Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009565.1 Corchorus olitorius cultivar O-4 contig09597, 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: 3534
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Found at i:2119 original size:13 final size:13
Alignment explanation
Indices: 2086--2119 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2076 ATTTTACCAA
2086 TTACTCTTTCATT
1 TTACTCTTTCATT
*
2099 AT-CTCTTTCATT
1 TTACTCTTTCATT
2111 TTACTCTTT
1 TTACTCTTT
2120 AATTACCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (13 bp):
TTACTCTTTCATT
Found at i:2226 original size:19 final size:19
Alignment explanation
Indices: 2170--2289 Score: 117
Period size: 19 Copynumber: 6.4 Consensus size: 19
2160 AATTTTCATT
2170 CTTACCAAATTCTTTTTTA
1 CTTACCAAATTCTTTTTTA
2189 CTTTACCAAAATTTCTTTTTTA
1 C-TTACC-AAA-TTCTTTTTTA
2211 -TTACCAAATTCTTTTTTA
1 CTTACCAAATTCTTTTTTA
* *
2229 GTTACC-AATTC-CTTTTA
1 CTTACCAAATTCTTTTTTA
**
2246 CTTTA-TTAA-T-TTTTTTA
1 C-TTACCAAATTCTTTTTTA
*
2263 ATTACCAAATTCTTTTTTA
1 CTTACCAAATTCTTTTTTA
2282 CTTACCAA
1 CTTACCAA
2290 TTTTACTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.04
17 13 0.16
18 21 0.25
19 23 0.28
20 10 0.12
21 3 0.04
22 10 0.12
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (19 bp):
CTTACCAAATTCTTTTTTA
Found at i:2253 original size:40 final size:39
Alignment explanation
Indices: 2171--2244 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
2161 ATTTTCATTC
* *
2171 TTACCAAATTCTTTTTTACTTTACCAAAATTTCTTTTTTA
1 TTACCAAATTCTTTTTTACGTTACC-AAATTCCTTTTTTA
2211 TTACCAAATTCTTTTTTA-GTTACC-AATTCCTTTT
1 TTACCAAATTCTTTTTTACGTTACCAAATTCCTTTT
2245 ACTTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 9 0.28
39 5 0.16
40 18 0.56
ACGTcount: A:0.26, C:0.19, G:0.01, T:0.54
Consensus pattern (39 bp):
TTACCAAATTCTTTTTTACGTTACCAAATTCCTTTTTTA
Found at i:2313 original size:27 final size:27
Alignment explanation
Indices: 2274--2749 Score: 272
Period size: 27 Copynumber: 18.1 Consensus size: 27
2264 TTACCAAATT
* *
2274 CTTTTTTACTTACCAATTTTACTTTTG
1 CTTTTTTAATTACCAATTTTACTTTTA
* *
2301 CTCTTTTAATTACCAAATTCTT--TTTAATT
1 CTTTTTTAATTACC-AATT-TTACTTT--TA
*
2330 CTTTTTAATTACTTACCAATTTTACTTTTA
1 C-TTTT--TTAATTACCAATTTTACTTTTA
* *
2360 CTCTTTTAATTACCAAATTCTT--TTTAA
1 CTTTTTTAATTACC-AATT-TTACTTTTA
*
2387 TTCTTTTTAATTACTTGCCAATTTTACTTTTA
1 CT-TTTTTAATTA----CCAATTTTACTTTTA
*
2419 CTCTTTTAATTACCAA----A---TT-
1 CTTTTTTAATTACCAATTTTACTTTTA
*
2438 C-TTTTTACTTACCAATTTTACTTTTA
1 CTTTTTTAATTACCAATTTTACTTTTA
* *
2464 CTCTTTTAATTACCAA-ATT-CTCTTT-
1 CTTTTTTAATTACCAATTTTACT-TTTA
2489 -TTTTTTAATTACCAATTTTACTTTTA
1 CTTTTTTAATTACCAATTTTACTTTTA
* *
2515 CTTTTTTTAATTACCAA-ATT-CTCTT-
1 C-TTTTTTAATTACCAATTTTACTTTTA
2540 -TTTTTTAATTACCAATTTTACTTTTA
1 CTTTTTTAATTACCAATTTTACTTTTA
*
2566 CTTTTTTTACTTACCAAATTCTT-CTTTTA
1 C-TTTTTTAATTACC-AATT-TTACTTTTA
* *
2595 CTTTTTTTTACTTACCAA-ATT-CTTTT-
1 C--TTTTTTAATTACCAATTTTACTTTTA
*
2621 TTTCTTTTAATTACCAATTTTACTTTTA
1 CTT-TTTTAATTACCAATTTTACTTTTA
*
2649 CTTTTTTACTTACCAA----A---TT-
1 CTTTTTTAATTACCAATTTTACTTTTA
2668 CGTTTTTTAATTACCAATTTTACTTTTA
1 C-TTTTTTAATTACCAATTTTACTTTTA
* *
2696 CTTTTTTTACTTACCAA-ATT-C--TT-
1 C-TTTTTTAATTACCAATTTTACTTTTA
*
2719 CTTTTTTAATTACCAATTTTACTTTTG
1 CTTTTTTAATTACCAATTTTACTTTTA
2746 CTTT
1 CTTT
2750 CTTTTTACTT
Statistics
Matches: 352, Mismatches: 38, Indels: 118
0.69 0.07 0.23
Matches are distributed among these distances:
18 12 0.03
19 2 0.01
20 18 0.05
22 15 0.04
23 20 0.06
24 22 0.06
25 25 0.07
26 17 0.05
27 78 0.22
28 61 0.17
29 22 0.06
30 25 0.07
31 17 0.05
32 18 0.05
ACGTcount: A:0.24, C:0.18, G:0.01, T:0.57
Consensus pattern (27 bp):
CTTTTTTAATTACCAATTTTACTTTTA
Found at i:2354 original size:59 final size:59
Alignment explanation
Indices: 2279--2444 Score: 314
Period size: 59 Copynumber: 2.8 Consensus size: 59
2269 AAATTCTTTT
*
2279 TTACTTACCAATTTTACTTTTGCTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
1 TTACTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
2338 TTACTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
1 TTACTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
*
2397 TTACTTGCCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTA
1 TTACTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTA
2445 CTTACCAATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 105 1.00
ACGTcount: A:0.26, C:0.17, G:0.01, T:0.55
Consensus pattern (59 bp):
TTACTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
Found at i:2444 original size:32 final size:31
Alignment explanation
Indices: 2290--2447 Score: 106
Period size: 32 Copynumber: 5.3 Consensus size: 31
2280 TACTTACCAA
2290 TTTTACTTTTGCTCTTTTAATTACCAAATTCT
1 TTTTACTTTT-CTCTTTTAATTACCAAATTCT
* ** * *
2322 TTTTA--ATTCT-TTTTAATTA-CTTA-CCAA
1 TTTTACTTTTCTCTTTTAATTACCAAATTC-T
2349 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1 TTTTACTTTT-CTCTTTTAATTACCAAATTCT
* *
2381 TTTTA--ATTCT-TTTTAATTA-C---TTGCCAA
1 TTTTACTTTTCTCTTTTAATTACCAAATT--C-T
2408 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1 TTTTACTTTT-CTCTTTTAATTACCAAATTCT
2440 TTTTACTT
1 TTTTACTT
2448 ACCAATTTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 36
0.65 0.10 0.25
Matches are distributed among these distances:
24 2 0.02
26 2 0.02
27 13 0.14
28 18 0.19
29 8 0.09
30 8 0.09
31 18 0.19
32 21 0.22
33 2 0.02
35 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTACTTTTCTCTTTTAATTACCAAATTCT
Found at i:2513 original size:22 final size:23
Alignment explanation
Indices: 2459--2744 Score: 115
Period size: 28 Copynumber: 11.4 Consensus size: 23
2449 CCAATTTTAC
*
2459 TTTTAC-TCTTTTAATTACCAAA
1 TTTTACTTTTTTTAATTACCAAA
*
2481 TTCTCT-TTTTTTTTAATTACCAATTTTA
1 TT-T-TACTTTTTTTAATTACCAA----A
2509 CTTTTACTTTTTTTAATTACCAAA
1 -TTTTACTTTTTTTAATTACCAAA
*
2533 TTCT-CTTTTTTTTAATTACCAATTTTA
1 TTTTAC-TTTTTTTAATTACCAA----A
*
2560 CTTTTACTTTTTTTACTTACCAAA
1 -TTTTACTTTTTTTAATTACCAAA
*
2584 TTCTTCTTTTACTTTTTTTTACTTACCAAA
1 ------TTTTAC-TTTTTTTAATTACCAAA
**
2614 TTCTTTTTTTCTTTTAATTACC-AA
1 TT-TTACTTT-TTTTAATTACCAAA
*
2638 TTTTACTTTTACTTTTTTACTTACCAAA
1 TTTTAC---T--TTTTTTAATTACCAAA
*
2666 --TT-CGTTTTTTAATTACCAATTTTA
1 TTTTACTTTTTTTAATTACCAA----A
*
2690 CTTTTACTTTTTTTACTTACCAAA
1 -TTTTACTTTTTTTAATTACCAAA
2714 TTCTT-C-TTTTTTAATTACC-AA
1 TT-TTACTTTTTTTAATTACCAAA
2735 TTTTACTTTT
1 TTTTACTTTT
2745 GCTTTCTTTT
Statistics
Matches: 206, Mismatches: 17, Indels: 82
0.68 0.06 0.27
Matches are distributed among these distances:
20 16 0.08
21 5 0.02
22 18 0.09
23 25 0.12
24 30 0.15
25 13 0.06
26 3 0.01
27 14 0.07
28 55 0.27
29 10 0.05
30 17 0.08
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTACTTTTTTTAATTACCAAA
Found at i:2571 original size:51 final size:50
Alignment explanation
Indices: 2342--2593 Score: 307
Period size: 51 Copynumber: 4.9 Consensus size: 50
2332 TTTTAATTAC
*
2342 TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAA
1 TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTC--TCT--TT-TTTTTAA
*
2397 TTACTTGCCAATTTTACTTTTACTCTTTTAATTACCAAA-T-TC---TTTTTAC
1 TTA----CCAATTTTACTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTAA
2446 TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTTAA
1 TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTC-TTTTTTTTAA
*
2497 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAA
1 TTACCAATTTTACTTTTAC-TCTTTTAATTACCAAATTCTCTTTTTTTTAA
* *
2548 TTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTCTTTT
1 TTACCAATTTTACTTTTAC-TCTTTTAATTACCAAATTC-TCTTTT
2594 ACTTTTTTTT
Statistics
Matches: 180, Mismatches: 5, Indels: 27
0.85 0.02 0.13
Matches are distributed among these distances:
45 32 0.18
46 1 0.01
47 2 0.01
49 9 0.05
51 73 0.41
52 26 0.14
55 4 0.02
58 1 0.01
59 32 0.18
ACGTcount: A:0.25, C:0.18, G:0.00, T:0.57
Consensus pattern (50 bp):
TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTAA
Found at i:2594 original size:35 final size:33
Alignment explanation
Indices: 2555--2629 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 33
2545 TAATTACCAA
2555 TTTTACTTTTACTTTTTTTACTTACCAAATTCTT
1 TTTTACTTTTA-TTTTTTTACTTACCAAATTCTT
2589 CTTTTAC---T-TTTTTTTACTTACCAAATTCTT
1 -TTTTACTTTTATTTTTTTACTTACCAAATTCTT
*
2619 TTTTTCTTTTA
1 TTTTACTTTTA
2630 ATTACCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
29 5 0.14
30 22 0.63
32 2 0.06
35 6 0.17
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTTACTTTTATTTTTTTACTTACCAAATTCTT
Found at i:2681 original size:47 final size:47
Alignment explanation
Indices: 2566--2967 Score: 422
Period size: 47 Copynumber: 8.2 Consensus size: 47
2556 TTTACTTTTA
*
2566 CTTTTTTTACTTACCAAATTCTT-CTTTTACTTTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACC-AATT-TTACTTTTAC--TTTTTTACTTACCAAATT
2616 CTTTTTTTCTTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATT
1 C----TTT-TTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATT
*
2668 CGTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACCAATTTTACTTTTAC-TTTTTTACTTACCAAATT
*
2716 CTTCTTTTTTAATTACCAATTTTACTTTTGCTTTCTTTTTACTTACCAAATT
1 C-T-TTTTTTAATTACCAATTTTACTTTTAC--T-TTTTTACTTACCAAATT
* * *
2768 C--TCTTTACTTACCAATTTTACTTTTATTTTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACCAATTTTACTTTTA--CTTTTTTACTTACCAAATT
* *
2815 C--TCTTTACTTACCAATTTTACTTTTACTCTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACCAATTTTACTTTTA--CTTTTTTACTTACCAAATT
** * *
2862 CTATTTTTTTGCTTACCAATTTTACTTTTACTCTTTTAATTACC-AATT
1 C--TTTTTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATT
2910 -TTTTTTTAATTACCAATTTTACTTTTACTTTCTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACCAATTTTACTTTTA----CTTTTTTACTTACCAAATT
2960 CTTTTTTT
1 CTTTTTTT
2968 TATCAATTTT
Statistics
Matches: 311, Mismatches: 18, Indels: 45
0.83 0.05 0.12
Matches are distributed among these distances:
45 25 0.08
47 88 0.28
48 48 0.15
49 24 0.08
50 31 0.10
51 32 0.10
52 37 0.12
53 2 0.01
54 14 0.05
55 10 0.03
ACGTcount: A:0.23, C:0.19, G:0.01, T:0.58
Consensus pattern (47 bp):
CTTTTTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATT
Found at i:2693 original size:130 final size:131
Alignment explanation
Indices: 2439--2723 Score: 447
Period size: 130 Copynumber: 2.2 Consensus size: 131
2429 TACCAAATTC
2439 TTTTTACTTACC-AATT-TTACTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTTAATTACC
1 TTTTTACTTACCAAATTCTT-CTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTTAATTACC
*
2502 AATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAATTACCAATTTTACTTTTAC
65 AATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTGTTTTTTAATTACCAATTTTACTTTTAC
2567 TT
130 TT
* * *
2569 TTTTTACTTACCAAATTCTTCTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTCTTTTAATTA
1 TTTTTACTTACCAAATTCTTCTTTTAC--TCTTTTAATTACCAAATTCTCTTTTT-TTTTAATTA
*
2634 CCAATTTTACTTTTAC-TTTTTTACTTACCAAA-T-TC-GTTTTTTAATTACCAATTTTACTTTT
63 CCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTGTTTTTTAATTACCAATTTTACTTTT
2695 ACTT
128 ACTT
2699 TTTTTACTTACCAAATTCTTCTTTT
1 TTTTTACTTACCAAATTCTTCTTTT
2724 TTAATTACCA
Statistics
Matches: 145, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
130 66 0.46
131 13 0.09
132 3 0.02
133 38 0.26
134 25 0.17
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (131 bp):
TTTTTACTTACCAAATTCTTCTTTTACTCTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCA
ATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTGTTTTTTAATTACCAATTTTACTTTTACT
T
Found at i:2774 original size:18 final size:18
Alignment explanation
Indices: 2748--2782 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2738 TACTTTTGCT
*
2748 TTCTTTTTACTTACCAAA
1 TTCTCTTTACTTACCAAA
2766 TTCTCTTTACTTACCAA
1 TTCTCTTTACTTACCAA
2783 TTTTACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCTCTTTACTTACCAAA
Found at i:2791 original size:18 final size:17
Alignment explanation
Indices: 2753--2838 Score: 60
Period size: 18 Copynumber: 5.2 Consensus size: 17
2743 TTGCTTTCTT
*
2753 TTTACTTACCAAATTCTC
1 TTTACTTACC-AATTTTC
2771 TTTACTTACCAATTTTAC
1 TTTACTTACCAATTTT-C
2789 TTTTA-TT-----TTTT-
1 -TTTACTTACCAATTTTC
*
2800 TTTACTTACCAAATTCTC
1 TTTACTTACC-AATTTTC
2818 TTTACTTACCAATTTTAC
1 TTTACTTACCAATTTT-C
2836 TTT
1 TTT
2839 TACTCTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
10 4 0.07
11 2 0.04
13 4 0.07
17 13 0.24
18 27 0.50
19 4 0.07
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTACTTACCAATTTTC
Found at i:2799 original size:145 final size:146
Alignment explanation
Indices: 2567--2966 Score: 503
Period size: 145 Copynumber: 2.7 Consensus size: 146
2557 TTACTTTTAC
2567 TTTTTTTACTTACCAAATTCTT-CTTTTACTTT-TTTTTACTTACCAAATTCTTTTTTTCTTTTA
1 TTTTTTTACTTACC-AATT-TTACTTTTACTTTCTTTTTACTTACCAAATTC------TC-TTTA
*
2630 ATTACCAATTTTACTTTTA-CTTTTTTACTTACCAAATTCGTTTTTTAATTACCAATTTTACTTT
57 ATTACCAATTTTACTTTTATTTTTTTTACTTACCAAATTC-TTTTTTAATTACCAATTTTACTTT
2694 TACT-TTTTTTACTTACCAAATTCT-
121 TACTCTTTTTTACTTACCAAATTCTA
* * *
2718 TCTTTTTTAATTACCAATTTTACTTTTGCTTTCTTTTTACTTACCAAATTCTCTTTACTTACCAA
1 T-TTTTTTACTTACCAATTTTACTTTTACTTTCTTTTTACTTACCAAATTCTCTTTAATTACCAA
* *
2783 TTTTACTTTTATTTTTTTTTACTTACCAAATTC-TCTTTACTTACCAATTTTACTTTTACTCTTT
65 TTTTACTTTTA-TTTTTTTTACTTACCAAATTCTTTTTTAATTACCAATTTTACTTTTACTCTTT
2847 TTTACTTACCAAATTCTA
129 TTTACTTACCAAATTCTA
* * * * *
2865 TTTTTTTGCTTACCAATTTTACTTTTAC--TC-TTTTAATTACCAATTTTTTTTTAATTACCAAT
1 TTTTTTTACTTACCAATTTTACTTTTACTTTCTTTTTACTTACCAAATTCTCTTTAATTACCAAT
2927 TTTACTTTTACTTTCTTTTTTACTTACCAAATTCTTTTTT
66 TTTACTTTTA--TT-TTTTTTACTTACCAAATTCTTTTTT
2967 TTATCAATTT
Statistics
Matches: 224, Mismatches: 15, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
143 37 0.17
144 5 0.02
145 66 0.29
146 50 0.22
147 20 0.09
150 2 0.01
151 14 0.06
152 30 0.13
ACGTcount: A:0.23, C:0.18, G:0.01, T:0.58
Consensus pattern (146 bp):
TTTTTTTACTTACCAATTTTACTTTTACTTTCTTTTTACTTACCAAATTCTCTTTAATTACCAAT
TTTACTTTTATTTTTTTTACTTACCAAATTCTTTTTTAATTACCAATTTTACTTTTACTCTTTTT
TACTTACCAAATTCTA
Found at i:2820 original size:98 final size:98
Alignment explanation
Indices: 2568--2966 Score: 482
Period size: 98 Copynumber: 4.1 Consensus size: 98
2558 TACTTTTACT
*
2568 TTTTTTACTTACCAAATTCTT-CTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTCTTTTAAT
1 TTTTTTACTTACC-AATT-TTACTTTTA-TTTTTTTTACTTACCAAATTC--TTCTT-TTTTAAT
2632 TACCAATTTTACTTTTAC--TTTTTTACTTACCAAATTC
60 TACCAATTTTACTTTTACTTTTTTTTACTTACCAAATTC
* *
2669 GTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTCTTTTTTAATTACCA
1 -TTTTTTACTTACCAATTTTACTTTTATTTTTTTTACTTACCAAATTCTTCTTTTTTAATTACCA
*
2734 ATTTTACTTTTGCTTTCTTTTTACTTACCAAATTC
65 ATTTTACTTTTACTTT-TTTTTACTTACCAAATTC
* *
2769 -TCTTTACTTACCAATTTTACTTTTATTTTTTTTTACTTACCAAATTC-TC---TTTACTTACCA
1 TTTTTTACTTACCAATTTTACTTTTA-TTTTTTTTACTTACCAAATTCTTCTTTTTTAATTACCA
*
2829 ATTTTACTTTTACTCTTTTTTACTTACCAAATTC
65 ATTTTACTTTTACTTTTTTTTACTTACCAAATTC
* * * *
2863 TATTTTTTTGCTTACCAATTTTACTTTTA-CTCTTTTAATTACC-AA-T-TT-TTTTTTAATTAC
1 ---TTTTTTACTTACCAATTTTACTTTTATTTTTTTTACTTACCAAATTCTTCTTTTTTAATTAC
2923 CAATTTTACTTTTACTTTCTTTTTTACTTACCAAATTC
63 CAATTTTACTTTTAC-TT-TTTTTTACTTACCAAATTC
2961 TTTTTT
1 TTTTTT
2967 TTATCAATTT
Statistics
Matches: 265, Mismatches: 17, Indels: 37
0.83 0.05 0.12
Matches are distributed among these distances:
94 20 0.08
95 32 0.12
96 34 0.13
97 25 0.09
98 71 0.27
99 21 0.08
100 40 0.15
101 10 0.04
102 12 0.05
ACGTcount: A:0.23, C:0.19, G:0.01, T:0.58
Consensus pattern (98 bp):
TTTTTTACTTACCAATTTTACTTTTATTTTTTTTACTTACCAAATTCTTCTTTTTTAATTACCAA
TTTTACTTTTACTTTTTTTTACTTACCAAATTC
Found at i:2854 original size:29 final size:29
Alignment explanation
Indices: 2818--2911 Score: 98
Period size: 27 Copynumber: 3.6 Consensus size: 29
2808 CCAAATTCTC
2818 TTTACTTACCAATTTTACTTTTACTCTTT
1 TTTACTTACCAATTTTACTTTTACTCTTT
*
2847 TTTACTTACCAA----A-TTCTA-T-TTT
1 TTTACTTACCAATTTTACTTTTACTCTTT
*
2869 TTTGCTTACCAATTTTACTTTTACTC--T
1 TTTACTTACCAATTTTACTTTTACTCTTT
*
2896 TTTAATTACCAATTTT
1 TTTACTTACCAATTTT
2912 TTTTTAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
22 14 0.26
23 1 0.02
24 4 0.08
25 1 0.02
26 1 0.02
27 19 0.36
28 1 0.02
29 12 0.23
ACGTcount: A:0.23, C:0.19, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTACTTACCAATTTTACTTTTACTCTTT
Found at i:2890 original size:21 final size:22
Alignment explanation
Indices: 2843--2890 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2833 TACTTTTACT
2843 CTTTTTTACTTACCAAATTCTA
1 CTTTTTTACTTACCAAATTCTA
* * *
2865 TTTTTTTGCTTACC-AATTTTA
1 CTTTTTTACTTACCAAATTCTA
2886 CTTTT
1 CTTTT
2891 ACTCTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (22 bp):
CTTTTTTACTTACCAAATTCTA
Found at i:2916 original size:18 final size:18
Alignment explanation
Indices: 2895--2929 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2885 ACTTTTACTC
2895 TTTTAATTACCAATTTTT
1 TTTTAATTACCAATTTTT
2913 TTTTAATTACCAATTTT
1 TTTTAATTACCAATTTT
2930 ACTTTTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATTACCAATTTTT
Done.