Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 24 of 127
Found at i:5324199 original size:42 final size:41
Alignment explanation
Indices: 5324140--5324227 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 41
5324130 GCACCACGAA
5324140 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTG
*
5324182 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
5324223 CTCCT
1 CTCCT
5324228 TGACAATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
Found at i:5324201 original size:67 final size:66
Alignment explanation
Indices: 5324074--5324205 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 66
5324064 AAATAAATTG
*
5324074 CTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
5324139 A
66 A
5324140 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
5324205 A
65 A
5324206 CTTTGGAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 28 0.44
67 36 0.56
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (66 bp):
CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
A
Found at i:5324216 original size:108 final size:107
Alignment explanation
Indices: 5324033--5324227 Score: 354
Period size: 108 Copynumber: 1.8 Consensus size: 107
5324023 AAGTAAATTG
*
5324033 CTCCTCTAAACAGAGGCACCACGACTATGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACGA
1 CTCCTCTAAACAGAGGCACCACGACTATGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGA
5324098 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAA
66 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAA
*
5324140 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCACGACTATGAAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACG
*
5324205 ACTTTGGAAAGTAAATTGCTCCT
65 ACTTTGAAAAGTAAATTGCTCCT
5324228 TGACAATCAT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
107 33 0.39
108 51 0.61
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.21
Consensus pattern (107 bp):
CTCCTCTAAACAGAGGCACCACGACTATGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGA
CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAA
Found at i:5325401 original size:16 final size:15
Alignment explanation
Indices: 5325376--5325444 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 15
5325366 TCAATTTGAA
5325376 TCTCTTTTTTCATTT
1 TCTCTTTTTTCATTT
5325391 TCTCATTTTTTCATTT
1 TCTC-TTTTTTCATTT
* *
5325407 TTTCTTCTTTC--TT
1 TCTCTTTTTTCATTT
*
5325420 TCTTTTTTTTC-TTT
1 TCTCTTTTTTCATTT
5325434 T-T-TTTTTTCAT
1 TCTCTTTTTTCAT
5325445 CATCTTCTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.15
13 12 0.26
14 3 0.07
15 10 0.22
16 14 0.30
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTCTTTTTTCATTT
Found at i:5325408 original size:8 final size:8
Alignment explanation
Indices: 5325380--5325410 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5325370 TTTGAATCTC
5325380 TTTTTTCA
1 TTTTTTCA
*
5325388 TTTTCTCA
1 TTTTTTCA
5325396 TTTTTTCA
1 TTTTTTCA
5325404 TTTTTTC
1 TTTTTTC
5325411 TTCTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5325438 original size:9 final size:9
Alignment explanation
Indices: 5325396--5325438 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
5325386 CATTTTCTCA
5325396 TTTTTTCATT
1 TTTTTTC-TT
5325406 TTTTCTTC-T
1 TTTT-TTCTT
*
5325415 TTCTTTCTT
1 TTTTTTCTT
5325424 TTTTTTCTT
1 TTTTTTCTT
5325433 TTTTTT
1 TTTTTT
5325439 TTTCATCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 3 0.10
9 19 0.66
10 4 0.14
11 3 0.10
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:5325442 original size:21 final size:20
Alignment explanation
Indices: 5325396--5325442 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
5325386 CATTTTCTCA
* *
5325396 TTTTTTCATTTTTTC-TTCT
1 TTTTTTCTTTTTTTCTTTTT
*
5325415 TTCTTTCTTTTTTTTCTTTTT
1 TTTTTTC-TTTTTTTCTTTTT
5325436 TTTTTTC
1 TTTTTTC
5325443 ATCATCTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTTTTTCTTTTT
Found at i:5325457 original size:19 final size:19
Alignment explanation
Indices: 5325428--5325470 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5325418 TTTCTTTTTT
5325428 TTCTT-TTTTTTTTTCATCA
1 TTCTTCTTTTTTTTTC-TCA
5325447 -TCTTCTTTTTTTTTCTCA
1 TTCTTCTTTTTTTTTCTCA
5325465 TTCTTC
1 TTCTTC
5325471 ACCTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (19 bp):
TTCTTCTTTTTTTTTCTCA
Found at i:5329433 original size:57 final size:57
Alignment explanation
Indices: 5329307--5329688 Score: 526
Period size: 57 Copynumber: 6.7 Consensus size: 57
5329297 TCTTGTGTAG
* *
5329307 GGAAAATTGATACTTTCAACTTTT-CCCTAAAATA-TTTTT-GAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
5329361 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* * *
5329418 GGAAAATTGATACTTTCAACTTTT-CCTAAAAA-A-TTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
5329472 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* *
5329529 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA----TTTTTTGGAAA-TTT-ATTTCTAA
* *** *
5329592 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTT-GAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* *
5329648 CGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5329689 TTTGGATTTT
Statistics
Matches: 292, Mismatches: 24, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
54 66 0.23
55 17 0.06
56 54 0.18
57 94 0.32
58 4 0.01
59 5 0.02
61 10 0.03
62 3 0.01
63 39 0.13
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:5329495 original size:27 final size:28
Alignment explanation
Indices: 5329411--5329496 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 28
5329401 TGGAAATTTA
5329411 TTTCTAAGGAAAATTGATACTTTCAACT
1 TTTCTAAGGAAAATTGATACTTTCAACT
* *
5329439 TTTCCTAA--AAAATTTTTGAAAATTT--A-T
1 TTT-CTAAGGAAAA---TTGATACTTTCAACT
5329466 TTT-TAAGGAAAATTGATACTTTCAACT
1 TTTCTAAGGAAAATTGATACTTTCAACT
5329493 TTTC
1 TTTC
5329497 CCCAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
24 8 0.18
25 3 0.07
26 1 0.02
27 16 0.36
28 4 0.09
29 4 0.09
30 8 0.18
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (28 bp):
TTTCTAAGGAAAATTGATACTTTCAACT
Found at i:5329501 original size:111 final size:113
Alignment explanation
Indices: 5329307--5329687 Score: 565
Period size: 111 Copynumber: 3.4 Consensus size: 113
5329297 TCTTGTGTAG
*
5329307 GGAAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTG-AAATTTATTTTTAAGAAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTGAAAATTTATTTTTAAGGAAAATTG
5329370 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
5329418 GGAAAATTGATACTTTCAACTTTT-CCTAAAAA-ATTTTTGAAAATTTATTTTTAAGGAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTGAAAATTTATTTTTAAGGAAAATTG
5329481 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* * **
5329529 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTTGAAACTTTGATTTCCAAGG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA------TTTTTGAAAATTT-ATTTTTAAGG
* *** *
5329594 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTT-GAAATTTATTTTTAA
59 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
5329648 CGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTT
5329688 TTTTGGATTT
Statistics
Matches: 247, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
110 10 0.04
111 122 0.49
112 7 0.03
113 6 0.02
119 59 0.24
120 43 0.17
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (113 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTGAAAATTTATTTTTAAGGAAAATTG
ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:5329668 original size:119 final size:119
Alignment explanation
Indices: 5329451--5329691 Score: 376
Period size: 119 Copynumber: 2.0 Consensus size: 119
5329441 TCCTAAAAAA
** * *
5329451 TTTTTGAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
1 TTTTTGAAAATTTATTTCCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTTGGA
*
5329516 AATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
66 AATTTATTTCTAACGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
* * *
5329570 TTTTTGAAACTTTGATTTCCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTT-G
1 TTTTTGAAAATTT-ATTTCCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTTGG
* *
5329634 AAATTTATTTTTAACGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
65 AAATTTATTTCTAACGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5329689 TTT
1 TTT
5329692 GGATTTTTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 68 0.61
120 43 0.39
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (119 bp):
TTTTTGAAAATTTATTTCCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTTGGA
AATTTATTTCTAACGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
Found at i:5329743 original size:20 final size:20
Alignment explanation
Indices: 5329713--5329804 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 20
5329703 ATTTTTATTT
5329713 AAAGA-AAATAAAATAATAA
1 AAAGATAAATAAAATAATAA
5329732 AAAGATAAAT-AAA-AAT-A
1 AAAGATAAATAAAATAATAA
*
5329749 AAA-ATAAATAAAGAAAAGTAA
1 AAAGATAAATAAA-ATAA-TAA
*
5329770 AACAGA-AATAAAAAATAA-AA
1 AA-AGATAA-ATAAAATAATAA
5329790 TAAAGATAAA-AAAAT
1 -AAAGATAAATAAAAT
5329805 TAGATAAACC
Statistics
Matches: 60, Mismatches: 2, Indels: 22
0.71 0.02 0.26
Matches are distributed among these distances:
16 6 0.10
17 6 0.10
18 4 0.07
19 15 0.25
20 11 0.18
21 7 0.12
22 6 0.10
23 5 0.08
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAGATAAATAAAATAATAA
Found at i:5329749 original size:6 final size:6
Alignment explanation
Indices: 5329717--5329801 Score: 50
Period size: 6 Copynumber: 13.7 Consensus size: 6
5329707 TTATTTAAAG
* *
5329717 AAAATAA AATAATA AAAAGA TAAATA AAAATA AAAATA AATAA-A GAAAAGT-
1 AAAAT-A AA-AATA AAAATA AAAATA AAAATA AAAATA AA-AATA -AAAA-TA
* * *
5329768 AAAACA GAAATA AAAA-A TAAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA -AAAATA AAAATA AAAA
5329802 AATTAGATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
5 1 0.02
6 46 0.77
7 10 0.17
8 3 0.05
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:5329753 original size:32 final size:33
Alignment explanation
Indices: 5329717--5329795 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
5329707 TTATTTAAAG
5329717 AAAATAAAATAATA-AAAAGATAAATA-A-AAAT-A
1 AAAATAAAATAA-AGAAAAG-TAAA-ACAGAAATAA
5329749 AAAAT-AAATAAAGAAAAGTAAAACAGAAATAA
1 AAAATAAAATAAAGAAAAGTAAAACAGAAATAA
5329781 AAAATAAAATAAAGA
1 AAAATAAAATAAAGA
5329796 TAAAAAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
29 1 0.02
30 6 0.14
31 15 0.36
32 11 0.26
33 9 0.21
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (33 bp):
AAAATAAAATAAAGAAAAGTAAAACAGAAATAA
Found at i:5329755 original size:16 final size:15
Alignment explanation
Indices: 5329717--5329765 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5329707 TTATTTAAAG
*
5329717 AAAATAAAATAATAAA
1 AAAAT-AAATAAAAAA
*
5329733 AAGATAAATAAAAATA
1 AAAATAAATAAAAA-A
5329749 AAAATAAATAAAGAAA
1 AAAATAAATAAA-AAA
5329765 A
1 A
5329766 GTAAAACAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 8 0.29
16 18 0.64
17 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAATAAATAAAAAA
Found at i:5330412 original size:26 final size:27
Alignment explanation
Indices: 5330365--5330421 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
5330355 AATCTGGAAA
*
5330365 TTTC-CCAAAAATTTCCAGAAAAAT-T
1 TTTCGCCAAAAATTTCCAAAAAAATAT
* *
5330390 TTTCGCCAAAAATTTCTAAAAAAGTAT
1 TTTCGCCAAAAATTTCCAAAAAAATAT
5330417 TTTCG
1 TTTCG
5330422 ATCCCTACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 17 0.63
27 6 0.22
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (27 bp):
TTTCGCCAAAAATTTCCAAAAAAATAT
Found at i:5330783 original size:30 final size:30
Alignment explanation
Indices: 5330711--5330810 Score: 105
Period size: 30 Copynumber: 3.2 Consensus size: 30
5330701 TTAAATAAAT
*
5330711 ATAAAAAAATAATAGATA-ATTAGAACAGATAA
1 ATAAAAAAA-AATAGATATATTAG--TAGATAA
*
5330743 ATCGAAAAAAAATAGATATATTA-TAGGATAA
1 AT-AAAAAAAAATAGATATATTAGTA-GATAA
* *
5330774 ATAAAAAAAAATAGATATATAATTAGATAA
1 ATAAAAAAAAATAGATATATTAGTAGATAA
5330804 ATAAAAA
1 ATAAAAA
5330811 TACAAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 31 0.52
31 9 0.15
32 10 0.17
33 10 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (30 bp):
ATAAAAAAAAATAGATATATTAGTAGATAA
Found at i:5330821 original size:26 final size:25
Alignment explanation
Indices: 5330773--5330856 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 25
5330763 TTATAGGATA
* * * * *
5330773 AATAAAAAAAAATAGATATATAATT
1 AATAAATAAAAATACAAAAATAAAT
5330798 AGATAAATAAAAATACAAAAATAAAT
1 A-ATAAATAAAAATACAAAAATAAAT
5330824 AA-AATATAAAAATA-ATAATAAT-AAT
1 AATAA-ATAAAAATACA-AA-AATAAAT
5330849 AATAAATA
1 AATAAATA
5330857 TATAACTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
24 3 0.06
25 21 0.43
26 25 0.51
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (25 bp):
AATAAATAAAAATACAAAAATAAAT
Found at i:5330846 original size:17 final size:17
Alignment explanation
Indices: 5330803--5330885 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
5330793 TAATTAGATA
* *
5330803 AATAAAAATACAAAAAT
1 AATAATAATATAAAAAT
5330820 AAATAA-AATATAAAAAT
1 -AATAATAATATAAAAAT
5330837 AATAATAATAATAATAAAT
1 AATAATAAT-ATAA-AAAT
*
5330856 -AT-ATAACTATATAAAT
1 AATAATAA-TATAAAAAT
5330872 AAT-ATACATATAAA
1 AATAATA-ATATAAA
5330886 TCTATTCTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
16 9 0.16
17 30 0.54
18 13 0.23
19 4 0.07
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATAATATAAAAAT
Found at i:5330861 original size:23 final size:23
Alignment explanation
Indices: 5330821--5330883 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 23
5330811 TACAAAAATA
5330821 AATAA-AATATAAA-A-ATAA-T
1 AATAATAATATAAATATATAACT
5330840 AATAATAATAATAAATATATAACT
1 AATAATAAT-ATAAATATATAACT
*
5330864 ATATAAATAATATACATATA
1 A-AT-AATAATATAAATATA
5330884 AATCTATTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 5 0.14
22 1 0.03
23 4 0.11
24 2 0.06
25 10 0.28
26 6 0.17
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAATAATATAAATATATAACT
Found at i:5330866 original size:8 final size:8
Alignment explanation
Indices: 5330788--5330883 Score: 53
Period size: 8 Copynumber: 12.6 Consensus size: 8
5330778 AAAAAAATAG
5330788 ATATATAA
1 ATATATAA
* *
5330796 TTAGATAA
1 ATATATAA
5330804 ATA-A-AA
1 ATATATAA
* *
5330810 ATACAAAA
1 ATATATAA
*
5330818 ATAAATAA
1 ATATATAA
5330826 A-ATATAA
1 ATATATAA
*
5330833 AAATA-ATA
1 ATATATA-A
5330841 ATA-AT-A
1 ATATATAA
5330847 ATA-ATAA
1 ATATATAA
5330854 ATATATAA
1 ATATATAA
*
5330862 CTATATAA
1 ATATATAA
*
5330870 ATAATATAC
1 AT-ATATAA
5330879 ATATA
1 ATATA
5330884 AATCTATTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
6 11 0.16
7 14 0.20
8 38 0.54
9 7 0.10
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (8 bp):
ATATATAA
Found at i:5332472 original size:1 final size:1
Alignment explanation
Indices: 5332461--5332490 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
5332451 CGTTTTCTAG
*
5332461 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5332491 ATCTGTCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:5333950 original size:2 final size:2
Alignment explanation
Indices: 5333943--5333986 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5333933 ACCCGTATCT
5333943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5333985 TA
1 TA
5333987 ATAAATAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5334694 original size:47 final size:46
Alignment explanation
Indices: 5334601--5334694 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 46
5334591 ACATGTATAA
* * * * *
5334601 TTAATTGGCATACCTTAAAGATATTGTTCTATGAGCAGGATGGAAT
1 TTAACTGGCATACATTAAAGATATTGTTCAATGAGCAAGATAGAAT
* *
5334647 TTAACTGGCATACATTAAAGAATATTGTTCAATGCGCAAGTTAGAAT
1 TTAACTGGCATACATTAAAG-ATATTGTTCAATGAGCAAGATAGAAT
5334694 T
1 T
5334695 CATTAATGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 18 0.45
47 22 0.55
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (46 bp):
TTAACTGGCATACATTAAAGATATTGTTCAATGAGCAAGATAGAAT
Found at i:5335195 original size:16 final size:16
Alignment explanation
Indices: 5335176--5335224 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
5335166 AAAAAATTGG
5335176 AGACAAAAAAGAAAGA
1 AGACAAAAAAGAAAGA
5335192 AGACAAAGAAA-AAAGA
1 AGACAAA-AAAGAAAGA
5335208 A-A-AAAAAATGAAAGA
1 AGACAAAAAA-GAAAGA
5335223 AG
1 AG
5335225 GAAAATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 7 0.24
16 13 0.45
17 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (16 bp):
AGACAAAAAAGAAAGA
Found at i:5335718 original size:2 final size:2
Alignment explanation
Indices: 5335711--5335741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5335701 TGTGGGTTTG
5335711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5335742 ATTTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5336616 original size:27 final size:26
Alignment explanation
Indices: 5336559--5336619 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
5336549 ATAAAATTTG
*
5336559 ATTTAAATTTATATTAAAATTTAAAT
1 ATTTAAATTTATATTAAAATTTAAAA
* *
5336585 TTTTATAATATTATA-TAATATTTAAAA
1 ATTTA-AAT-TTATATTAAAATTTAAAA
5336612 ATTTAAAT
1 ATTTAAAT
5336620 CAAATCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 17 0.59
28 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTAAATTTATATTAAAATTTAAAA
Found at i:5336855 original size:14 final size:14
Alignment explanation
Indices: 5336836--5336865 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5336826 ATAAAATTAC
*
5336836 TTAATTTTTTTTAT
1 TTAATTTTTTATAT
5336850 TTAATTTTTTATAT
1 TTAATTTTTTATAT
5336864 TT
1 TT
5336866 TTTAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTAATTTTTTATAT
Found at i:5338498 original size:8 final size:9
Alignment explanation
Indices: 5338479--5338503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5338469 TTCAATTGAA
5338479 TTTTAAATT
1 TTTTAAATT
5338488 TTTTAAATT
1 TTTTAAATT
5338497 TTTTAAA
1 TTTTAAA
5338504 AAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTAAATT
Found at i:5339582 original size:23 final size:22
Alignment explanation
Indices: 5339531--5339586 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5339521 AAATTACTAA
* *
5339531 TAAATTAAAT-AATATTATTTT
1 TAAAATAAATAAATATTATTCT
*
5339552 TATTAATAAATAAATATTAATTCT
1 TA-AAATAAATAAATATT-ATTCT
5339576 TAAAATAAATA
1 TAAAATAAATA
5339587 CATAAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 6 0.21
23 14 0.50
24 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATAAATAAATATTATTCT
Found at i:5342409 original size:6 final size:6
Alignment explanation
Indices: 5342398--5342431 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5342388 TAATTAAAGA
5342398 AAAATC AAAATC -AAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
5342432 AGAAAGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:5342415 original size:11 final size:12
Alignment explanation
Indices: 5342398--5342431 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
5342388 TAATTAAAGA
5342398 AAAATCAAAATC
1 AAAATCAAAATC
5342410 -AAATCAAAATC
1 AAAATCAAAATC
5342421 AAAATCAAAAT
1 AAAATCAAAAT
5342432 AGAAAGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATCAAAATC
Found at i:5342587 original size:57 final size:57
Alignment explanation
Indices: 5342468--5342849 Score: 517
Period size: 56 Copynumber: 6.7 Consensus size: 57
5342458 TTGTGTAGGA
* * * *
5342468 AAAATTGATACTTTCAA-TTTTTCCCTAAAATAATTTTTT-GAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTGGAAA-TTTATTTCTAAGG
5342525 AAAATTGAATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
1 AAAATTG-ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
* *
5342583 -AAATTGATACTTTCAACTTTT-CCTAAAAA-ATTTTTTGAAAATTTATTT-TAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
5342636 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
* *
5342693 AAAATTGATACTTTCAACTTTTCCCCCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGG
1 AAAATTGATACTTTCAACTTTT-CCCCAAAAATA--TTTTTTGGAAA-TTT-ATTTCTAAGG
* *** *
5342755 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTT-GAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
*
5342811 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5342850 TTAGATTTTT
Statistics
Matches: 292, Mismatches: 21, Indels: 25
0.86 0.06 0.07
Matches are distributed among these distances:
53 5 0.02
54 39 0.13
55 14 0.05
56 75 0.26
57 43 0.15
58 43 0.15
59 21 0.07
60 10 0.03
61 11 0.04
62 31 0.11
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
Found at i:5342885 original size:5 final size:5
Alignment explanation
Indices: 5342877--5342964 Score: 58
Period size: 5 Copynumber: 16.8 Consensus size: 5
5342867 TTATTTAAAG
5342877 AAAAT AAAAT AATAA- ATAAAT -AAAT AAAAAT AAAAT -AAAT AAAGA-
1 AAAAT AAAAT AA-AAT A-AAAT AAAAT -AAAAT AAAAT AAAAT AAA-AT
* *
5342922 AAAGT AAAAC AGAAAT AAAAAT AAAAAT AAAAT AAAGAT AAAA
1 AAAAT AAAAT A-AAAT -AAAAT -AAAAT AAAAT AAA-AT AAAA
5342965 AATTAGATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
4 8 0.12
5 33 0.49
6 26 0.38
7 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5342892 original size:8 final size:9
Alignment explanation
Indices: 5342878--5342919 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
5342868 TATTTAAAGA
5342878 AAATAAAAT
1 AAATAAAAT
5342887 -AAT-AAAT
1 AAATAAAAT
*
5342894 AAATAAATAA
1 AAATAAA-AT
5342904 AAATAAAAT
1 AAATAAAAT
5342913 AAATAAA
1 AAATAAA
5342920 GAAAAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 4 0.14
8 6 0.21
9 10 0.36
10 8 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5342903 original size:15 final size:15
Alignment explanation
Indices: 5342877--5342957 Score: 66
Period size: 15 Copynumber: 5.5 Consensus size: 15
5342867 TTATTTAAAG
5342877 AAAATAAAATAATAAAT
1 AAAAT-AAATAA-AAAT
5342894 -AAATAAATAAAAAT
1 AAAATAAATAAAAAT
*
5342908 AAAATAAATAAAGA-
1 AAAATAAATAAAAAT
*
5342922 AAAGTAAA-ACAGAAAT
1 AAAATAAATA-A-AAAT
5342938 --AA-AAATAAAAAT
1 AAAATAAATAAAAAT
5342950 AAAATAAA
1 AAAATAAA
5342958 GATAAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
12 4 0.08
13 5 0.10
14 16 0.31
15 23 0.44
16 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:5342953 original size:11 final size:11
Alignment explanation
Indices: 5342877--5342964 Score: 65
Period size: 11 Copynumber: 7.8 Consensus size: 11
5342867 TTATTTAAAG
5342877 AAAATAAAATA
1 AAAATAAAATA
5342888 ATAAATAAATAAATA
1 A-AAAT--A-AAATA
5342903 AAAATAAAAT-
1 AAAATAAAATA
*
5342913 -AAAT-AAAGA
1 AAAATAAAATA
* *
5342922 AAAGTAAAACA
1 AAAATAAAATA
*
5342933 GAAATAAAAATA
1 AAAAT-AAAATA
5342945 AAAATAAAATA
1 AAAATAAAATA
*
5342956 AAGATAAAA
1 AAAATAAAA
5342965 AATTAGATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 3 0.05
11 26 0.43
12 14 0.23
14 5 0.08
15 6 0.10
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:5343572 original size:26 final size:28
Alignment explanation
Indices: 5343525--5343582 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
5343515 AATCTGGAAA
*
5343525 TTTC-CCAGAAATTTCTAGAAAAA-T-T
1 TTTCGCCAAAAATTTCTAGAAAAAGTAT
5343550 TTTCGCCAAAAATTTCTTA-AAAAAGTAT
1 TTTCGCCAAAAATTTC-TAGAAAAAGTAT
5343578 TTTCG
1 TTTCG
5343583 ATCCCTACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.14
26 15 0.54
27 3 0.11
28 6 0.21
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (28 bp):
TTTCGCCAAAAATTTCTAGAAAAAGTAT
Found at i:5343947 original size:29 final size:29
Alignment explanation
Indices: 5343870--5343966 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 29
5343860 TCAAATAAAT
*
5343870 ATAAAAAATAATAGATA-ATTAGAACAGATAA
1 ATAAAAAA-AATAGATATATTAG--TAGATAA
* *
5343901 ATCGAAAAAAACAGATATATTA-TAGGATAA
1 AT-AAAAAAAATAGATATATTAGTA-GATAA
* *
5343931 ATAAAAAAAATAGATATATAATTAGATAA
1 ATAAAAAAAATAGATATATTAGTAGATAA
5343960 ATAAAAA
1 ATAAAAA
5343967 TACAAAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
29 29 0.52
30 9 0.16
31 9 0.16
32 9 0.16
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (29 bp):
ATAAAAAAAATAGATATATTAGTAGATAA
Found at i:5343979 original size:18 final size:18
Alignment explanation
Indices: 5343956--5343998 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
5343946 ATATAATTAG
5343956 ATAAATAAAAATACAAAA
1 ATAAATAAAAATACAAAA
*
5343974 ATAAAT-AAAATATAAAA
1 ATAAATAAAAATACAAAA
*
5343991 ATTAATAA
1 ATAAATAA
5343999 TAAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAATAAAAATACAAAA
Found at i:5344001 original size:3 final size:3
Alignment explanation
Indices: 5343993--5344023 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5343983 ATATAAAAAT
5343993 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5344024 TAACTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5344002 original size:20 final size:20
Alignment explanation
Indices: 5343977--5344026 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5343967 TACAAAAATA
5343977 AATAAAAT-ATAAAAATTAAT
1 AATAAAATAATAAAAA-TAAT
*
5343997 AATAAAATAATAATAATAAT
1 AATAAAATAATAAAAATAAT
*
5344017 AATAATATAA
1 AATAAAATAA
5344027 CTATATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAAAATAATAAAAATAAT
Found at i:5348348 original size:16 final size:16
Alignment explanation
Indices: 5348329--5348361 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5348319 AAAAAATTGG
5348329 AGACAAA-AAAGAAAGA
1 AGACAAAGAAA-AAAGA
5348345 AGACAAAGAAAAAAGA
1 AGACAAAGAAAAAAGA
5348361 A
1 A
5348362 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (16 bp):
AGACAAAGAAAAAAGA
Found at i:5348380 original size:13 final size:13
Alignment explanation
Indices: 5348334--5348371 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5348324 ATTGGAGACA
*
5348334 AAAAAGAAAGAAG
1 AAAAAGAAAAAAG
*
5348347 ACAAAGAAAAAAG
1 AAAAAGAAAAAAG
5348360 AAAAAGAAAAAA
1 AAAAAGAAAAAA
5348372 ATGAAAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:5348874 original size:2 final size:2
Alignment explanation
Indices: 5348867--5348901 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5348857 TGTGGGTTTG
5348867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5348902 ATTTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5349777 original size:27 final size:26
Alignment explanation
Indices: 5349720--5349780 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
5349710 ATAAAATTTG
*
5349720 ATTTAAATTTATATTAAAATTTAAAT
1 ATTTAAATTTATATTAAAATTTAAAA
* *
5349746 TTTTATAATATTATA-TAATATTTAAAA
1 ATTTA-AAT-TTATATTAAAATTTAAAA
5349773 ATTTAAAT
1 ATTTAAAT
5349781 CAAATCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 17 0.59
28 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTAAATTTATATTAAAATTTAAAA
Found at i:5349994 original size:24 final size:23
Alignment explanation
Indices: 5349967--5350031 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 23
5349957 TTCTTCATAC
5349967 AATTTTTTAAATATTTTTGTATAA
1 AATTTTTTAAATATTTTT-TATAA
** * **
5349991 AATTACTTAATTATTTTTTATTT
1 AATTTTTTAAATATTTTTTATAA
5350014 AATTTTTT--ATATTTTTTA
1 AATTTTTTAAATATTTTTTA
5350032 AGTTTTCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 9 0.27
23 9 0.27
24 15 0.45
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
AATTTTTTAAATATTTTTTATAA
Found at i:5351161 original size:20 final size:19
Alignment explanation
Indices: 5351128--5351170 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5351118 GTAGGTCTGG
* *
5351128 TTTTTTATGCAAATCTCATT
1 TTTTTTAAGAAAAT-TCATT
*
5351148 TTTTTTAAGAAAATTTATT
1 TTTTTTAAGAAAATTCATT
5351167 TTTT
1 TTTT
5351171 AAATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTTTAAGAAAATTCATT
Found at i:5353927 original size:16 final size:16
Alignment explanation
Indices: 5353906--5353961 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
5353896 ATTATTTTTT
5353906 AAATATAAATATTTAA
1 AAATATAAATATTTAA
* * *
5353922 AAATATCATTATATAA
1 AAATATAAATATTTAA
* * *
5353938 ATATATATATAATTAA
1 AAATATAAATATTTAA
5353954 AAAT-TAAA
1 AAATATAAA
5353962 AAATTAATTA
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATAAATATTTAA
Found at i:5353927 original size:30 final size:32
Alignment explanation
Indices: 5353891--5353957 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
5353881 CGAAATTAAT
* * * *
5353891 AAAATATTATTTTTTAAATATA-A-ATATTTA
1 AAAATATCATTATATAAATATATATATAATTA
5353921 AAAATATCATTATATAAATATATATATAATTA
1 AAAATATCATTATATAAATATATATATAATTA
5353953 AAAAT
1 AAAAT
5353958 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 19 0.61
31 1 0.03
32 11 0.35
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATATCATTATATAAATATATATATAATTA
Found at i:5353972 original size:12 final size:12
Alignment explanation
Indices: 5353955--5353979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5353945 TATAATTAAA
5353955 AATTAAAAAATT
1 AATTAAAAAATT
5353967 AATTAAAAAATT
1 AATTAAAAAATT
5353979 A
1 A
5353980 TTTTTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTAAAAAATT
Found at i:5355390 original size:61 final size:61
Alignment explanation
Indices: 5355286--5355456 Score: 252
Period size: 61 Copynumber: 2.8 Consensus size: 61
5355276 TTTTTGGTAA
** * * * * *
5355286 TTAAGGATGTTGGTACCTGGTACGTGGAACAAATACTGAGGGTTTGATCCTTTATTGCAAT
1 TTAAGGATGTTGGTATTTGGTAGGTGGGACAAATAATGTGGGTTTGATACTTTATTGCAAT
* *
5355347 TTAAAGATGTTGGTATTTGGTTGGTGGGACAAATAATGTGGGTTTGATACTTTATTGCAAT
1 TTAAGGATGTTGGTATTTGGTAGGTGGGACAAATAATGTGGGTTTGATACTTTATTGCAAT
*
5355408 TTAAGGATGTTGGTATTTGGTAGGTGAGACAAATAATGTGGGTTTGATA
1 TTAAGGATGTTGGTATTTGGTAGGTGGGACAAATAATGTGGGTTTGATA
5355457 TATATATATA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 98 1.00
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (61 bp):
TTAAGGATGTTGGTATTTGGTAGGTGGGACAAATAATGTGGGTTTGATACTTTATTGCAAT
Found at i:5355530 original size:20 final size:20
Alignment explanation
Indices: 5355487--5355528 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5355477 TATATAATTG
* *
5355487 AATTTTTTATTTTATTTTTA
1 AATTATTTATTTTATTTATA
5355507 AATTATTTATTTTATTATATA
1 AATTATTTATTTTATT-TATA
5355528 A
1 A
5355529 TTGATTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTATTTATTTTATTTATA
Found at i:5355591 original size:14 final size:15
Alignment explanation
Indices: 5355560--5355594 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5355550 TGCATAAATT
5355560 TTTTAAAATTTATAA
1 TTTTAAAATTTATAA
5355575 TTTTAAAATTT-TAA
1 TTTTAAAATTTATAA
5355589 TTTTAA
1 TTTTAA
5355595 TGATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAATTTATAA
Found at i:5356060 original size:4 final size:4
Alignment explanation
Indices: 5356053--5356081 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5356043 TATTGATTTT
5356053 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
5356082 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:5356769 original size:15 final size:15
Alignment explanation
Indices: 5356749--5356779 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5356739 GCATCCCATA
5356749 TTTTTTCAATACACT
1 TTTTTTCAATACACT
5356764 TTTTTTCAATACACT
1 TTTTTTCAATACACT
5356779 T
1 T
5356780 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTTCAATACACT
Found at i:5357818 original size:34 final size:31
Alignment explanation
Indices: 5357773--5357839 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
5357763 TATTTTAAAA
5357773 TTTTTAATATGT-ATTTTTGATAAATTATATAAT
1 TTTTTAATATGTAATTTTT-AT--ATTATATAAT
5357806 TTTTTGAATATGTAATTTTTATATTATATAAT
1 TTTTT-AATATGTAATTTTTATATTATATAAT
5357838 TT
1 TT
5357840 ACCAAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 12 0.38
33 5 0.16
34 9 0.28
35 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (31 bp):
TTTTTAATATGTAATTTTTATATTATATAAT
Found at i:5357837 original size:16 final size:16
Alignment explanation
Indices: 5357796--5357839 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5357786 TTTTTGATAA
5357796 ATTATATAATTTTTTG
1 ATTATATAATTTTTTG
* *
5357812 AATATGTAATTTTTAT-
1 ATTATATAATTTTT-TG
5357828 ATTATATAATTT
1 ATTATATAATTT
5357840 ACCAAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTATATAATTTTTTG
Found at i:5359845 original size:39 final size:40
Alignment explanation
Indices: 5359800--5359905 Score: 105
Period size: 39 Copynumber: 2.7 Consensus size: 40
5359790 TTTTGTATTT
* *
5359800 TATGTATTGTATTATTTATTATTATTATATG-TATTA-ATA
1 TATGTATTATATTATTTATTATTATTAT-TGTTAATATATA
*
5359839 TATGTA-TATATTTATTTATTTATT-TT-TTGTTAATATTTA
1 TATGTATTATA-TTATTTA-TTATTATTATTGTTAATATATA
*
5359878 TATGTATTTTATTATTTATGTATTATTA
1 TATGTATTATATTATTTAT-TATTATTA
5359906 CTAATATGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
37 2 0.04
38 9 0.16
39 34 0.62
40 10 0.18
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (40 bp):
TATGTATTATATTATTTATTATTATTATTGTTAATATATA
Found at i:5359853 original size:35 final size:34
Alignment explanation
Indices: 5359807--5359920 Score: 94
Period size: 35 Copynumber: 3.3 Consensus size: 34
5359797 TTTTATGTAT
5359807 TGTAT-TATTTATTATTATTATATGTATTAATATA
1 TGTATATATTTATTATTATT-TATGTATTAATATA
* *
5359841 TGTATATATTTATTTATTTATTT-TTTGTTAATAT-
1 TGTATATATTTA-TTA-TTATTTATGTATTAATATA
*
5359875 T-TATATGTATT-TTATTATTTATGTATTATTACTAATA
1 TGTATATAT-TTATTATTATTTATGTATTA--A-T-ATA
5359912 TGTATATAT
1 TGTATATAT
5359921 ATATATTTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
31 6 0.10
32 8 0.13
33 6 0.10
34 9 0.14
35 16 0.25
36 6 0.10
37 6 0.10
38 6 0.10
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (34 bp):
TGTATATATTTATTATTATTTATGTATTAATATA
Found at i:5359941 original size:14 final size:17
Alignment explanation
Indices: 5359924--5359960 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
5359914 TATATATATA
5359924 TATTTTA-TC-TTTTT-
1 TATTTTATTCATTTTTG
5359938 TATTTTATTCATTTTTG
1 TATTTTATTCATTTTTG
5359955 TATTTT
1 TATTTT
5359961 TACTTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
16 5 0.25
17 6 0.30
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTATTCATTTTTG
Found at i:5359977 original size:57 final size:57
Alignment explanation
Indices: 5359882--5360006 Score: 130
Period size: 57 Copynumber: 2.2 Consensus size: 57
5359872 TATTTATATG
* *
5359882 TATTTTATTATTTATGTATTATTACTAATATGTATATATATAT-AT-TTTATCTTTTT
1 TATTTTATTATTTATGTATTATTACT-ATATCTATATATATATGATATATATCTTTTT
* * * *
5359938 TATTTTATTCATTTTTGTATTTTTACT-TATCTAATTATATATCTGATATATATTTTTTT
1 TATTTTATT-ATTTATGTATTATTACTATATCT-A-TATATATATGATATATATCTTTTT
5359997 TATTATTATT
1 TATT-TTATT
5360007 TTATTTATCC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
55 4 0.07
56 10 0.18
57 23 0.40
58 2 0.04
59 13 0.23
60 5 0.09
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (57 bp):
TATTTTATTATTTATGTATTATTACTATATCTATATATATATGATATATATCTTTTT
Found at i:5360835 original size:13 final size:13
Alignment explanation
Indices: 5360817--5360844 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5360807 TTTTTTTTTG
5360817 TTTATTTGTTTAT
1 TTTATTTGTTTAT
5360830 TTTATTTGTTTAT
1 TTTATTTGTTTAT
5360843 TT
1 TT
5360845 ATTAGATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:5360837 original size:21 final size:20
Alignment explanation
Indices: 5360804--5360844 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5360794 GCCGCTCCAG
*
5360804 GTTTTTTTTTTTGTTTATTT
1 GTTTTTTTATTTGTTTATTT
5360824 GTTTATTTTATTTGTTTATTT
1 GTTT-TTTTATTTGTTTATTT
5360845 ATTAGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (20 bp):
GTTTTTTTATTTGTTTATTT
Found at i:5361016 original size:57 final size:57
Alignment explanation
Indices: 5360935--5361513 Score: 716
Period size: 57 Copynumber: 9.7 Consensus size: 57
5360925 AAAATTCCAA
5360935 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * * * *
5360993 AAAAAATATTTTTGGGGAAAAGTTGAAAATATCAATTTTTCTCAGAAATAAATTTCAAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC----C
*
5361054 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATTAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
5361111 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
5361173 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * *
5361232 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC--C
*
5361291 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTTCAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAA-TTTC-C
* * *
5361355 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTACTTAGAAATAAATTTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
5361412 AAAAAA-AGGGTTTTT-GAAGAAAAGTTAAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
* *
5361473 AAAAAATATTTTT-GAGAAAAAGTTGAAAGTATCAATCTTCC
1 AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCC
5361514 CTACAAAAAA
Statistics
Matches: 465, Mismatches: 29, Indels: 53
0.85 0.05 0.10
Matches are distributed among these distances:
56 1 0.00
57 149 0.32
58 10 0.02
59 123 0.26
60 2 0.00
61 68 0.15
62 15 0.03
64 93 0.20
65 4 0.01
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:5361406 original size:239 final size:235
Alignment explanation
Indices: 5360915--5361513 Score: 857
Period size: 239 Copynumber: 2.5 Consensus size: 235
5360905 TTTCTTTAAA
* *
5360915 TAAGAATAAAAAAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
1 TAAGAA-AATAAATTTCCAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* *
5360980 GAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAATATCAATTTTTCTCAGAAATAAA
64 GAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA
*
5361045 TTTCAAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATTAATTTTCCTTAGAAATAAATTTC
129 TTTC-AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* *
5361110 CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
193 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTACT
5361153 TAAAAGAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 T--AAG-AAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT
5361218 AGAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAA
63 AGAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAA
5361283 ATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAA
128 ATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAA
*
5361347 ATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTACT
188 A-TTTC-AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTACT
* *** * *
5361397 T-AG-AAATAAATTTTCAAAAAAAGGGTTTTT-GAAGAAAAGTTAAAAGTATCAATTTTCCTT-G
1 TAAGAAAATAAATTTCCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * *
5361458 AAAATCGAAATTTCCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATCTTCC
65 -AAAT--AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
5361514 CTACAAAAAA
Statistics
Matches: 330, Mismatches: 17, Indels: 25
0.89 0.05 0.07
Matches are distributed among these distances:
237 45 0.14
238 3 0.01
239 159 0.48
240 21 0.06
241 50 0.15
242 7 0.02
243 4 0.01
244 41 0.12
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (235 bp):
TAAGAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA
AATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATT
TCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAAA
AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTACT
Found at i:5362348 original size:17 final size:16
Alignment explanation
Indices: 5362295--5362348 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
5362285 AGCAAATAAA
5362295 AAAATAAAAAATAATGAT
1 AAAAT-AAAAAT-ATGAT
*
5362313 ATAAATAAAAATATAAT
1 A-AAATAAAAATATGAT
*
5362330 AAAATAAATCATATGAT
1 AAAATAAA-AATATGAT
5362347 AA
1 AA
5362349 TTAAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 13 0.42
18 7 0.23
19 4 0.13
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (16 bp):
AAAATAAAAATATGAT
Found at i:5365225 original size:24 final size:24
Alignment explanation
Indices: 5365173--5365219 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5365163 AATCTTTTTT
*
5365173 ATTATAATTATAACAATTTTTCTA
1 ATTATAATTATAACAATTTTTATA
* *
5365197 ATTATAATTATAATATTTTTTAT
1 ATTATAATTATAACAATTTTTAT
5365220 TTTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATAATTATAACAATTTTTATA
Found at i:5366655 original size:34 final size:34
Alignment explanation
Indices: 5366612--5366680 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
5366602 TATTTTGAAC
*
5366612 TTTTGAATATGT-ATTTTTAATAACGTATATAATT
1 TTTTGAATATGTAATTTTT-ATAAAGTATATAATT
* *
5366646 TTTTGAATATTTAATTTTTATAAATTATATAATT
1 TTTTGAATATGTAATTTTTATAAAGTATATAATT
5366680 T
1 T
5366681 ATCAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (34 bp):
TTTTGAATATGTAATTTTTATAAAGTATATAATT
Found at i:5367036 original size:26 final size:26
Alignment explanation
Indices: 5367007--5367069 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
5366997 TCTGTGAAAA
* *
5367007 AAATTAATTAATTATTA-TTAATAATT
1 AAATTAATAAATT-TTATTTAATAAAT
5367033 AAA-TAATAAATTTTATTTTAATAAAT
1 AAATTAATAAATTTTA-TTTAATAAAT
5367059 AAATTATATAA
1 AAATTA-ATAA
5367070 TAATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 3 0.10
25 8 0.26
26 14 0.45
27 2 0.06
28 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTAATAAATTTTATTTAATAAAT
Found at i:5367059 original size:19 final size:19
Alignment explanation
Indices: 5367037--5367079 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5367027 ATAATTAAAT
* **
5367037 AATAAATTTTATTTTAATA
1 AATAAATTATATAATAATA
5367056 AATAAATTATATAATAATA
1 AATAAATTATATAATAATA
5367075 AATAA
1 AATAA
5367080 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAATTATATAATAATA
Found at i:5367118 original size:41 final size:40
Alignment explanation
Indices: 5367016--5367118 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 40
5367006 AAAATTAATT
*
5367016 AATTATTATTAATAATTAAATAATAAATTTTATTTTAATA
1 AATTATTATTAATAATTAAATAATAAATTTTATTTAAATA
*
5367056 AATAAATTATATAATAA-TAAATAAT-AA-TTT-TTTAAATA
1 AAT-TATTAT-TAATAATTAAATAATAAATTTTATTTAAATA
5367094 ATATTATTATGTACATAATTTAAAT
1 A-ATTATTAT-TA-ATAA-TTAAAT
5367119 GAAAAAAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
38 15 0.28
39 9 0.17
40 5 0.09
41 18 0.34
42 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (40 bp):
AATTATTATTAATAATTAAATAATAAATTTTATTTAAATA
Found at i:5369858 original size:16 final size:18
Alignment explanation
Indices: 5369819--5369863 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
5369809 TTTGATTTTA
*
5369819 GAAAAAAAGAATTAAAGAT
1 GAAAAAAA-TATTAAAGAT
5369838 GAAAAAAATATTAAA-AT
1 GAAAAAAATATTAAAGAT
5369855 -AAAAAAATA
1 GAAAAAAATA
5369864 ACAATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 2 0.08
18 6 0.24
19 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (18 bp):
GAAAAAAATATTAAAGAT
Found at i:5374685 original size:27 final size:27
Alignment explanation
Indices: 5374642--5374694 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5374632 GACAGGTACA
*
5374642 GGATTTCCATAGGTAATCCTTTATGGG
1 GGATTTCCATAGATAATCCTTTATGGG
* *
5374669 GGATTTCCGTAGATAATTCTTTATGG
1 GGATTTCCATAGATAATCCTTTATGG
5374695 TGGAGGGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.40
Consensus pattern (27 bp):
GGATTTCCATAGATAATCCTTTATGGG
Found at i:5376052 original size:32 final size:32
Alignment explanation
Indices: 5375981--5376087 Score: 126
Period size: 32 Copynumber: 3.3 Consensus size: 32
5375971 TCTTTTGAAA
* * *
5375981 CATTTTAAAAAATTAAGTACAAATTTCCTTATT
1 CATTTTAAAAAATTAAATAAAAATTTCCATA-T
* **
5376014 GA-TTTAAAAAATTAAATAAAAAACTCCATAT
1 CATTTTAAAAAATTAAATAAAAATTTCCATAT
* *
5376045 CATTTTAAAATATTAAATAAAAATTTTCATAT
1 CATTTTAAAAAATTAAATAAAAATTTCCATAT
5376077 CATTTTAAAAA
1 CATTTTAAAAA
5376088 TCGATTTATT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.03
32 58 0.95
33 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.38
Consensus pattern (32 bp):
CATTTTAAAAAATTAAATAAAAATTTCCATAT
Found at i:5376392 original size:32 final size:32
Alignment explanation
Indices: 5376351--5376443 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
5376341 AATAAATTTA
* *
5376351 TTTTTTATTTACTATTGTAAAATGATATGAAG
1 TTTTTTATTTACTTTTCTAAAATGATATGAAG
* * * *
5376383 TTTTTTATTTAATTTTCTAAACTAATATGAAT
1 TTTTTTATTTACTTTTCTAAAATGATATGAAG
* *
5376415 TTTTTTACTTACTTTTTTAAAATGATATG
1 TTTTTTATTTACTTTTCTAAAATGATATG
5376444 GAGTAATTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (32 bp):
TTTTTTATTTACTTTTCTAAAATGATATGAAG
Found at i:5376594 original size:29 final size:29
Alignment explanation
Indices: 5376537--5376595 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 29
5376527 ATAATAAAAA
* *
5376537 ATAAAAATTATTTTAAATTATCATATTTT
1 ATAAAAATTATTTAAAATTATAATATTTT
*
5376566 ATAAAAATATATTTGAAAATT-TAATTTTTT
1 ATAAAAAT-TATTT-AAAATTATAATATTTT
5376596 GTTTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
ATAAAAATTATTTAAAATTATAATATTTT
Found at i:5376704 original size:19 final size:20
Alignment explanation
Indices: 5376672--5376715 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5376662 GAATTTGATA
*
5376672 TTTTAAATAGAAAAT-ATAT
1 TTTTAAATAAAAAATAATAT
*
5376691 TTTTAGATAAAAAATAATAT
1 TTTTAAATAAAAAATAATAT
5376711 TTTTA
1 TTTTA
5376716 TTATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTAAATAAAAAATAATAT
Found at i:5377960 original size:17 final size:17
Alignment explanation
Indices: 5377926--5377965 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5377916 ATTTTGTTTT
*
5377926 TTTTATCTAATATGATTA
1 TTTT-TCTAATATAATTA
*
5377944 TTTTTCTATTATAATTA
1 TTTTTCTAATATAATTA
5377961 TTTTT
1 TTTTT
5377966 TATCTCACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTCTAATATAATTA
Found at i:5379973 original size:14 final size:14
Alignment explanation
Indices: 5379931--5379973 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5379921 TAATGTGGCT
5379931 TAAATGGCCAATAA
1 TAAATGGCCAATAA
* *
5379945 TAAACT-GTCATTAA
1 TAAA-TGGCCAATAA
5379959 TAAATGGCCAATAA
1 TAAATGGCCAATAA
5379973 T
1 T
5379974 TTACATGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (14 bp):
TAAATGGCCAATAA
Found at i:5382234 original size:52 final size:52
Alignment explanation
Indices: 5382126--5382234 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
5382116 TGAGTGTTAT
* * **
5382126 AATTTTGTATAATTTGAAAATTATAAATTATTTAATCAAAAGCAATGTTTGT
1 AATTTTGTATAATTTCAAAATTATAAATTATTTAATCAAAAGCAATGTATCC
*
5382178 AATTTTGTATAATTTCAAAATTATAAATTATTTAATCAAAAG-TATGATATCC
1 AATTTTGTATAATTTCAAAATTATAAATTATTTAATCAAAAGCAATG-TATCC
5382230 AATTT
1 AATTT
5382235 AATTTAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 3 0.06
52 48 0.94
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (52 bp):
AATTTTGTATAATTTCAAAATTATAAATTATTTAATCAAAAGCAATGTATCC
Found at i:5382905 original size:153 final size:154
Alignment explanation
Indices: 5382612--5382887 Score: 425
Period size: 153 Copynumber: 1.8 Consensus size: 154
5382602 AAGTGTGAAC
* *
5382612 TCTAAAAGTATTAAAAATGAATGACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATC
1 TCTAAAAGTATTAAAAATGAATAACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATA
* *
5382677 TTTAAATTTTTAACATTTTTTTATCTATTTAATAAAGATTATTTATCATTAAATATATAACTTTT
66 TTTAAATTTGTAACATTTATTTATCTATTTAATAAAGATTATTTATCATTAAATATATAACTTTT
5382742 ACTAGTTAGTTATTTAAATTTAAA
131 ACTAGTTAGTTATTTAAATTTAAA
*
5382766 TCTAAAAGTGTT-AAAATGAATAACATAAATA-CTCTTATAAATTTTAAAAAATAACAAATTTAT
1 TCTAAAAGTATTAAAAATGAATAACATAAATATC-CTTATAAATTTTAAAAAATAACAAATTTAT
* * * *
5382829 ATTTCAATTTGTAGCA-TTATTTATTTATTTAATAATGATTATTTGA-CATTAAATATATA
65 ATTTAAATTTGTAACATTTATTTATCTATTTAATAAAGATTATTT-ATCATTAAATATATA
5382888 GTTTTTTATT
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
152 39 0.35
153 61 0.55
154 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (154 bp):
TCTAAAAGTATTAAAAATGAATAACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATA
TTTAAATTTGTAACATTTATTTATCTATTTAATAAAGATTATTTATCATTAAATATATAACTTTT
ACTAGTTAGTTATTTAAATTTAAA
Found at i:5386678 original size:34 final size:34
Alignment explanation
Indices: 5386635--5386702 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5386625 GGTGATTGAA
5386635 TGCCACAAAGTAGACATATTTGCTTCAGAACGTG
1 TGCCACAAAGTAGACATATTTGCTTCAGAACGTG
5386669 TGCCACAAAGTAGACATATTTGCTTCAGAACGTG
1 TGCCACAAAGTAGACATATTTGCTTCAGAACGTG
5386703 CTTGCTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (34 bp):
TGCCACAAAGTAGACATATTTGCTTCAGAACGTG
Found at i:5396305 original size:22 final size:22
Alignment explanation
Indices: 5396244--5396301 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
5396234 TCGATTCGAC
5396244 TTAAAATTAATAAAATATTATTTT
1 TTAAAA-T-ATAAAATATTATTTT
*
5396268 TTTAAATATAAAATATTA-TTT
1 TTAAAATATAAAATATTATTTT
5396289 TTAAAATATAAAA
1 TTAAAATATAAAA
5396302 ATATAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 15 0.47
22 11 0.34
23 1 0.03
24 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATATAAAATATTATTTT
Found at i:5396321 original size:22 final size:21
Alignment explanation
Indices: 5396255--5396324 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
5396245 TAAAATTAAT
* * *
5396255 AAAATATTATTTTTTTAAATA
1 AAAATATAATTTATATAAATA
* * *
5396276 TAAAATATTATTTTTAAAATATA
1 -AAAATATAATTTATATAA-ATA
5396299 AAAATATAATTATATATAAATA
1 AAAATATAATT-TATATAAATA
5396321 AAAA
1 AAAA
5396325 ATTTAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 33 0.80
23 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATATAATTTATATAAATA
Found at i:5401236 original size:32 final size:32
Alignment explanation
Indices: 5401171--5401245 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
5401161 TAGACATGAT
* * *
5401171 ATTTATATATTTATATCATATAAAATATTAAA
1 ATTTATATATTAATATAATATAAAATATAAAA
***
5401203 ATTTATATATTAATATAATATTTTATATAAAA
1 ATTTATATATTAATATAATATAAAATATAAAA
5401235 A-TTATATATTA
1 ATTTATATATTA
5401246 TAATTCGTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 10 0.27
32 27 0.73
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTTATATATTAATATAATATAAAATATAAAA
Found at i:5401276 original size:18 final size:18
Alignment explanation
Indices: 5401255--5401289 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5401245 ATAATTCGTG
5401255 TTAATATAAATTAATTTT
1 TTAATATAAATTAATTTT
* *
5401273 TTAATTTTAATTAATTT
1 TTAATATAAATTAATTT
5401290 ATATATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATAAATTAATTTT
Found at i:5402544 original size:30 final size:29
Alignment explanation
Indices: 5402508--5402614 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 29
5402498 AAATTAATTT
5402508 ATATTAAGAATTTATTTAGGTATAAATTAA
1 ATATTAA-AATTTATTTAGGTATAAATTAA
* * * * *
5402538 ATATTAACACTTGTTTAGATATAAAATAA
1 ATATTAAAATTTATTTAGGTATAAATTAA
*
5402567 AGATTAAAGATTTATTT-GGATATAAATTAGA
1 ATATTAAA-ATTTATTTAGG-TATAAATTA-A
*
5402598 A-ATAAAATATTTATTTA
1 ATATTAAA-ATTTATTTA
5402615 AGTGCAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 24 0.40
30 34 0.57
31 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (29 bp):
ATATTAAAATTTATTTAGGTATAAATTAA
Found at i:5405716 original size:23 final size:22
Alignment explanation
Indices: 5405683--5405725 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5405673 TTAATAATTT
5405683 AAATTTAAATATAATATTATAAA
1 AAATTTAAATATAA-ATTATAAA
*
5405706 AAATTTTAATATAAATTATA
1 AAATTTAAATATAAATTATA
5405726 TTTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTTAAATATAAATTATAAA
Found at i:5416726 original size:357 final size:356
Alignment explanation
Indices: 5416071--5417318 Score: 1533
Period size: 357 Copynumber: 3.5 Consensus size: 356
5416061 TATAATAATT
* * * *
5416071 TATTAAAGGTGGTTTATAATTAAAGACGCCTTTAATAATCCATGAAAATTTTTTGAAG-AAAATT
1 TATTAAAGGTGATTTATAATAAAAGACGCCTTTAATAATCCGT-AAAATTTTTTTAAGAAAAATT
* * * * * * * *
5416135 ATTGAAGGCGTTGTTTTTTACAACC-ACATTCATTTATTATCTACAAACTATGATAAAAATTATT
65 ATTAAAGGCATTATTTTCTGCAACCGTC-TTCAGTTATTATCTACAAACTATGATAGAAATTATT
* * * *
5416199 AAAGGCGTCTTTCTTGGATGTACTCCTTCAATAATAGTGTTAGAATTTGTGTGACAGTATATAAA
129 AAAGGCATCTTTCTTAGATGTACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAGTATATAAA
* * * * * * *
5416264 AAGCATTTTAAAATAGAAAACGCATTTAATAATTCTCAAAATATTTAATGAGAAAATTTTAAAAG
194 AGGCATTTGAAAATAGAAAATGCCTTTAATAATTCTTAAAATATTTAATGAAAAAATTTTAAAGG
* * * **
5416329 CGTCTGTTGTTAATAAATGCCTTCACTAATGGATTACTAAGTTTAAAGGTATATTAAATACGTCT
259 CGTCTGTTATTAACAAATGCCTTCACTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCGTCT
*
5416394 TTTCTAATAAATGCCTTCCATTACGATTGTGGTA
324 TTTCTAATAAATGCCTT-CATTACCATTGTGGTA
* *
5416428 TATTAAAGGTGATTTATAATAAAAGACGCCTGTAATAATCCGTGAAATTTTTTTAAGAAAAATTA
1 TATTAAAGGTGATTTATAATAAAAGACGCCTTTAATAATCCGTAAAATTTTTTTAAGAAAAATTA
* * * *
5416493 TTAAAAGCGTTGTTTTCTGCAACCGTCTTCAGTTATTATCTACAAACTGTGATAGAAATTATTAA
66 TTAAAGGCATTATTTTCTGCAACCGTCTTCAGTTATTATCTACAAACTATGATAGAAATTATTAA
* * * **
5416558 AGGCATCTTTCTTAGATGTACGCCTTCAATAATAGTGTTAAAATTTGTGTGACGGTATATGGAAG
131 AGGCATCTTTCTTAGATGTACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAGTATATAAAAG
* * *
5416623 GCATTTGACAATAGAAAATACCTTTAATAATTCTTAAAATATTTAATGAAAAAATTTTGAAGGCG
196 GCATTTGAAAATAGAAAATGCCTTTAATAATTCTTAAAATATTTAATGAAAAAATTTTAAAGGCG
* * *
5416688 TCTGTTATTAACAAATGCCTTTACTAATGGATTACTAAGTTTAAAGGTATATTGAAGGTGTTTTT
261 TCTGTTATTAACAAATGCCTTCACTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCGTCTTT
** *
5416753 TCTAATAAATGCCTTTCGCTACCATCGTGGTA
326 TCTAATAAATGCC-TTCATTACCATTGTGGTA
* * * ** *
5416785 TATTGAAGGTGATTTATAACAAAAGACACCTTTAATAATCCGTAAAAAATTTTTAAGAGAAATTA
1 TATTAAAGGTGATTTATAATAAAAGACGCCTTTAATAATCCGTAAAATTTTTTTAAGAAAAATTA
* * * * * * * **
5416850 TTGAAGGCATTATTTTTTTCAATCGCCTTCAATTATTATCAACAAACCGTGATATG-AATTATTA
66 TTAAAGGCATTATTTTCTGCAACCGTCTTCAGTTATTATCTACAAACTATGATA-GAAATTATTA
* * *
5416914 AA-GCATCTTTTTTAGATGTACGCCTTTAATAACAGTGTTAGAATTTATGTGACAGTATATAAAA
130 AAGGCATCTTTCTTAGATGTACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAGTATATAAAA
* * * * *
5416978 GGTATTTGATAGTA-AAAATGCCTTTAATAATTCGTAAAATATTTAGTGAAAAAATTTTAAAGGC
195 GGCATTTGAAAATAGAAAATGCCTTTAATAATTCTTAAAATATTTAATGAAAAAATTTTAAAGGC
* * *
5417042 GTTTGTTATTAACAAATGCCTTCACTAATGGAATACTAAGTTTAAAAGTATATTGAAGGCG-CAT
260 GTCTGTTATTAACAAATGCCTTCACTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCGTC-T
*
5417106 TTTCTAATAAACGCCTTCATTACCATTGTGGTA
324 TTTCTAATAAATGCCTTCATTACCATTGTGGTA
* * * * *
5417139 TATTGAAGG-CATGTCATAATAAAAGATGCCTTTAATAATTCG-AAAATTTTTTTTAA-AAAAAT
1 TATTAAAGGTGAT-TTATAATAAAAGACGCCTTTAATAATCCGTAAAA-TTTTTTTAAGAAAAAT
* * * * * *
5417201 TATTAAAGGCATTATTTTCTGCAACCGTCTTCAGTAATTAACTACAAATTATGAGATAAATTACT
64 TATTAAAGGCATTATTTTCTGCAACCGTCTTCAGTTATTATCTACAAACTATGATAGAAATTATT
* * * * *
5417266 AAAGGCGTCTTTGTTGGATATATGCCTTCAATAACAGTGTTAGAATTTGTGTG
129 AAAGGCATCTTTCTTAGATGTACGCCTTCAATAACAGTGTTAGAATTTGTGTG
5417319 GCGATATATT
Statistics
Matches: 764, Mismatches: 118, Indels: 21
0.85 0.13 0.02
Matches are distributed among these distances:
353 63 0.08
354 97 0.13
355 117 0.15
356 77 0.10
357 406 0.53
358 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (356 bp):
TATTAAAGGTGATTTATAATAAAAGACGCCTTTAATAATCCGTAAAATTTTTTTAAGAAAAATTA
TTAAAGGCATTATTTTCTGCAACCGTCTTCAGTTATTATCTACAAACTATGATAGAAATTATTAA
AGGCATCTTTCTTAGATGTACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAGTATATAAAAG
GCATTTGAAAATAGAAAATGCCTTTAATAATTCTTAAAATATTTAATGAAAAAATTTTAAAGGCG
TCTGTTATTAACAAATGCCTTCACTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCGTCTTT
TCTAATAAATGCCTTCATTACCATTGTGGTA
Found at i:5425106 original size:99 final size:99
Alignment explanation
Indices: 5424919--5425133 Score: 220
Period size: 99 Copynumber: 2.2 Consensus size: 99
5424909 CGAACGTCGC
* *
5424919 TAATATTGAGCCATTTTTAGATTCAAATGCCTCTAAAGTAACAGCATCTCAAAGATATAAATGTC
1 TAATATTGAGCCATTTTCAGATTCAAATGCCTCTAAAGTAACAGCATCTCAAAGATATAAACGTC
** * *
5424984 GCTAAAATAGCAGTGCTCCTGATATAAACGCCGT
66 GCTAAAATAGCAGCACTCCTGATACAAACGCCAT
* ** *
5425018 TAATATTGAG-CAGTTTTCATATTCAAATGCCTCTAAAGT-AGTGACGTCTCAAAGATATAAACG
1 TAATATTGAGCCA-TTTTCAGATTCAAATGCCTCTAAAGTAACAG-CATCTCAAAGATATAAACG
* ** ** *
5425081 -CTGCTAAAATGGTGGCACTTTTGATACAAACGTCAT
64 TC-GCTAAAATAGCAGCACTCCTGATACAAACGCCAT
* *
5425117 TAATATCGAGGCATTTT
1 TAATATTGAGCCATTTT
5425134 TATTAAAACA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
98 5 0.05
99 88 0.93
100 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (99 bp):
TAATATTGAGCCATTTTCAGATTCAAATGCCTCTAAAGTAACAGCATCTCAAAGATATAAACGTC
GCTAAAATAGCAGCACTCCTGATACAAACGCCAT
Found at i:5431635 original size:3 final size:3
Alignment explanation
Indices: 5431627--5431662 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5431617 AGTTCAAAAA
5431627 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5431663 GTAATCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5433739 original size:8 final size:8
Alignment explanation
Indices: 5433726--5433751 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5433716 AACAATACTA
5433726 ATAAAAAT
1 ATAAAAAT
5433734 ATAAAAAT
1 ATAAAAAT
5433742 ATAAAAAT
1 ATAAAAAT
5433750 AT
1 AT
5433752 GTTTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:5434990 original size:2 final size:2
Alignment explanation
Indices: 5434983--5435007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5434973 GTATGATGTA
5434983 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5435008 ATGATTCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5435346 original size:21 final size:20
Alignment explanation
Indices: 5435314--5435353 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5435304 AATATATTAA
5435314 TTTAATTAATTAAAATAAAAT
1 TTTAATTAATT-AAATAAAAT
5435335 TTTATATT-ATTAAATAAAA
1 TTTA-ATTAATTAAATAAAA
5435354 AATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 7 0.39
22 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATTAATTAAATAAAAT
Found at i:5437110 original size:34 final size:35
Alignment explanation
Indices: 5437071--5437136 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
5437061 AAAAATTACT
* * *
5437071 TCTAAAAATGTATTTCTAAAT-AATTGTAATGCTA
1 TCTAAAAATGCATTTCCAAATAAATTGCAATGCTA
5437105 TCTAAAAATGCATTTCCAAATAAATTGCAATG
1 TCTAAAAATGCATTTCCAAATAAATTGCAATG
5437137 TTTTCAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (35 bp):
TCTAAAAATGCATTTCCAAATAAATTGCAATGCTA
Found at i:5444683 original size:2 final size:2
Alignment explanation
Indices: 5444676--5444703 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5444666 GAGGGTAGTG
5444676 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5444704 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5444708 original size:2 final size:2
Alignment explanation
Indices: 5444703--5444735 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5444693 CTCTCTCTCT
5444703 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
5444736 GCTTGCACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5446464 original size:2 final size:2
Alignment explanation
Indices: 5446451--5446490 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5446441 CTGAACATTC
*
5446451 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5446491 CCAGTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5457992 original size:34 final size:34
Alignment explanation
Indices: 5457954--5458018 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
5457944 AGTTTTTGAA
*
5457954 AAATTGATATCC-AAAAAGTTTTGAGAATTATTAG
1 AAATTGATATCCGAAAAA-TTTTAAGAATTATTAG
*
5457988 AAATTGATATCCGATAAATTTTAAGAATTAT
1 AAATTGATATCCGAAAAATTTTAAGAATTAT
5458019 ACGATATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (34 bp):
AAATTGATATCCGAAAAATTTTAAGAATTATTAG
Found at i:5461522 original size:32 final size:33
Alignment explanation
Indices: 5461473--5461535 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
5461463 TTTACTTAAA
* *
5461473 AAGTTTTTAAGTAATTTATTTTTTGATAAAATT
1 AAGTTTTTAAGTAATTTATTATTTGACAAAATT
*
5461506 AAGTTTTTAA-TTATTTATTATTTGACAAAA
1 AAGTTTTTAAGTAATTTATTATTTGACAAAA
5461536 AATAATTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (33 bp):
AAGTTTTTAAGTAATTTATTATTTGACAAAATT
Found at i:5464407 original size:231 final size:231
Alignment explanation
Indices: 5464004--5464471 Score: 873
Period size: 231 Copynumber: 2.0 Consensus size: 231
5463994 TAGTTTCCCT
*
5464004 TCTAAACAGATACTAGTCAAGTAAACAATAACCATTCAGTGGTACTTTTCAAACCGACATCCACT
1 TCTAAACAGATACCAGTCAAGTAAACAATAACCATTCAGTGGTACTTTTCAAACCGACATCCACT
*
5464069 TTTCTTCTGATTGGAGCATCAAATGGTAAATGTTTTAGGGTGTACTTTTGAGGTTTTGAATGCAA
66 TTTCTTCTGATTGGAGCATCAAATAGTAAATGTTTTAGGGTGTACTTTTGAGGTTTTGAATGCAA
5464134 TCTTCATTATTATTTCTGGTCTTCACTTTTGCTTTTCATATATTATGCTGTCTTACTGAATTTTG
131 TCTTCATTATTATTTCTGGTCTTCACTTTTGCTTTTCATATATTATGCTGTCTTACTGAATTTTG
5464199 TTTAATGTAGCATGGAGTATGCTATTATGTTCCTGA
196 TTTAATGTAGCATGGAGTATGCTATTATGTTCCTGA
*
5464235 TCTAAACAGATACCAGTCAAGTAAACAATAACCATTCAGTGGTACTTTTCAAACTGACATCCACT
1 TCTAAACAGATACCAGTCAAGTAAACAATAACCATTCAGTGGTACTTTTCAAACCGACATCCACT
* *
5464300 TTTCTTCTGATTGGAGCATTAAATAGTAAATGTTTTAGGGTGTCCTTTTGAGGTTTTGAATGCAA
66 TTTCTTCTGATTGGAGCATCAAATAGTAAATGTTTTAGGGTGTACTTTTGAGGTTTTGAATGCAA
*
5464365 TCTTCATTATTATTTCTGGTCTTCACTTTTGCTTTTCATATATTATGCTGTCTTACTGATTTTTG
131 TCTTCATTATTATTTCTGGTCTTCACTTTTGCTTTTCATATATTATGCTGTCTTACTGAATTTTG
5464430 TTTAATGTAGCATGGAGTATGCTATTATGTTCCTGA
196 TTTAATGTAGCATGGAGTATGCTATTATGTTCCTGA
*
5464466 TTTAAA
1 TCTAAA
5464472 TTAATCAACA
Statistics
Matches: 230, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
231 230 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (231 bp):
TCTAAACAGATACCAGTCAAGTAAACAATAACCATTCAGTGGTACTTTTCAAACCGACATCCACT
TTTCTTCTGATTGGAGCATCAAATAGTAAATGTTTTAGGGTGTACTTTTGAGGTTTTGAATGCAA
TCTTCATTATTATTTCTGGTCTTCACTTTTGCTTTTCATATATTATGCTGTCTTACTGAATTTTG
TTTAATGTAGCATGGAGTATGCTATTATGTTCCTGA
Found at i:5474157 original size:24 final size:21
Alignment explanation
Indices: 5474123--5474166 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5474113 TACAACTCAT
*
5474123 TATATAATTTGTATTAAATTTA
1 TATATAATTTGT-TAAAATTTA
5474145 TATATAATTTTTGTTAAAATTT
1 TATATAA--TTTGTTAAAATTT
5474167 TAAATTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TATATAATTTGTTAAAATTTA
Found at i:5475378 original size:16 final size:16
Alignment explanation
Indices: 5475341--5475375 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5475331 ACACCTTTCA
*
5475341 AATTAAATAAAAGATT
1 AATTAAATAAAAGAAT
5475357 AATTAAATAAAA-AAT
1 AATTAAATAAAAGAAT
5475372 AATT
1 AATT
5475376 TAAGGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATTAAATAAAAGAAT
Found at i:5481791 original size:11 final size:11
Alignment explanation
Indices: 5481775--5481804 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5481765 TAGAAATAAC
5481775 GTAGTAACATA
1 GTAGTAACATA
5481786 GTAGTAACATA
1 GTAGTAACATA
*
5481797 ATAGTAAC
1 GTAGTAAC
5481805 CTTAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (11 bp):
GTAGTAACATA
Found at i:5485623 original size:3 final size:3
Alignment explanation
Indices: 5485615--5485648 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5485605 AAGTACCATC
* *
5485615 GCA GCA GCA GCC GCA GCA GCA GCC GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
5485649 TAGCGTTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.38, G:0.35, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:5485631 original size:12 final size:12
Alignment explanation
Indices: 5485614--5485648 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5485604 GAAGTACCAT
5485614 CGCAGCAGCAGC
1 CGCAGCAGCAGC
5485626 CGCAGCAGCAGC
1 CGCAGCAGCAGC
5485638 CGCAGCAGCAG
1 CGCAGCAGCAG
5485649 TAGCGTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.40, G:0.34, T:0.00
Consensus pattern (12 bp):
CGCAGCAGCAGC
Found at i:5486575 original size:13 final size:13
Alignment explanation
Indices: 5486557--5486587 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5486547 AGTGAGTGAC
5486557 TGTATAAATTAAT
1 TGTATAAATTAAT
5486570 TGTATAAATTAAT
1 TGTATAAATTAAT
5486583 TGTAT
1 TGTAT
5486588 TGTATAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
TGTATAAATTAAT
Found at i:5493891 original size:22 final size:22
Alignment explanation
Indices: 5493863--5493909 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5493853 AACCAACTAG
5493863 ACACCAACTCTATACATCTCCA
1 ACACCAACTCTATACATCTCCA
5493885 ACACCAACTCTATACATCTCCA
1 ACACCAACTCTATACATCTCCA
5493907 ACA
1 ACA
5493910 ATGGGGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (22 bp):
ACACCAACTCTATACATCTCCA
Found at i:5498064 original size:5 final size:5
Alignment explanation
Indices: 5498054--5498081 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5498044 ACATATAAAT
5498054 AAAGG AAAGG AAAGG AAAGG AAAGG AAA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAA
5498082 AGAATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:5503887 original size:34 final size:34
Alignment explanation
Indices: 5503827--5503933 Score: 135
Period size: 34 Copynumber: 3.1 Consensus size: 34
5503817 ACTATTAAGC
* *
5503827 TTCCAGATTTGCAAATCCGGAGGCTTTTAAAAGT
1 TTCCAGATTTGCAAATCTGGAAGCTTTTAAAAGT
***
5503861 TTTTGGATTTGCCAAAT-TGGAAGCTTTTAAAAGT
1 TTCCAGATTTG-CAAATCTGGAAGCTTTTAAAAGT
* *
5503895 CTCCAGATTTGCAAATCTGAAAGCTTTTAAAAGT
1 TTCCAGATTTGCAAATCTGGAAGCTTTTAAAAGT
5503929 TTCCA
1 TTCCA
5503934 AATTCACATA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 5 0.08
34 50 0.83
35 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (34 bp):
TTCCAGATTTGCAAATCTGGAAGCTTTTAAAAGT
Found at i:5504826 original size:21 final size:20
Alignment explanation
Indices: 5504771--5504826 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
5504761 CCAAAGATTT
*
5504771 TAATCTCACCACAATAATAC
1 TAATCTCACCACTATAATAC
* * *
5504791 TCAATCTTACAACTATAGTAAC
1 T-AATCTCACCACTATAAT-AC
5504813 TAATCTCACCACTA
1 TAATCTCACCACTA
5504827 CTACACTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (20 bp):
TAATCTCACCACTATAATAC
Found at i:5509396 original size:2 final size:2
Alignment explanation
Indices: 5509383--5509417 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5509373 GTAGCAGCAA
*
5509383 GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5509418 CATGTACAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (2 bp):
GT
Found at i:5513157 original size:13 final size:14
Alignment explanation
Indices: 5513139--5513167 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5513129 CTTCTCCACA
5513139 AAAAATAAA-AAAT
1 AAAAATAAATAAAT
5513152 AAAAATAAATAAAT
1 AAAAATAAATAAAT
5513166 AA
1 AA
5513168 GAGAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:5514358 original size:2 final size:2
Alignment explanation
Indices: 5514351--5514390 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5514341 TAGGTGTTAA
* *
5514351 AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5514391 ACATAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:5514653 original size:21 final size:21
Alignment explanation
Indices: 5514629--5514674 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5514619 TTTGAACTCG
5514629 ATTTAATTTTATATTT-ATTAA
1 ATTTAATTTTA-ATTTGATTAA
*
5514650 ATTTAATTTTAATTTGATTTA
1 ATTTAATTTTAATTTGATTAA
5514671 ATTT
1 ATTT
5514675 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTAATTTTAATTTGATTAA
Found at i:5514776 original size:14 final size:14
Alignment explanation
Indices: 5514768--5514807 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
5514758 AATATTATTT
5514768 TTTAAATATAAATA
1 TTTAAATATAAATA
5514782 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
5514798 TATAAATATA
1 TTTAAATATA
5514808 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:5514794 original size:16 final size:16
Alignment explanation
Indices: 5514773--5514809 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5514763 TATTTTTTAA
*
5514773 ATATAAATATTTAAAT
1 ATATAAATATATAAAT
*
5514789 ATATAATTATATAAAT
1 ATATAAATATATAAAT
5514805 ATATA
1 ATATA
5514810 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAATATATAAAT
Found at i:5514816 original size:14 final size:14
Alignment explanation
Indices: 5514770--5514817 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5514760 TATTATTTTT
* *
5514770 TAAATATAAATATT
1 TAAATATATATATA
5514784 TAAATATATAATTATA
1 TAAATATAT-A-TATA
*
5514800 TAAATATATATAAA
1 TAAATATATATATA
5514814 TAAA
1 TAAA
5514818 AAATATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATATATA
Done.