCTTACTGATTGCTA
* * *
2675 TTTTACTCTTACTGATTACTA-TTTACTTTTTTGCCGATTACTATTTTACTCTTACTAATTACCT
1 TTTTACTCTTACTGATTACTATTTTAC--TTTTACTGATTAC-CTTTTACTCTTACTAATTACCT
*
2739 TTTACTTTTTACTGATTGCTA
63 TTTACTTCTTACTGATTGCTA
* ** * *
2760 TTTTACTCTTACTGATTACCT-TCTTACTTTCTACTGATTATTATTTTACTTTTTTACTGATTAC
1 TTTTACTCTTACTGATTA-CTATTTTACTTT-TACTGATTA-CCTTTTAC--TCTTACTAATTAC
2824 CTTTTACTTCTTACTGATTGCTA
61 CTTTTACTTCTTACTGATTGCTA
* *
2847 TTTTACTCTTACTGATTACTA-TTTACTTTTTTGCCGATTA-CTATTATACTCTTACTAATTACC
1 TTTTACTCTTACTGATTACTATTTTAC--TTTTACTGATTACCT-TT-TACTCTTACTAATTACC
* *
2910 TTTTACTTTTTACTGATTACTA
62 TTTTACTTCTTACTGATTGCTA
* * * * * *
2932 -TTCACTTTTTTGCCGATTACTATTTTACTCTTACTAATTACCTTTTACT
1 TTTTAC--TCTTACTGATTACTATTTTACTTTTACTGATTACCTTTTACT
2981 TTTTACTGAC
Statistics
Matches: 258, Mismatches: 29, Indels: 40
0.79 0.09 0.12
Matches are distributed among these distances:
84 21 0.08
85 133 0.52
86 35 0.14
87 66 0.26
88 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (83 bp):
TTTTACTCTTACTGATTACTATTTTACTTTTACTGATTACCTTTTACTCTTACTAATTACCTTTT
ACTTCTTACTGATTGCTA
Found at i:9683 original size:21 final size:20
Alignment explanation
Indices: 9658--9696 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9648 TATAGAAAAT
9658 AACAAATAATGTACAAATGCA
1 AACAAATAAT-TACAAATGCA
* *
9679 AACAACTAATTTCAAATG
1 AACAAATAATTACAAATG
9697 AACGAATAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (20 bp):
AACAAATAATTACAAATGCA
Found at i:25162 original size:13 final size:14
Alignment explanation
Indices: 25146--25176 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25136 ATAGATAAAG
25146 AAAATAAC-TTAAT
1 AAAATAACTTTAAT
25159 AAAATAACTTTAAT
1 AAAATAACTTTAAT
25173 AAAA
1 AAAA
25177 ACAAAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAACTTTAAT
Found at i:26568 original size:35 final size:35
Alignment explanation
Indices: 26522--26662 Score: 212
Period size: 35 Copynumber: 4.0 Consensus size: 35
26512 GGATTATTTA
*
26522 AGATCAACTCTGATCATCGAAAACTTTTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
26557 AGATCAACTCTGATCGTCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
26592 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* * *
26627 AGATCAACTTTGATC-TCTGAAAGCTTTTTGAAATG
1 AGATCAACTCTGATCATC-GAAAACTTCTTGAAATG
26662 A
1 A
26663 CCGCACTGGA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
34 2 0.02
35 95 0.98
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:36242 original size:13 final size:13
Alignment explanation
Indices: 36213--36260 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
36203 CTGTTTGGGT
*
36213 ATTTTGGTTTATT
1 ATTTTGGTTTATG
*
36226 ATTTTGGTTTGTG
1 ATTTTGGTTTATG
*
36239 ATTTT-GATTATG
1 ATTTTGGTTTATG
*
36251 ATATTGGTTT
1 ATTTTGGTTT
36261 TAACGATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62
Consensus pattern (13 bp):
ATTTTGGTTTATG
Found at i:44103 original size:15 final size:15
Alignment explanation
Indices: 44085--44117 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
44075 TAAATTTCAA
44085 TAAAATA-AAATATAT
1 TAAAATATAAATAT-T
44100 TAAAATATAAATATT
1 TAAAATATAAATATT
44115 TAA
1 TAA
44118 TTTGTATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATAAATATT
Found at i:53570 original size:50 final size:51
Alignment explanation
Indices: 53511--53606 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
53501 TAGTCATTAT
* *
53511 GTTTGACAAACTAA-AAACTAAATTTGACAGAAAAATAGAACCATATTTTG
1 GTTTGACAAACCAACAAACTAAATTTGACAGAAAAATAAAACCATATTTTG
*
53561 GTTTGACAAACCAACAAACTAAATTTGACTGAAAAATAAAACCATA
1 GTTTGACAAACCAACAAACTAAATTTGACAGAAAAATAAAACCATA
53607 ATAAGGTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 13 0.31
51 29 0.69
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (51 bp):
GTTTGACAAACCAACAAACTAAATTTGACAGAAAAATAAAACCATATTTTG
Done.