Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008337.1 Hibiscus syriacus cultivar Beakdansim tig00111057_pilon, 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: 840327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:320400 original size:86 final size:86
Alignment explanation
Indices: 320302--320886 Score: 665
Period size: 86 Copynumber: 7.0 Consensus size: 86
320292 ACAACTATAA
320302 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
320367 TTAAAATTAATCAATTCATAC
66 TTAAAATAAATCAATTCATAC
* * *
320388 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACAAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
320453 TTAAAATAAATCAATCCATAC
66 TTAAAATAAATCAATTCATAC
* *
320474 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
320539 TTAAAATAAATCAA-TC---C
66 TTAAAATAAATCAATTCATAC
** * ** * * * **
320556 --AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-A-AATCAATCCA-T
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATACT-AATAAATT
320612 ATTTTAAAATAAATCAATTCATAC
64 A-TTTAAAATAAATCAATTCATAC
** * ** * * * * ** *
320636 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-AAATTAATCCATAA
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATACTAATAAATTA
*
320700 TTTAAAATAAATCAATCCATAC
65 TTTAAAATAAATCAATTCATAC
*
320722 AAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
320787 TTAAAATAAATCAATCCATAC
66 TTAAAATAAATCAATTCATAC
*
320808 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATT
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATT
320865 ATTTAAAATAAATCAATTCATA
64 ATTTAAAATAAATCAATTCATA
320887 TTTTAAAATA
Statistics
Matches: 444, Mismatches: 37, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
75 4 0.01
76 40 0.09
77 13 0.03
78 1 0.00
79 2 0.00
80 69 0.16
82 4 0.01
84 2 0.00
85 15 0.03
86 291 0.66
87 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (86 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
TTAAAATAAATCAATTCATAC
Found at i:320453 original size:140 final size:140
Alignment explanation
Indices: 320303--320931 Score: 958
Period size: 140 Copynumber: 4.5 Consensus size: 140
320293 CAACTATAAT
320303 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
* * *
320368 TAAAATTAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATC
66 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATC
320433 AATCCATACA
131 AATCCATACA
* * * * * *
320443 AATAAATTATTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCTA
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AAT-AA-AT-
320503 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
62 TA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
*
320568 AAATCAATCCATACT
126 AAATCAATCCATACA
320583 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
* *
320648 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATAATTTAAAATAAATC
66 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATC
320713 AATCCATACA
131 AATCCATACA
320723 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
*
320788 TAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAAT
66 TAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
* *
320846 CAATCTATACT
130 CAATCCATACA
* *
320857 AATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
*
320922 TTAAATAAAT
66 TAAAATAAAT
320932 TATTTTAAAA
Statistics
Matches: 451, Mismatches: 27, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
134 108 0.24
135 6 0.01
136 11 0.02
137 2 0.00
138 3 0.01
139 4 0.01
140 295 0.65
141 2 0.00
142 2 0.00
143 2 0.00
144 10 0.02
145 6 0.01
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (140 bp):
AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATT
TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATC
AATCCATACA
Found at i:320535 original size:22 final size:22
Alignment explanation
Indices: 320486--320534 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
320476 ATAAATTATT
* **
320486 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
320508 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
320531 TAAA
1 TAAA
320535 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:320564 original size:22 final size:22
Alignment explanation
Indices: 320538--320580 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
320528 TAATAAATTA
320538 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
320560 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
320581 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:320589 original size:22 final size:22
Alignment explanation
Indices: 320540--320588 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
320530 ATAAATTATT
**
320540 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
320562 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
320585 TAAA
1 TAAA
320589 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:320618 original size:22 final size:22
Alignment explanation
Indices: 320592--320634 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
320582 TAATAAATTA
320592 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
320614 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
320635 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:320643 original size:22 final size:22
Alignment explanation
Indices: 320594--320642 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
320584 ATAAATTATT
**
320594 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
320616 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
320639 TAAA
1 TAAA
320643 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:320693 original size:22 final size:22
Alignment explanation
Indices: 320668--320711 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
320658 CAATCCATAC
*
320668 TAATAAATTATTTAAAATAAAT
1 TAATAAATAATTTAAAATAAAT
**
320690 TAATCCATAATTTAAAATAAAT
1 TAATAAATAATTTAAAATAAAT
320712 CAATCCATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAAATAATTTAAAATAAAT
Found at i:320716 original size:22 final size:22
Alignment explanation
Indices: 320677--320720 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
320667 CTAATAAATT
*
320677 ATTTAAAATAAATTAATCCATA
1 ATTTAAAATAAATCAATCCATA
320699 ATTTAAAATAAATCAATCCATA
1 ATTTAAAATAAATCAATCCATA
320721 CAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTAAAATAAATCAATCCATA
Found at i:320729 original size:22 final size:22
Alignment explanation
Indices: 320680--320728 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
320670 ATAAATTATT
* **
320680 TAAAATAAATTAATCCATAATT
1 TAAAATAAATCAATCCATAAAA
320702 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
320725 TAAA
1 TAAA
320729 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:320758 original size:22 final size:22
Alignment explanation
Indices: 320732--320774 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
320722 AAATAAATTA
320732 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
320754 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
320775 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:320783 original size:22 final size:22
Alignment explanation
Indices: 320734--320782 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
320724 ATAAATTATT
**
320734 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
320756 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
320779 TAAA
1 TAAA
320783 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:320873 original size:32 final size:32
Alignment explanation
Indices: 320834--320931 Score: 108
Period size: 32 Copynumber: 3.4 Consensus size: 32
320824 CAATCCATAT
320834 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
320866 TTTAAAATAAATCAA--T-T-C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
320888 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
320920 TTTTAAATAAAT
1 TTTAAAATAAAT
320932 TATTTTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
22 15 0.28
23 1 0.02
24 1 0.02
25 1 0.02
26 3 0.06
28 3 0.06
29 1 0.02
30 2 0.04
31 1 0.02
32 26 0.48
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:320892 original size:22 final size:22
Alignment explanation
Indices: 320866--320966 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
320856 TAATAAATTA
*
320866 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
320888 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
320911 AATAAATTATTTTAAATAAATTAT
1 TTTAAAATA-AATCAATCCA-TAT
320935 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
320957 TTTATAATAA
1 TTTAAAATAA
320967 TTTATTTTAA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 32 0.55
23 12 0.21
24 12 0.21
25 2 0.03
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:320944 original size:15 final size:15
Alignment explanation
Indices: 320911--321028 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
320901 AATCCATACT
320911 AATAAATTATTTT-A
1 AATAAATTATTTTAA
320925 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
320940 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
320962 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
320977 AATAAATTATTTTAT
1 AATAAATTATTTTAA
320992 AATAAATTATTTTAA
1 AATAAATTATTTTAA
321007 AATAAATTATTTTAA
1 AATAAATTATTTTAA
321022 AATAAAT
1 AATAAAT
321029 AACCTTATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 13 0.14
15 60 0.67
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:320956 original size:69 final size:67
Alignment explanation
Indices: 320856--321013 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 67
320846 CAATCTATAC
* *
320856 TAATAAATTA-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-CATA-AAATAAATTA
320920 TTTTA
63 TTTTA
* ** **
320925 -AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTT
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTT
320989 TA
66 TA
320991 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
321014 TATTTTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
66 14 0.17
67 24 0.30
68 14 0.17
69 28 0.35
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.44
Consensus pattern (67 bp):
TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTT
TA
Found at i:322654 original size:10 final size:11
Alignment explanation
Indices: 322621--322653 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
322611 TCAACACTCG
322621 AATCG-CTCAA
1 AATCGACTCAA
*
322631 AATCGACTCGA
1 AATCGACTCAA
322642 AATCGACTCAA
1 AATCGACTCAA
322653 A
1 A
322654 TTCTTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.18
Consensus pattern (11 bp):
AATCGACTCAA
Found at i:322873 original size:11 final size:11
Alignment explanation
Indices: 322859--322909 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
322849 AATCGAGTTT
*
322859 GAGCTTGAATC
1 GAGCTTCAATC
322870 GAGCTTCAATC
1 GAGCTTCAATC
322881 GAGC-TCGAGACTC
1 GAGCTTC-A-A-TC
*
322894 AAGCTTCAATC
1 GAGCTTCAATC
322905 GAGCT
1 GAGCT
322910 CCTGAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 2 0.06
11 21 0.64
12 2 0.06
13 6 0.18
14 2 0.06
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (11 bp):
GAGCTTCAATC
Found at i:324891 original size:6 final size:6
Alignment explanation
Indices: 324880--324934 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
324870 GACACGTATT
* *
324880 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
324928 ACCACG A
1 ACCACG A
324935 GCCGAGCCGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:325568 original size:165 final size:163
Alignment explanation
Indices: 325299--325627 Score: 615
Period size: 165 Copynumber: 2.0 Consensus size: 163
325289 TTCATCTACC
325299 CACTCACTCTGGGTTATGACTTATTAAGATATATATTCAGCCAAAATTGGTAAATTCATCAAGTC
1 CACTCACTCTGGGTTATGACTTATTAAGATATATATTCAGCCAAAATTGGTAAATTCATCAAGTC
325364 TTCTCACTAAGACCACCCAAAGCCTGGGCTATGAATTTATTAAAAGCAATTAAGCTCATCATGGG
66 TTCTCACTAAGACCACCCAAAGCCTGGGCTATGAATTTATTAAAAGCAATTAAGCTCATCATGGG
325429 -TGCACATTATTCATCATAGGGATAGGCAGTAG
131 ATGCACATTATTCATCATAGGGATAGGCAGTAG
325461 CACTCACTCTGGGTTATGAACTTATTAAGAATATATATTCAGCCAAAATTGGTAAATTCATCAAG
1 CACTCACTCTGGGTTATG-ACTTATTAAG-ATATATATTCAGCCAAAATTGGTAAATTCATCAAG
325526 TCTTTCTCACTAAGACCACCCAAAGCCTGGGCTATGAATTTATTAAAAGCAATTAAGCTCATCAT
64 TC-TTCTCACTAAGACCACCCAAAGCCTGGGCTATGAATTTATTAAAAGCAATTAAGCTCATCAT
325591 GGGCATGCACATTATTCATCATAGGGATAGGCAGTAG
128 GGG-ATGCACATTATTCATCATAGGGATAGGCAGTAG
325628 GAATGTGCAC
Statistics
Matches: 162, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
162 18 0.11
163 10 0.06
164 37 0.23
165 65 0.40
167 32 0.20
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (163 bp):
CACTCACTCTGGGTTATGACTTATTAAGATATATATTCAGCCAAAATTGGTAAATTCATCAAGTC
TTCTCACTAAGACCACCCAAAGCCTGGGCTATGAATTTATTAAAAGCAATTAAGCTCATCATGGG
ATGCACATTATTCATCATAGGGATAGGCAGTAG
Found at i:330541 original size:6 final size:6
Alignment explanation
Indices: 330530--330578 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
330520 GACACGTATT
* *
330530 ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
330578 A
1 A
330579 GCCGATCCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:335244 original size:6 final size:6
Alignment explanation
Indices: 335233--335281 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
335223 GACACGTATT
* *
335233 ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
335281 A
1 A
335282 GCCGAACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:336552 original size:21 final size:21
Alignment explanation
Indices: 336510--336599 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 21
336500 GCGGGCGGGA
* * *
336510 CCTCTTGAACGATGACAAGGG
1 CCTCTTAAACGATGAGAGGGG
* *
336531 CCTCTTAAACGGTGGGAGGGG
1 CCTCTTAAACGATGAGAGGGG
* * *
336552 CCTTTTCAATGATGAGAGGGG
1 CCTCTTAAACGATGAGAGGGG
* *
336573 CCTCTTCAATGATGAGAGGGG
1 CCTCTTAAACGATGAGAGGGG
*
336594 CATCTT
1 CCTCTT
336600 GAATGATAGG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTAAACGATGAGAGGGG
Found at i:336604 original size:21 final size:21
Alignment explanation
Indices: 336546--336606 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
336536 TAAACGGTGG
* *
336546 GAGGGGCCTTTTCAATGATGA
1 GAGGGGCATCTTCAATGATGA
*
336567 GAGGGGCCTCTTCAATGATGA
1 GAGGGGCATCTTCAATGATGA
*
336588 GAGGGGCATCTTGAATGAT
1 GAGGGGCATCTTCAATGAT
336607 AGGAGTCGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (21 bp):
GAGGGGCATCTTCAATGATGA
Found at i:336605 original size:42 final size:42
Alignment explanation
Indices: 336512--336606 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 42
336502 GGGCGGGACC
* * * *
336512 TCTTGAACGATGACAAGGGCCTCTTAAACGGTGGGAGGGGCC
1 TCTTGAATGATGACAAGGGCCTCTTAAACGATGAGAGGGGCA
* * * * * *
336554 TTTTCAATGATGAGAGGGGCCTCTTCAATGATGAGAGGGGCA
1 TCTTGAATGATGACAAGGGCCTCTTAAACGATGAGAGGGGCA
336596 TCTTGAATGAT
1 TCTTGAATGAT
336607 AGGAGTCGTC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (42 bp):
TCTTGAATGATGACAAGGGCCTCTTAAACGATGAGAGGGGCA
Found at i:336971 original size:21 final size:21
Alignment explanation
Indices: 336945--336992 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
336935 CATTGTCTTC
**
336945 ACGTAAAGTACCGACCTCATG
1 ACGTAAAACACCGACCTCATG
*
336966 ACGTAAAACACCGACCTCATT
1 ACGTAAAACACCGACCTCATG
336987 ACGTAA
1 ACGTAA
336993 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.19
Consensus pattern (21 bp):
ACGTAAAACACCGACCTCATG
Found at i:338681 original size:20 final size:20
Alignment explanation
Indices: 338658--338747 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
338648 AAACTTAAAT
338658 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
338678 TCGCAACGGGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
338698 TCGCAACGCGAAAATTAAAA
1 TCGCAACGCGAAAATGAAAA
*
338718 TCGCAACGCGAAACTAGAAAA
1 TCGCAACGCGAAAAT-GAAAA
338739 TCGCAACGC
1 TCGCAACGC
338748 AAATATCGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 49 0.79
21 13 0.21
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:338798 original size:20 final size:20
Alignment explanation
Indices: 338759--338798 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
338749 AATATCGCAA
* *
338759 GCGTTGCAATTTTTATTTTC
1 GCGTTGCAATTTTAAGTTTC
*
338779 GCGTTGCGATTTTAAGTTTC
1 GCGTTGCAATTTTAAGTTTC
338799 AGAAACTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (20 bp):
GCGTTGCAATTTTAAGTTTC
Found at i:339341 original size:20 final size:20
Alignment explanation
Indices: 339316--339425 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
339306 TAAACGCGCT
*
339316 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
339336 TTGCGAATTTTGACTT-TAGTG
1 TTGCGAA-TTTGACTTCT-GTG
339357 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
* * *
339377 CTGCGAATTTGACTTCAGTA
1 TTGCGAATTTGACTTCTGTG
* *
339397 TTACGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
339417 TTGC-AATTT
1 TTGCGAATTT
339426 ACAAATTCGC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.06
20 54 0.69
21 19 0.24
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:339364 original size:41 final size:41
Alignment explanation
Indices: 339316--339425 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 41
339306 TAAACGCGCT
* * *
339316 TTGCGAATTTGACTTTTGTGTTGCGAATTTTGACTTTAGTG
1 TTGCGAATTTGACTTATGTGTTGCGAATTTTGACTTCAGTA
* *
339357 TTGCGAATTTGACTTCTGTGCTGCGAA-TTTGACTTCAGTA
1 TTGCGAATTTGACTTATGTGTTGCGAATTTTGACTTCAGTA
*
339397 TTACGAATTTGACTTATGTGTTGC-AATTT
1 TTGCGAATTTGACTTATGTGTTGCGAATTT
339426 ACAAATTCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.03
40 34 0.56
41 25 0.41
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (41 bp):
TTGCGAATTTGACTTATGTGTTGCGAATTTTGACTTCAGTA
Found at i:339444 original size:40 final size:39
Alignment explanation
Indices: 339316--339448 Score: 126
Period size: 40 Copynumber: 3.3 Consensus size: 39
339306 TAAACGCGCT
* * *
339316 TTGCGAATTTGACTTTTGTGTTGCGAATTTTGACTTTAGTG
1 TTGCGAATTTGACTTATGTGTTGCGAA-TTT-ACATTCGTG
* * *
339357 TTGCGAATTTGACTTCTGTGCTGCGAATTTGAC-TTCAGTA
1 TTGCGAATTTGACTTATGTGTTGCGAATTT-ACATTC-GTG
* *
339397 TTACGAATTTGACTTATGTGTTGC-AATTTACAAATTCGCG
1 TTGCGAATTTGACTTATGTGTTGCGAATTTAC--ATTCGTG
339437 TTGCGAATTTGA
1 TTGCGAATTTGA
339449 AAACGGTGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
38 2 0.03
39 7 0.09
40 41 0.53
41 28 0.36
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (39 bp):
TTGCGAATTTGACTTATGTGTTGCGAATTTACATTCGTG
Found at i:340950 original size:2 final size:2
Alignment explanation
Indices: 340943--340995 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
340933 ACCCAAATGG
340943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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 AT
340984 AT AT AT AT AT AT
1 AT AT AT AT AT AT
340996 TGTTGAATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:341647 original size:21 final size:20
Alignment explanation
Indices: 341623--341686 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
341613 AACTTTGAAA
341623 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
341644 AAATG-TTT---A-TTT-GA
1 AAATGTTTTCAAAGTTTGGT
341658 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
341679 AAATGTTT
1 AAATGTTT
341687 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:341661 original size:35 final size:35
Alignment explanation
Indices: 341616--341736 Score: 163
Period size: 35 Copynumber: 3.4 Consensus size: 35
341606 GGTAATCAAC
341616 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
341652 ATTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 -TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
341687 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
341724 GTTGAAAAATGAT
1 TTTGAAAAATGAT
341737 AATGGGATAA
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (35 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:343981 original size:13 final size:13
Alignment explanation
Indices: 343963--343987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343953 CCATGACACC
343963 ACAGCAGAATGGA
1 ACAGCAGAATGGA
343976 ACAGCAGAATGG
1 ACAGCAGAATGG
343988 CGTAGCAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (13 bp):
ACAGCAGAATGGA
Found at i:346287 original size:36 final size:36
Alignment explanation
Indices: 346174--346292 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
346164 GTAACCAACT
346174 TTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
346211 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
* * *
346246 TTTGAAAAATAGTTTTTCAAAATTTGGTAGATGTTT-
1 TTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTC
*
346282 GTTGAAAAATG
1 TTTGAAAAATG
346293 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 26 0.34
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
Found at i:356205 original size:17 final size:19
Alignment explanation
Indices: 356164--356212 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
356154 TTGGACCCTT
* *
356164 AGTGCATCGGTGCACTTAG
1 AGTGCATCGATGCACTGAG
356183 AGTGCATCGATGCA-TGA-
1 AGTGCATCGATGCACTGAG
356200 AGTGCATTCGATG
1 AGTGCA-TCGATG
356213 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (19 bp):
AGTGCATCGATGCACTGAG
Found at i:356232 original size:64 final size:65
Alignment explanation
Indices: 356158--356304 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 65
356148 CGACCGTTGG
* * * *
356158 ACCCTTAGTGCATCGGTGCACT-TAGAGTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AA
1 ACCCTGAGTGCATCGATGCA-TGTAGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA
356220 A
65 A
* ***
356221 TAGCCTGAGTGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA
1 -ACCCTGAGTGCATCGATGCATGTAGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA
356286 A
65 A
356287 ACCCTGAGTGCATCGATG
1 ACCCTGAGTGCATCGATG
356305 GATAAAATGC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 45 0.63
65 22 0.31
66 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (65 bp):
ACCCTGAGTGCATCGATGCATGTAGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
Found at i:356321 original size:64 final size:63
Alignment explanation
Indices: 356158--356322 Score: 154
Period size: 64 Copynumber: 2.6 Consensus size: 63
356148 CGACCGTTGG
* * * * * * *
356158 ACCCTTAGTGCATCGGTGCACTTAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAAT
1 ACCCTGAGTGCATCGATGCA-GTAAAATGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT
* ****
356222 AGCCTGAGTGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ACCCTGAGTGCATCGATGCA-GTAAAATGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAA
356287 -
63 T
*
356287 ACCCTGAGTGCATCGATGGA-TAAAATGCATTCGATG
1 ACCCTGAGTGCATCGATGCAGTAAAATGCA-TCGATG
356323 TTCAATTTAT
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 5 0.06
64 51 0.62
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (63 bp):
ACCCTGAGTGCATCGATGCAGTAAAATGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT
Found at i:356360 original size:20 final size:20
Alignment explanation
Indices: 356335--356372 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
356325 CAATTTATTC
356335 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
356355 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
356373 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:356970 original size:2 final size:2
Alignment explanation
Indices: 356963--356996 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
356953 CAAACCAAAC
356963 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
356997 TAAGATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359158 original size:17 final size:19
Alignment explanation
Indices: 359122--359159 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
359112 TCAAAAGGGA
359122 TGCATCGATGCACTATTAAG
1 TGCATCGATG-ACTATTAAG
359142 TGCATCGATG-C-ATTAAG
1 TGCATCGATGACTATTAAG
359159 T
1 T
359160 AAAAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
20 10 0.56
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCATCGATGACTATTAAG
Found at i:364886 original size:19 final size:19
Alignment explanation
Indices: 364864--364915 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
364854 TTGGACCCTT
*
364864 AGTGCATCGGTGGACTAAG
1 AGTGCATCGGTGCACTAAG
*
364883 AGTGCATCAGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
364902 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
364916 TGAAGTGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:364989 original size:64 final size:65
Alignment explanation
Indices: 364903--365026 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
364893 TGCACTAAGA
* * * *
364903 GTGCATCGATGCATGAAGTGCATTTGAT-TTTTCA-AAATAGCCTGAGTGCATTGATGCATGTCT
1 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGTCT
364966 T
65 T
364967 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
365027 AAAATACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
64 26 0.48
65 25 0.46
66 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGTCTT
Found at i:365079 original size:20 final size:20
Alignment explanation
Indices: 365054--365091 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
365044 CAATTTATTC
365054 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
365074 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
365092 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:369619 original size:13 final size:13
Alignment explanation
Indices: 369601--369626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
369591 TTGTTGAAAA
369601 TTGGTGTGAATGC
1 TTGGTGTGAATGC
369614 TTGGTGTGAATGC
1 TTGGTGTGAATGC
369627 ACTGAATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
TTGGTGTGAATGC
Found at i:379030 original size:16 final size:16
Alignment explanation
Indices: 379009--379040 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
378999 ATAAATAAAC
379009 GAACATAAACAAACAA
1 GAACATAAACAAACAA
*
379025 GAACATAAACGAACAA
1 GAACATAAACAAACAA
379041 AATTTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.19, G:0.09, T:0.06
Consensus pattern (16 bp):
GAACATAAACAAACAA
Found at i:379158 original size:16 final size:16
Alignment explanation
Indices: 379104--379156 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
379094 CATTTAATAA
*
379104 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
*
379120 ATAAACGAACACGAAT
1 ATAAACGAACACGAAC
*
379136 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
379152 ATAAA
1 ATAAA
379157 TGTTGGAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.58, C:0.17, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:379917 original size:14 final size:14
Alignment explanation
Indices: 379898--379926 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
379888 GAACATAAAT
379898 GAACATAACCGAAC
1 GAACATAACCGAAC
379912 GAACATAACCGAAC
1 GAACATAACCGAAC
379926 G
1 G
379927 TTCACGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:379925 original size:10 final size:10
Alignment explanation
Indices: 379878--379911 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
379868 ATAAATGAAT
379878 GAACATAAAC
1 GAACATAAAC
*
379888 GAACATAAAT
1 GAACATAAAC
*
379898 GAACATAACC
1 GAACATAAAC
379908 GAAC
1 GAAC
379912 GAACATAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:382930 original size:29 final size:29
Alignment explanation
Indices: 382885--382942 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
382875 GTGTTGGCCG
382885 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
* * *
382914 TAGGTCGCCATGTCTTCCTGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
382943 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTAC
Found at i:383004 original size:14 final size:14
Alignment explanation
Indices: 382985--383017 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
382975 CGCTGGGCAT
382985 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
382999 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
383013 ACGAG
1 CCGAG
383018 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:383053 original size:33 final size:33
Alignment explanation
Indices: 383016--383080 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
383006 CATCCGAACG
*
383016 AGCTATGCGAGGGCATCCGAGGGCAA-CCGAGCT
1 AGCTATGCGAGGGAATCCGAGGG-AAGCCGAGCT
383049 AGCTATGCGAGGGAATCCGAGGGAAGCCGAGC
1 AGCTATGCGAGGGAATCCGAGGGAAGCCGAGC
383081 GAGGGTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (33 bp):
AGCTATGCGAGGGAATCCGAGGGAAGCCGAGCT
Found at i:383120 original size:29 final size:29
Alignment explanation
Indices: 383087--383142 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
383077 GAGCGAGGGT
383087 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
383116 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
383143 TGTGTTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.30, G:0.39, T:0.11
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:383192 original size:20 final size:20
Alignment explanation
Indices: 383169--383208 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
383159 TGTGCCATGC
383169 AACACGTTCATTCTCTCTGT
1 AACACGTTCATTCTCTCTGT
383189 AACACGTTCATTCTCTCTGT
1 AACACGTTCATTCTCTCTGT
383209 TTGAGCAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (20 bp):
AACACGTTCATTCTCTCTGT
Found at i:388689 original size:13 final size:13
Alignment explanation
Indices: 388671--388695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
388661 ATGATTGGAA
388671 AATTTTATTTATG
1 AATTTTATTTATG
388684 AATTTTATTTAT
1 AATTTTATTTAT
388696 TTAATTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AATTTTATTTATG
Found at i:390538 original size:217 final size:217
Alignment explanation
Indices: 389878--390812 Score: 1549
Period size: 217 Copynumber: 4.3 Consensus size: 217
389868 GAAGATAAAT
* * * *
389878 ATATAAATTATAGAAAAAATATTTAATCTAATGATGACGTGTGTCACCATTTAATTGGTGGATTA
1 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
* ** * *
389943 AATTTATTGAATTAAATTTATTTTAGGAACAATTTGATAGAATATATAAGTATTGATGACTAAAT
66 AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
* * * *
390008 ATATAATTATATCGATTTTATTAACCTTAAACCATATGATGACACGTGT---CATCTGGTTGGAA
131 GTATAATTATACCGATTTTATTAACCTTCAACTATATGATGACACGTGTCACCATCTGGTTGGAA
390070 GATAAATATATAAATTAAATAA
196 GATAAATATATAAATTAAATAA
*
390092 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGAGGATTA
1 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
* *
390157 AATTTATTGAATTAAATTTATTTTAGGAACAAA-TGATAGAATGTACAAGTATTGACGACTAAAT
66 AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
* * * * * *
390221 GTATAATTATATCGATTTTATTAACCTTCAACTAGATGATGACACATGTCACCATATAGTCGGAA
131 GTATAATTATACCGATTTTATTAACCTTCAACTATATGATGACACGTGTCACCATCTGGTTGGAA
390286 GATAAATATATAAATTAAATAA
196 GATAAATATATAAATTAAATAA
* *
390308 ATATAAATTATAGAAAAAATATTAAATCTAATGGTAACATGTGCCACCATCTAATTGGTGGATTA
1 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
390373 AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
66 AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
* *
390438 GTATAATTATACCGATTTTATTAATCTTCAACTATATGATGACATGTGTCACCATCTGGTTGGAA
131 GTATAATTATACCGATTTTATTAACCTTCAACTATATGATGACACGTGTCACCATCTGGTTGGAA
390503 GATAAATATATAAATTAAATAA
196 GATAAATATATAAATTAAATAA
*
390525 ATATAAATTATAGAAAAAATATTAAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
1 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
*
390590 AATTTATTAAATTAAATTTATTTTAAGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
66 AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
* *
390655 GTATAATTATACCGATTTTATTAATCTTCAACTATATGATGACATGTGTCACCATCTGGTTGGAA
131 GTATAATTATACCGATTTTATTAACCTTCAACTATATGATGACACGTGTCACCATCTGGTTGGAA
390720 GATAAATATATAAATTAAATAA
196 GATAAATATATAAATTAAATAA
*
390742 ATATAAATTAT--AAAAAATATTTAATCTAATGGTGACATGTGTCACCATCTAATTGGTGGATTA
1 ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
390805 AATTTATT
66 AATTTATT
390813 TTAGGAACAA
Statistics
Matches: 683, Mismatches: 34, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
213 72 0.11
214 92 0.13
215 58 0.08
216 126 0.18
217 335 0.49
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (217 bp):
ATATAAATTATAGAAAAAATATTTAATCTAATGGTAACATGTGTCACCATCTAATTGGTGGATTA
AATTTATTAAATTAAATTTATTTTAGGAACAAACTGATAGAATGTATAAGTATTGACGACTAAAT
GTATAATTATACCGATTTTATTAACCTTCAACTATATGATGACACGTGTCACCATCTGGTTGGAA
GATAAATATATAAATTAAATAA
Found at i:390747 original size:15 final size:16
Alignment explanation
Indices: 390727--390761 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
390717 GAAGATAAAT
*
390727 ATATAAATTA-AATAA
1 ATATAAATTATAAAAA
390742 ATATAAATTATAAAAA
1 ATATAAATTATAAAAA
390758 ATAT
1 ATAT
390762 TTAATCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATTATAAAAA
Found at i:390884 original size:22 final size:22
Alignment explanation
Indices: 390831--390887 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
390821 AAATTGATAG
*
390831 AATGTATAAGTATTGATGACTT
1 AATGTATAATTATTGATGACTT
390853 AATGTATAATTATTGATGACTT
1 AATGTATAATTATTGATGACTT
390875 AATGTATAATTAT
1 AATGTATAATTAT
390888 ATCAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.44
Consensus pattern (22 bp):
AATGTATAATTATTGATGACTT
Found at i:402583 original size:2 final size:2
Alignment explanation
Indices: 402576--402631 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
402566 AAACATGTAA
* * *
402576 AT AT AT AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402618 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
402632 GACATTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:402593 original size:14 final size:14
Alignment explanation
Indices: 402576--402631 Score: 103
Period size: 14 Copynumber: 4.0 Consensus size: 14
402566 AAACATGTAA
402576 ATATATATACATAT
1 ATATATATACATAT
402590 ATATATATACATAT
1 ATATATATACATAT
402604 ATATATATACATAT
1 ATATATATACATAT
*
402618 ATATATATATATAT
1 ATATATATACATAT
402632 GACATTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:402742 original size:17 final size:17
Alignment explanation
Indices: 402722--402779 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
402712 ATAATATTTA
402722 TAATATAAAAATAATAT
1 TAATATAAAAATAATAT
*
402739 TAATGATAAAAAGATATAT
1 TAAT-ATAAAAATA-ATAT
** *
402758 GCATATAAATATAATAT
1 TAATATAAAAATAATAT
*
402775 AAATA
1 TAATA
402780 ATATTAACAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 11 0.34
18 15 0.47
19 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
TAATATAAAAATAATAT
Found at i:406119 original size:21 final size:21
Alignment explanation
Indices: 406093--406135 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
406083 AGAGATTATG
406093 AAATGATTACGGAGTAAAGAT
1 AAATGATTACGGAGTAAAGAT
406114 AAATGATTACGGAGTAAAGAT
1 AAATGATTACGGAGTAAAGAT
406135 A
1 A
406136 CCCATGGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (21 bp):
AAATGATTACGGAGTAAAGAT
Found at i:410419 original size:20 final size:20
Alignment explanation
Indices: 410365--410438 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
410355 TTCTACCTGC
*
410365 GAGTATCGATACTCAT-TCTAA
1 GAGTACCGATACT-ATCTC-AA
* *
410386 GAGTATCAATACTATCTCAA
1 GAGTACCGATACTATCTCAA
*
410406 GGGTACCGATACTATCTCAA
1 GAGTACCGATACTATCTCAA
*
410426 GAGTGCCGATACT
1 GAGTACCGATACT
410439 CAAGGGATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 32 0.70
21 14 0.30
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (20 bp):
GAGTACCGATACTATCTCAA
Found at i:413047 original size:29 final size:29
Alignment explanation
Indices: 413014--413094 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
413004 CTTTTTCATT
413014 TAAGTATATAAAATAATTTTTGGTCAAAA
1 TAAGTATATAAAATAATTTTTGGTCAAAA
** * *
413043 TAAGTATCCAAAATTATCTTTTTGGTTAAAA
1 TAAGTATATAAAA-TA-ATTTTTGGTCAAAA
* * *
413074 TAGGTACATAAAATATTTTTT
1 TAAGTATATAAAATAATTTTT
413095 TTTATCAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 16 0.39
30 4 0.10
31 21 0.51
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (29 bp):
TAAGTATATAAAATAATTTTTGGTCAAAA
Found at i:413244 original size:28 final size:26
Alignment explanation
Indices: 413204--413259 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
413194 AAAATGTTTG
413204 AATATTTGAGGTACCTATTTTGACATAA
1 AATATTTGAGGTACCTATTTT--CATAA
*
413232 AATACTTT-AGGTACTTATTTTCATAA
1 AATA-TTTGAGGTACCTATTTTCATAA
413258 AA
1 AA
413260 AATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.27
28 16 0.62
29 3 0.12
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (26 bp):
AATATTTGAGGTACCTATTTTCATAA
Found at i:415659 original size:11 final size:11
Alignment explanation
Indices: 415643--415667 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
415633 AAATTGACTG
415643 TTATTTTAAAA
1 TTATTTTAAAA
415654 TTATTTTAAAA
1 TTATTTTAAAA
415665 TTA
1 TTA
415668 ATGAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:418542 original size:64 final size:64
Alignment explanation
Indices: 418474--418629 Score: 210
Period size: 64 Copynumber: 2.4 Consensus size: 64
418464 CGTACCCAAT
*
418474 TCGAATGCAATTTATGCACCGATGCACAA-ACCATGCATCGATGCACTCTGGCTATTTTAAAAAA
1 TCGAATGCAATTTATGCACCGATGCACAAGA-CATGCATCGATGCACCCTGGCTATTTTAAAAAA
* * * *
418538 TCGAATTG-ATTTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGTTATTTTGAAACA
1 TCGAA-TGCAATTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGCTATTTTAAAAAA
*
418602 TCGAA-GCCGATTTATGCACCGATGCACA
1 TCGAATG-CAATTTATGCACCGATGCACA
418630 CCCTAGTGCA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
62 1 0.01
64 77 0.95
65 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
TCGAATGCAATTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGCTATTTTAAAAAA
Found at i:420229 original size:40 final size:40
Alignment explanation
Indices: 420185--420338 Score: 193
Period size: 40 Copynumber: 3.9 Consensus size: 40
420175 TGAATATTTT
* *
420185 TCCCGAAGGACCATTACTTCCCTAAGGACCACTGGATATG
1 TCCCGAAGGACCACTACTTCCCGAAGGACCACTGGATATG
** *
420225 TCCCGAAGGACCACTACGTT-TAGAAGGACCATTGGATATG
1 TCCCGAAGGACCACTAC-TTCCCGAAGGACCACTGGATATG
* *
420265 TCCCGAAAGACCACTACGTCCCGAAGGACCACTGGATATG
1 TCCCGAAGGACCACTACTTCCCGAAGGACCACTGGATATG
* * * *
420305 TCCCGAATGACCACTACGTCTCGAATGACCACTG
1 TCCCGAAGGACCACTACTTCCCGAAGGACCACTG
420339 TAACCCTCCA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 96 0.97
41 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (40 bp):
TCCCGAAGGACCACTACTTCCCGAAGGACCACTGGATATG
Found at i:420233 original size:22 final size:22
Alignment explanation
Indices: 420203--420319 Score: 99
Period size: 22 Copynumber: 5.7 Consensus size: 22
420193 GACCATTACT
*
420203 TCCCTAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
*
420225 TCCCGAAGGACCACTACG-T-T-
1 TCCCGAAGGACCACT-GGATATG
* *
420245 T--AGAAGGACCATTGGATATG
1 TCCCGAAGGACCACTGGATATG
* *
420265 TCCCGAAAGACCAC----TACG
1 TCCCGAAGGACCACTGGATATG
420283 TCCCGAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
*
420305 TCCCGAATGACCACT
1 TCCCGAAGGACCACT
420320 ACGTCTCGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.01
18 27 0.37
19 1 0.01
20 2 0.03
21 1 0.01
22 40 0.55
23 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATATG
Found at i:420287 original size:18 final size:18
Alignment explanation
Indices: 420264--420337 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
420254 CATTGGATAT
*
420264 GTCCCGAAAGACCACTAC
1 GTCCCGAATGACCACTAC
* *
420282 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAATGACCAC----TAC
420304 GTCCCGAATGACCACTAC
1 GTCCCGAATGACCACTAC
*
420322 GTCTCGAATGACCACT
1 GTCCCGAATGACCACT
420338 GTAACCCTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 31 0.66
22 16 0.34
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.18
Consensus pattern (18 bp):
GTCCCGAATGACCACTAC
Found at i:420335 original size:80 final size:80
Alignment explanation
Indices: 420185--420335 Score: 230
Period size: 80 Copynumber: 1.9 Consensus size: 80
420175 TGAATATTTT
* * * * *
420185 TCCCGAAGGACCATTACTTCCCTAAGGACCACTGGATATGTCCCGAAGGACCACTACGTTTAGAA
1 TCCCGAAAGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTACGTCTAGAA
420250 GGACCATTGGATATG
66 GGACCATTGGATATG
* *
420265 TCCCGAAAGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAATGACCACTACGTCTCGAA
1 TCCCGAAAGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTACGTCTAGAA
*
420330 TGACCA
66 GGACCA
420336 CTGTAACCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (80 bp):
TCCCGAAAGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTACGTCTAGAA
GGACCATTGGATATG
Found at i:420951 original size:63 final size:63
Alignment explanation
Indices: 420876--421038 Score: 173
Period size: 63 Copynumber: 2.6 Consensus size: 63
420866 GATGCATCCC
*
420876 TTAACGGGTGCATCGATGCACTACCTGTGCATCGGTACACAAATCCCATTCGATGTTTGAATA
1 TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
* * * ** ** ** *
420939 TTAAGGGGTGCATCGATTCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATT
1 TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
* * * * *
421002 TTAAATGAGTGCATCGATACACTTCATGTGCATCGAT
1 TT-AACGGGTGCATCGATGCACTACCTGTGCATCGAT
421039 GCACCTTCAA
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
63 54 0.65
64 29 0.35
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (63 bp):
TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
Found at i:427204 original size:18 final size:18
Alignment explanation
Indices: 427177--427286 Score: 121
Period size: 18 Copynumber: 5.9 Consensus size: 18
427167 GTGAATATTT
*
427177 GTCCCAAAGGACCATTAC
1 GTCCCAAAGGACCACTAC
* *
427195 GTCCCTAAGGACCACTAGATAT
1 GTCCCAAAGGACCAC----TAC
427217 GTCCCAAAGGACCACTAC
1 GTCCCAAAGGACCACTAC
**
427235 GTCCCGTAGGACCACTAC
1 GTCCCAAAGGACCACTAC
* *
427253 GTTCCGAAGGACCACTAC
1 GTCCCAAAGGACCACTAC
427271 GTCCCAAAGGACCACT
1 GTCCCAAAGGACCACT
427287 GTAACCCTCG
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
18 61 0.79
22 16 0.21
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (18 bp):
GTCCCAAAGGACCACTAC
Found at i:427236 original size:40 final size:38
Alignment explanation
Indices: 427176--427286 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 38
427166 AGTGAATATT
*
427176 TGTCCCAAAGGACCATTACGTCCCTAAGGACCACTA-G
1 TGTCCCAAAGGACCACTACGTCCCTAAGGACCACTACG
427213 ATATGTCCCAAAGGACCACTACGTCCCGT-AGGACCACTACG
1 ---TGTCCCAAAGGACCACTACGTCCC-TAAGGACCACTACG
* *
427254 T-T-CCGAAGGACCACTACGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACTACGTCCCTAAGGACCACT
427287 GTAACCCTCG
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
36 28 0.43
37 1 0.02
38 1 0.02
40 33 0.51
41 2 0.03
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.17
Consensus pattern (38 bp):
TGTCCCAAAGGACCACTACGTCCCTAAGGACCACTACG
Found at i:432070 original size:21 final size:21
Alignment explanation
Indices: 432046--432125 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
432036 TTATGCATAA
432046 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
*
432067 TGCATCGATGTATCACTATGAATG
1 TGCATCGA--TA-CACTATGAAGG
*
432091 TGCATCGATACA-TCATGAAGA
1 TGCATCGATACACT-ATGAAGG
* *
432112 TGCATTGATGCACT
1 TGCATCGATACACT
432126 CCTTGAATGT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.02
21 25 0.51
22 3 0.06
23 2 0.04
24 18 0.37
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:432105 original size:24 final size:24
Alignment explanation
Indices: 432056--432105 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
432046 TGCATCGATA
**
432056 CACTATGAAGGTGCATCGATGTAT
1 CACTATGAAGGTGCATCGATACAT
*
432080 CACTATGAATGTGCATCGATACAT
1 CACTATGAAGGTGCATCGATACAT
432104 CA
1 CA
432106 TGAAGATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (24 bp):
CACTATGAAGGTGCATCGATACAT
Found at i:432110 original size:45 final size:44
Alignment explanation
Indices: 432046--432140 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 44
432036 TTATGCATAA
* *
432046 TGCATCGATACACTATGAAGGTGCATCGATGTA-TCACTATGAATG
1 TGCATCGATACACTATGAAGATGCATCGATGCACTC-CT-TGAATG
*
432091 TGCATCGATACA-TCATGAAGATGCATTGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATGAAGATGCATCGATGCACTCCTTGAATG
432135 TGCATC
1 TGCATC
432141 AATGCACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 13 0.29
45 30 0.67
46 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCATCGATGCACTCCTTGAATG
Found at i:434868 original size:64 final size:65
Alignment explanation
Indices: 434799--434946 Score: 212
Period size: 64 Copynumber: 2.3 Consensus size: 65
434789 TTCGAATGCA
* *
434799 ATTTATGCACCGATGCACAA-ACCATGCATCGATGCACTCTGGCTA-TTTTAAAACATCGAA-TT
1 ATTTATGCACCGATGCACAAGA-CATGCATCGATGCACCCTGGCTATTTTTAAAACATCGAAGCT
434861 G
65 G
* *
434862 ATTTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGTTATTTTTGAAACATCGAAGCT
1 A-TTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGCTATTTTTAAAACATCGAAGCT
434927 G
65 G
*
434928 ATTTATGCACTGATGCACA
1 ATTTATGCACCGATGCACA
434947 CCCAAGTGCA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
63 1 0.01
64 40 0.53
65 32 0.42
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (65 bp):
ATTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGCTATTTTTAAAACATCGAAGCTG
Found at i:440785 original size:251 final size:251
Alignment explanation
Indices: 440342--440801 Score: 735
Period size: 251 Copynumber: 1.8 Consensus size: 251
440332 AAAATTTTGG
* *
440342 ATGTATTAGGAGCTCTCCGTATTTTGTAAACTGATTATACATTTTTATTTTATACAACTATGGAT
1 ATGTATTAGGAGCTCTCCGTATTTTGTAAACTAAATATACATTTTTATTTTATACAACTATGGAT
*
440407 GGGTTTTTATGATGCTTTACAATTGTTTTTAAAGAAATATTTTGGGTTAATCACTTTGGTGGTCC
66 GGGTGTTTATGATGCTTTACAATTGTTTTTAAAGAAATATTTTGGGTTAATCACTTTGGTGGTCC
*
440472 CGTGTAACACTTTAATCCTTTGATATTCGAGTAAGACTAGATTAGAGTATTACATTTAGTGGTAT
131 CGTATAACACTTTAATCCTTTGATATTCGAGTAAGACTAGATTAGAGTATTACATTTAGTGGTAT
440537 CAAAGCATCAAGTTCAATCATTCCTAGGACTCGCGATTTAGAATCAGTTGGTGTCT
196 CAAAGCATCAAGTTCAATCATTCCTAGGACTCGCGATTTAGAATCAGTTGGTGTCT
* *
440593 ATGTATTAGGAGCTC-CTTGTATTTTGTAAATTAAATATAACATTTTTATTTTATACAACTATGG
1 ATGTATTAGGAGCTCTC-CGTATTTTGTAAACTAAATAT-ACATTTTTATTTTATACAACTATGG
* *
440657 AT-GGTGTTTATGATGCTTTATAATTGTTTTTAAAGAAATATTTTGGGTTAGTCACTTTGGTGGT
64 ATGGGTGTTTATGATGCTTTACAATTGTTTTTAAAGAAATATTTTGGGTTAATCACTTTGGTGGT
* * * ** * * * *
440721 CCCGTATAACACTTTAATCCTTTGATTTTTGGGTCGGGCTAGATTAGGGTGTTATATTTAGTGGT
129 CCCGTATAACACTTTAATCCTTTGATATTCGAGTAAGACTAGATTAGAGTATTACATTTAGTGGT
440786 ATCAAAGCATCAAGTT
194 ATCAAAGCATCAAGTT
440802 TCTGGTTGGA
Statistics
Matches: 190, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
250 1 0.01
251 162 0.85
252 27 0.14
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (251 bp):
ATGTATTAGGAGCTCTCCGTATTTTGTAAACTAAATATACATTTTTATTTTATACAACTATGGAT
GGGTGTTTATGATGCTTTACAATTGTTTTTAAAGAAATATTTTGGGTTAATCACTTTGGTGGTCC
CGTATAACACTTTAATCCTTTGATATTCGAGTAAGACTAGATTAGAGTATTACATTTAGTGGTAT
CAAAGCATCAAGTTCAATCATTCCTAGGACTCGCGATTTAGAATCAGTTGGTGTCT
Found at i:441932 original size:18 final size:18
Alignment explanation
Indices: 441909--441945 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
441899 TGGGGGATCT
*
441909 ACAACAATAACAATAATA
1 ACAACAAAAACAATAATA
*
441927 ACAACAAAAATAATAATA
1 ACAACAAAAACAATAATA
441945 A
1 A
441946 TAATGCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (18 bp):
ACAACAAAAACAATAATA
Found at i:443361 original size:60 final size:60
Alignment explanation
Indices: 443297--443412 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
443287 TAGGTATCAT
* * * * * *
443297 TTTAAAATGAGGGTGATAGTTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGATTTA
1 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGATTTA
* *
443357 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTTAAATATTTAAAAGTTGAAGGA
1 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGA
443413 CCAATTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (60 bp):
TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGATTTA
Found at i:443420 original size:60 final size:60
Alignment explanation
Indices: 443297--443442 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 60
443287 TAGGTATCAT
* * * * * * ***
443297 TTTAAAATGAGGGTGATAGTTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGATTTA
1 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGACCAA
* *
443357 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTTAAATATTTAAAAGTTGAAGGACCAA
1 TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGACCAA
* * *
443417 TTTAAAA-AACATTCATAGTTTAGAGA
1 TTTAAAATGAGAGTCATAGTTTAGAGA
443443 AATATGATGC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 16 0.22
60 56 0.78
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (60 bp):
TTTAAAATGAGAGTCATAGTTTAGAGATAAAATTGAAATATTCAAAAGTTGAAGGACCAA
Found at i:445866 original size:32 final size:32
Alignment explanation
Indices: 445820--445893 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
445810 TTCGGGTTGG
*
445820 GTCGAGTTTTTTAAGTGTGATATTCAGGTCGA
1 GTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
* *
445852 GTCGGGTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
445884 GTTCGGGTTT
1 G-TCGGGTTT
445894 AGTGTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 30 0.79
33 8 0.21
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (32 bp):
GTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
Found at i:448304 original size:16 final size:16
Alignment explanation
Indices: 448285--448318 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
448275 CAATATACGA
448285 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
448301 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
448317 AT
1 AT
448319 TTAGATGTAT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:448392 original size:16 final size:18
Alignment explanation
Indices: 448360--448393 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
448350 TATTAATGTA
448360 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
448378 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
448394 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:449066 original size:130 final size:130
Alignment explanation
Indices: 448862--449109 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
448852 AATTTTCTTC
* *
448862 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
448927 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
448992 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
449057 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
449110 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:449556 original size:35 final size:35
Alignment explanation
Indices: 449506--449581 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
449496 AATTGAATTT
* *
449506 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
449541 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
449576 AATTGA
1 AATTGA
449582 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:452248 original size:10 final size:10
Alignment explanation
Indices: 452215--452253 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
452205 CCCTTTTATG
452215 CATTTTGATA
1 CATTTTGATA
* * *
452225 CATTCTAATG
1 CATTTTGATA
452235 CATTTTGATA
1 CATTTTGATA
452245 CATTTTGAT
1 CATTTTGAT
452254 GTGATGTTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (10 bp):
CATTTTGATA
Found at i:453332 original size:2 final size:2
Alignment explanation
Indices: 453320--453349 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
453310 TTTAATTGGA
*
453320 AT AT TT 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
453350 CGATTAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:476253 original size:3 final size:3
Alignment explanation
Indices: 476245--476321 Score: 109
Period size: 3 Copynumber: 25.7 Consensus size: 3
476235 TAATATAAAT
* *
476245 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
476293 GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
476322 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:476773 original size:113 final size:113
Alignment explanation
Indices: 476575--477335 Score: 1208
Period size: 113 Copynumber: 6.7 Consensus size: 113
476565 TCTTGATGAG
476575 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCT
476639 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
476688 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
476753 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
476801 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
476866 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
476914 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * * * * * *
476979 GCAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
477027 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTT-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
* * * * *
477091 GGAAATGTTGATCCATCAAGTGATGAATTTAGGTAAAAGGTTGAACAAA
65 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
477140 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTT-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
* * * *
477204 GGAAATGTTGATCCATCAAATGATGAATTTAAACAACAA-GTTGAACAAG
65 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAA-AAGGTTGAACAAA
* *
477253 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* *
477317 GTAATGAATGATCCATCAA
66 GCAATG-TTGATCCATCAA
477336 GTGGATTTGA
Statistics
Matches: 614, Mismatches: 29, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
112 11 0.02
113 600 0.98
114 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:477973 original size:50 final size:50
Alignment explanation
Indices: 477898--478089 Score: 375
Period size: 50 Copynumber: 3.8 Consensus size: 50
477888 ATACACTTCT
*
477898 TCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
477948 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
477998 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
478048 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
478090 GGTAAATTCA
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 141 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (50 bp):
TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
Found at i:478226 original size:133 final size:133
Alignment explanation
Indices: 477999--478239 Score: 482
Period size: 133 Copynumber: 1.8 Consensus size: 133
477989 TCTGTCTAAT
477999 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
478064 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCAAATTCACTGATTGGTTCTGTTC
478129 AAC
131 AAC
478132 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
478197 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCA
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCA
478240 TTTAATGTTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 108 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (133 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCAAATTCACTGATTGGTTCTGTTC
AAC
Found at i:479017 original size:16 final size:17
Alignment explanation
Indices: 478979--479023 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
478969 AATATAAAAG
*
478979 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
478997 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
479013 AATAAATTGAA
1 AATAAATTGAA
479024 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:479367 original size:10 final size:10
Alignment explanation
Indices: 479352--479425 Score: 82
Period size: 10 Copynumber: 7.7 Consensus size: 10
479342 CTTGACCCCC
479352 TTTTCTTTTT
1 TTTTCTTTTT
479362 TTTTCTTTTT
1 TTTTCTTTTT
*
479372 TTTTCTTTCT
1 TTTTCTTTTT
479382 TTTTC---TT
1 TTTTCTTTTT
* *
479389 TTCTCCTTTT
1 TTTTCTTTTT
*
479399 TTTTCTTTCT
1 TTTTCTTTTT
*
479409 TTTTCTTTCT
1 TTTTCTTTTT
479419 TTTTCTT
1 TTTTCTT
479426 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 5 0.09
10 50 0.91
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:479390 original size:27 final size:27
Alignment explanation
Indices: 479353--479416 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
479343 TTGACCCCCT
479353 TTTCTTTTT-TTTTCT--TTTTTTTTC
1 TTTCTTTTTCTTTTCTCCTTTTTTTTC
479377 TTTCTTTTTCTTTTCTCCTTTTTTTTC
1 TTTCTTTTTCTTTTCTCCTTTTTTTTC
479404 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
479417 CTTTTTCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
24 9 0.24
25 6 0.16
27 22 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTCTTTTTCTTTTCTCCTTTTTTTTC
Found at i:479399 original size:37 final size:35
Alignment explanation
Indices: 479351--479425 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 35
479341 CCTTGACCCC
*
479351 CTTTTCTTTTTTTTTCTTTTTTTTTCTTTCTTTTT
1 CTTTTCTTTTTTTTTCTTTCTTTTTCTTTCTTTTT
479386 CTTTTCTCCTTTTTTTTCTTTCTTTTTCTTTCTTTTT
1 CTTTTCT--TTTTTTTTCTTTCTTTTTCTTTCTTTTT
479423 CTT
1 CTT
479426 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 7 0.19
37 30 0.81
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (35 bp):
CTTTTCTTTTTTTTTCTTTCTTTTTCTTTCTTTTT
Found at i:490070 original size:17 final size:17
Alignment explanation
Indices: 490030--490071 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
490020 ATACTTGCAA
*
490030 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
490048 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
490065 ATAAAAA
1 ATAAAAA
490072 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:492179 original size:3 final size:3
Alignment explanation
Indices: 492171--492256 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
492161 TAATATAAAT
* *
492171 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
492219 TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
492257 TGGATAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:497391 original size:69 final size:69
Alignment explanation
Indices: 497309--497447 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
497299 CAACATGGTA
497309 TCTTTCGCTAGACGATCCAGGCGGTCTTCTCGTGTTCTCGCTGCTTAAAGAAAGGTTCATCATGG
1 TCTTTCGCTAGACGATCCAGGCGGTCTTCTCGTGTTCTCGCTGCTTAAAGAAAGGTTCATCATGG
497374 ATGT
66 ATGT
*
497378 TCTTTCGCTAGACGATCCGGGCGGTCTTCTCGTGTTCTCGCTGCTTAAAGAAAGGTTCATCATGG
1 TCTTTCGCTAGACGATCCAGGCGGTCTTCTCGTGTTCTCGCTGCTTAAAGAAAGGTTCATCATGG
497443 ATGT
66 ATGT
497447 T
1 T
497448 GATCGGTTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (69 bp):
TCTTTCGCTAGACGATCCAGGCGGTCTTCTCGTGTTCTCGCTGCTTAAAGAAAGGTTCATCATGG
ATGT
Found at i:501097 original size:22 final size:22
Alignment explanation
Indices: 501072--501117 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
501062 CGACCGGATG
501072 TGGCGTTTAGTGTGAACAAGGC
1 TGGCGTTTAGTGTGAACAAGGC
501094 TGGCGTTTAGTGTGAACAAGGC
1 TGGCGTTTAGTGTGAACAAGGC
501116 TG
1 TG
501118 CTCAGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (22 bp):
TGGCGTTTAGTGTGAACAAGGC
Found at i:504393 original size:17 final size:17
Alignment explanation
Indices: 504343--504395 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
504333 ATTTATATTA
504343 TTTTAATCTAATTAAAT
1 TTTTAATCTAATTAAAT
* *
504360 ATTT-ATTTGATATTTAAAT
1 TTTTAATCT-A-A-TTAAAT
504379 TTTTAATCTAATTAAAT
1 TTTTAATCTAATTAAAT
504396 ACATTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 2 0.07
19 10 0.36
20 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAATCTAATTAAAT
Found at i:510453 original size:7 final size:7
Alignment explanation
Indices: 510441--510591 Score: 302
Period size: 7 Copynumber: 21.6 Consensus size: 7
510431 TCACTTTAAG
510441 GCTTCAA
1 GCTTCAA
510448 GCTTCAA
1 GCTTCAA
510455 GCTTCAA
1 GCTTCAA
510462 GCTTCAA
1 GCTTCAA
510469 GCTTCAA
1 GCTTCAA
510476 GCTTCAA
1 GCTTCAA
510483 GCTTCAA
1 GCTTCAA
510490 GCTTCAA
1 GCTTCAA
510497 GCTTCAA
1 GCTTCAA
510504 GCTTCAA
1 GCTTCAA
510511 GCTTCAA
1 GCTTCAA
510518 GCTTCAA
1 GCTTCAA
510525 GCTTCAA
1 GCTTCAA
510532 GCTTCAA
1 GCTTCAA
510539 GCTTCAA
1 GCTTCAA
510546 GCTTCAA
1 GCTTCAA
510553 GCTTCAA
1 GCTTCAA
510560 GCTTCAA
1 GCTTCAA
510567 GCTTCAA
1 GCTTCAA
510574 GCTTCAA
1 GCTTCAA
510581 GCTTCAA
1 GCTTCAA
510588 GCTT
1 GCTT
510592 TCATTATTGT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 144 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (7 bp):
GCTTCAA
Found at i:516695 original size:91 final size:89
Alignment explanation
Indices: 516542--516715 Score: 303
Period size: 91 Copynumber: 1.9 Consensus size: 89
516532 ATTCGATCAA
* * *
516542 ACTCTAAACATAGGATACTATATGCATAGATTATCCAAAATAGAAAATAATGGCCCATGCAGGTT
1 ACTCTAAACATAGGAGACTATATGCATAAATTACCCAAAATAGAAAATAATGGCCCATGCAGGTT
516607 GCATGGTCTCGAACGCGAAGATCG
66 GCATGGTCTCGAACGCGAAGATCG
516631 ACTCTAAACATAGGAGACTATATATGCATAAATTACCCAAAATAGAAAATAATGGCCCATGCAGG
1 ACTCTAAACATAGGAGAC--TATATGCATAAATTACCCAAAATAGAAAATAATGGCCCATGCAGG
516696 TTGCATGGTCTCGAACGCGA
64 TTGCATGGTCTCGAACGCGA
516716 CCTTCACGTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 17 0.21
91 63 0.79
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (89 bp):
ACTCTAAACATAGGAGACTATATGCATAAATTACCCAAAATAGAAAATAATGGCCCATGCAGGTT
GCATGGTCTCGAACGCGAAGATCG
Found at i:518944 original size:75 final size:75
Alignment explanation
Indices: 518818--519051 Score: 335
Period size: 75 Copynumber: 3.1 Consensus size: 75
518808 GCGGCCATTG
*
518818 CGGTGGAGGGGCAAATTTTGATTGAACTGGAGCTTCTATTTTCTCAACAGCTTTTAAAACAATCC
1 CGGTGGAGGGGCAAATTTTGATTGAACCGGAGCTTCTATTTTCTCAACAGCTTTTAAAACAATCC
* *
518883 CTTGATACGA
66 CATGAGACGA
* * * *
518893 CGGTGGAGGGGTAAATTTTGATTGAACCGGAGCTTCAATTTTCTCAGCAGCTGTTAAAACAATCC
1 CGGTGGAGGGGCAAATTTTGATTGAACCGGAGCTTCTATTTTCTCAACAGCTTTTAAAACAATCC
518958 CATGAGAC-A
66 CATGAGACGA
* ** * * *
518967 GCGGTGAAGGCCCAGATTTTGATTGAACCGGAGCTTCTCTTTTCTCAACAGCTTTTAAAGCAATC
1 -CGGTGGAGGGGCAAATTTTGATTGAACCGGAGCTTCTATTTTCTCAACAGCTTTTAAAACAATC
519032 CCATGAGACGA
65 CCATGAGACGA
519043 CGGTGGAGG
1 CGGTGGAGG
519052 AGTTAAAGGA
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
74 1 0.01
75 137 0.99
76 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (75 bp):
CGGTGGAGGGGCAAATTTTGATTGAACCGGAGCTTCTATTTTCTCAACAGCTTTTAAAACAATCC
CATGAGACGA
Found at i:520133 original size:30 final size:30
Alignment explanation
Indices: 520098--520159 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
520088 ATAAGCACTT
520098 GAACGAGTAAAATGCAAAGGTAAGACTTGA
1 GAACGAGTAAAATGCAAAGGTAAGACTTGA
*
520128 GAACGAGTAAAATGCAAAGGTAAGATTTGA
1 GAACGAGTAAAATGCAAAGGTAAGACTTGA
520158 GA
1 GA
520160 GAGATGTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (30 bp):
GAACGAGTAAAATGCAAAGGTAAGACTTGA
Found at i:520872 original size:18 final size:19
Alignment explanation
Indices: 520849--520890 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
520839 GAAACACAAA
*
520849 TTTAATATAAATATAAG-G
1 TTTAATATAAAAATAAGTG
520867 TTTAATATAAAAATAAGTG
1 TTTAATATAAAAATAAGTG
520886 TTTAA
1 TTTAA
520891 ACTATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TTTAATATAAAAATAAGTG
Found at i:523190 original size:64 final size:64
Alignment explanation
Indices: 523089--523241 Score: 225
Period size: 64 Copynumber: 2.4 Consensus size: 64
523079 AGACTAGTAA
* * *
523089 CATATCTTCCAGAACCTGTATCACTCTCTCAACTACCATGGAATTCGAGCACACAACCCCGTAG
1 CATATCTTCCAGAACCTGTATCACTCTCTCAACTACCACGGAAATCAAGCACACAACCCCGTAG
** *
523153 CATATCTTCCAGAACCTGTATCACTCTCTCAACTACCACGGAAATCAATTACACAACCTCGTAG
1 CATATCTTCCAGAACCTGTATCACTCTCTCAACTACCACGGAAATCAAGCACACAACCCCGTAG
* * *
523217 CATATCCTCCAAAACATGTATCACT
1 CATATCTTCCAGAACCTGTATCACT
523242 TCATCAGTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.32, C:0.33, G:0.10, T:0.25
Consensus pattern (64 bp):
CATATCTTCCAGAACCTGTATCACTCTCTCAACTACCACGGAAATCAAGCACACAACCCCGTAG
Found at i:526795 original size:23 final size:20
Alignment explanation
Indices: 526765--526822 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
526755 GCACCCCTGC
526765 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCAT---A-T
*
526788 AGTGCATCGATGCACCATAT
1 AGTGCATCCATGCACCATAT
526808 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
526823 TCCATTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
23 15 0.47
24 1 0.03
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATAT
Found at i:526873 original size:20 final size:20
Alignment explanation
Indices: 526842--526894 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
526832 AATTCAATTA
* *
526842 GTGCATCGATGCATCTTGCT
1 GTGCATCCATGCATCCTGCT
*
526862 GTGCGTCCATGCATCCTGCT
1 GTGCATCCATGCATCCTGCT
526882 GTGCATCCATGCA
1 GTGCATCCATGCA
526895 CCAAGGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGCATCCATGCATCCTGCT
Found at i:530018 original size:21 final size:21
Alignment explanation
Indices: 529992--530031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
529982 AAACAATTGG
*
529992 TAACAATTGATATCATTTTGT
1 TAACAATTAATATCATTTTGT
*
530013 TAACAATTAATATCTTTTT
1 TAACAATTAATATCATTTT
530032 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TAACAATTAATATCATTTTGT
Found at i:535749 original size:19 final size:19
Alignment explanation
Indices: 535721--535769 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
535711 AATTGGAATA
* *
535721 TATAATATATTTACATATT
1 TATAAAATATTTAAATATT
**
535740 TATAAAATATAAAAATATT
1 TATAAAATATTTAAATATT
535759 TATAAAA-ATTT
1 TATAAAATATTT
535770 TGTTTAACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TATAAAATATTTAAATATT
Found at i:539414 original size:32 final size:32
Alignment explanation
Indices: 539377--539440 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
539367 TCACTCTTAA
539377 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
1 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
539409 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
1 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
539441 CATAAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.44, G:0.06, T:0.34
Consensus pattern (32 bp):
TTTCCCCATCTAACATCCTATGCCTGCTTCCC
Found at i:548758 original size:3 final size:3
Alignment explanation
Indices: 548752--548835 Score: 154
Period size: 3 Copynumber: 28.7 Consensus size: 3
548742 ATATTATTAT
548752 TAA TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
548798 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
548836 TCCCGGACAA
Statistics
Matches: 79, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 75 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:549120 original size:55 final size:55
Alignment explanation
Indices: 549048--549391 Score: 501
Period size: 55 Copynumber: 6.3 Consensus size: 55
549038 GAAAAATGGA
** * * *
549048 ACTCGAA-AATCTTCAACAATCGTATCTGCTCTCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
* *
549102 ACTCGAACAATTTTCAACAATCGTGCCTGCACCCTATATCTTCAGAGAGTAAAAG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
* *
549157 ACTCGAACAATTTTCAACAATCGTGCCTGCTCCTTATATCTTCAGAGAGTAAAAG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
* *
549212 ACACGAACAATCTTCAACAATCGCGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
* * * * *
549267 ACTCGAACAATCTTCAATAATCGCGCTTGCTCCCTATATCTTCAGATAGTAAAGG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
** * *
549322 ACTCGAACAATCTTCAACAATCGCACCTTCTCCCTATATCTTCAGAGAGTAAAGG
1 ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
549377 ACTCGAACAATCTTC
1 ACTCGAACAATCTTC
549392 TTCTTACGGG
Statistics
Matches: 266, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
54 7 0.03
55 259 0.97
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAG
Found at i:549543 original size:54 final size:52
Alignment explanation
Indices: 549377--549915 Score: 543
Period size: 54 Copynumber: 10.1 Consensus size: 52
549367 AGAGTAAAGG
** * *
549377 ACTCGAACAATCTTCTTCTTACGGGTTTGCTCCCTCTTTCTTCAGGAAGTATAAA
1 ACTCGAAC-ATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTT-AGGAAGTATAGA
** * * **
549432 ACTAAAAAAATCGTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGA
1 ACT-CGAACATC-TTTTCAAACGGGTTCGCTCCCTCTTTCTT-AGGAAGTATAGA
* ** * * *
549487 ACTTGAACATCTTTTTCAAACAAGTTCACTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATC-TTTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGAAGTATAGA
*
549541 ACTC-AGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGA
1 ACTCGA-ACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTT-AGGAAGTATAGA
* * *
549595 ACTTGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGA
1 ACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTT-AGGAAGTATAGA
** *
549649 ACTCGAACATCTTTTTCAAACAAGTTCGCTCCATCTTTCTTCAGGAAGTATAGA
1 ACTCGAACATC-TTTTCAAACGGGTTCGCTCCCTCTTTCTT-AGGAAGTATAGA
*
549703 ACTCGAACAATC--TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
1 ACTCGAAC-ATCTTTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGAAGTATAGA
*
549755 ACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGA
1 ACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTC-TTAGGAAGTATAGA
* * * *
549809 ACTCGAACAATC--TTCAAACGGGTTCGCTCTCTTTTTCTCTAGGGAGTATGGA
1 ACTCGAAC-ATCTTTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGAAGTATAGA
* * *
549861 ACTCGGACATC--TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGAAGTATAGA
549912 ACTC
1 ACTC
549916 AAATAATCTT
Statistics
Matches: 421, Mismatches: 47, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
51 48 0.11
52 83 0.20
53 5 0.01
54 226 0.54
55 56 0.13
56 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (52 bp):
ACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTTAGGAAGTATAGA
Found at i:549579 original size:108 final size:106
Alignment explanation
Indices: 549397--549927 Score: 619
Period size: 106 Copynumber: 5.0 Consensus size: 106
549387 TCTTCTTCTT
* * * ** * * ** *
549397 ACGGGTTTGCTCCCTCTTTCT-TCAGGAAGTATAAAACTAAAAAAATCGTCTTCTTACGGGTTCG
1 ACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACT-CGAACATCTTCTTCAAACAGGTTCG
*
549461 CTCCCTCTTTCTTCAGGAAGTATAGAACTTGAAC-ATCTTTTTCAA
64 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATC---TTCAA
** * *
549506 ACAAGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTTCTTCAAACAGGTTCGC
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACAGGTTCGC
* *
549570 TCCCTCTTTCTTCAGGAAGTATAGAACTTGGACATATTCTTCAA
65 TCCCTCTTTCTTCAGGAAGTATAGAACTCGAACA-A-TCTTCAA
* * *
549614 ACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGAACATCTTTTTCAAACAAGTTCGC
1 ACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCTTCAAACAGGTTCGC
*
549678 TCCATCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAA
65 TCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAA
* *
549720 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACAGGTTCGCT
*
549785 CCCTCTTTCTTTAGGAAGTATAGAACTCGAACAATCTTCAA
66 CCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAA
* * * * *
549826 ACGGGTTCGCTCTCTTTTTCTCTAGGGAGTATGGAACTCGGACA---TCTTCAAACGGGTTCGCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACAGGTTCGCT
* * * *
549888 CCCTCTTTC-TCTAGGGAGTATGGAACTCAAATAATCTTCA
66 CCCTCTTTCTTC-AGGAAGTATAGAACTCGAACAATCTTCA
549928 TTTGCTTCAC
Statistics
Matches: 373, Mismatches: 40, Indels: 24
0.85 0.09 0.05
Matches are distributed among these distances:
102 1 0.00
103 51 0.14
106 144 0.39
107 4 0.01
108 139 0.37
109 30 0.08
110 2 0.01
111 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (106 bp):
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACAGGTTCGCT
CCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAA
Found at i:550362 original size:36 final size:36
Alignment explanation
Indices: 550304--550533 Score: 275
Period size: 36 Copynumber: 6.4 Consensus size: 36
550294 ACTCTTCTGA
* * **
550304 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
550341 GAAGACTTAAGATGGTTTGCTTCGCTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
550377 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
550413 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
550449 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
550485 GAAGGCTTAGGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
550521 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
550534 TGACTTTGCT
Statistics
Matches: 170, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
35 2 0.01
36 155 0.91
37 13 0.08
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:550468 original size:108 final size:108
Alignment explanation
Indices: 550304--550536 Score: 308
Period size: 108 Copynumber: 2.1 Consensus size: 108
550294 ACTCTTCTGA
* * ** *
550304 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGTGAAGACTTAAGATGGTTTGCTTCGCTA
1 GAAGGCTTAAGATTGAT-TGCTTCACTA-TTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTA
* *
550368 CTCTCTGGTGAAGACTTATGATGGTTTGCTTCACTAT-TCTCCGGT
64 CTCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCCGGT
* * * *
550413 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTATT
1 GAAGGCTTAAGATTGATTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACT
* *
550478 CTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
550521 GAAGGCTTAAGATTGA
1 GAAGGCTTAAGATTGA
550537 CTTTGCTCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.03
108 91 0.84
109 14 0.13
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (108 bp):
GAAGGCTTAAGATTGATTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACT
CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
Done.