Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold180
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: 1398530
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 86668 characters in sequence are not A, C, G, or T
File 1 of 6
Found at i:2077 original size:26 final size:26
Alignment explanation
Indices: 2036--2093 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2026 ATAAGAGCAA
* *
2036 TAATCAGGAAATTCACAAAGAACTTT
1 TAATCAGGAAACTCACAAAGAACCTT
* * *
2062 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAACTCACAAAGAACCTT
2088 TAATCA
1 TAATCA
2094 AGAGCTCCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (26 bp):
TAATCAGGAAACTCACAAAGAACCTT
Found at i:3410 original size:26 final size:26
Alignment explanation
Indices: 3381--3438 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
3371 ATAAGAGCAA
* *
3381 TAATCAAGAAGTTCACAAAGAACTTT
1 TAATCAAGAAGCTCACAAAGAACCTT
*
3407 TAATCAAGAAGCTCACAAAGAGCCTT
1 TAATCAAGAAGCTCACAAAGAACCTT
3433 TAATCA
1 TAATCA
3439 GGAGCTCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (26 bp):
TAATCAAGAAGCTCACAAAGAACCTT
Found at i:4343 original size:6 final size:6
Alignment explanation
Indices: 4334--4372 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
4324 GCTTTTATTT
*
4334 TTTTTA TTTTTA -TTTT- TTGTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
4373 TACAAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 7 0.24
6 22 0.76
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:4351 original size:22 final size:22
Alignment explanation
Indices: 4326--4374 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4316 GATTTACAGC
*
4326 TTTTATTTTTTTTATTTTTATT
1 TTTTATTATTTTTATTTTTATT
*
4348 TTTTGTTATTTTTATTTTTATT
1 TTTTATTATTTTTATTTTTATT
4370 TTTTA
1 TTTTA
4375 CAAACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTATTATTTTTATTTTTATT
Found at i:4356 original size:16 final size:15
Alignment explanation
Indices: 4326--4366 Score: 73
Period size: 16 Copynumber: 2.7 Consensus size: 15
4316 GATTTACAGC
4326 TTTTATTTTTTTTAT
1 TTTTATTTTTTTTAT
4341 TTTTATTTTTTGTTAT
1 TTTTATTTTTT-TTAT
4357 TTTTATTTTT
1 TTTTATTTTT
4367 ATTTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTTTTAT
Found at i:4983 original size:3 final size:3
Alignment explanation
Indices: 4969--5030 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
4959 AAATTGTTAT
*
4969 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA
* *
5015 TTA TTT TTA TTT TTA T
1 TTA TTA TTA TTA TTA T
5031 ATTCATGCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.90
4 4 0.08
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5470 original size:23 final size:23
Alignment explanation
Indices: 5444--5487 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
5434 CGATTTTGTT
5444 TATT-CATT-TATTCATATTATTTC
1 TATTCCATTGTATT-AT-TTATTTC
5467 TATTCCATTGTATTATTTATT
1 TATTCCATTGTATTATTTATT
5488 ATTGCATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 6 0.32
25 4 0.21
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTCCATTGTATTATTTATTTC
Found at i:5495 original size:20 final size:19
Alignment explanation
Indices: 5458--5504 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5448 CATTTATTCA
5458 TATTATTTCTATTCCATTG
1 TATTATTTCTATTCCATTG
* *
5477 TATTATTTATTATTGCATTG
1 TATTATTT-CTATTCCATTG
5497 TA-TATTTC
1 TATTATTTC
5505 ATGTAGCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTATTTCTATTCCATTG
Found at i:7887 original size:113 final size:114
Alignment explanation
Indices: 7719--7945 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 114
7709 CTACTCATAG
7719 TATTATTATTCACAATTATCAATATTTTTTTTGTCAAAATCATGGTGTTCATTGTCGGTAAAAAT
1 TATTATTATTCACAATTATCAATATTTTTTTTGTCAAAATCATGGTGTTCATTGTCGGTAAAAAT
7784 GACTAATCCCTTTATTGCGGGTGATGTTCAAAAAAGTAAATGATGGCCA
66 GACTAATCCCTTTATTGCGGGTGATGTTCAAAAAAGTAAATGATGGCCA
7833 TATTATTATTCACAATTATCAATA-TTTTTTTGTCAAAATCATGGTGTTCATTGTCGGTAAAAAT
1 TATTATTATTCACAATTATCAATATTTTTTTTGTCAAAATCATGGTGTTCATTGTCGGTAAAAAT
7897 GACTAATCCCTTTATTGCGGGTGATGTTCAAAAAAGTAAATGATGGCCA
66 GACTAATCCCTTTATTGCGGGTGATGTTCAAAAAAGTAAATGATGGCCA
7946 AGAAATGTGA
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 89 0.79
114 24 0.21
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (114 bp):
TATTATTATTCACAATTATCAATATTTTTTTTGTCAAAATCATGGTGTTCATTGTCGGTAAAAAT
GACTAATCCCTTTATTGCGGGTGATGTTCAAAAAAGTAAATGATGGCCA
Found at i:10560 original size:8 final size:8
Alignment explanation
Indices: 10549--10592 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
10539 TATATTTAAA
10549 TATATTTT
1 TATATTTT
*
10557 TATATATT
1 TATATTTT
10565 TATATTTTT
1 TATA-TTTT
10574 TATAAATTTT
1 TAT--ATTTT
10584 TATATTTT
1 TATATTTT
10592 T
1 T
10593 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 17 0.55
9 6 0.19
10 7 0.23
11 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATATTTT
Found at i:10594 original size:10 final size:9
Alignment explanation
Indices: 10534--10593 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
10524 GTTTTAGTGA
10534 TTTTATATAT
1 TTTTATAT-T
**
10544 TTAAATATAT
1 TTTTATAT-T
10554 TTTTATA-T
1 TTTTATATT
*
10562 ATTTATATT
1 TTTTATATT
*
10571 TTTTATAAAT
1 TTTTAT-ATT
10581 TTTTATATT
1 TTTTATATT
10590 TTTT
1 TTTT
10594 TTTCAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
8 7 0.17
9 12 0.30
10 21 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTATATT
Found at i:10665 original size:25 final size:26
Alignment explanation
Indices: 10611--10668 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
10601 ATACTATAAG
*
10611 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTGTAATTGTATAC
* *
10637 ATTTTTATA-ATTT-TATATTTTATAT
1 ATTTTTATATATTTGTA-ATTGTATAC
10662 ATTTTTA
1 ATTTTTA
10669 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 17 0.61
26 9 0.32
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (26 bp):
ATTTTTATATATTTGTAATTGTATAC
Found at i:11590 original size:31 final size:31
Alignment explanation
Indices: 11531--11620 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 31
11521 TATGTGATAG
* * *
11531 TACAGGGTTTGAATATG-AAATATTAATGA-
1 TACATGGTATGAATATGAAAATATGAATGAT
11560 TA-ATAGGATATGAATATGAAAATATGAATGAT
1 TACAT-GG-TATGAATATGAAAATATGAATGAT
11592 TACATGGTATGAATATGAAAATATGAATG
1 TACATGGTATGAATATGAAAATATGAATG
11621 GTTGATACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 9 0.17
31 33 0.62
32 4 0.08
33 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (31 bp):
TACATGGTATGAATATGAAAATATGAATGAT
Found at i:12351 original size:37 final size:38
Alignment explanation
Indices: 12301--12375 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
12291 TGTATATAAA
12301 GGAAAATTAGTGGGAAAAGATGAC-AAATTCATCATCT
1 GGAAAATTAGTGGGAAAAGATGACAAAATTCATCATCT
12338 GGAAAATTAGTGGGAAAAGATGACAAAATTCATCATCT
1 GGAAAATTAGTGGGAAAAGATGACAAAATTCATCATCT
12376 TCCTCGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 24 0.65
38 13 0.35
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (38 bp):
GGAAAATTAGTGGGAAAAGATGACAAAATTCATCATCT
Found at i:15434 original size:23 final size:23
Alignment explanation
Indices: 15404--15453 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
15394 TACATACGTA
*
15404 ATCAGGAAGCTCACAAAGAGCCT
1 ATCAGGAAGCTCACAAAAAGCCT
*
15427 ATCAGGAAGCTCACAAAAAGCTT
1 ATCAGGAAGCTCACAAAAAGCCT
15450 ATCA
1 ATCA
15454 TCCATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAAAGCCT
Found at i:15606 original size:26 final size:26
Alignment explanation
Indices: 15572--15636 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
15562 ATGAGAGCAA
* * *
15572 TAATTAGGAAGTTCAC-AATGAACTTT
1 TAATCAGGAAGCTCACGAA-GAACCTT
*
15598 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACGAAGAACCTT
15624 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
15637 CGGATAGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.15
26 27 0.79
27 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
TAATCAGGAAGCTCACGAAGAACCTT
Found at i:18093 original size:21 final size:22
Alignment explanation
Indices: 18052--18094 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18042 TCAAAGAACT
18052 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
18074 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
18095 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:25752 original size:64 final size:64
Alignment explanation
Indices: 25636--25812 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
25626 ACAAACATTT
*
25636 GAACCACATATG--TAT-AATTTACA-ACATTAAATTTCAGCTCAAAGAA-TTTGTAACCTATAT
1 GAACCACATATGTATATAAAATT-CATACATTAAA-TTCAGCTCAAA-AACTTTGTAACCTATAT
25696 TC
63 TC
* * * *
25698 GAACCTCATATGTATGTAAAATTCATACATTAAATTCCGCTCAAAAACTTTGTAACCTATATTT
1 GAACCACATATGTATATAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTATATTC
* * *
25762 GAACCACATATGTATATATAATTCATACATTAAATACAGCTCAAGAACTTT
1 GAACCACATATGTATATAAAATTCATACATTAAATTCAGCTCAAAAACTTT
25813 AAATATATAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
62 11 0.11
63 2 0.02
64 74 0.75
65 12 0.12
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (64 bp):
GAACCACATATGTATATAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTATATTC
Found at i:51610 original size:58 final size:57
Alignment explanation
Indices: 51465--51646 Score: 133
Period size: 58 Copynumber: 3.1 Consensus size: 57
51455 NNNNNNNNNN
* * *
51465 TATTACATGAAATAATATAGAAATATTCAAAATATTTCCTTATTTAAAAGAATTTCTATTT
1 TATTACATGAAATAATATAGAAATATTC---A-ATTACCTTATTCAAAAAAATTTCTATTT
* *
51526 TATTA-A--AAAT-ATAAAAGTAAAT-TTCAATTACTTTATTCAAAACAACATTT-TATTT
1 TATTACATGAAATAAT-ATAG-AAATATTCAATTACCTTATTCAAAA-AA-ATTTCTATTT
* * *
51581 TATTACATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTCTATTT
1 TATTACATGAAATAATATAGAAATATTC---A-ATTACCTTATTCAAAAAAATTTCTATTT
*
51642 CATTA
1 TATTA
51647 AAAATATAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
54 13 0.14
55 12 0.12
56 5 0.05
57 6 0.06
58 20 0.21
59 6 0.06
60 5 0.05
61 16 0.17
62 13 0.14
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (57 bp):
TATTACATGAAATAATATAGAAATATTCAATTACCTTATTCAAAAAAATTTCTATTT
Found at i:51666 original size:30 final size:29
Alignment explanation
Indices: 51625--51709 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 29
51615 TTGCCTTATT
51625 TAAAAGAATTTCTATTTCATTAAA-AATA
1 TAAAAGAATTTCTATTTCATTAAATAATA
*
51653 TAAAAGTAAATTTCTATTTTTTGCATGAAATAATA
1 TAAAAG--AATTTCTA---TTT-CATTAAATAATA
51688 TAAAAGAATTTCTATTTCATTA
1 TAAAAGAATTTCTATTTCATTA
51710 CATGAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
28 6 0.12
29 4 0.08
30 11 0.23
33 11 0.23
34 6 0.12
35 10 0.21
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (29 bp):
TAAAAGAATTTCTATTTCATTAAATAATA
Found at i:51719 original size:34 final size:33
Alignment explanation
Indices: 51625--51726 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 33
51615 TTGCCTTATT
51625 TAAAAGAATTTCTATTTCA-T--T-AAA-AATA
1 TAAAAGAATTTCTATTTCATTCATGAAATAATA
*
51653 TAAAAGTAAATTTCTATTT-TTTGCATGAAATAATA
1 TAAAAG--AATTTCTATTTCATT-CATGAAATAATA
51688 TAAAAGAATTTCTATTTCATTACATGAAATAATA
1 TAAAAGAATTTCTATTTCATT-CATGAAATAATA
51722 TAAAA
1 TAAAA
51727 ATATTCAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
28 6 0.10
30 12 0.19
33 12 0.19
34 22 0.35
35 10 0.16
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (33 bp):
TAAAAGAATTTCTATTTCATTCATGAAATAATA
Found at i:55759 original size:17 final size:18
Alignment explanation
Indices: 55732--55765 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55722 AAAATTGGGA
*
55732 GAAATTTTTAAATTTTAT
1 GAAATTTTTAAAATTTAT
55750 GAAA-TTTTAAAATTTA
1 GAAATTTTTAAAATTTA
55766 AACTGTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
GAAATTTTTAAAATTTAT
Found at i:59087 original size:8 final size:9
Alignment explanation
Indices: 59057--59085 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
59047 ATTTAGGCCC
59057 TTTAAAATT
1 TTTAAAATT
59066 TTTAAAATT
1 TTTAAAATT
59075 TTTAAAATT
1 TTTAAAATT
59084 TT
1 TT
59086 AACCCTCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:62911 original size:44 final size:44
Alignment explanation
Indices: 62863--63239 Score: 152
Period size: 44 Copynumber: 8.4 Consensus size: 44
62853 CTACTACGTT
* **
62863 TTCAGAGAGATATGACTCGTAGCTTCAATCTACTCTGCTGCAAC
1 TTCAGAGAGATAAGACTCGTAGCTTCAATCTACTCCACTGCAAC
* * * *
62907 TTCAGGGAGATAAGATTGGTATCTTCAATCTACTCCACTGCAAC
1 TTCAGAGAGATAAGACTCGTAGCTTCAATCTACTCCACTGCAAC
* ** * * * * * *
62951 TTC-GGGTAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTGTAGC
1 TTCAGAG-AGATAAGACTCGT-AGCTTCAATCTACTCCACTGCAAC
* * * * * *
62996 TTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGAC-CTACTGCAAC
1 TTCAGAGAGATAAGAC------TCGTAGCTTCAATCT-ACTCCACTGCAAC
* * * * * * *
63046 TTTAGAG-GTATAAGATTCATCA-TTTTAATCTGCTCCAATGCAAC
1 TTCAGAGAG-ATAAGACTCGT-AGCTTCAATCTACTCCACTGCAAC
* * * * * *
63090 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAAC
1 TTCAGAGAGATAAGACTCGTAGCTTCAATCTACTCCACTGCAAC
* * * * * *
63134 TTCA-AGGAGATAAGATTGGTATCTTCAACCTGCTTCACTGCAAC
1 TTCAGA-GAGATAAGACTCGTAGCTTCAATCTACTCCACTGCAAC
* ** * * * *
63178 TTCAGATAGATAAGGTTTGTCATCTTTAGTCTACTCCACTGCAAC
1 TTCAGAGAGATAAGACTCGT-AGCTTCAATCTACTCCACTGCAAC
* *
63223 TTTAGGGAGATAAGACT
1 TTCAGAGAGATAAGACT
63240 TGTTATGGTA
Statistics
Matches: 253, Mismatches: 62, Indels: 35
0.72 0.18 0.10
Matches are distributed among these distances:
43 5 0.02
44 151 0.60
45 63 0.25
46 3 0.01
49 1 0.00
50 26 0.10
51 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
TTCAGAGAGATAAGACTCGTAGCTTCAATCTACTCCACTGCAAC
Found at i:63282 original size:227 final size:226
Alignment explanation
Indices: 62863--64273 Score: 1272
Period size: 227 Copynumber: 6.3 Consensus size: 226
62853 CTACTACGTT
* * * * * *
62863 TTCAGAGAGATATGACTCGTAGCTTCAATCTACTCTGCTGCAACTTCAGGGAGATAAGATTGGTA
1 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTA
* * *
62928 TCTTCAATCTACTCCACTGCAACTTC-GGGTAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTG
66 GCTTCAATCTGCTCCACTGCAACTTCAGGG-AGATAAGGTTTGT-ATCTTCAGTCTACTCCACTG
* * * *
62992 TAGCTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGCAACTTTAGAGGTAT
129 CAACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGACCTACTGCAACTTCAGAGGTAT
* *
63057 AAGATTCATCATTTTAATCTGCTCCAATGCAAC
194 AAGATTCATCATTTTAATCCGCTCCACTGCAAC
*
63090 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTGGTA
1 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTA
* * * ** *
63155 TCTTCAACCTGCTTCACTGCAACTTCAGATAGATAAGGTTTGTCATCTTTAGTCTACTCCACTGC
66 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-ATCTTCAGTCTACTCCACTGC
*
63220 AACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCAACTTCAGAGGTATA
130 AACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGACCTACTGCAACTTCAGAGGTATA
**
63285 AGATTCATCATTTTAATCCGCTCCACTATAAC
195 AGATTCATCATTTTAATCCGCTCCACTGCAAC
* * * * * *
63317 TTAAGGGAGATAGGATTAGTAGCTTCAA--T-CT--ACT-C--CTTCTGGGACATAGGATTAGTA
1 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTA
* * * * ** *
63374 GCTTCAATCTGCTTCGCTGCAACTTCAGGGAGATATA-ATTGGTATCTTCAACCTGCTCCACTGC
66 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA-AGGTTTGTATCTTCAGTCTACTCCACTGC
* * ** * ** * *
63438 AACTTGAGGAAGATAAGGTTTGTCA---T-C-TTTGGTCTG-CTCCACTGCAACTTCAG-GGAGA
130 AACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGAC-CTACTGCAACTTCAGAGG-TA
* * * * *
63496 TAAGACTTGTTATGGTAGATTTAATCCGATCTACTGCAAC
193 TAAGA--T-TCAT--CA-TTTTAATCCGCTCCACTGCAAC
* * * * * * * *
63536 TTCAGAGG-TATAAGATTCA-TCA-TTTTAATCTACTACACTGCAACTTCAGGGAGATAGGATTA
1 TTCAG-GGAGATAGGATT-AGT-AGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATT-
* * * * **
63598 GG-AGCTTCAATCTGTTCCACTGCAACTTCAGGGAGCTAA-GATCGATATCTTCAACCTACTCCA
62 GGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TATCTTCAGTCTACTCCA
* * ** * * * *
63661 CTGCAACTTCAAGGAGATAAGGTTTGTCA---T-C-TTTAGTCTG-CTCCACTACAACTTCAG-G
126 CTGCAACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGAC-CTACTGCAACTTCAGAG
* * * * * *
63719 GATATAAGACTTGTTATGGTAGATTTAATCTGAC-CTACAGCAAC
190 G-TATAAGA--T-TCAT--CA-TTTTAATCCG-CTCCACTGCAAC
* * * * ** * * * *
63763 TTCAGAGG-TATAGGATTCA-TCA-TTTTAATCCGCTCCATTACAACTTCAGGGAGAGAGGATTA
1 TTCAG-GGAGATAGGATT-AGT-AGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTG
* * * * *
63825 GTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCA-ACTTGCTCCAC
63 GTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATCTTCAGTC-TACTCCAC
* *
63889 TGCAACTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTACAACTTCAGAGGT
127 TGCAACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGACCTACTGCAACTTCAGAGGT
* * * *
63954 ATAGGATTTATTATTTTAATCCGCTCCACTACAAC
192 ATAAGATTCATCATTTTAATCCGCTCCACTGCAAC
* *
63989 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGTAACTTGAGGGAGATAAGATTGGTA
1 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTA
* * * * *
64054 TCTTCAACCTACTCCACTGTAACTTCAGGGAGATAAGGTTTGTCATCTTTAGTCTACTCCACTGC
66 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-ATCTTCAGTCTACTCCACTGC
* * *
64119 AACTTCAGGCAGATAATACTTGTTATGGTACATTTAAT-TCGACCTACTGCAACTTCAGAGGTAT
130 AACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCT-GACCTACTGCAACTTCAGAGGTAT
*
64183 AAGATTCATCATTTTAATCCACTCCACTGCAAC
194 AAGATTCATCATTTTAATCCGCTCCACTGCAAC
*
64216 TTCAGGGTGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAG
1 TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAG
64274 GTCTGCAATT
Statistics
Matches: 995, Mismatches: 148, Indels: 82
0.81 0.12 0.07
Matches are distributed among these distances:
212 3 0.00
213 26 0.03
214 1 0.00
215 2 0.00
216 3 0.00
218 38 0.04
219 84 0.08
220 5 0.01
221 2 0.00
222 4 0.00
224 5 0.01
225 7 0.01
226 103 0.10
227 670 0.67
228 5 0.01
229 4 0.00
230 2 0.00
232 28 0.03
233 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (226 bp):
TTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTA
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATCTTCAGTCTACTCCACTGCA
ACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCTGACCTACTGCAACTTCAGAGGTATAA
GATTCATCATTTTAATCCGCTCCACTGCAAC
Found at i:63589 original size:263 final size:263
Alignment explanation
Indices: 63089--63610 Score: 850
Period size: 263 Copynumber: 2.0 Consensus size: 263
63079 TCCAATGCAA
*
63089 CTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTGGT
1 CTTCAGGGACATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTGGT
*
63154 ATCTTCAACCTGCTTCACTGCAACTTCAGATAGATAAGGTTTGTCATCTTTAGTCTACTCCACTG
66 ATCTTCAACCTGCTCCACTGCAACTTCAGATAGATAAGGTTTGTCATCTTTAGTCTACTCCACTG
*
63219 CAACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCAACTTCAGAGGTAT
131 CAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCAACTTCAGAGGTAT
* * * *
63284 AAGATTCATCATTTTAATCCGCTCCACTATAACTTAAGGGAGATAGGATTAGTAGCTTCAATCTA
196 AAGATTCATCATTTTAATCCACTACACTACAACTTAAGGGAGATAGGATTAGGAGCTTCAATCTA
63349 CTC
261 CTC
* * *
63352 CTTCTGGGACATAGGATTAGTAGCTTCAATCTGCTTCGCTGCAACTTCAGGGAGATATA-ATTGG
1 CTTCAGGGACATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGGAGATA-AGATTGG
* * *
63416 TATCTTCAACCTGCTCCACTGCAACTTGAGGA-AGATAAGGTTTGTCATCTTTGGTCTGCTCCAC
65 TATCTTCAACCTGCTCCACTGCAACTTCA-GATAGATAAGGTTTGTCATCTTTAGTCTACTCCAC
* *
63480 TGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGATCTACTGCAACTTCAGAGGT
129 TGCAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCAACTTCAGAGGT
* * *
63545 ATAAGATTCATCATTTTAATCTACTACACTGCAACTTCAGGGAGATAGGATTAGGAGCTTCAATC
194 ATAAGATTCATCATTTTAATCCACTACACTACAACTTAAGGGAGATAGGATTAGGAGCTTCAATC
63610 T
259 T
63611 GTTCCACTGC
Statistics
Matches: 239, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
263 236 0.99
264 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (263 bp):
CTTCAGGGACATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTGGT
ATCTTCAACCTGCTCCACTGCAACTTCAGATAGATAAGGTTTGTCATCTTTAGTCTACTCCACTG
CAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCAACTTCAGAGGTAT
AAGATTCATCATTTTAATCCACTACACTACAACTTAAGGGAGATAGGATTAGGAGCTTCAATCTA
CTC
Found at i:63816 original size:490 final size:490
Alignment explanation
Indices: 62881--63842 Score: 1518
Period size: 490 Copynumber: 2.0 Consensus size: 490
62871 GATATGACTC
*
62881 GTAGCTTCAATCTACTCTGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTACTCCACT
1 GTAGCTTCAATCTACTCTGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTACTCCACT
* * * *
62946 GCAACTTCGGGTAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTGTAGCTTTAGGGAGATAAGA
66 GCAACTTCGGGAAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* *
63011 CTTGTTATGGTAGATTTAATCTGACCTACTGCAACTTTAGAGGTATAAGATTCATCATTTTAATC
131 CTTGTTATGGTAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAAGATTCATCATTTTAATC
* * * *
63076 TGCTCCAATGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAAGG
196 TACTACAATGCAACTTCAGGGAGATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCAAGG
* * * * *
63141 AGATAAGATTGGTATCTTCAACCTGCTTCACTGCAACTTCAGATAGATAAGGTTTGTCATCTTTA
261 AGATAAGATCGATATCTTCAACCTACTCCACTGCAACTTCAGAGAGATAAGGTTTGTCATCTTTA
* * *
63206 GTCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACTGCA
326 GTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACAGCA
* *
63271 ACTTCAGAGGTATAAGATTCATCATTTTAATCCGCTCCACTATAACTTAAGGGAGATAGGATTAG
391 ACTTCAGAGGTATAAGATTCATCATTTTAATCCGCTCCACTACAACTTAAGGGAGAGAGGATTAG
63336 TAGCTTCAATCTACTCCTTCTGGGACATAGGATTA
456 TAGCTTCAATCTACTCCTTCTGGGACATAGGATTA
* *
63371 GTAGCTTCAATCTGCT-TCGCTGCAACTTCAGGGAGATATA-ATTGGTATCTTCAACCTGCTCCA
1 GTAGCTTCAATCTACTCT-GCTGCAACTTCAGGGAGATA-AGATTGGTATCTTCAACCTACTCCA
**
63434 CTGCAACTT-GAGGAAGATAAGGTTTGTCATCTTTGGTCTGCTCCACTGCAACTTCAGGGAGATA
64 CTGCAACTTCG-GGAAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
*
63498 AGACTTGTTATGGTAGATTTAATCCGATCTACTGCAACTTCAGAGGTATAAGATTCATCATTTTA
128 AGACTTGTTATGGTAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAAGATTCATCATTTTA
* *
63563 ATCTACTACACTGCAACTTCAGGGAGATAGGATTAGGAGCTTCAATCTGTTCCACTGCAACTTCA
193 ATCTACTACAATGCAACTTCAGGGAGATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCA
* *
63628 GGGAGCTAAGATCGATATCTTCAACCTACTCCACTGCAACTTCA-AGGAGATAAGGTTTGTCATC
258 AGGAGATAAGATCGATATCTTCAACCTACTCCACTGCAACTTCAGA-GAGATAAGGTTTGTCATC
* * * *
63692 TTTAGTCTGCTCCACTACAACTTCAGGGATATAAGACTTGTTATGGTAGATTTAATCTGACCTAC
322 TTTAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTAC
* * *
63757 AGCAACTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCATTACAACTTCAGGGAGAGAGGA
387 AGCAACTTCAGAGGTATAAGATTCATCATTTTAATCCGCTCCACTACAACTTAAGGGAGAGAGGA
*
63822 TTAGTAGCTTCAATCTGCTCC
452 TTAGTAGCTTCAATCTACTCC
63843 GCTGCAACTT
Statistics
Matches: 430, Mismatches: 38, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
489 3 0.01
490 426 0.99
491 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (490 bp):
GTAGCTTCAATCTACTCTGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTACTCCACT
GCAACTTCGGGAAGATAAGGTTTGTCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
CTTGTTATGGTAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAAGATTCATCATTTTAATC
TACTACAATGCAACTTCAGGGAGATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCAAGG
AGATAAGATCGATATCTTCAACCTACTCCACTGCAACTTCAGAGAGATAAGGTTTGTCATCTTTA
GTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTTATGGTACATTTAATCCGACCTACAGCA
ACTTCAGAGGTATAAGATTCATCATTTTAATCCGCTCCACTACAACTTAAGGGAGAGAGGATTAG
TAGCTTCAATCTACTCCTTCTGGGACATAGGATTA
Found at i:63926 original size:409 final size:409
Alignment explanation
Indices: 63393--64317 Score: 1316
Period size: 409 Copynumber: 2.3 Consensus size: 409
63383 TGCTTCGCTG
** * * * * * *
63393 CAACTTCAGGGAGATATAATTGGTATCTTCAACCTGCTCCACTGCAACTTGAGGAAGATAAGGTT
1 CAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGTT
* ***
63458 TGTCATCTT-TGGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATC
66 GGT-ATCTTCAACT-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATC
* * * *
63522 CGATCTACTGCAACTTCAGAGGTATAAGATTCATCATTTTAATCTACTACACTGCAACTTCAGGG
129 CGACCTACTACAACTTCAGAGGTATAAGATTCATCATTTTAATCCACTACACTACAACTTCAGGG
* *
63587 AGATAGGATTAGGAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGCTAAGATCGATATCTTCAA
194 AGATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCGATATCTTCAA
*
63652 CCTACTCCACTGCAACTTCAAGGAGATAAGGTTTGTCATCTTTAGTCTGCTCCACTACAACTTCA
259 CCTACTCCACTGCAACTTCAAGGAGATAAGGTTTGTCATCTTTAGTCTACTCCACTACAACTTCA
* * * *
63717 GGGATATAAGACTTGTTATGGTAGATTTAA-TCTGACCTACAGCAACTTCAGAGGTATAGGATTC
324 GGCAGATAAGACTTGTTATGGTACATTTAATTC-GACCTACAGCAACTTCAGAGGTATAAGATTC
* *
63781 ATCATTTTAATCCGCTCCATTA
388 ATCATTTTAATCCACTCCACTA
* *
63803 CAACTTCAGGGAGAGAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATT
1 CAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGTT
* *
63868 GGTATCTTCAACTTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTG
66 GGTATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCCG
* * * * *
63933 ACCTACTACAACTTCAGAGGTATAGGATTTATTATTTTAATCCGCTCCACTACAACTTCAGGGAG
131 ACCTACTACAACTTCAGAGGTATAAGATTCATCATTTTAATCCACTACACTACAACTTCAGGGAG
* * * * * *
63998 ATAGGATTAGTAGCTTCAATCTGCTCCGCTGTAACTTGAGGGAGATAAGATTGGTATCTTCAACC
196 ATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCGATATCTTCAACC
* * *
64063 TACTCCACTGTAACTTCAGGGAGATAAGGTTTGTCATCTTTAGTCTACTCCACTGCAACTTCAGG
261 TACTCCACTGCAACTTCAAGGAGATAAGGTTTGTCATCTTTAGTCTACTCCACTACAACTTCAGG
* *
64128 CAGATAATACTTGTTATGGTACATTTAATTCGACCTACTGCAACTTCAGAGGTATAAGATTCATC
326 CAGATAAGACTTGTTATGGTACATTTAATTCGACCTACAGCAACTTCAGAGGTATAAGATTCATC
*
64193 ATTTTAATCCACTCCACTG
391 ATTTTAATCCACTCCACTA
*
64212 CAACTTCAGGGTGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGTC
1 CAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGT-
** * * * *
64277 TGCAAT-TTCAACATGCCCCACTGTAACTTCAGGGGGATAAG
65 TGGTATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAG
64318 GCTAGTGTCT
Statistics
Matches: 456, Mismatches: 56, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
409 392 0.86
410 64 0.14
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (409 bp):
CAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGTT
GGTATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCCG
ACCTACTACAACTTCAGAGGTATAAGATTCATCATTTTAATCCACTACACTACAACTTCAGGGAG
ATAGGATTAGGAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCGATATCTTCAACC
TACTCCACTGCAACTTCAAGGAGATAAGGTTTGTCATCTTTAGTCTACTCCACTACAACTTCAGG
CAGATAAGACTTGTTATGGTACATTTAATTCGACCTACAGCAACTTCAGAGGTATAAGATTCATC
ATTTTAATCCACTCCACTA
Found at i:63928 original size:138 final size:138
Alignment explanation
Indices: 63470--64047 Score: 320
Period size: 138 Copynumber: 4.2 Consensus size: 138
63460 TCATCTTTGG
* * * *
63470 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGATCTACTGCAA
1 TCTGCTCCACTGCAACTTGAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGACCCACTACAA
* * * * * * ** * * *
63535 CTTCAGAGGTATAAGATTCA-TCATTTTAATCTACTACACTGCAACTTCAGGGAGATAGGATTAG
66 CTTCAGAGGGAGAGGATTTAGT-ACTTCAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAG
*
63599 GAGCTTCAA
130 TAGCTTCAA
* * * * ** * * *
63608 TCTGTTCCACTGCAACTTCAGGGAGCTAAGA-TCG--A---TATCTTCAA-CCTACTCCACTGCA
1 TCTGCTCCACTGCAACTTGAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGAC-CCACTACA
* * * * *
63666 ACTTCA-AGGAGATAAGG-TTT-GTCATCTTTAGTCTGCTCCACTACAACTTCAGGGATATAAGA
65 ACTTCAGAGG-GA-GAGGATTTAGT-A-CTTCAATCCGCTCCACTACAACTTCAGGGAGATAAGA
* *
63728 CTTGTTATGGTAGATTTAA
126 ----TTA--GTAGCTTCAA
* * * * * * * * *
63747 TCTGAC-CTACAGCAACTTCAGAGG-TATAGGA--T-TCAT--CA-TTTTAATCCG-CTCCATTA
1 TCTG-CTCCACTGCAACTTGAG-GGAGATAAGACTTGTTATGGTAGATTTAATCCGAC-CCACTA
* * *
63803 CAACTTCAG-GGAGAGAGGA-TTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGA
63 CAACTTCAGAGG-GAGAGGATTTAGTA-CTTCAATCCGCTCCACTACAACTTCAGGGAGATAAGA
* *
63866 TTGGTATCTTCAA
126 TTAGTAGCTTCAA
* * *
63879 -CTTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTACA
1 TC-TGCTCCACTGCAACTTGAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGACCCACTACA
* * * * * *
63943 ACTTCAGAGGTATAGGATTTATTATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAG
65 ACTTCAGAGGGAGAGGATTTAGTACTTCAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAG
64008 TAGCTTCAA
130 TAGCTTCAA
* *
64017 TCTGCTCCGCTGTAACTTGAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTGAGGGAGATAAGA
64048 TTGGTATCTT
Statistics
Matches: 335, Mismatches: 72, Indels: 66
0.71 0.15 0.14
Matches are distributed among these distances:
131 10 0.03
132 51 0.15
133 32 0.10
134 3 0.01
135 4 0.01
137 6 0.02
138 161 0.48
139 63 0.19
140 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (138 bp):
TCTGCTCCACTGCAACTTGAGGGAGATAAGACTTGTTATGGTAGATTTAATCCGACCCACTACAA
CTTCAGAGGGAGAGGATTTAGTACTTCAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAGT
AGCTTCAA
Found at i:63947 original size:182 final size:182
Alignment explanation
Indices: 63646--64090 Score: 669
Period size: 182 Copynumber: 2.4 Consensus size: 182
63636 AGATCGATAT
* * * * * * * * *
63646 CTTCAACCTACTCCACTGCAACTTCAAGGAGATAAGGTTTGTCATCTT-TAGTCTGCTCCACTAC
1 CTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGT-ATCTTCAACT-TGCTCCACTGC
*
63710 AACTTCAGGGATATAAGACTTGTTATGGTAGATTTAATCTGACCTACAGCAACTTCAGAGGTATA
64 AACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACAGCAACTTCAGAGGTATA
*
63775 GGATTCATCATTTTAATCCGCTCCATTACAACTTCAGGGAGAGAGGATTAGTAG
129 GGATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGAGAGGATTAGTAG
63829 CTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACTTGCTCCACTGCAA
1 CTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACTTGCTCCACTGCAA
*
63894 CTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTA-CAACTTCAGAGGTATAG
66 CTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTAC-AGCAACTTCAGAGGTATAG
* * *
63958 GATTTATTATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAGTAG
130 GATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGAGAGGATTAGTAG
* * * * *
64011 CTTCAATCTGCTCCGCTGTAACTTGAGGGAGATAAGATTGGTATCTTCAACCTACTCCACTGTAA
1 CTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACTTGCTCCACTGCAA
64076 CTTCAGGGAGATAAG
66 CTTCAGGGAGATAAG
64091 GTTTGTCATC
Statistics
Matches: 239, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
182 200 0.84
183 39 0.16
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (182 bp):
CTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACTTGCTCCACTGCAA
CTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACAGCAACTTCAGAGGTATAGG
ATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGAGAGGATTAGTAG
Found at i:64117 original size:45 final size:44
Alignment explanation
Indices: 63368--64344 Score: 336
Period size: 44 Copynumber: 21.6 Consensus size: 44
63358 GGACATAGGA
* * * * *
63368 TTAGTAGCTTCAATCTGCTTCGCTGCAACTTCAGGGAGATATA-A
1 TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATA-AGG
* * * * *
63412 TTGGTATCTTCAACCTGCTCCACTGCAACTTGAGGAAGATAAGG
1 TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* *** *
63456 TTTGTCATCTTTGGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
1 TTAGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG----G
** * * * * *
63505 TTATGGTAGATTTAATCCGA-TCTACTGCAACTTCAGAGG-TATAAGA
1 TTA--GTATCTTCAAT-CTACTCCACTGCAACTTCAG-GGAGATAAGG
* *
63551 TTCA-TCAT-TTTAATCTACTACACTGCAACTTCAGGGAGAT-AGG
1 TT-AGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * ** *
63594 ATTAGGAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGCTAA-G
1 -TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * *
63638 ATCGATATCTTCAACCTACTCCACTGCAACTTCAAGGAGATAAGG
1 TTAG-TATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * * * *
63683 TTTGTCATCTTTAGTCTGCTCCACTACAACTTCAGGGATATAAGACTTG
1 TTAGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG----G
** * * * *
63732 TTATGGTAGATTTAATCTGAC-CTACAGCAACTTCA--GAGGTATAGG
1 TTA--GTATCTTCAATCT-ACTCCACTGCAACTTCAGGGAGATA-AGG
* ** * * *
63777 ATTCA-TCAT-TTTAATCCGCTCCATTACAACTTCAGGGAGA-GAGG
1 -TT-AGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * *
63821 ATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGA
1 -TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * *
63866 TTGGTATCTTCAA-CTTGCTCCACTGCAACTTTAGGGAGATAAGACTTG
1 TTAGTATCTTCAATC-TACTCCACTGCAACTTCAGGGAGATAAG----G
** * * * *
63914 TTATGGTAGATTTAATCTGAC-CTACTACAACTTCA--GAGGTATAGG
1 TTA--GTATCTTCAATCT-ACTCCACTGCAACTTCAGGGAGATA-AGG
* * ** *
63959 ATTTATTAT-TTTAATCCGCTCCACTACAACTTCAGGGAGAT-AGG
1 --TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * * * *
64003 ATTAGTAGCTTCAATCTGCTCCGCTGTAACTTGAGGGAGATAAGA
1 -TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * *
64048 TTGGTATCTTCAACCTACTCCACTGTAACTTCAGGGAGATAAGG
1 TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * * *
64092 TTTGTCATCTTTAGTCTACTCCACTGCAACTTCAGGCAGATAATACTTG
1 TTAGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGAT-A-A--GG
* * * * *
64141 TTATGGTA-CATTTAATTCGAC-CTACTGCAACTTCAGAGG-TATAAGA
1 TTA--GTATC-TTCAA-TCTACTCCACTGCAACTTCAG-GGAGATAAGG
* * *
64187 TTCA-TCAT-TTTAATCCACTCCACTGCAACTTCAGGGTGAT-AGG
1 TT-AGT-ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * *
64230 ATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGG
1 -TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
* * * * *
64275 TCT-GCAAT-TTCAA-CATGCCCCACTGTAACTTCAGGGGGATAAGG
1 T-TAG-TATCTTCAATC-TACTCCACTGCAACTTCAGGGAGATAAGG
* * * *
64319 CTAGTGTCTTCGATCTACTTCACTGC
1 TTAGTATCTTCAATCTACTCCACTGC
64345 CAATACAAGA
Statistics
Matches: 694, Mismatches: 159, Indels: 160
0.69 0.16 0.16
Matches are distributed among these distances:
43 34 0.05
44 397 0.57
45 114 0.16
46 14 0.02
47 7 0.01
48 12 0.02
49 15 0.02
50 84 0.12
51 17 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
TTAGTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
Found at i:65785 original size:8 final size:8
Alignment explanation
Indices: 65772--65833 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
65762 TGCTCCGAAG
65772 GTTTTTTT
1 GTTTTTTT
65780 G--TTTTT
1 GTTTTTTT
65786 G-TTTTTT
1 GTTTTTTT
* *
65793 ATTTTCTT
1 GTTTTTTT
*
65801 ATTTTTTT
1 GTTTTTTT
65809 GTTTGTTTT
1 GTTT-TTTT
65818 -TGTTTTTT
1 GT-TTTTTT
65826 GTTTTTTT
1 GTTTTTTT
65834 CCTCCACTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
6 6 0.13
7 5 0.11
8 27 0.60
9 7 0.16
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (8 bp):
GTTTTTTT
Found at i:65790 original size:5 final size:6
Alignment explanation
Indices: 65775--65831 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
65765 TCCGAAGGTT
* *
65775 TTTTTG TTTTTG TTTTT- TATTTTC TTATT- TTTTTG --TTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG TTTTTG
65820 TTTTTTG TTTTT
1 -TTTTTG TTTTT
65832 TTCCTCCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 4 0.09
5 5 0.12
6 27 0.63
7 7 0.16
ACGTcount: A:0.04, C:0.02, G:0.11, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:65791 original size:7 final size:7
Alignment explanation
Indices: 65774--65832 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
65764 CTCCGAAGGT
65774 TTTTTTG
1 TTTTTTG
65781 -TTTTTG
1 TTTTTTG
*
65787 TTTTTTA
1 TTTTTTG
65794 TTTTCTT-
1 TTTT-TTG
*
65801 ATTTTT-
1 TTTTTTG
*
65807 TTGTTTG
1 TTTTTTG
65814 -TTTTTG
1 TTTTTTG
65820 TTTTTTG
1 TTTTTTG
65827 TTTTTT
1 TTTTTT
65833 TCCTCCACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
6 17 0.40
7 24 0.56
8 2 0.05
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:72804 original size:15 final size:13
Alignment explanation
Indices: 72773--72812 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 13
72763 CACCAATTTT
72773 TTTAAAATAAA-A
1 TTTAAAATAAATA
72785 TTTAAAATAAATCTA
1 TTTAAAATAAA--TA
72800 TTTAAAATAAATA
1 TTTAAAATAAATA
72813 GATTAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
15 12 0.48
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAATAAATA
Found at i:74802 original size:3 final size:3
Alignment explanation
Indices: 74796--74832 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
74786 ATAACATTAT
* *
74796 TAA TAA TAA TAG TAA TAA TAA TAA TAC TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
74833 GAAAGCAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:74814 original size:15 final size:15
Alignment explanation
Indices: 74796--74854 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
74786 ATAACATTAT
74796 TAATAATAATAGTAA
1 TAATAATAATAGTAA
*
74811 TAATAATAATACTAA
1 TAATAATAATAGTAA
*
74826 TAATAATGAA-AGCAA
1 TAATAAT-AATAGTAA
* *
74841 TAATTATAAGAGTA
1 TAATAATAATAGTA
74855 CAAAAATAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (15 bp):
TAATAATAATAGTAA
Found at i:79553 original size:6 final size:6
Alignment explanation
Indices: 79542--79572 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
79532 TTAAATTTTA
79542 TAATTT TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT T
79573 TAAACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:79631 original size:16 final size:16
Alignment explanation
Indices: 79610--79643 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
79600 TCCCTAGCTA
79610 AATTGAATCAAGAGTG
1 AATTGAATCAAGAGTG
* *
79626 AATTGAATGAGGAGTG
1 AATTGAATCAAGAGTG
79642 AA
1 AA
79644 AAATTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (16 bp):
AATTGAATCAAGAGTG
Found at i:80247 original size:5 final size:5
Alignment explanation
Indices: 80237--80262 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
80227 TGAGCATTCG
80237 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
80263 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:81275 original size:9 final size:9
Alignment explanation
Indices: 81261--81306 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
81251 TATATTTTGA
81261 TATTCGAAT
1 TATTCGAAT
81270 TATTCGAAT
1 TATTCGAAT
81279 TATTCGAAT
1 TATTCGAAT
*
81288 TATTCGAGT
1 TATTCGAAT
81297 TATTCGAAT
1 TATTCGAAT
81306 T
1 T
81307 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:82591 original size:20 final size:20
Alignment explanation
Indices: 82566--82605 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
82556 ATCAAGCCTC
*
82566 TATTTATTTTTTGTAACTTA
1 TATTTATTCTTTGTAACTTA
82586 TATTTATTCTTTGTAACTTA
1 TATTTATTCTTTGTAACTTA
82606 AATAGAGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (20 bp):
TATTTATTCTTTGTAACTTA
Found at i:97636 original size:26 final size:25
Alignment explanation
Indices: 97606--97686 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
97596 CCGGAGCTCT
97606 TGATTAAAAGCTCTTCATGAGCTTCC
1 TGATTAAAAGCTCTT-ATGAGCTTCC
* * *
97632 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAAGCTC-TTATGAGCTTCC
* **
97658 TAATT-ATTGCTCTTATGAGCTTCC
1 TGATTAAAAGCTCTTATGAGCTTCC
97682 T-ATTA
1 TGATTA
97687 TATAGCCCAG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.07
24 11 0.25
25 4 0.09
26 24 0.55
27 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (25 bp):
TGATTAAAAGCTCTTATGAGCTTCC
Found at i:97818 original size:23 final size:23
Alignment explanation
Indices: 97788--97831 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
97778 TGGATGAAAA
*
97788 GCTCTTTGTGAGCTTCTTGATAG
1 GCTCTTTGTGAGCTTCCTGATAG
97811 GCTCTTTGTGAGCTTCCTGAT
1 GCTCTTTGTGAGCTTCCTGAT
97832 TACATATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (23 bp):
GCTCTTTGTGAGCTTCCTGATAG
Found at i:99008 original size:26 final size:26
Alignment explanation
Indices: 98977--99032 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
98967 GGAGCTTTTG
* *
98977 ATTAAAGGCTCTTCGTGAGCTTCCTA
1 ATTAAAAGCTCTTCGTGAACTTCCTA
* * *
99003 ATTAAAAGTTCTTTGTGAACTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTA
99029 ATTA
1 ATTA
99033 TTGCTCTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (26 bp):
ATTAAAAGCTCTTCGTGAACTTCCTA
Found at i:107967 original size:21 final size:20
Alignment explanation
Indices: 107933--107983 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
107923 GAAACAGAAA
107933 AAAACTC-CAAACAAAGTT-C
1 AAAACTCACAAAC-AAGTTAC
107952 AAAACTCACAACACAAGTTAC
1 AAAACTCACAA-ACAAGTTAC
107973 ACAAA-TCACAA
1 A-AAACTCACAA
107984 GCAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
20 8 0.29
21 10 0.36
22 3 0.11
ACGTcount: A:0.55, C:0.27, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAACTCACAAACAAGTTAC
Found at i:109053 original size:3 final size:3
Alignment explanation
Indices: 109033--109127 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
109023 TTAATTTTAA
* * * * * * * * *
109033 TAT TTT TAT TAT TGT TAT TAT TAT TAA TAC CAT CAT CAT CAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
109081 TAT TAT TAA TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
109128 AATTGTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:112899 original size:18 final size:18
Alignment explanation
Indices: 112867--112905 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
112857 ACCTTTTATG
* *
112867 TATCCTCCTCCTCAAATA
1 TATCCTCCACATCAAATA
*
112885 TATCCTCCACATCAATTA
1 TATCCTCCACATCAAATA
112903 TAT
1 TAT
112906 GAAAACCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
TATCCTCCACATCAAATA
Found at i:113871 original size:454 final size:454
Alignment explanation
Indices: 113024--113931 Score: 1816
Period size: 454 Copynumber: 2.0 Consensus size: 454
113014 CGTCATTCCT
113024 CTAATTGGTGAAAACTAAATTGTACCACTACCATTATTTGTAAGGTATGTTTTTTTTTAAAGAAA
1 CTAATTGGTGAAAACTAAATTGTACCACTACCATTATTTGTAAGGTATGTTTTTTTTTAAAGAAA
113089 ACTTTTGTTAAAGTTCTTAATTTTGATGATATTAAAACATTTAAAATATATCCTTAGATAAATGA
66 ACTTTTGTTAAAGTTCTTAATTTTGATGATATTAAAACATTTAAAATATATCCTTAGATAAATGA
113154 ATGGAGTATATTTTATGAAAAGATAATTAAAATCGAAGCATGTTAAACTACATATGAAAGTAGAA
131 ATGGAGTATATTTTATGAAAAGATAATTAAAATCGAAGCATGTTAAACTACATATGAAAGTAGAA
113219 TGAGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTAATGTGAATCTATACATTTATCTATTCC
196 TGAGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTAATGTGAATCTATACATTTATCTATTCC
113284 TTTTTTCCTTTTGAAGCATAGAATGTTTATATCTTCATCATCTTCAAAGCTGTCAAGAAATATTG
261 TTTTTTCCTTTTGAAGCATAGAATGTTTATATCTTCATCATCTTCAAAGCTGTCAAGAAATATTG
113349 AAGATATTTCTCAAGTATGAATTTTCAATTATTTTATCTATAAAAACTTTCAAACTTATTAAATA
326 AAGATATTTCTCAAGTATGAATTTTCAATTATTTTATCTATAAAAACTTTCAAACTTATTAAATA
113414 TGATAAATGTTTAATACTTCCCTTTTTTTACTTTGTTATTAGTTAATATAACATTCTTAGAAAA
391 TGATAAATGTTTAATACTTCCCTTTTTTTACTTTGTTATTAGTTAATATAACATTCTTAGAAAA
113478 CTAATTGGTGAAAACTAAATTGTACCACTACCATTATTTGTAAGGTATGTTTTTTTTTAAAGAAA
1 CTAATTGGTGAAAACTAAATTGTACCACTACCATTATTTGTAAGGTATGTTTTTTTTTAAAGAAA
113543 ACTTTTGTTAAAGTTCTTAATTTTGATGATATTAAAACATTTAAAATATATCCTTAGATAAATGA
66 ACTTTTGTTAAAGTTCTTAATTTTGATGATATTAAAACATTTAAAATATATCCTTAGATAAATGA
113608 ATGGAGTATATTTTATGAAAAGATAATTAAAATCGAAGCATGTTAAACTACATATGAAAGTAGAA
131 ATGGAGTATATTTTATGAAAAGATAATTAAAATCGAAGCATGTTAAACTACATATGAAAGTAGAA
113673 TGAGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTAATGTGAATCTATACATTTATCTATTCC
196 TGAGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTAATGTGAATCTATACATTTATCTATTCC
113738 TTTTTTCCTTTTGAAGCATAGAATGTTTATATCTTCATCATCTTCAAAGCTGTCAAGAAATATTG
261 TTTTTTCCTTTTGAAGCATAGAATGTTTATATCTTCATCATCTTCAAAGCTGTCAAGAAATATTG
113803 AAGATATTTCTCAAGTATGAATTTTCAATTATTTTATCTATAAAAACTTTCAAACTTATTAAATA
326 AAGATATTTCTCAAGTATGAATTTTCAATTATTTTATCTATAAAAACTTTCAAACTTATTAAATA
113868 TGATAAATGTTTAATACTTCCCTTTTTTTACTTTGTTATTAGTTAATATAACATTCTTAGAAAA
391 TGATAAATGTTTAATACTTCCCTTTTTTTACTTTGTTATTAGTTAATATAACATTCTTAGAAAA
113932 TTTGTAAATA
Statistics
Matches: 454, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
454 454 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (454 bp):
CTAATTGGTGAAAACTAAATTGTACCACTACCATTATTTGTAAGGTATGTTTTTTTTTAAAGAAA
ACTTTTGTTAAAGTTCTTAATTTTGATGATATTAAAACATTTAAAATATATCCTTAGATAAATGA
ATGGAGTATATTTTATGAAAAGATAATTAAAATCGAAGCATGTTAAACTACATATGAAAGTAGAA
TGAGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTAATGTGAATCTATACATTTATCTATTCC
TTTTTTCCTTTTGAAGCATAGAATGTTTATATCTTCATCATCTTCAAAGCTGTCAAGAAATATTG
AAGATATTTCTCAAGTATGAATTTTCAATTATTTTATCTATAAAAACTTTCAAACTTATTAAATA
TGATAAATGTTTAATACTTCCCTTTTTTTACTTTGTTATTAGTTAATATAACATTCTTAGAAAA
Found at i:126396 original size:46 final size:46
Alignment explanation
Indices: 126301--126543 Score: 328
Period size: 46 Copynumber: 5.3 Consensus size: 46
126291 TACCCCGTTT
* * *
126301 TGGACAACATTTATACATCAAATTGGACAACATCAATATGCTC-AAA
1 TGGACAGCA-TTATACATCAAATTGGACAGCATCAATATACTCAAAA
* *
126347 TGGACAGTATTATACATCAAATTGGAGAGCATCAATATACTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
* * *
126393 TGGACAGCATTATGCATCAAATTGGACAGCTTTAATATACTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
* ** * *
126439 TGGACAGCATTATACATCAAAATGGACAGC-TTTATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
*
126484 TGGATAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
*
126530 TGGACAACATTATA
1 TGGACAGCATTATA
126544 ACATATAAAA
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
45 70 0.41
46 102 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (46 bp):
TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
Found at i:126481 original size:91 final size:92
Alignment explanation
Indices: 126301--126543 Score: 328
Period size: 91 Copynumber: 2.7 Consensus size: 92
126291 TACCCCGTTT
* * * *
126301 TGGACAACATTTATACATCAAATTGGACAACATCAATATGCTC-AAATGGACAGTATTATACATC
1 TGGACAGCA-TTATACATCAAATTGGACAGCATCAATATACTCAAAATGGACAGCATTATACATC
* *
126365 AAATTGGAGAGCATCAATATACTCAAAA
65 AAAATGGACAGCATCAATATACTCAAAA
* * *
126393 TGGACAGCATTATGCATCAAATTGGACAGCTTTAATATACTCAAAATGGACAGCATTATACATCA
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAATGGACAGCATTATACATCA
** * *
126458 AAATGGACAGC-TTTATATGCTCAAAT
66 AAATGGACAGCATCAATATACTCAAAA
* *
126484 TGGATAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAATGGACAACATTATA
1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAATGGACAGCATTATA
126544 ACATATAAAA
Statistics
Matches: 132, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
91 94 0.71
92 38 0.29
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (92 bp):
TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAATGGACAGCATTATACATCA
AAATGGACAGCATCAATATACTCAAAA
Found at i:126883 original size:18 final size:18
Alignment explanation
Indices: 126860--126897 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
126850 TCAAAAGTAC
126860 AAACTTATAAGGTACCGA
1 AAACTTATAAGGTACCGA
126878 AAACTTATAAGGTACCGA
1 AAACTTATAAGGTACCGA
126896 AA
1 AA
126898 TAGCAATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (18 bp):
AAACTTATAAGGTACCGA
Found at i:138280 original size:19 final size:21
Alignment explanation
Indices: 138241--138288 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
138231 ATCTCTTCAT
138241 ATAA-ATATCATATATCATAC
1 ATAATATATCATATATCATAC
*
138261 ATCATATATC-TATATC-TAC
1 ATAATATATCATATATCATAC
138280 ATAATATAT
1 ATAATATAT
138289 ATTATAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 9 0.36
21 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATATATCATATATCATAC
Found at i:139253 original size:50 final size:50
Alignment explanation
Indices: 139199--139405 Score: 405
Period size: 50 Copynumber: 4.1 Consensus size: 50
139189 AATAATAATA
139199 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
1 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
139249 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
1 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
139299 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
1 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
*
139349 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCTAGGACT
1 CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
139399 CTTTGAT
1 CTTTGAT
139406 ATTTGCTTTT
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 156 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (50 bp):
CTTTGATTAGTCAAATTTGAATATTTTAGGTAACTTTGGGAGCGAGGACT
Found at i:140526 original size:31 final size:31
Alignment explanation
Indices: 140478--140555 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
140468 ATAGGGTTTA
* * *
140478 AATATG-AAATATTAATGATTATAGGATATG
1 AATATGAAAATATGAATGACTACAGGATATG
* *
140508 AATGTGAAAATATGAATGACTACAGGGTATG
1 AATATGAAAATATGAATGACTACAGGATATG
*
140539 AATATGCAAATATGAAT
1 AATATGAAAATATGAAT
140556 AGTATGAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (31 bp):
AATATGAAAATATGAATGACTACAGGATATG
Found at i:146734 original size:40 final size:39
Alignment explanation
Indices: 146679--146789 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 39
146669 AGGGCTTCAA
* * *
146679 AAGTAGAAAAAGGGGCACGTATGTGCATTCAAGCGTACTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAAG-GTACTG
* *
146719 AAGTATAAACAGGGGCACATATGTGCATTCCTAGGTACTG
1 AAGTACAAACAGGGGCACATATGTGCATT-CAAGGTACTG
*
146759 AAGTACAAACAGGGGCACCTATGTGCATTCA
1 AAGTACAAACAGGGGCACATATGTGCATTCA
146790 GACAATAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 59 0.94
41 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (39 bp):
AAGTACAAACAGGGGCACATATGTGCATTCAAGGTACTG
Found at i:151198 original size:27 final size:27
Alignment explanation
Indices: 151159--151300 Score: 140
Period size: 27 Copynumber: 5.3 Consensus size: 27
151149 AAAGGTCGAT
* *
151159 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCAAAGGGTA
* * *
151186 AAATGACCAAAATATCCCTAAATGGTA
1 AAATGACCAAAATACCCCCAAAGGGTA
* ** **
151213 AAATAACTGAAATACCCCTGAAGGGTA
1 AAATGACCAAAATACCCCCAAAGGGTA
*
151240 AAATGACCAAAATACCCTCAAAGGGTA
1 AAATGACCAAAATACCCCCAAAGGGTA
** ** *
151267 AAACAATTAAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCAAAGGGTA
151294 AAATGAC
1 AAATGAC
151301 TGTTATACCC
Statistics
Matches: 89, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCAAAGGGTA
Found at i:151249 original size:54 final size:54
Alignment explanation
Indices: 151167--151300 Score: 191
Period size: 54 Copynumber: 2.5 Consensus size: 54
151157 ATAAATGACC
* *
151167 GAAATACCCCCATAGGGTAAAATGACCAAAATATCCCT-AAATGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACCAAAATA-CCCTCAAAGGGTAAAACAACT
* *
151221 GAAATACCCCTGA-AGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAACAATT
1 GAAATACCCC-CATAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAACAACT
*
151275 AAAATACCCCCATAGGGTAAAATGAC
1 GAAATACCCCCATAGGGTAAAATGAC
151301 TGTTATACCC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
53 5 0.07
54 65 0.92
55 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (54 bp):
GAAATACCCCCATAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAACAACT
Found at i:151294 original size:81 final size:81
Alignment explanation
Indices: 151159--151312 Score: 182
Period size: 81 Copynumber: 1.9 Consensus size: 81
151149 AAAGGTCGAT
* * ** * * *
151159 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATATCCCTAAATGGTAAAATAACTGAA
1 AAATGACCAAAATACCCCCAAAGGGTAAAACAACCAAAATACCCCCAAAGGGTAAAATAACTGAA
151224 ATACCCCTGAAGGGTA
66 ATACCCCTGAAGGGTA
* ** * * **
151240 AAATGACCAAAATACCCTCAAAGGGTAAAACAATTAAAATACCCCCATAGGGTAAAATGACTGTT
1 AAATGACCAAAATACCCCCAAAGGGTAAAACAACCAAAATACCCCCAAAGGGTAAAATAACTGAA
151305 ATACCCCT
66 ATACCCCT
151313 AGGATTCGAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 59 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (81 bp):
AAATGACCAAAATACCCCCAAAGGGTAAAACAACCAAAATACCCCCAAAGGGTAAAATAACTGAA
ATACCCCTGAAGGGTA
Found at i:151505 original size:26 final size:26
Alignment explanation
Indices: 151466--151519 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
151456 GGAAATATAT
151466 TGTTACTGGCAGCTTTGCTGCGATAC
1 TGTTACTGGCAGCTTTGCTGCGATAC
* *
151492 TGTTACTGGTAGCTTTGTTGCGATAC
1 TGTTACTGGCAGCTTTGCTGCGATAC
151518 TG
1 TG
151520 GTGTGTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.39
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTGCGATAC
Found at i:151627 original size:28 final size:28
Alignment explanation
Indices: 151595--151672 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
151585 GATATTATGC
*
151595 TGGGCAAAGGCCCACACTATTACTGTAT
1 TGGGCTAAGGCCCACACTATTACTGTAT
* * *
151623 TGGGCTGAGACCCACACTGTTACTGTAT
1 TGGGCTAAGGCCCACACTATTACTGTAT
*
151651 TGGGCTAAGGCCCACACAATTA
1 TGGGCTAAGGCCCACACTATTA
151673 TTGTTACTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (28 bp):
TGGGCTAAGGCCCACACTATTACTGTAT
Found at i:153987 original size:16 final size:16
Alignment explanation
Indices: 153966--154012 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
153956 CTGATTGTTT
153966 TTATTTTT-TTATTTTA
1 TTATTTTTCTT-TTTTA
153982 TTATTTTTCTTTTTTA
1 TTATTTTTCTTTTTTA
153998 TT-TTTTTCCTTTTTT
1 TTATTTTT-CTTTTTT
154013 CCTTTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.17
16 22 0.76
17 2 0.07
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (16 bp):
TTATTTTTCTTTTTTA
Found at i:154039 original size:9 final size:8
Alignment explanation
Indices: 153985--154062 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
153975 TATTTTATTA
153985 TTTTTC-T
1 TTTTTCTT
*
153992 TTTTTATT
1 TTTTTCTT
*
154000 TTTTTCCT
1 TTTTTCTT
*
154008 TTTTTCCT
1 TTTTTCTT
*
154016 TTTTTCCT
1 TTTTTCTT
154024 TTTTTCTT
1 TTTTTCTT
154032 TTTCTTCTT
1 TTT-TTCTT
154041 TCTTTT-TT
1 T-TTTTCTT
154049 TTCTCTTCTT
1 TT-T-TTCTT
154059 TTTT
1 TTTT
154063 GGGCCAAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
7 6 0.10
8 38 0.62
9 11 0.18
10 6 0.10
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:154048 original size:15 final size:15
Alignment explanation
Indices: 153985--154062 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
153975 TATTTTATTA
* *
153985 TTTTTCTTTTTTATT
1 TTTTTCTTCTTTCTT
*
154000 TTTTTCCTTTTTTCCTT
1 TTTTT-CTTCTTT-CTT
* *
154017 TTTTCCTT-TTT-TC
1 TTTTTCTTCTTTCTT
154030 TTTTTCTTCTTTC-T
1 TTTTTCTTCTTTCTT
154044 TTTTT-TTCTCTTCTT
1 TTTTTCTTCT-TTCTT
154059 TTTT
1 TTTT
154063 GGGCCAAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
13 12 0.23
14 11 0.21
15 13 0.25
16 10 0.19
17 6 0.12
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTTCTTTCTT
Found at i:154055 original size:24 final size:23
Alignment explanation
Indices: 153985--154055 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
153975 TATTTTATTA
153985 TTTTTCTT-TTTTATTTTTTTC-C
1 TTTTTCTTCTTTT-TTTTTTTCTC
*
154007 TTTTT-TCCTTTTTTCCTTTTT-TC
1 TTTTTCTTCTTTTTT--TTTTTCTC
154030 TTTTTCTTCTTTCTTTTTTTTCTC
1 TTTTTCTTCTTT-TTTTTTTTCTC
154054 TT
1 TT
154056 CTTTTTTGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
21 3 0.08
22 9 0.22
23 16 0.40
24 9 0.22
25 3 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTCTTTTTTTTTTTCTC
Found at i:154057 original size:14 final size:13
Alignment explanation
Indices: 153985--154062 Score: 65
Period size: 12 Copynumber: 6.2 Consensus size: 13
153975 TATTTTATTA
153985 TTTTTCTTT-TTT
1 TTTTTCTTTCTTT
* *
153997 ATTTT-TTTCCTT
1 TTTTTCTTTCTTT
*
154009 TTTTCCTTT-TTT
1 TTTTTCTTTCTTT
**
154021 CCTTT-TTTCTTT
1 TTTTTCTTTCTTT
*
154033 TTCTTCTTTCTTT
1 TTTTTCTTTCTTT
154046 TTTTTCTCTTCTTT
1 TTTTTCT-TTCTTT
154060 TTT
1 TTT
154063 GGGCCAAAAG
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
11 6 0.12
12 18 0.37
13 16 0.33
14 9 0.18
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:154062 original size:13 final size:12
Alignment explanation
Indices: 153985--154062 Score: 56
Period size: 13 Copynumber: 6.3 Consensus size: 12
153975 TATTTTATTA
153985 TTTTTCTTT-TT
1 TTTTTCTTTCTT
153996 TATTTT-TTTCCTT
1 T-TTTTCTTT-CTT
*
154009 TTTTCCTTT-TT
1 TTTTTCTTTCTT
*
154020 TCCTTT-TTTCTT
1 T-TTTTCTTTCTT
154032 TTTCTTCTTTCTTT
1 TTT-TTCTTTC-TT
154046 TTTTTCTCTTCTT
1 TTTTTCT-TTCTT
154059 TTTT
1 TTTT
154063 GGGCCAAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
11 11 0.21
12 14 0.26
13 20 0.38
14 8 0.15
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:154807 original size:28 final size:28
Alignment explanation
Indices: 154733--154856 Score: 70
Period size: 29 Copynumber: 4.2 Consensus size: 28
154723 GGCAAAAGCA
* * *
154733 TAATTTTATAAAAATATAGGGTCAAAATG
1 TAATTTTA-GAAAATTTAGGGCCAAAATG
* * * *
154762 TAATTTTTTGAAAGTTTAGGGCCCAAATT
1 TAA-TTTTAGAAAATTTAGGGCCAAAATG
** *
154791 TAATTTTAGAAAATTTAAAGGGTTAAAATA
1 TAATTTTAGAAAATTT--AGGGCCAAAATG
* * *
154821 TAATTAT-GAAAAATTTAAGAGCTAAAATG
1 TAATTTTAG-AAAATTT-AGGGCCAAAATG
154850 TAATTTT
1 TAATTTT
154857 TATTTTTTGT
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
28 11 0.15
29 37 0.51
30 25 0.34
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (28 bp):
TAATTTTAGAAAATTTAGGGCCAAAATG
Found at i:155304 original size:153 final size:147
Alignment explanation
Indices: 155060--155534 Score: 535
Period size: 153 Copynumber: 3.1 Consensus size: 147
155050 AAATAGTAGA
** * * *
155060 GTATGTGACCCAAAACTCAACTCACCTCTCG-AGTTATGAGTTGATCTTTGAGAAACAGAAATTG
1 GTATGTGACCCAAGGCTCAACTCACCTCTCGCA-TTATGAGTTGATTTTTGAAAAACAAAAATT-
* * * * * * **
155124 AAAATACCT--CATTGTGCCGCTCAAGGCTCAGCTCACCTCTTGGATTACAAGTTGATTTTTGAA
64 AAAATACCTCGCA-TGTGAC-C-CGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAA
155187 AAACGTAAATTAAAAGAAATACCTCG
126 AAACG-AAATT-AAAG--ATACCTCG
** * *
155213 GCGTGCGGCCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAAAAATTCA
1 GTATGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAAAAATT-A
* *
155278 AAATACCTCGGCATGTGACCCGAGGCTCAACACACCTCTCGTAATATGAGTTGATTTTTTGAAAA
65 AAATACCTC-GCATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGA-TTTTTGAAAA
*
155343 ACAGAAATTAAAGATACCACG
128 AC-GAAATTAAAGATACCTCG
* * * * *
155364 GTATGTGACCCGAGGCTCAAGTCACCTCTCGCAATATGAGTT-TTTTTTAAAAAACAAAAATTAA
1 GTATGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAAAAATTAA
*
155428 AGATACCTCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAA
66 A-ATACCTC-GCATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAA
*
155493 GAGAAATTAAAGATACCTCG
129 -CGAAATTAAAGATACCTCG
155513 GTATGTGACCCAAGGCTCAACT
1 GTATGTGACCCAAGGCTCAACT
155535 TAATTAAAGA
Statistics
Matches: 277, Mismatches: 37, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
149 51 0.18
150 66 0.24
151 42 0.15
153 91 0.33
154 19 0.07
155 6 0.02
156 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (147 bp):
GTATGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAAAAATTAA
AATACCTCGCATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAACG
AAATTAAAGATACCTCG
Found at i:155375 original size:76 final size:75
Alignment explanation
Indices: 155060--155534 Score: 505
Period size: 75 Copynumber: 6.3 Consensus size: 75
155050 AAATAGTAGA
* ** * * *
155060 GTATGTGACCCAAAACTCAACTCACCTCTCG-AGTTATGAGTTGATCTTTGAGAAACAGAAATTG
1 GTATGTGACCCGAGGCTCAACTCACCTCTCGCA-ATATGAGTTGATTTTTGAAAAACAGAAATT-
155124 AAA-ATACCTC-
64 AAAGATACCTCG
* * * * * * * **
155134 AT-TGTGCCGCTCAAGGCTCAGCTCACCTCTTGGATTACAAGTTGATTTTTGAAAAAC-GTAAAT
1 GTATGTGAC-C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG-AAAT
155197 TAAAAGAAATACCTCG
63 T-AAAG--ATACCTCG
** * * * * *
155213 GCGTGCGGCCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAAAAATTCA
1 GTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-A
155278 AA-ATACCTCG
65 AAGATACCTCG
* * *
155288 GCATGTGACCCGAGGCTCAACACACCTCTCGTAATATGAGTTGATTTTTTGAAAAACAGAAATTA
1 GTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTA
*
155353 AAGATACCACG
65 AAGATACCTCG
* * * *
155364 GTATGTGACCCGAGGCTCAAGTCACCTCTCGCAATATGAGTT-TTTTTTAAAAAACAAAAATTAA
1 GTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
155428 AGATACCTCA
66 AGATACCTCG
* *
155438 GTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAAGAGAAATTAA
1 GTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
155503 AGATACCTCG
66 AGATACCTCG
*
155513 GTATGTGACCCAAGGCTCAACT
1 GTATGTGACCCGAGGCTCAACT
155535 TAATTAAAGA
Statistics
Matches: 340, Mismatches: 48, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
73 5 0.01
74 70 0.21
75 140 0.41
76 64 0.19
78 56 0.16
79 1 0.00
80 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (75 bp):
GTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
AGATACCTCG
Found at i:155551 original size:39 final size:39
Alignment explanation
Indices: 155497--155573 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
155487 GAAAAAGAGA
155497 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
1 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
155536 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACT
1 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACT
155574 CACCTCTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (39 bp):
AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
Found at i:155622 original size:114 final size:114
Alignment explanation
Indices: 155422--155648 Score: 400
Period size: 114 Copynumber: 2.0 Consensus size: 114
155412 AAAAAACAAA
*
155422 AATTAAAGATACCTCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTT
1 AATTAAAGATACCTCAGTATGTGACCCAAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTT
* *
155487 GAAAAAGAGAAATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
66 GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCAAGGCTCAACTT
* *
155536 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTAAAGATACCTCAGTATGTGACCCAAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTT
*
155601 GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCGAGGCTCAACT
66 GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCAAGGCTCAACT
155649 CACCTCTCGC
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (114 bp):
AATTAAAGATACCTCAGTATGTGACCCAAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTT
GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCAAGGCTCAACTT
Found at i:155667 original size:189 final size:189
Alignment explanation
Indices: 155348--155725 Score: 625
Period size: 189 Copynumber: 2.0 Consensus size: 189
155338 GAAAAACAGA
* * *
155348 AATTAAAGATACCACGGTATGTGACCCGAGGCTCAAGTCACCTCTCGCAATATGAGTTTTTTTTA
1 AATTAAAGATACCACGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTATTTTTA
*
155413 AAAAACAAAAATTAAAGATACCTCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAG
66 AAAAACAAAAATTAAAGATACCCCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAG
155478 TTGA-TTTTTGAAAAAG-AGAAATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
131 TTGATTTTTTG-AAAAGCAGAAATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
*
155536 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTAAAGATACCACGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTT
* * * *
155601 GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
65 AAAAAACAAAAATTAAAGATACCCCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGA
*
155666 GTTGATTTTTTTGAAAAGCAGAAATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACT
130 GTTGA-TTTTTTGAAAAGCAGAAATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACT
155726 CACCTCTCGC
Statistics
Matches: 176, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
188 55 0.31
189 70 0.40
190 5 0.03
191 46 0.26
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (189 bp):
AATTAAAGATACCACGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTATTTTTA
AAAAACAAAAATTAAAGATACCCCAGTATGTGACCCGAGGCTCAACTCACCTCTCGAAATATGAG
TTGATTTTTTGAAAAGCAGAAATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTT
Found at i:155712 original size:77 final size:75
Alignment explanation
Indices: 155536--156068 Score: 809
Period size: 75 Copynumber: 7.1 Consensus size: 75
155526 GGCTCAACTT
*
155536 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
155601 GAAAAACAGA
66 GAAAAACAGA
*
155611 AATTAAAGATACCCCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
*
155676 TTGAAAAGCAGA
64 TTGAAAAACAGA
155688 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
**
155752 GAAAATTAGA
66 GAAAAACAGA
* *
155762 TATTAAAGATACC-CTGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTT
1 AATTAAAGATACCTC-GGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
* *
155826 TTTGAATAGCAGA
63 TTTGAAAAACAGA
* *
155839 AATTAAAGATACTTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTC
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
155904 AAAAAATAGA
66 GAAAAACAGA
* * *
155914 GATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTGTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
155979 GAGAAATAGA
66 GAAAAACAGA
* *
155989 AATTAAAGATACCTTGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
*
156054 TGAAAAACAAA
65 TGAAAAACAGA
156065 AATT
1 AATT
156069 GAAAAATATA
Statistics
Matches: 416, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
73 1 0.00
74 67 0.16
75 193 0.46
76 16 0.04
77 138 0.33
78 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (75 bp):
AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAAACAGA
Found at i:155816 original size:151 final size:152
Alignment explanation
Indices: 155536--156060 Score: 844
Period size: 151 Copynumber: 3.5 Consensus size: 152
155526 GGCTCAACTT
*
155536 AATTAAAGATACCTCGGTATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
155601 GAAAAACAGAAATTAAAGATACCCCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
66 GAAAAATAGAAATTAAAGATACCCTGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
155666 GTTGATTTTTTTGAAAAGCAGA
131 GTTGATTTTTTTGAAAAGCAGA
155688 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * *
155752 GAAAATTAGATATTAAAGATACCCTGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAGTATGA
66 GAAAAATAGAAATTAAAGATACCCTGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
155817 GTTGATTTTTTTGAATAGCAGA
131 GTTGATTTTTTTGAAAAGCAGA
* *
155839 AATTAAAGATACTTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTC
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * *
155904 AAAAAATAGAGATTAAAGATA-CCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCACAATATG
66 GAAAAATAGAAATTAAAGATACCCT-GGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
155968 AGTTGA--TTGTTGAGAAA-TAGA
130 AGTTGATTTTTTTGA-AAAGCAGA
* *
155989 AATTAAAGATACCTTGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1 AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
156054 TGAAAAA
65 TGAAAAA
156061 CAAAAATTGA
Statistics
Matches: 347, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
150 66 0.19
151 158 0.46
152 123 0.35
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (152 bp):
AATTAAAGATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAAATAGAAATTAAAGATACCCTGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTGAAAAGCAGA
Found at i:155992 original size:492 final size:491
Alignment explanation
Indices: 155060--156026 Score: 1326
Period size: 492 Copynumber: 2.0 Consensus size: 491
155050 AAATAGTAGA
* *
155060 GTATGTGACCCAAAACTCAACTCACCTCTCGAGTTATGAGTTGATCTTTGAGAAACAGAAATTGA
1 GTATGTGACCCAAAACTCAACTCACCTCTCGAGATATGAGTTGATCTTTGAAAAACAGAAATTGA
* * * * * *
155125 AAATACCTCATTGTGCCGCTCAAGGCTCAGCTCACCTCTTGGATTACAAGTTGATTTTTGAAAAA
66 AAATACCCCATTGTGACGCTCAAGGCTCAACTCACCTCTCGCAATACAAGTTGATTTTTGAAAAA
* * *
155190 CGTAAATTAAAAGAAATACCTCGGCGTGCGGCCCAAGGCTCAACTCACCTCTCGCATTATGAGTT
131 CGTAAATTAAAAG-AATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
*
155255 GATTTTTGAAAAACAAAAATTCAAAATACCTCGGCATGTGACCCGAGGCTCAACACACCTCTCGT
195 GATTTTTGAAAAACAAAAATTCAAAATACCTCGGCATGTGACCCGAGGCTCAACACACCTCTCGC
*
155320 AATATGAGTTGATTTTTTGAAAAACAGAAATTAAAGATACCACGGTATGTGACCCGAGGCTCAAG
260 AATATGAGTTGATTTTTTGAAAAACAGAAATTAAAGATACCACGGTATGTGACCCGAGGCTCAAC
* *
155385 TCACCTCTCGCAATATGAGTTTTTTTTAAAAAACAAAAATTAAAGATACCTCAGTATGTGACCCG
325 TCACCTCTCGCAATATGAGTTATTTTCAAAAAACAAAAATTAAAGATACCTCAGTATGTGACCCG
*
155450 AGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAAGAGAAATTAAAGATACCTCGGT
390 AGGCTCAACTCACCTCTCGAAATATGAGTTGATTGTTGAAAAAGAGAAATTAAAGATACCTCGGT
155515 ATGTGACCCAAGGCTCAACTTAATTAAAGATACCTCG
455 ATGTGACCCAAGGCTCAACTTAATTAAAGATACCTCG
** *
155552 GTATGTGACCCAAGGCTCAACTCACCTCTCGCA-ATATGAGTTGATTTTTGAAAAACAGAAATT-
1 GTATGTGACCCAAAACTCAACTCACCTCTCG-AGATATGAGTTGATCTTTGAAAAACAGAAATTG
* * **
155615 AAAGATACCCCGGTATGTGAC-C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
65 AAA-ATACCCC-AT-TGTGACGCTCAAGGCTCAACTCACCTCTCGCAATACAAGTTGA--TTTTT
* * * *
155678 GAAAAGCAG-AAATT-AAAG-ATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCAATA
125 GAAAAAC-GTAAATTAAAAGAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAATA
** * * * *
155740 TGAGTT-ATTTTTGAAAATTAGATATT-AAAGATACC-CTGGTATGTGACCCGAGGCTCAACTCA
189 TGAGTTGATTTTTGAAAAACAAAAATTCAAA-ATACCTC-GGCATGTGACCCGAGGCTCAACACA
* * * **
155802 CCTCTCGCAGTATGAGTTGATTTTTTTGAATAGCAGAAATTAAAGATACTTCGGTATGTGACCCG
252 CCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTAAAGATACCACGGTATGTGACCCG
* * * *
155867 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCAAAAAATAGAGATTAAAGATACCTCGGT
316 AGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTCAAAAAACAAAAATTAAAGATACCTCAGT
* *
155932 ATGTGACCCGAGGCTCAACTCACCTCTC-ACAATATGAGTTGATTGTTGAGAAATAGAAATTAAA
380 ATGTGACCCGAGGCTCAACTCACCTCTCGA-AATATGAGTTGATTGTTGAAAAAGAGAAATTAAA
* *
155996 GATACCTTGGTATGTGACCCGAGGCTCAACT
444 GATACCTCGGTATGTGACCCAAGGCTCAACT
156027 CACCTCTCGT
Statistics
Matches: 417, Mismatches: 46, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
489 4 0.01
490 62 0.15
491 117 0.28
492 205 0.49
493 7 0.02
494 21 0.05
495 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (491 bp):
GTATGTGACCCAAAACTCAACTCACCTCTCGAGATATGAGTTGATCTTTGAAAAACAGAAATTGA
AAATACCCCATTGTGACGCTCAAGGCTCAACTCACCTCTCGCAATACAAGTTGATTTTTGAAAAA
CGTAAATTAAAAGAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTCAAAATACCTCGGCATGTGACCCGAGGCTCAACACACCTCTCGCA
ATATGAGTTGATTTTTTGAAAAACAGAAATTAAAGATACCACGGTATGTGACCCGAGGCTCAACT
CACCTCTCGCAATATGAGTTATTTTCAAAAAACAAAAATTAAAGATACCTCAGTATGTGACCCGA
GGCTCAACTCACCTCTCGAAATATGAGTTGATTGTTGAAAAAGAGAAATTAAAGATACCTCGGTA
TGTGACCCAAGGCTCAACTTAATTAAAGATACCTCG
Found at i:156939 original size:13 final size:13
Alignment explanation
Indices: 156923--156952 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
156913 ACCTTGATTT
156923 TTTTCTTTTTTTG
1 TTTTCTTTTTTTG
*
156936 TTTTGTTTTTTTG
1 TTTTCTTTTTTTG
156949 TTTT
1 TTTT
156953 TAGGCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTTTTG
Found at i:168203 original size:7 final size:7
Alignment explanation
Indices: 168200--168250 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
168190 CTTTTTTGTT
168200 TTTTTTC
1 TTTTTTC
*
168207 TTTTCTC
1 TTTTTTC
168214 TTTTTTC
1 TTTTTTC
168221 TTTTTTCC
1 TTTTTT-C
168229 TTTTCTTC
1 TTTT-TTC
*
168237 CTTTTTC
1 TTTTTTC
168244 TATTTTT
1 T-TTTTT
168251 TTCATGTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 21 0.57
8 14 0.38
9 2 0.05
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:168217 original size:16 final size:16
Alignment explanation
Indices: 168198--168253 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
168188 GCCTTTTTTG
168198 TTTTTTTTCTTTTCTC
1 TTTTTTTTCTTTTCTC
168214 TTTTTTCTT-TTTTC-C
1 TTTTTT-TTCTTTTCTC
* *
168229 TTTTCTTCCTTTT-TC
1 TTTTTTTTCTTTTCTC
168244 TATTTTTTTC
1 T-TTTTTTTC
168254 ATGTAGTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 12 0.38
16 17 0.53
17 2 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTTCTTTTCTC
Found at i:168224 original size:23 final size:24
Alignment explanation
Indices: 168190--168253 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
168180 CAATTCGGGC
*
168190 CTTTTTTGTTTTTTTTCTTTTC-T
1 CTTTTTTCTTTTTTTTCTTTTCTT
*
168213 CTTTTTTC-TTTTTTCCTTTTCTT
1 CTTTTTTCTTTTTTTTCTTTTCTT
*
168236 CCTTTTTCTATTTTTTTC
1 CTTTTTTCT-TTTTTTTC
168254 ATGTAGTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.35
23 15 0.44
25 7 0.21
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (24 bp):
CTTTTTTCTTTTTTTTCTTTTCTT
Found at i:168457 original size:12 final size:12
Alignment explanation
Indices: 168442--168480 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
168432 TCGCTCTCTT
168442 TTTTCTTTTCTC
1 TTTTCTTTTCTC
168454 TTTTCTTTTCTC
1 TTTTCTTTTCTC
**
168466 CCTTCTTTT-TC
1 TTTTCTTTTCTC
168477 TTTT
1 TTTT
168481 TGGTTGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTTTCTC
Found at i:168462 original size:19 final size:18
Alignment explanation
Indices: 168438--168481 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
168428 CTCCTCGCTC
**
168438 TCTTTTTTCTTTTCTCTTT
1 TCTTTTTTCCCTTCT-TTT
*
168457 TCTTTTCTCCCTTCTTTT
1 TCTTTTTTCCCTTCTTTT
168475 TCTTTTT
1 TCTTTTT
168482 GGTTGCTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
TCTTTTTTCCCTTCTTTT
Found at i:174971 original size:29 final size:29
Alignment explanation
Indices: 174922--174981 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
174912 TGGGACAACT
174922 CACTAAGGGAGAAAGATGCCCAAACCATC
1 CACTAAGGGAGAAAGATGCCCAAACCATC
* *
174951 CACTAAGGGAGCAATGA-GCCCAAGCCATC
1 CACTAAGGGAG-AAAGATGCCCAAACCATC
174980 CA
1 CA
174982 TGTGACTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.38, C:0.30, G:0.22, T:0.10
Consensus pattern (29 bp):
CACTAAGGGAGAAAGATGCCCAAACCATC
Found at i:176263 original size:71 final size:72
Alignment explanation
Indices: 176143--176282 Score: 165
Period size: 71 Copynumber: 1.9 Consensus size: 72
176133 CACTGTGACA
* * ** *
176143 ATGGTCTATCGACTTTATGGAGCGACACTGTGACGGTGGTTATCAACTAG-CGCTAGAGTGACAC
1 ATGGTCTATCGACTCTATCGAGCGACACTGTGACGGCAGTTATCAACTAGCCACTAGAGTGACAC
176207 CGTGATG
66 CGTGATG
* * * * **
176214 ATGGTCTATTGACTCTATCGAGTGACATTGTGATGGCAGTTATTGACTAGCTCACTAGAGTGACA
1 ATGGTCTATCGACTCTATCGAGCGACACTGTGACGGCAGTTATCAACTAGC-CACTAGAGTGACA
176279 CCGT
65 CCGT
176283 CACAATGATA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
71 40 0.71
73 16 0.29
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (72 bp):
ATGGTCTATCGACTCTATCGAGCGACACTGTGACGGCAGTTATCAACTAGCCACTAGAGTGACAC
CGTGATG
Found at i:178294 original size:22 final size:22
Alignment explanation
Indices: 178269--178310 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
178259 AATTAATCAC
178269 TCACTCATCATT-CATTCTTCAT
1 TCACTCA-CATTCCATTCTTCAT
178291 TCACTCACATTCCATTCTTC
1 TCACTCACATTCCATTCTTC
178311 TCTTTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (22 bp):
TCACTCACATTCCATTCTTCAT
Found at i:188353 original size:42 final size:43
Alignment explanation
Indices: 188293--188375 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
188283 AGCATTTACA
** *
188293 AAAATAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAG
1 AAAATAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAG
188336 AAAA-AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT
1 AAAATAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT
188376 TCTTCACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (43 bp):
AAAATAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAG
Found at i:188430 original size:43 final size:43
Alignment explanation
Indices: 188298--188437 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 43
188288 TTACAAAAAT
** * * *
188298 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTAGAAAA
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTGTAAA
* *
188340 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTCT-TCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTT-TGTAAA
* * *
188383 AAACGCCGCTATAGAATATGA-CTTTTAGCGGCGCTTTTGTGAA
1 AAACGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTTTGTAAA
*
188426 AAACGCCACTAA
1 AAACGCCGCTAA
188438 TTTGGGATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
42 33 0.41
43 48 0.59
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTGTAAA
Found at i:206593 original size:20 final size:21
Alignment explanation
Indices: 206560--206608 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
206550 AATAAAAATT
*
206560 ATAAAAAT-TATTAAACTGTA
1 ATAAAAATATATTAAAATGTA
*
206580 ATAAAAATAT-TTAAAATTTA
1 ATAAAAATATATTAAAATGTA
*
206600 CTAAAAATA
1 ATAAAAATA
206609 GAATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAAAATATATTAAAATGTA
Found at i:206595 original size:29 final size:28
Alignment explanation
Indices: 206524--206597 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
206514 CACATATGAC
**
206524 AAAAATATTATAAAAAAATTAAAATCAAT
1 AAAAATATT-TAAAATTATTAAAATCAAT
* * *
206553 AAAAAT-TATAAAAATTATTAAACTGTAAT
1 AAAAATAT-TTAAAATTATTAAAAT-CAAT
206582 AAAAATATTTAAAATT
1 AAAAATATTTAAAATT
206598 TACTAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 12 0.33
29 23 0.64
30 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATATTTAAAATTATTAAAATCAAT
Found at i:208914 original size:18 final size:17
Alignment explanation
Indices: 208870--208914 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
208860 ATTTCAAAAT
208870 ATTATAAAAATATTAAA
1 ATTATAAAAATATTAAA
* *
208887 ATTTTCAAAAATATTGATA
1 ATTAT-AAAAATATT-AAA
208906 ATTATAAAA
1 ATTATAAAA
208915 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTATAAAAATATTAAA
Found at i:209139 original size:19 final size:18
Alignment explanation
Indices: 209089--209150 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
209079 GACATATTTC
209089 AAAATATTATAAAAATATT
1 AAAAT-TTATAAAAATATT
209108 AAAATTT-TCAAAAATATT
1 AAAATTTAT-AAAAATATT
* *
209126 GATAATTTATAAAATTATTT
1 -AAAATTTATAAAAATA-TT
209146 AAAAT
1 AAAAT
209151 GGTAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 21 0.58
20 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTTATAAAAATATT
Found at i:209171 original size:224 final size:224
Alignment explanation
Indices: 208804--209248 Score: 874
Period size: 224 Copynumber: 2.0 Consensus size: 224
208794 GCAAATTGAT
208804 ATCCAAGTTTATTTGAATGTAAACATTTTTTTTTTGTCCAGATTCATTGTAGACATATTTCAAAA
1 ATCCAAGTTTATTTGAATGTAAACATTTTTTTTTTGTCCAGATTCATTGTAGACATATTTCAAAA
208869 TATTATAAAAATATTAAAATTTTCAAAAATATTGATAATTATAAAATTTATTTAAAATGGTAAAA
66 TATTATAAAAATATTAAAATTTTCAAAAATATTGATAATTATAAAATTTATTTAAAATGGTAAAA
208934 ATTATAATAATTTTTAATGTTATTAAAAAATTCTAAAACATTGTAAAAATAAAAATATAAAAAAA
131 ATTATAATAATTTTTAATGTTATTAAAAAATTCTAAAACATTGTAAAAATAAAAATATAAAAAAA
208999 TTTGTTAAAATAATTTATTACAAATGTAA
196 TTTGTTAAAATAATTTATTACAAATGTAA
209028 ATCCAAGTTTATTTGAATGTAAACATTTTTTTTTTGTCCAGATTCATTGTAGACATATTTCAAAA
1 ATCCAAGTTTATTTGAATGTAAACATTTTTTTTTTGTCCAGATTCATTGTAGACATATTTCAAAA
209093 TATTATAAAAATATTAAAATTTTCAAAAATATTGATAATTTATAAAA-TTATTTAAAATGGTAAA
66 TATTATAAAAATATTAAAATTTTCAAAAATATTGATAA-TTATAAAATTTATTTAAAATGGTAAA
209157 AATTATAATAATTTTTAATGTTATTAAAAAATTCTAAAACATTGTAAAAATAAAAATATAAAAAA
130 AATTATAATAATTTTTAATGTTATTAAAAAATTCTAAAACATTGTAAAAATAAAAATATAAAAAA
209222 ATTTGTTAAAATAATTTATTACAAATG
195 ATTTGTTAAAATAATTTATTACAAATG
209249 CAATAGAATA
Statistics
Matches: 220, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
224 212 0.96
225 8 0.04
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (224 bp):
ATCCAAGTTTATTTGAATGTAAACATTTTTTTTTTGTCCAGATTCATTGTAGACATATTTCAAAA
TATTATAAAAATATTAAAATTTTCAAAAATATTGATAATTATAAAATTTATTTAAAATGGTAAAA
ATTATAATAATTTTTAATGTTATTAAAAAATTCTAAAACATTGTAAAAATAAAAATATAAAAAAA
TTTGTTAAAATAATTTATTACAAATGTAA
Found at i:211347 original size:16 final size:16
Alignment explanation
Indices: 211326--211358 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
211316 AGAAGGATTC
211326 AAACCCAAAAATTCTT
1 AAACCCAAAAATTCTT
211342 AAACCCAAAAATTCTT
1 AAACCCAAAAATTCTT
211358 A
1 A
211359 CACACACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACCCAAAAATTCTT
Found at i:214552 original size:15 final size:16
Alignment explanation
Indices: 214532--214565 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
214522 AGATTAAATT
214532 AATTAG-CTAAATGCA
1 AATTAGCCTAAATGCA
214547 AATTAGCCTAAATGCA
1 AATTAGCCTAAATGCA
214563 AAT
1 AAT
214566 GGGATGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (16 bp):
AATTAGCCTAAATGCA
Found at i:214587 original size:75 final size:75
Alignment explanation
Indices: 214498--214651 Score: 281
Period size: 75 Copynumber: 2.1 Consensus size: 75
214488 AAGAAAACAT
*
214498 AATAATTTAAGGTGATAAATGTTAAGATTAAATTAATTAGCTAAATGCAAATTAGCCTAAATGCA
1 AATAATTTAAGGTGATAAATGTTAAGATTAAATTAATTAGCTAAATGCAAATTAACCTAAATGCA
214563 AATGGGATGA
66 AATGGGATGA
**
214573 AATAATTTGGGGTGATAAATGTTAAGATTAAATTAATTAGCTAAATGCAAATTAACCTAAATGCA
1 AATAATTTAAGGTGATAAATGTTAAGATTAAATTAATTAGCTAAATGCAAATTAACCTAAATGCA
214638 AATGGGATGA
66 AATGGGATGA
214648 AATA
1 AATA
214652 TGAAAGGTGA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (75 bp):
AATAATTTAAGGTGATAAATGTTAAGATTAAATTAATTAGCTAAATGCAAATTAACCTAAATGCA
AATGGGATGA
Found at i:218900 original size:147 final size:147
Alignment explanation
Indices: 218737--219020 Score: 514
Period size: 147 Copynumber: 1.9 Consensus size: 147
218727 ACAAAAATAA
*
218737 TTTTTTATGTGTATGTAAATATAAAACCGCTCAACTTAATTTAGTAACAAAATAATGATTCATAC
1 TTTTTTATGTGTATGTAAATATAAAACCGCTCAACTTAATTTAGTAACAAAATAATGATTCATAA
* *
218802 CATATATCAAAGTATTTCGAAATAAATACTTTCGCTTTTTATTTTTAATAGTTGGAGTTGATACG
66 CATATATCAAAGTATTTCAAAATAAAGACTTTCGCTTTTTATTTTTAATAGTTGGAGTTGATACG
218867 TTAGATAAAAAAATTTT
131 TTAGATAAAAAAATTTT
218884 TTTTTTATGTGTATGTAAATATAAAACCGCTCAACTTAATTTAGTAACAAAATAATGATTCATAA
1 TTTTTTATGTGTATGTAAATATAAAACCGCTCAACTTAATTTAGTAACAAAATAATGATTCATAA
* * *
218949 CATATTTCAAAGTATTTCAAAATAAAGACTTTCGCTTTTTCTTTTTAATATTTGGAGTTGATACG
66 CATATATCAAAGTATTTCAAAATAAAGACTTTCGCTTTTTATTTTTAATAGTTGGAGTTGATACG
219014 TTAGATA
131 TTAGATA
219021 CAGATAGATC
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 131 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (147 bp):
TTTTTTATGTGTATGTAAATATAAAACCGCTCAACTTAATTTAGTAACAAAATAATGATTCATAA
CATATATCAAAGTATTTCAAAATAAAGACTTTCGCTTTTTATTTTTAATAGTTGGAGTTGATACG
TTAGATAAAAAAATTTT
Found at i:219057 original size:9 final size:11
Alignment explanation
Indices: 219031--219056 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
219021 CAGATAGATC
219031 ATATATTGTAA
1 ATATATTGTAA
219042 ATATATTGTAA
1 ATATATTGTAA
219053 ATAT
1 ATAT
219057 TTGGAGTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
ATATATTGTAA
Found at i:220225 original size:14 final size:14
Alignment explanation
Indices: 220208--220234 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
220198 ATGAGGAGAA
220208 ATAATTTTTCTTGG
1 ATAATTTTTCTTGG
220222 ATAATTTTTCTTG
1 ATAATTTTTCTTG
220235 CAAACTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
ATAATTTTTCTTGG
Found at i:224006 original size:14 final size:14
Alignment explanation
Indices: 223975--224069 Score: 50
Period size: 14 Copynumber: 6.8 Consensus size: 14
223965 ATTTAAATTT
*
223975 TAAATCCTAAAC-C
1 TAAATTCTAAACAC
223988 ATAAATTCTAAACAC
1 -TAAATTCTAAACAC
* * ***
224003 TAAATTTTATATTT
1 TAAATTCTAAACAC
* * *
224017 TGAACTCTAAACCC
1 TAAATTCTAAACAC
* *
224031 TATATTC-AAATCAT
1 TAAATTCTAAA-CAC
224045 TAAATTCTAAACAC
1 TAAATTCTAAACAC
*
224059 TAAATTTTAAA
1 TAAATTCTAAA
224070 TCTCAAACTC
Statistics
Matches: 57, Mismatches: 21, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
13 3 0.05
14 50 0.88
15 4 0.07
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (14 bp):
TAAATTCTAAACAC
Found at i:224053 original size:28 final size:28
Alignment explanation
Indices: 224019--224103 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
224009 TTATATTTTG
*
224019 AACTCTAAACCCTATATTCAAATCATTA
1 AACTCTAAACCCTATATTTAAATCATTA
* * * *
224047 AATTCTAAACACTAAATTTTAAATC-TCA
1 AACTCTAAACCCTATA-TTTAAATCATTA
*
224075 AACTCAAAACCCTATATTTAAATCATTA
1 AACTCTAAACCCTATATTTAAATCATTA
224103 A
1 A
224104 GTGCATCATA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 8 0.18
28 30 0.67
29 7 0.16
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (28 bp):
AACTCTAAACCCTATATTTAAATCATTA
Found at i:224053 original size:56 final size:56
Alignment explanation
Indices: 223989--224103 Score: 176
Period size: 56 Copynumber: 2.1 Consensus size: 56
223979 TCCTAAACCA
* * ** *
223989 TAAATTCTAAACACTAAATTTTATATTTTGAACTCTAAACCCTATATTCAAATCAT
1 TAAATTCTAAACACTAAATTTTAAATCTCAAACTCAAAACCCTATATTCAAATCAT
*
224045 TAAATTCTAAACACTAAATTTTAAATCTCAAACTCAAAACCCTATATTTAAATCAT
1 TAAATTCTAAACACTAAATTTTAAATCTCAAACTCAAAACCCTATATTCAAATCAT
224101 TAA
1 TAA
224104 GTGCATCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (56 bp):
TAAATTCTAAACACTAAATTTTAAATCTCAAACTCAAAACCCTATATTCAAATCAT
Found at i:224153 original size:20 final size:19
Alignment explanation
Indices: 224117--224156 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
224107 CATCATACTC
* *
224117 ATAAAAACAAAATATAGAA
1 ATAAAAAAAAAACATAGAA
224136 ATAAAAAAATAAACATAGAA
1 ATAAAAAAA-AAACATAGAA
224156 A
1 A
224157 ATATAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (19 bp):
ATAAAAAAAAAACATAGAA
Found at i:224854 original size:24 final size:24
Alignment explanation
Indices: 224809--224854 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
224799 TAACTAAAAT
** *
224809 AAATAATATATAACCTATATAATA
1 AAATAATATATAAAATAAATAATA
*
224833 AAATAATATTTAAAATAAATAA
1 AAATAATATATAAAATAAATAA
224855 CATTCTATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAATATATAAAATAAATAATA
Found at i:226112 original size:76 final size:76
Alignment explanation
Indices: 226029--226355 Score: 349
Period size: 76 Copynumber: 4.3 Consensus size: 76
226019 TGGTAATTCC
* * *
226029 GAGGCTCAACTCATTTCTTGAAAACATAATCAATTTTTGATAAAATGATAATTGAAAGGACCTCA
1 GAGGCTCAACCCATTTCTTGAAAACATAATCAATTTTTGATAAAATGACAACTGAAAGGACCTCA
*
226094 ACAACAATCCT
66 ACGACAATCCT
* * ** * * * *
226105 GACGCTCAACCCATTTCTTGAAAACAGAATCGCTTTTTGATAAAATGATAGCTGAAAGAACCTAA
1 GAGGCTCAACCCATTTCTTGAAAACATAATCAATTTTTGATAAAATGACAACTGAAAGGACCTCA
*
226170 ATGACAATCCT
66 ACGACAATCCT
* * * *
226181 GAGGCTCGACCCATTTCTTGAAAACA-AATTCAATTTTTGATAAAATGACAACTAAAAAGACATC
1 GAGGCTCAACCCATTTCTTGAAAACATAA-TCAATTTTTGATAAAATGACAACTGAAAGGACCTC
*
226245 AACGTCAAT-CT
65 AACGACAATCCT
* * * *
226256 CGAGGCTCGATCCATTTCTTGAAAACAT-ATCCAATTTTTCATCAAATGACAACTGAAAGGACCT
1 -GAGGCTCAACCCATTTCTTGAAAACATAAT-CAATTTTTGATAAAATGACAACTGAAAGGACCT
** *
226320 TGACGATAAT-CT
64 CAACGACAATCCT
*
226332 CAAGGCTCAACCCATTTCTT-AAAA
1 -GAGGCTCAACCCATTTCTTGAAAA
226356 TGAATTCGAT
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
75 9 0.04
76 201 0.96
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (76 bp):
GAGGCTCAACCCATTTCTTGAAAACATAATCAATTTTTGATAAAATGACAACTGAAAGGACCTCA
ACGACAATCCT
Found at i:237633 original size:9 final size:9
Alignment explanation
Indices: 237619--237645 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
237609 CAAGTATTTG
237619 CTTGAAAGA
1 CTTGAAAGA
237628 CTTGAAAGA
1 CTTGAAAGA
237637 CTTGAAAGA
1 CTTGAAAGA
237646 AACTCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (9 bp):
CTTGAAAGA
Found at i:247476 original size:16 final size:16
Alignment explanation
Indices: 247455--247485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
247445 TATGTTAGAG
247455 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
247471 CATATATATTTGAAA
1 CATATAAATTTGAAA
247486 AAAATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:247690 original size:19 final size:20
Alignment explanation
Indices: 247666--247731 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
247656 ATAAATATTG
247666 GAATTTTTATAAA-TATTTT
1 GAATTTTTATAAATTATTTT
*
247685 GAA-TTTTA-AAAGTTATCTT
1 GAATTTTTATAAA-TTATTTT
247704 GAATTTTT-TAAAATTATTTT
1 GAATTTTTAT-AAATTATTTT
247724 GAATTTTT
1 GAATTTTT
247732 TTTTATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.08
18 5 0.12
19 11 0.28
20 18 0.45
21 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
GAATTTTTATAAATTATTTT
Found at i:266725 original size:23 final size:20
Alignment explanation
Indices: 266695--266755 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 20
266685 AAAGAGAAAG
266695 AATTTCTGTAAAATCAGTCAA
1 AATTTCTGTAAAATCAGT-AA
*
266716 TTAATTTCTGTAAAATTTCTGTAA
1 --AATTTCTGTAAAA--TCAGTAA
266740 AATTTCTGTAAAATCA
1 AATTTCTGTAAAATCA
266756 AACAATCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.06
22 13 0.38
23 13 0.38
24 2 0.06
25 4 0.12
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (20 bp):
AATTTCTGTAAAATCAGTAA
Found at i:266734 original size:11 final size:11
Alignment explanation
Indices: 266718--266753 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
266708 TCAGTCAATT
266718 AATTTCTGTAA
1 AATTTCTGTAA
266729 AATTTCTGTAA
1 AATTTCTGTAA
266740 AATTTCTGTAA
1 AATTTCTGTAA
266751 AAT
1 AAT
266754 CAAACAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
AATTTCTGTAA
Found at i:270674 original size:20 final size:19
Alignment explanation
Indices: 270628--270674 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
270618 ACAAATATTT
270628 AATTTT-TATATTTAAATA
1 AATTTTATATATTTAAATA
* * *
270646 TAGTTTATATATTCTAATTA
1 AATTTTATATATT-TAAATA
270666 AATTTTATA
1 AATTTTATA
270675 AATAATTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTATATATTTAAATA
Found at i:270847 original size:13 final size:13
Alignment explanation
Indices: 270786--270849 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
270776 ACACTCAAAT
*
270786 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
*
270799 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
270812 TTTTGCATAA-CAC
1 TTTT-CAAAAGCAC
270825 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
270838 TTTTCAAAAGCA
1 TTTTCAAAAGCA
270850 ATGAAGAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:275560 original size:27 final size:27
Alignment explanation
Indices: 275530--275616 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
275520 TACTGACCAT
275530 TCCAACACCAAATCTATCCATCATGCA
1 TCCAACACCAAATCTATCCATCATGCA
275557 TCC-ACTA-CAACA-CATATCC-T-ACTGACCA
1 TCCAAC-ACCAA-ATC-TATCCATCA-TG--CA
275585 TTCCAACACCAAATCTATCCATCATGCA
1 -TCCAACACCAAATCTATCCATCATGCA
275613 TCCA
1 TCCA
275617 CTACTATACC
Statistics
Matches: 48, Mismatches: 0, Indels: 24
0.67 0.00 0.33
Matches are distributed among these distances:
25 1 0.02
26 9 0.19
27 14 0.29
28 4 0.08
29 10 0.21
30 9 0.19
31 1 0.02
ACGTcount: A:0.36, C:0.38, G:0.03, T:0.23
Consensus pattern (27 bp):
TCCAACACCAAATCTATCCATCATGCA
Found at i:275585 original size:56 final size:57
Alignment explanation
Indices: 275503--275620 Score: 211
Period size: 56 Copynumber: 2.1 Consensus size: 57
275493 ACCTCAAAAA
275503 TACAACACATATAAGCCTACTGACCATTCCAACACCAAATCTATCCATCATGCATCCAC
1 TACAACACATAT-A-CCTACTGACCATTCCAACACCAAATCTATCCATCATGCATCCAC
275562 TACAACACATAT-CCTACTGACCATTCCAACACCAAATCTATCCATCATGCATCCAC
1 TACAACACATATACCTACTGACCATTCCAACACCAAATCTATCCATCATGCATCCAC
275618 TAC
1 TAC
275621 TATACCGAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 47 0.80
59 12 0.20
ACGTcount: A:0.36, C:0.36, G:0.04, T:0.23
Consensus pattern (57 bp):
TACAACACATATACCTACTGACCATTCCAACACCAAATCTATCCATCATGCATCCAC
Found at i:278862 original size:23 final size:23
Alignment explanation
Indices: 278830--278881 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
278820 AACATAGTGT
*
278830 CTACTATTAAAGCACTTCGGTGC
1 CTACTATTAAAGCACTTCGATGC
* *
278853 CTACTGTTAAATCACTTCGATGC
1 CTACTATTAAAGCACTTCGATGC
278876 CTACTA
1 CTACTA
278882 CTGTGGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (23 bp):
CTACTATTAAAGCACTTCGATGC
Found at i:281550 original size:21 final size:22
Alignment explanation
Indices: 281511--281555 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
281501 CATTAAACTG
*
281511 AATTCAAACAAATAAAAAGTAA
1 AATTCAAACAAATAAAAAGAAA
281533 AATTCATAA-AAA-AAAAAGAAA
1 AATTCA-AACAAATAAAAAGAAA
281554 AA
1 AA
281556 AAAAAGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 9 0.43
23 2 0.10
ACGTcount: A:0.73, C:0.07, G:0.04, T:0.16
Consensus pattern (22 bp):
AATTCAAACAAATAAAAAGAAA
Found at i:283357 original size:23 final size:23
Alignment explanation
Indices: 283331--283382 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
283321 AGATTATTAC
283331 TATAATTTCAATGAATATATCAT
1 TATAATTTCAATGAATATATCAT
*
283354 TATAATTTCAATGTATATATCAT
1 TATAATTTCAATGAATATATCAT
283377 TATAAT
1 TATAAT
283383 ATTTTGACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (23 bp):
TATAATTTCAATGAATATATCAT
Found at i:285119 original size:71 final size:71
Alignment explanation
Indices: 285003--285138 Score: 272
Period size: 71 Copynumber: 1.9 Consensus size: 71
284993 GCTTAGACTA
285003 AAAAAAAAAAAAAAAGGGAAACGTAGGAGTTTATATAAGAAAGATAAAGTTTTAATAGAGAGAAA
1 AAAAAAAAAAAAAAAGGGAAACGTAGGAGTTTATATAAGAAAGATAAAGTTTTAATAGAGAGAAA
285068 TTAAAC
66 TTAAAC
285074 AAAAAAAAAAAAAAAGGGAAACGTAGGAGTTTATATAAGAAAGATAAAGTTTTAATAGAGAGAAA
1 AAAAAAAAAAAAAAAGGGAAACGTAGGAGTTTATATAAGAAAGATAAAGTTTTAATAGAGAGAAA
285139 GAAAGAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (71 bp):
AAAAAAAAAAAAAAAGGGAAACGTAGGAGTTTATATAAGAAAGATAAAGTTTTAATAGAGAGAAA
TTAAAC
Found at i:287949 original size:18 final size:18
Alignment explanation
Indices: 287905--287949 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
287895 CATTCGTTTC
*
287905 CAAAACATTATTCATTTA
1 CAAAACGTTATTCATTTA
*
287923 CAAATCGTTATTCAATTT-
1 CAAAACGTTATTC-ATTTA
287941 CAAAACGTT
1 CAAAACGTT
287950 TTCTTATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCATTTA
Found at i:291677 original size:24 final size:24
Alignment explanation
Indices: 291650--291695 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
291640 GATTTGAAAA
291650 AAAATAATT-TTTAGCAAAAACTTT
1 AAAATAATTATTTAG-AAAAACTTT
**
291674 AAAATTGTTATTTAGAAAAACT
1 AAAATAATTATTTAGAAAAACT
291696 CATGCGCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (24 bp):
AAAATAATTATTTAGAAAAACTTT
Found at i:292161 original size:34 final size:35
Alignment explanation
Indices: 292081--292174 Score: 120
Period size: 34 Copynumber: 2.7 Consensus size: 35
292071 ACTTATACAA
* *
292081 ATATTAGATCAGAATGTTATATTACCAAAAAAACAT
1 ATATGAGATCAGAATGTCATATTACC-AAAAAACAT
*
292117 GTATTG-GATCAGAATGTCATATTACC-AAAAACAT
1 ATA-TGAGATCAGAATGTCATATTACCAAAAAACAT
*
292151 ATATGAGATCAGAATGTCCTATTA
1 ATATGAGATCAGAATGTCATATTA
292175 AATCAGAGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.04
34 27 0.53
36 21 0.41
37 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (35 bp):
ATATGAGATCAGAATGTCATATTACCAAAAAACAT
Done.