Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 129 of 297
Found at i:44604252 original size:15 final size:15
Alignment explanation
Indices: 44604232--44604262 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44604222 TTCCTCTAAC
44604232 AGACATGGGTATCTT
1 AGACATGGGTATCTT
44604247 AGACATGGGTATCTT
1 AGACATGGGTATCTT
44604262 A
1 A
44604263 AGTTTACTTA
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:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (15 bp):
AGACATGGGTATCTT
Found at i:44604585 original size:22 final size:21
Alignment explanation
Indices: 44604534--44604591 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
44604524 TTTTTAAATT
*
44604534 ATAAATTATAAATTATTTTTAA
1 ATAAATT-CAAATTATTTTTAA
* *
44604556 AGATATTCAAATTATTTTTTAA
1 ATAAATTCAAATTA-TTTTTAA
44604578 ATAAATTCATAATT
1 ATAAATTCA-AATT
44604592 TAAAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 19 0.66
23 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAAATTCAAATTATTTTTAA
Found at i:44604630 original size:31 final size:28
Alignment explanation
Indices: 44604576--44604637 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 28
44604566 ATTATTTTTT
*
44604576 AAATAAATTCATAATTTAAAATATTATA
1 AAATAAATTAATAATTTAAAATATTATA
44604604 AAATAAATTAAATAATATCTAAAATATTATA
1 AAATAAATT-AATAAT-T-TAAAATATTATA
44604635 AAA
1 AAA
44604638 CTAATAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.30
29 5 0.17
30 1 0.03
31 15 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (28 bp):
AAATAAATTAATAATTTAAAATATTATA
Found at i:44604703 original size:28 final size:26
Alignment explanation
Indices: 44604660--44604722 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
44604650 TTGAAAGTTT
* *
44604660 AAAATACTTAAATATTTTATATTATTAA
1 AAAATA-TTTAATATTTAATATT-TTAA
44604688 AAATATATTTAATATTTAATATTTTAA
1 AAA-ATATTTAATATTTAATATTTTAA
44604715 AAAATATT
1 AAAATATT
44604723 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 7 0.22
28 17 0.53
29 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATTTAATATTTAATATTTTAA
Found at i:44604773 original size:35 final size:34
Alignment explanation
Indices: 44604699--44604788 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 34
44604689 AATATATTTA
*
44604699 ATATTTAATATTTTAAAAAAT-ATTAAAAAATAAT
1 ATATTTAA-AATTTAAAAAATAATTAAAAAATAAT
* *
44604733 A-ATTTAAAATTTAGAAAAATAATTTAAAAATTAT
1 ATATTTAAAATTTA-AAAAATAATTAAAAAATAAT
44604767 ATATTTAAAATTTTAAAAAATA
1 ATATTTAAAA-TTTAAAAAATA
44604789 TATATTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 5 0.10
33 12 0.24
34 13 0.27
35 15 0.31
36 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
ATATTTAAAATTTAAAAAATAATTAAAAAATAAT
Found at i:44604783 original size:23 final size:24
Alignment explanation
Indices: 44604755--44604801 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
44604745 AGAAAAATAA
*
44604755 TTTAAAAATTATATATT-TAAAAT
1 TTTAAAAAATATATATTATAAAAT
44604778 TTTAAAAAATATATATTATAAAAT
1 TTTAAAAAATATATATTATAAAAT
44604802 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAAAATATATATTATAAAAT
Found at i:44604872 original size:21 final size:21
Alignment explanation
Indices: 44604848--44605062 Score: 61
Period size: 21 Copynumber: 10.8 Consensus size: 21
44604838 TAAAACAAAT
44604848 TAAATAATATTTAAAATATTA
1 TAAATAATATTTAAAATATTA
* *
44604869 TAAA-ACTA-GTAACAA-ATT-
1 TAAATAATATTTAA-AATATTA
* *
44604887 TGAA-AGT-TT-AAAATATT-
1 TAAATAATATTTAAAATATTA
* *
44604904 TAAAT-AT-TTTATAGTATTA
1 TAAATAATATTTAAAATATTA
* *
44604923 -AAAAATATATTTAATAT-TTA
1 TAAATA-ATATTTAAAATATTA
* *
44604943 GAAAATAATATTTAAAATTTTA
1 -TAAATAATATTTAAAATATTA
*
44604965 AAAATAATATTTAAAAT-TTA
1 TAAATAATATTTAAAATATTA
* *
44604985 AAACAGTAAT-TTCAAAATA-TA
1 TAA-A-TAATATTTAAAATATTA
** *
44605006 TATTTAAAATTTAAAA-A-TA
1 TAAATAATATTTAAAATATTA
* * * *
44605025 TATATATTA-ATAAAATATTT
1 TAAATAATATTTAAAATATTA
*
44605045 TAAATATATATTTCAAAT
1 TAAATA-ATATTTAAAAT
44605063 TTTTTAAAGT
Statistics
Matches: 144, Mismatches: 30, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.01
17 11 0.08
18 19 0.13
19 19 0.13
20 28 0.19
21 49 0.34
22 16 0.11
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (21 bp):
TAAATAATATTTAAAATATTA
Found at i:44604934 original size:22 final size:21
Alignment explanation
Indices: 44604906--44604987 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
44604896 AAAATATTTA
*
44604906 AATATTTTATAGTATTAAAAAAT
1 AATATTTAATA-T-TTAAAAAAT
*
44604929 -ATATTTAATATTTAGAAAAT
1 AATATTTAATATTTAAAAAAT
* *
44604949 AATATTTAAAATTTTAAAAAT
1 AATATTTAATATTTAAAAAAT
*
44604970 AATATTTAAAATTTAAAA
1 AATATTTAATATTTAAAA
44604988 CAGTAATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.15
21 35 0.67
22 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATTTAATATTTAAAAAAT
Found at i:44604996 original size:20 final size:20
Alignment explanation
Indices: 44604923--44604987 Score: 96
Period size: 21 Copynumber: 3.2 Consensus size: 20
44604913 TATAGTATTA
*
44604923 AAAAAT-ATATTTAATATTT
1 AAAAATAATATTTAAAATTT
44604942 AGAAAATAATATTTAAAATTTT
1 A-AAAATAATATTTAAAA-TTT
44604964 AAAAATAATATTTAAAATTT
1 AAAAATAATATTTAAAATTT
44604984 AAAA
1 AAAA
44604988 CAGTAATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 1 0.02
20 12 0.29
21 25 0.60
22 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAATAATATTTAAAATTT
Found at i:44605024 original size:236 final size:237
Alignment explanation
Indices: 44604590--44605070 Score: 726
Period size: 236 Copynumber: 2.0 Consensus size: 237
44604580 AAATTCATAA
*
44604590 TTTAAAATATTATAAAATAAATTAAATAATATCTAAAATATTATAAAACTAATAACAAATTTGAA
1 TTTAAAATATTATAAAACAAATTAAATAATATCTAAAATATTATAAAACTAATAACAAATTTGAA
*
44604655 AGTTTAAAATACTTAAATATTTTATATTATTAAAAATATATTTAATATTTAATATTTTAAAAAAT
66 AGTTTAAAATACTTAAATATTTTATAGTATTAAAAATATATTTAATATTTAATATTTT-AAAAAT
44604720 ATTAAAAAATAATAATTTAAAATTTAGAAAAATAATTTAAAAATTATATATTTAAAATTTTAAAA
130 ATTAAAAAATAATAATTTAAAATTTAGAAAAATAATTTAAAAATTATATATTTAAAATTTTAAAA
* *
44604785 A-ATATATATT-ATAAAATATTTTAAATATGCATTTCAAGTTT
195 ATATATATATTAATAAAATATTTTAAATATACATTTCAAATTT
* *
44604826 TTTAAAATATTATAAAACAAATTAAATAATATTTAAAATATTATAAAACTAGTAACAAATTTGAA
1 TTTAAAATATTATAAAACAAATTAAATAATATCTAAAATATTATAAAACTAATAACAAATTTGAA
*
44604891 AGTTTAAAATATTTAAATATTTTATAGTATTAAAAAATATATTTAATATTTAGAAAATAATATTT
66 AGTTTAAAATACTTAAATATTTTATAGTATT-AAAAATATATTTAATATTT----AAT-AT-TTT
* * *
44604956 -AAAAT-TTTAAAAATAAT-ATTTAAAATTTA-AAACAGTAATTTCAAAA-TATATATTTAAAA-
124 AAAAATATTAAAAAATAATAATTTAAAATTTAGAAA-AATAATTTAAAAATTATATATTTAAAAT
*
44605015 TTTAAAAATATATATATTAATAAAATATTTTAAATATATATTTCAAATTT
188 TTTAAAAATATATATATTAATAAAATATTTTAAATATACATTTCAAATTT
44605065 TTTAAA
1 TTTAAA
44605071 GTTAATAATA
Statistics
Matches: 224, Mismatches: 11, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
236 91 0.41
237 27 0.12
238 25 0.11
239 57 0.25
240 11 0.05
241 8 0.04
242 2 0.01
243 3 0.01
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (237 bp):
TTTAAAATATTATAAAACAAATTAAATAATATCTAAAATATTATAAAACTAATAACAAATTTGAA
AGTTTAAAATACTTAAATATTTTATAGTATTAAAAATATATTTAATATTTAATATTTTAAAAATA
TTAAAAAATAATAATTTAAAATTTAGAAAAATAATTTAAAAATTATATATTTAAAATTTTAAAAA
TATATATATTAATAAAATATTTTAAATATACATTTCAAATTT
Found at i:44605110 original size:20 final size:20
Alignment explanation
Indices: 44605074--44605115 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44605064 TTTTAAAGTT
44605074 AATAATAATAAATAAAATAA
1 AATAATAATAAATAAAATAA
*
44605094 AATAA-AATGAATAAAAATAA
1 AATAATAATAAAT-AAAATAA
44605114 AA
1 AA
44605116 GACAAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (20 bp):
AATAATAATAAATAAAATAA
Found at i:44605133 original size:27 final size:26
Alignment explanation
Indices: 44605092--44605162 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 26
44605082 TAAATAAAAT
*
44605092 AAAATAAAATGAATAAAAATAAA-AGACA
1 AAAATAAAA--AATAAAAA-AAAGAAACA
44605120 AAACATAAAAAATAAAAAAAAGAAACA
1 AAA-ATAAAAAATAAAAAAAAGAAACA
*
44605147 AAAGTAAAAAATAAAA
1 AAAATAAAAAATAAAA
44605163 GAGAAACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 15 0.38
27 15 0.38
28 3 0.08
29 6 0.15
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (26 bp):
AAAATAAAAAATAAAAAAAAGAAACA
Found at i:44605138 original size:9 final size:9
Alignment explanation
Indices: 44605080--44605157 Score: 50
Period size: 10 Copynumber: 8.0 Consensus size: 9
44605070 AGTTAATAAT
*
44605080 AATAAATAA
1 AATAAAAAA
44605089 AATAAAATAA
1 AATAAAA-AA
*
44605099 AATGAATAAA
1 AAT-AAAAAA
44605109 AATAAAAGACA
1 AATAAAA-A-A
44605120 AA-ACATAAAA
1 AATA-A-AAAA
44605130 AATAAAAAA
1 AATAAAAAA
*
44605139 AAGAAACAAA
1 AATAAA-AAA
*
44605149 AGTAAAAAA
1 AATAAAAAA
44605158 TAAAAGAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
9 21 0.38
10 23 0.42
11 9 0.16
12 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (9 bp):
AATAAAAAA
Found at i:44605145 original size:22 final size:21
Alignment explanation
Indices: 44605106--44605146 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44605096 TAAAATGAAT
* *
44605106 AAAAATAAAAGACAAAACATA
1 AAAAATAAAAAAAAAAACATA
44605127 AAAAATAAAAAAAAGAAACA
1 AAAAATAAAAAAAA-AAACA
44605147 AAAGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAAAAAAAACATA
Found at i:44605616 original size:15 final size:15
Alignment explanation
Indices: 44605561--44605617 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
44605551 TTATACTAAA
*
44605561 AAAATATTTGTTATT
1 AAAATATTTATTATT
* *
44605576 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
44605593 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
44605610 AAAATATT
1 AAAATATT
44605618 AAATAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:44605643 original size:25 final size:26
Alignment explanation
Indices: 44605593--44605657 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
44605583 TTATAATTGT
44605593 AATAAA-TATTTATTATTAAAATATTA
1 AATAAATTA-TTATTATTAAAATATTA
44605619 AATAAATTATTATT-TTAATAA-ATTA
1 AATAAATTATTATTATTAA-AATATTA
*
44605644 TATAAATTA-TATTA
1 AATAAATTATTATTA
44605658 ATAACTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
24 4 0.11
25 16 0.46
26 13 0.37
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAATTATTATTATTAAAATATTA
Found at i:44607540 original size:24 final size:24
Alignment explanation
Indices: 44607503--44607575 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
44607493 GGTAAGACAT
44607503 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
* *
44607527 TTTCCACTGTTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
44607551 TTTCCACAGCTCCTCTATTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
44607575 T
1 T
44607576 ATCGATTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:44630851 original size:20 final size:20
Alignment explanation
Indices: 44630814--44630852 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44630804 ACATATATTG
**
44630814 AATAAATTTAATTTAAATTA
1 AATAAATTTAATAGAAATTA
*
44630834 AATAATTTTAATAGAAATT
1 AATAAATTTAATAGAAATT
44630853 GAGTTTTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATAAATTTAATAGAAATTA
Found at i:44633411 original size:18 final size:19
Alignment explanation
Indices: 44633375--44633412 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
44633365 TATATTACAT
44633375 TTTTCAAAAAATCATATTA
1 TTTTCAAAAAATCATATTA
*
44633394 TTTTCCAAAAATCA-ATTA
1 TTTTCAAAAAATCATATTA
44633412 T
1 T
44633413 CGGAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTCAAAAAATCATATTA
Found at i:44635750 original size:30 final size:30
Alignment explanation
Indices: 44635714--44635775 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
44635704 AATTTGGGTT
* *
44635714 TTTTATTTTTTTAATGTGAATAATATTTAA
1 TTTTATTTCTTTAATGTGAAAAATATTTAA
44635744 TTTTATTTCTTTAATGTGAAAAATATTTAA
1 TTTTATTTCTTTAATGTGAAAAATATTTAA
44635774 TT
1 TT
44635776 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (30 bp):
TTTTATTTCTTTAATGTGAAAAATATTTAA
Found at i:44638381 original size:46 final size:46
Alignment explanation
Indices: 44638331--44638506 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
44638321 TGGTTGAGCA
44638331 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
44638377 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
44638422 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
44638470 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44638507 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:44638487 original size:93 final size:93
Alignment explanation
Indices: 44638328--44638499 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44638318 GGATGGTTGA
* *
44638328 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
44638393 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
44638421 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
44638486 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
44638500 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:44645952 original size:46 final size:46
Alignment explanation
Indices: 44645902--44646077 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
44645892 TGGTTGAGCA
44645902 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
44645948 TCCGAACTCTTTGAGTTGAGTCCGAGTTCA-TGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
44645993 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
44646041 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44646078 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:44646058 original size:93 final size:93
Alignment explanation
Indices: 44645899--44646069 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
44645889 GGATGGTTGA
* * * *
44645899 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCTTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
44645964 TGAGTCCGAGTTCATGAAATGTAACTAG
66 TGAGTCCGAGTTCATGAAATGTAACTAG
*
44645992 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
44646057 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
44646070 GCTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAAATGTAACTAG
Found at i:44648778 original size:3 final size:3
Alignment explanation
Indices: 44648770--44648815 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
44648760 CAATGATGTT
*
44648770 AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
44648816 TAAAAGCAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44649145 original size:18 final size:19
Alignment explanation
Indices: 44649122--44649161 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
44649112 CGGGTTTAGA
44649122 TTGGGCCCAACC-AAAATT
1 TTGGGCCCAACCTAAAATT
44649140 TTGGGCCCAACCTAAAATT
1 TTGGGCCCAACCTAAAATT
44649159 TTG
1 TTG
44649162 CCCAAGCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (19 bp):
TTGGGCCCAACCTAAAATT
Found at i:44650035 original size:16 final size:16
Alignment explanation
Indices: 44649997--44650060 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
44649987 CATAATATGC
44649997 AATAATAATAATGAAA
1 AATAATAATAATGAAA
44650013 AGA-AATAATAACT-AAA
1 A-ATAATAATAA-TGAAA
44650029 AATAAT-AT-AT--AA
1 AATAATAATAATGAAA
*
44650041 AATAATAAAAATGTAAA
1 AATAATAATAATG-AAA
44650058 AAT
1 AAT
44650061 CAAAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 3 0.08
15 3 0.08
16 16 0.41
17 7 0.18
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (16 bp):
AATAATAATAATGAAA
Found at i:44653841 original size:6 final size:6
Alignment explanation
Indices: 44653832--44653856 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44653822 CGTTATTCAC
44653832 TTCATT TTCATT TTCATT TTCATT T
1 TTCATT TTCATT TTCATT TTCATT T
44653857 ATCTTCGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCATT
Found at i:44655052 original size:19 final size:20
Alignment explanation
Indices: 44655028--44655070 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
44655018 GATCCTTTTG
*
44655028 TGAAATTTAATGCACATG-A
1 TGAAATGTAATGCACATGCA
*
44655047 TGAAATGTAATGCAGATGCA
1 TGAAATGTAATGCACATGCA
44655067 TGAA
1 TGAA
44655071 TACAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCACATGCA
Found at i:44656796 original size:3 final size:3
Alignment explanation
Indices: 44656788--44656843 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
44656778 CAAAATATGC
* * *
44656788 AAT AAT AAT -GT AA- AAT AAT AAT AGT AAT AAT AAT AAT AACT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
44656832 AAT AAT ATAT AA
1 AAT AAT A-AT AA
44656844 ATTAATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.07
3 34 0.79
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:44656823 original size:31 final size:28
Alignment explanation
Indices: 44656788--44656861 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 28
44656778 CAAAATATGC
44656788 AATAATAATGTAAAATAATAATAGTAATAAT
1 AATAATAATGTAAAATAAT-ATA-TAA-AAT
* *
44656819 AATAATAACT-AAAAATAATATATAAATT
1 AATAATAA-TGTAAAATAATATATAAAAT
*
44656847 AATAAAAATGTAAAA
1 AATAATAATGTAAAA
44656862 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 13 0.35
29 3 0.08
30 3 0.08
31 16 0.43
32 1 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (28 bp):
AATAATAATGTAAAATAATATATAAAAT
Found at i:44658437 original size:24 final size:24
Alignment explanation
Indices: 44658408--44658453 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
44658398 TTTACCAAAT
44658408 CAAACCA-CATACCAAAACCAAAAC
1 CAAACCATCA-ACCAAAACCAAAAC
*
44658432 CAAACCATCACCCAAAACCAAA
1 CAAACCATCAACCAAAACCAAA
44658454 CCATAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.57, C:0.39, G:0.00, T:0.04
Consensus pattern (24 bp):
CAAACCATCAACCAAAACCAAAAC
Found at i:44663231 original size:47 final size:46
Alignment explanation
Indices: 44663175--44663307 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 46
44663165 ATGCAAACAT
*
44663175 CATAAATGAAAAAAAATCAAGCATA-ATTGAAAATTTGATTATAA-TTG
1 CATAAATGAAAAAAAATCAA--ATATATTGAAAATTTAATTA-AATTTG
* *
44663222 CATAAATGAAAAAATATAAAATAATATTGCAAAA-TTAATTAAATTTG
1 CATAAATGAAAAAAAATCAAAT-ATATTG-AAAATTTAATTAAATTTG
44663269 CATAAATGAAAAAAATATCAAATAGTATTGAAAATTTAA
1 CATAAATGAAAAAAA-ATCAAATA-TATTGAAAATTTAA
44663308 AATTATCACT
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
45 2 0.03
46 3 0.04
47 50 0.68
48 19 0.26
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.30
Consensus pattern (46 bp):
CATAAATGAAAAAAAATCAAATATATTGAAAATTTAATTAAATTTG
Found at i:44663461 original size:11 final size:11
Alignment explanation
Indices: 44663445--44663484 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
44663435 TAAACAAATG
44663445 ATTTTGATAGA
1 ATTTTGATAGA
44663456 ATTTTGATAGA
1 ATTTTGATAGA
*
44663467 AATTTGATAGA
1 ATTTTGATAGA
44663478 ATTTTGA
1 ATTTTGA
44663485 GAAAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (11 bp):
ATTTTGATAGA
Found at i:44663475 original size:22 final size:22
Alignment explanation
Indices: 44663447--44663509 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
44663437 AACAAATGAT
44663447 TTTGATAGAATTTTGATAGAAA
1 TTTGATAGAATTTTGATAGAAA
*
44663469 TTTGATAGAATTTTGAGA-AAA
1 TTTGATAGAATTTTGATAGAAA
* *
44663490 TTTCA-ATGAAATTTGATAGA
1 TTTGATA-GAATTTTGATAGA
44663510 TTTTTTAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 16 0.46
22 18 0.51
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTGATAGAATTTTGATAGAAA
Found at i:44663491 original size:11 final size:11
Alignment explanation
Indices: 44663445--44663492 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
44663435 TAAACAAATG
*
44663445 ATTTTGATAGA
1 ATTTTGATAAA
44663456 ATTTTGATAGAA
1 ATTTTGATA-AA
*
44663468 A-TTTGATAGA
1 ATTTTGATAAA
*
44663478 ATTTTGAGAAA
1 ATTTTGATAAA
44663489 ATTT
1 ATTT
44663493 CAATGAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (11 bp):
ATTTTGATAAA
Found at i:44665102 original size:20 final size:20
Alignment explanation
Indices: 44665065--44665103 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44665055 ATATATATCG
**
44665065 AATAAATTTAATTTAAATTA
1 AATAAATTTAATAGAAATTA
*
44665085 AATAATTTTAATAGAAATT
1 AATAAATTTAATAGAAATT
44665104 GAGTTTTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATAAATTTAATAGAAATTA
Found at i:44668253 original size:20 final size:20
Alignment explanation
Indices: 44668228--44668272 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
44668218 ATATCAGTAT
*
44668228 TTTTATCCTGAATTTTAGGA
1 TTTTATCCTGAATTTCAGGA
*
44668248 TTTTATCCTGAATTTCAGTA
1 TTTTATCCTGAATTTCAGGA
44668268 TTTTA
1 TTTTA
44668273 ATTTAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTATCCTGAATTTCAGGA
Found at i:44673664 original size:17 final size:16
Alignment explanation
Indices: 44673637--44673668 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
44673627 AAGATTAAAA
44673637 TTTTAAAATATTCTAT
1 TTTTAAAATATTCTAT
44673653 TTTTATAAATATTCTA
1 TTTTA-AAATATTCTA
44673669 CAAAAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAAATATTCTAT
Found at i:44673982 original size:20 final size:20
Alignment explanation
Indices: 44673953--44673995 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44673943 ACATATATTG
**
44673953 AATAAATTTAATTTAAATTA
1 AATAAATTTAATAGAAATTA
*
44673973 AATAATTTTAATAGAAATTA
1 AATAAATTTAATAGAAATTA
44673993 AAT
1 AAT
44673996 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AATAAATTTAATAGAAATTA
Found at i:44676253 original size:25 final size:27
Alignment explanation
Indices: 44676216--44676265 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
44676206 TCAAACATGC
44676216 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
44676242 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
44676266 ATAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:44677809 original size:15 final size:15
Alignment explanation
Indices: 44677789--44677819 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44677779 AATGCTAATG
44677789 CCCATCATCCATTAA
1 CCCATCATCCATTAA
44677804 CCCATCATCCATTAA
1 CCCATCATCCATTAA
44677819 C
1 C
44677820 TATTAAAATG
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:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCATCATCCATTAA
Found at i:44678764 original size:9 final size:9
Alignment explanation
Indices: 44678750--44678776 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44678740 GAAGTGTACC
44678750 AAAATAGCA
1 AAAATAGCA
44678759 AAAATAGCA
1 AAAATAGCA
44678768 AAAATAGCA
1 AAAATAGCA
44678777 TATAATTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAATAGCA
Found at i:44682261 original size:3 final size:3
Alignment explanation
Indices: 44682253--44682296 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
44682243 TGCATTCCAA
44682253 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44682297 AATGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:44683600 original size:27 final size:27
Alignment explanation
Indices: 44683570--44683624 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
44683560 TATAGACATT
*
44683570 TTTTAATA-TGTATATACTATATAAATA
1 TTTTAAAATTGTATATA-TATATAAATA
* *
44683597 TTTTAAAATTTTATATATATATATATA
1 TTTTAAAATTGTATATATATATAAATA
44683624 T
1 T
44683625 ATTGTGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTAAAATTGTATATATATATAAATA
Found at i:44685679 original size:48 final size:48
Alignment explanation
Indices: 44685620--44685728 Score: 191
Period size: 48 Copynumber: 2.3 Consensus size: 48
44685610 TAATTGTTTG
* *
44685620 TATCTGCCATTGTATGAATGCCATTATCAAATTGATGTTTATTATGTA
1 TATCTGCCATTGTATAAATGCCATTATCAAACTGATGTTTATTATGTA
*
44685668 TATCTGCCATTGTATAAATGCCATTATCAAACTGATGTTTATTCTGTA
1 TATCTGCCATTGTATAAATGCCATTATCAAACTGATGTTTATTATGTA
44685716 TATCTGCCATTGT
1 TATCTGCCATTGT
44685729 TTGTATCCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (48 bp):
TATCTGCCATTGTATAAATGCCATTATCAAACTGATGTTTATTATGTA
Found at i:44695011 original size:6 final size:6
Alignment explanation
Indices: 44694995--44695079 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
44694985 GAAACACTCA
* ** * * *
44694995 TTGATT CTGATT TTGATT TTGATT TCAATT TCGATC TCGATT TTGATT
1 TTGATT TTGATT TTGATT TTGATT TTGATT TTGATT TTGATT TTGATT
* * * * * *
44695043 TAGAAT TTAATT TTGATT TGGATT TAGATT TCGATT T
1 TTGATT TTGATT TTGATT TTGATT TTGATT TTGATT T
44695080 AGGGTTATTT
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.55
Consensus pattern (6 bp):
TTGATT
Found at i:44695060 original size:24 final size:25
Alignment explanation
Indices: 44695004--44695079 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 25
44694994 ATTGATTCTG
* *
44695004 ATTTTGATTTTGATTT-CAATTTCG
1 ATTTTGATTTTGATTTAGAATTTCA
* *
44695028 ATCTCGATTTTGATTTAGAATTT-A
1 ATTTTGATTTTGATTTAGAATTTCA
* *
44695052 ATTTTGATTTGGATTTAG-ATTTCG
1 ATTTTGATTTTGATTTAGAATTTCA
44695076 ATTT
1 ATTT
44695080 AGGGTTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 4 0.10
24 33 0.79
25 5 0.12
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (25 bp):
ATTTTGATTTTGATTTAGAATTTCA
Found at i:44695185 original size:48 final size:48
Alignment explanation
Indices: 44695114--44695238 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
44695104 TTTGTTTGTA
* * * * *
44695114 TGATGTTTATTGTTTATATCTGTCATTGTATGAATGCCCTTATCAAAT
1 TGATGTTTATTATGTATATCTGTCATTGTATAAATGCCATTATCAAAC
44695162 TGATGTTTATTATGTATATCTGTCATTGTATAAATGCCATTATCAAAC
1 TGATGTTTATTATGTATATCTGTCATTGTATAAATGCCATTATCAAAC
* * * *
44695210 TGATGTTTACTCTGTATATCAGCCATTGT
1 TGATGTTTATTATGTATATCTGTCATTGT
44695239 TTATATCCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (48 bp):
TGATGTTTATTATGTATATCTGTCATTGTATAAATGCCATTATCAAAC
Found at i:44696179 original size:21 final size:21
Alignment explanation
Indices: 44696149--44696195 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
44696139 AAGTTGGTGT
*
44696149 CCCAACTCAGCAACA-GGCTAC
1 CCCAAATCAGCAACATGG-TAC
*
44696170 CCCAAATCAGCAAGATGGTAC
1 CCCAAATCAGCAACATGGTAC
44696191 CCCAA
1 CCCAA
44696196 CTCAACAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.36, C:0.38, G:0.15, T:0.11
Consensus pattern (21 bp):
CCCAAATCAGCAACATGGTAC
Found at i:44696684 original size:23 final size:23
Alignment explanation
Indices: 44696654--44696703 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
44696644 TGAGTTAAGC
* *
44696654 AACTGTTAAGCATTTTGTATACT
1 AACTGTTAAGCAATTTGTATACG
*
44696677 AACTGTTAAGCAATTTGTCTACG
1 AACTGTTAAGCAATTTGTATACG
44696700 AACT
1 AACT
44696704 ATTATCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (23 bp):
AACTGTTAAGCAATTTGTATACG
Found at i:44697374 original size:23 final size:23
Alignment explanation
Indices: 44697347--44697390 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
44697337 TCTCTATTTT
44697347 TCCTCTTCTCCTTCTTCTTCTCC
1 TCCTCTTCTCCTTCTTCTTCTCC
* *
44697370 TCCTCTTCTTCTTTTTCTTCT
1 TCCTCTTCTCCTTCTTCTTCT
44697391 TTTTTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (23 bp):
TCCTCTTCTCCTTCTTCTTCTCC
Found at i:44697380 original size:20 final size:20
Alignment explanation
Indices: 44697347--44697387 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44697337 TCTCTATTTT
*
44697347 TCCTCTTCTCCTTCTTCTTC
1 TCCTCCTCTCCTTCTTCTTC
* *
44697367 TCCTCCTCTTCTTCTTTTTC
1 TCCTCCTCTCCTTCTTCTTC
44697387 T
1 T
44697388 TCTTTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (20 bp):
TCCTCCTCTCCTTCTTCTTC
Found at i:44697398 original size:8 final size:9
Alignment explanation
Indices: 44697375--44697404 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44697365 TCTCCTCCTC
44697375 TTCTTCTTT
1 TTCTTCTTT
44697384 TTCTTCTTT
1 TTCTTCTTT
44697393 TT-TTCTTT
1 TTCTTCTTT
44697401 TTCT
1 TTCT
44697405 CTAACCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:44698251 original size:17 final size:16
Alignment explanation
Indices: 44698224--44698255 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
44698214 AAGATTAAAA
44698224 TTTTAAAATATTCTAT
1 TTTTAAAATATTCTAT
44698240 TTTTATAAATATTCTA
1 TTTTA-AAATATTCTA
44698256 CAAAAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAAATATTCTAT
Found at i:44698569 original size:20 final size:20
Alignment explanation
Indices: 44698540--44698582 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44698530 ACATATATTG
**
44698540 AATAAATTTAATTTAAATTA
1 AATAAATTTAATAGAAATTA
*
44698560 AATAATTTTAATAGAAATTA
1 AATAAATTTAATAGAAATTA
44698580 AAT
1 AAT
44698583 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AATAAATTTAATAGAAATTA
Found at i:44704750 original size:210 final size:210
Alignment explanation
Indices: 44704415--44704836 Score: 601
Period size: 210 Copynumber: 2.0 Consensus size: 210
44704405 CATGGTGTTG
*
44704415 TAAGTAACTATATTAGGTGCACAACCCTTCTCAATCATCAAGCTGAAAACCCTTCTAGCTTTATC
1 TAAGTAACTATATCAGGTGCACAACCCTTCTCAATCATCAAGCTGAAAACCCTTCTAGCTTTATC
* *
44704480 CATTTCATTCTGTAAGCAGTGACCATTAACTAACACACTATAGGTAACAACATTAGGCTCAATGC
66 CATTTCATTCTGCAAGCAATGACCATTAACTAACACACTATAGGTAACAACATTAGGCTCAATGC
* * * * ** * * *
44704545 CTCTCTTTCTCATTGAGTCAACAATATCCTTGGCTTCAAAGACCATCCCTTGCTTGCAATGTGCA
131 CTCGCTTTATCATTGAGTCAACAAAACCCTCAGCTTCAAAGACCATCCCTTCCTTGCAAAGCGCA
44704610 TCAACCAATATATTA
196 TCAACCAATATATTA
* *
44704625 TAAGTAACTATATCAGGTGCACAACCCTTCTCAATCATCAAGTTGAAAACTCTTCTAGCTTTATC
1 TAAGTAACTATATCAGGTGCACAACCCTTCTCAATCATCAAGCTGAAAACCCTTCTAGCTTTATC
* * * * * ** * *
44704690 CATTTCGTTCTGCAAGCAATGGCCGTTGATTAATGCATTATGGGTAACAACATTAGGCTCAATGC
66 CATTTCATTCTGCAAGCAATGACCATTAACTAACACACTATAGGTAACAACATTAGGCTCAATGC
* *
44704755 CTCGCTTTATCATTGCGTCAACAAAACCCTCAGCTTCAGAGACCATCCCTTCCTTGCAAAGCGCA
131 CTCGCTTTATCATTGAGTCAACAAAACCCTCAGCTTCAAAGACCATCCCTTCCTTGCAAAGCGCA
* *
44704820 TCAACCAGTGTATTA
196 TCAACCAATATATTA
44704835 TA
1 TA
44704837 CCTGACAACA
Statistics
Matches: 185, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
210 185 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (210 bp):
TAAGTAACTATATCAGGTGCACAACCCTTCTCAATCATCAAGCTGAAAACCCTTCTAGCTTTATC
CATTTCATTCTGCAAGCAATGACCATTAACTAACACACTATAGGTAACAACATTAGGCTCAATGC
CTCGCTTTATCATTGAGTCAACAAAACCCTCAGCTTCAAAGACCATCCCTTCCTTGCAAAGCGCA
TCAACCAATATATTA
Found at i:44706472 original size:3 final size:3
Alignment explanation
Indices: 44706464--44706488 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44706454 ATAAATTTCT
44706464 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
44706489 AGCTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44706613 original size:5 final size:5
Alignment explanation
Indices: 44706603--44706629 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
44706593 GTATTTGATT
44706603 GAGTC GAGTC GAGTC GAGTC GAGTC GA
1 GAGTC GAGTC GAGTC GAGTC GAGTC GA
44706630 ATTAAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (5 bp):
GAGTC
Found at i:44707465 original size:38 final size:38
Alignment explanation
Indices: 44707414--44707492 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
44707404 CCATTCCATT
44707414 AGTTGGGATACAAATCCGAACAAATTAGGTGATGAAAG
1 AGTTGGGATACAAATCCGAACAAATTAGGTGATGAAAG
*
44707452 AGTTGGGATACAAATCCGAACAAATTAGGTGATGATAG
1 AGTTGGGATACAAATCCGAACAAATTAGGTGATGAAAG
44707490 AGT
1 AGT
44707493 GTCATATTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.23
Consensus pattern (38 bp):
AGTTGGGATACAAATCCGAACAAATTAGGTGATGAAAG
Found at i:44710012 original size:17 final size:17
Alignment explanation
Indices: 44709986--44710023 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
44709976 GTTATATATT
*
44709986 TATTTCAAATTATTTTA
1 TATTTCAAATTATTGTA
*
44710003 TATTTTAAATTATTGTA
1 TATTTCAAATTATTGTA
44710020 TATT
1 TATT
44710024 ATGTATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTTCAAATTATTGTA
Found at i:44711565 original size:17 final size:17
Alignment explanation
Indices: 44711539--44711576 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
44711529 GTTATATATT
*
44711539 TATTTCAAATTATTTTA
1 TATTTCAAATTATTGTA
*
44711556 TATTTTAAATTATTGTA
1 TATTTCAAATTATTGTA
44711573 TATT
1 TATT
44711577 ATGTATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTTCAAATTATTGTA
Found at i:44716168 original size:24 final size:25
Alignment explanation
Indices: 44716107--44716169 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
44716097 TACTCAATAC
**
44716107 TTTTAAAAGTCAAAACCCATTAAAA
1 TTTTAAAAACCAAAACCCATTAAAA
* * *
44716132 CTTTAAAACCCAATACCCATT-AAA
1 TTTTAAAAACCAAAACCCATTAAAA
44716156 TTTTAAAAACCAAA
1 TTTTAAAAACCAAA
44716170 TTGAAATGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.27
Consensus pattern (25 bp):
TTTTAAAAACCAAAACCCATTAAAA
Found at i:44718115 original size:70 final size:70
Alignment explanation
Indices: 44718002--44718142 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
44717992 AGTTGAGTTT
*
44718002 TGAATGTTTAAAGCTTATTTCATATTTTAAATGGATCTTATTTTTTGGGCTTAATATTATTTTTC
1 TGAATGGTTAAAGCTTATTTCATATTTTAAATGGATCTTATTTTTTGGGCTTAATATTATTTTTC
44718067 AAATC
66 AAATC
44718072 TGAATGGTTAAAGCTTATTTCATATTTTAAATGGATCTTATTTTTTGGGCTTAATATTATTTTTC
1 TGAATGGTTAAAGCTTATTTCATATTTTAAATGGATCTTATTTTTTGGGCTTAATATTATTTTTC
44718137 AAATC
66 AAATC
44718142 T
1 T
44718143 TCTTAAAATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (70 bp):
TGAATGGTTAAAGCTTATTTCATATTTTAAATGGATCTTATTTTTTGGGCTTAATATTATTTTTC
AAATC
Found at i:44720118 original size:286 final size:286
Alignment explanation
Indices: 44719606--44720466 Score: 1713
Period size: 286 Copynumber: 3.0 Consensus size: 286
44719596 AAATTGTTTC
*
44719606 TCTTTCTCGACTAGATTTGTGTCTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
1 TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
44719671 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
66 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
44719736 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
131 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
44719801 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
196 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
44719866 GTGTTCACGGAAAATCGATTAGACAA
261 GTGTTCACGGAAAATCGATTAGACAA
44719892 TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
1 TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
44719957 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
66 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
44720022 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
131 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
44720087 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
196 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
44720152 GTGTTCACGGAAAATCGATTAGACAA
261 GTGTTCACGGAAAATCGATTAGACAA
44720178 TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
1 TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
44720243 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
66 TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
44720308 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
131 TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
44720373 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
196 TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
44720438 GTGTTCACGGAAAATCGATTAGACAA
261 GTGTTCACGGAAAATCGATTAGACAA
44720464 TCT
1 TCT
44720467 ATCCTTTCGG
Statistics
Matches: 574, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
286 574 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (286 bp):
TCTTTCTCGACTAGATTTGTGTTTGGGCAGTTGTCGTGCCCAAAAAATTTGGGGAGAGGATAAAA
TTGAAAACCTGAAACCTGAAATAAACAGGAAAAAAATGCGTGAAAAGTAAAAGCTGAAAATAAAA
TAATAAAAACAGTTAAATAAATCTGAAGAAAAATTAATTAAACTAAGCTCAGCTTTAGGCACGGG
TTTTTTCGAGGTTCCAGGTTCCAGGTTCCATAGGTTTTAGGTTCATGGAACCTGGAACCTGAAAT
GTGTTCACGGAAAATCGATTAGACAA
Found at i:44720938 original size:14 final size:13
Alignment explanation
Indices: 44720915--44720956 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
44720905 AACTTTGCTT
44720915 AAAAACTTGATGA
1 AAAAACTTGATGA
44720928 AAAACACTTGATG-
1 AAAA-ACTTGATGA
*
44720941 AAAGACTTGATGA
1 AAAAACTTGATGA
44720954 AAA
1 AAA
44720957 GCTTAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:44725740 original size:114 final size:113
Alignment explanation
Indices: 44725535--44725970 Score: 441
Period size: 114 Copynumber: 3.8 Consensus size: 113
44725525 TGGCATGGGA
* ** *
44725535 ATCTTTTACATGGTC-AAAGTTCATATCTACTGGAATGGTAATGCTCCTCTCTGAGGATGT-AAC
1 ATCTTTTACATGGTCTAAA-TTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGAT-TCAAC
* * * * *
44725598 TTTAGCCATAGGAGAAGTTACAGGATTCTTGGGGCTATTGGGCAAACCGTT
64 TTTAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAACC-TT
* *
44725649 ATCTGTTACATGGTCTAAATTCGTATCTACTGGAATTGTAACACTCGTCTCTGCA-GATTCAACT
1 ATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTG-AGGATTCAACT
* *
44725713 TTAGCCATGGGATAACTTACAGGATTCTTGGGGTTGTTGGATAAACCTTT
65 TTAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAACC-TT
* ** * * * * *
44725763 ACCTTTTACATATTCTAAATTCGTATTTACCGGAATGGTAACACTTGTCTCTGAGGATGCTACTT
1 ATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATTCAACTT
* * * *
44725828 CAGCCTTGGGATAAGTTACAAGATTCTTGGGGTTGTTGGACAAATCTT
66 TAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAACCTT
* * * * * *
44725876 CATCCTTTACATGGTCTAAGTTGGTCTCTACTGGAATGGTAGTACCAC-CGTGCTCCCG-GGATG
1 -ATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTA--A-CACTCGT-CT-CTGAGGATT
* *
44725939 CAACTTTAGCCATAGGATTAGTTACAGGATTC
60 CAACTTTAGCCATGGGATAAGTTACAGGATTC
44725971 ATAGAGTTGG
Statistics
Matches: 265, Mismatches: 47, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
113 4 0.02
114 216 0.82
115 4 0.02
116 3 0.01
117 36 0.14
118 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (113 bp):
ATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATTCAACTT
TAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAACCTT
Found at i:44730704 original size:93 final size:93
Alignment explanation
Indices: 44730540--44730791 Score: 321
Period size: 93 Copynumber: 2.7 Consensus size: 93
44730530 TTTTTGAAAG
* * * * *
44730540 TATTGATAGTTCAAGTACCACATTGGACATTTTCAAGGTGCAAGCACCACATTAGACATTTTATG
1 TATTGATAGTTCAAGCACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGAAATTTTATG
44730605 AAAGTACAAGTAACATAATAAAA-ACACA
66 AAAGTACAAGTAACATAATAAAATACA-A
* * * *
44730633 TATTGATAGTTCAAGCACCAAATTGGATATTTTCAAAGTTCAAGTACCACATTAGATATTTTATG
1 TATTGATAGTTCAAGCACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGAAATTTTATG
* * *
44730698 ATAGTACATGTACCATAATAAAATACAA
66 AAAGTACAAGTAACATAATAAAATACAA
* * * * *
44730726 -ATTGATAGTTCAAGGACCACATTGGGCATTTTCAAAATACAAATACGACATTA-AAATTTTATG
1 TATTGATAGTTCAAGCACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGAAATTTTATG
44730789 AAA
66 AAA
44730792 ACATACATAC
Statistics
Matches: 138, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
91 11 0.08
92 45 0.33
93 79 0.57
94 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (93 bp):
TATTGATAGTTCAAGCACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGAAATTTTATG
AAAGTACAAGTAACATAATAAAATACAA
Found at i:44732976 original size:28 final size:28
Alignment explanation
Indices: 44732936--44732994 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
44732926 GCTGGATTTA
44732936 TTGCACTGTTAGAAAACCATGAATAGTC
1 TTGCACTGTTAGAAAACCATGAATAGTC
*
44732964 TTGCACTGTTAGAAAACCATGGATAGTC
1 TTGCACTGTTAGAAAACCATGAATAGTC
44732992 TTG
1 TTG
44732995 TGACCATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (28 bp):
TTGCACTGTTAGAAAACCATGAATAGTC
Found at i:44733138 original size:38 final size:38
Alignment explanation
Indices: 44733089--44733333 Score: 263
Period size: 38 Copynumber: 6.9 Consensus size: 38
44733079 TATGACTCAT
* *
44733089 ATAACAAACAAACTTACTTTTTTTATTCATACATTTTC
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
44733127 ATAACAAACAAACTTACTTTTATGA--C-T-CA---T-
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
* *
44733157 ATAACAAACAAACTTACTTTTTTTATTCATACATTTTC
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
44733195 ATAACAAACAAACTTACTTTTATGA--C-T-CA---T-
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
* *
44733225 ATAACAAACAAACTTACTTTTTTTATTCATACATTTTC
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
*
44733263 ATAACAAACAAACTTACTTTTATGACTCATAC-TTTTGC
1 ATAACAAACAAACTTACTTTTATGATTCATACATTTT-C
** * *
44733301 ATAACAAACAATTTTATTTTTATGACTCATACA
1 ATAACAAACAAACTTACTTTTATGATTCATACA
44733334 AAATAGTGAA
Statistics
Matches: 175, Mismatches: 14, Indels: 35
0.78 0.06 0.16
Matches are distributed among these distances:
30 46 0.26
31 2 0.01
32 2 0.01
33 2 0.01
34 8 0.05
35 2 0.01
36 2 0.01
37 6 0.03
38 105 0.60
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (38 bp):
ATAACAAACAAACTTACTTTTATGATTCATACATTTTC
Found at i:44733138 original size:68 final size:68
Alignment explanation
Indices: 44733058--44733293 Score: 472
Period size: 68 Copynumber: 3.5 Consensus size: 68
44733048 ATCTTCTTTA
44733058 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
1 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
44733123 TTT
66 TTT
44733126 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
1 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
44733191 TTT
66 TTT
44733194 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
1 CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
44733259 TTT
66 TTT
44733262 CATAACAAACAAACTTACTTTTATGACTCATA
1 CATAACAAACAAACTTACTTTTATGACTCATA
44733294 CTTTTGCATA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 168 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (68 bp):
CATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTTTTATTCATACAT
TTT
Found at i:44733225 original size:106 final size:106
Alignment explanation
Indices: 44733089--44733333 Score: 247
Period size: 106 Copynumber: 2.3 Consensus size: 106
44733079 TATGACTCAT
* *
44733089 ATAACAAACAAACTTACTTTTTTTATTCATACATTTTCATAACAAACAAACTTACTTTTATGA-C
1 ATAACAAACAAACTTACTTTTATGA-TCATACA---T-ATAACAAACAAACTTACTTTTATGATC
* * *
44733153 -T-CA-T-ATAACAAACAAACTTACTTTTTTTATTCATACATTTT-C
61 ATACATTCATAACAAACAAACTTACTTTTATGACTCATAC-TTTTGC
* *
44733195 ATAACAAACAAACTTACTTTTATGA-C-T-CATATAACAAACAAACTTACTTTTTTTATTCATAC
1 ATAACAAACAAACTTACTTTTATGATCATACATATAACAAACAAACTTACTTTTATGA-TCATAC
44733257 ATTTTCATAACAAACAAACTTACTTTTATGACTCATACTTTTGC
65 A--TTCATAACAAACAAACTTACTTTTATGACTCATACTTTTGC
** *
44733301 ATAACAAACAATTTTATTTTTATGACTCATACA
1 ATAACAAACAAACTTACTTTTATGA-TCATACA
44733334 AAATAGTGAA
Statistics
Matches: 116, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
98 23 0.20
99 1 0.01
100 1 0.01
101 1 0.01
102 4 0.03
103 1 0.01
104 1 0.01
105 5 0.04
106 75 0.65
108 1 0.01
109 1 0.01
110 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (106 bp):
ATAACAAACAAACTTACTTTTATGATCATACATATAACAAACAAACTTACTTTTATGATCATACA
TTCATAACAAACAAACTTACTTTTATGACTCATACTTTTGC
Found at i:44733683 original size:30 final size:30
Alignment explanation
Indices: 44733649--44733709 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
44733639 TCTCCTTTAC
*
44733649 ATAACAAATAAACTTACTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
44733679 ATAACAAACAAACTTACTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
44733709 A
1 A
44733710 CAAAATAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.34
Consensus pattern (30 bp):
ATAACAAACAAACTTACTTTTATGACTCAT
Found at i:44739267 original size:30 final size:30
Alignment explanation
Indices: 44739211--44739267 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
44739201 ATTAGCAATA
* * *
44739211 AATATCAATTTTATACATGCACTTTGATCC
1 AATATCAATTTTACACATGAAATTTGATCC
44739241 AATATGCAA-TTTACACATGAAATTTGA
1 AATAT-CAATTTTACACATGAAATTTGA
44739268 ATTGTAGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (30 bp):
AATATCAATTTTACACATGAAATTTGATCC
Found at i:44752123 original size:5 final size:5
Alignment explanation
Indices: 44752113--44752148 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
44752103 TTATTATTAA
44752113 TATAT TATAT TATAT TATAT TATAT TATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
44752149 AACAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:44752133 original size:15 final size:16
Alignment explanation
Indices: 44752073--44752148 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 16
44752063 ATTCTAGTTA
44752073 ATATATATATTATA-T
1 ATATATATATTATATT
* *
44752088 ATATGTA-AGTAATGATT
1 ATATATATA-TTAT-ATT
44752105 ATTATTAATATATTATATT
1 A-TA-T-ATATATTATATT
44752124 ATAT-TATATTATATT
1 ATATATATATTATATT
44752139 ATATATATAT
1 ATATATATAT
44752149 AACAAAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 1 0.02
15 24 0.49
16 6 0.12
17 3 0.06
18 4 0.08
19 5 0.10
20 5 0.10
21 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
ATATATATATTATATT
Found at i:44752175 original size:16 final size:15
Alignment explanation
Indices: 44752154--44752183 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44752144 TATATAACAA
44752154 AAGAAAGAATAGAAAT
1 AAGAAAGAA-AGAAAT
44752170 AAGAAAGAAAGAAA
1 AAGAAAGAAAGAAA
44752184 CAGAGAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAGAAAGAAAGAAAT
Found at i:44753255 original size:23 final size:22
Alignment explanation
Indices: 44753228--44753312 Score: 113
Period size: 21 Copynumber: 4.0 Consensus size: 22
44753218 CTTTGCCGAC
44753228 CAGGCACTTTATGTGTCGTATCT
1 CAGGCACTTTATGTGTCGTAT-T
44753251 CAGGCACTTTATGTGTCGTA-T
1 CAGGCACTTTATGTGTCGTATT
* **
44753272 CAGGCACCTCGTGTGTCGT-TT
1 CAGGCACTTTATGTGTCGTATT
44753293 CAGGCAC-TTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
44753313 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 9 0.16
21 26 0.47
23 20 0.36
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (22 bp):
CAGGCACTTTATGTGTCGTATT
Found at i:44753278 original size:44 final size:41
Alignment explanation
Indices: 44753228--44753312 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
44753218 CTTTGCCGAC
* *
44753228 CAGGCACTTTATGTGTCGTATCTCAGGCACTTTATGTGTCGTAT
1 CAGGCACCTCATGTGTCGT-T-TCAGGCAC-TTATGTGTCGTAT
*
44753272 CAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCGTAT
1 CAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGTAT
44753313 ACTGATCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 13 0.34
42 8 0.21
43 1 0.03
44 16 0.42
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (41 bp):
CAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGTAT
Found at i:44754036 original size:17 final size:17
Alignment explanation
Indices: 44754014--44754064 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
44754004 ATGTGGCATG
44754014 TACCTAAGTAATGTATA
1 TACCTAAGTAATGTATA
44754031 TACCTAAGTAATGTATA
1 TACCTAAGTAATGTATA
*
44754048 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
44754065 GGGATTAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:44755229 original size:42 final size:42
Alignment explanation
Indices: 44755183--44755333 Score: 196
Period size: 42 Copynumber: 3.6 Consensus size: 42
44755173 ACAGTTAGCT
*
44755183 ATGGTCTTACACGATTCTCATATCGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
* * *
44755225 ATGGTCTTACACGAATCTCATATCGGTGCCAATGTCCCAGAT
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
* * * *
44755267 ATGGCCTTACATGAATCACATGAT-GAAGCCAATGTCCTAGAC
1 ATGGTCTTACACGAATCTCAT-ATCGATGCCAATGTCCTAGAC
*
44755309 ATGGTCTTACACGTAATCACATATC
1 ATGGTCTTACACG-AATCTCATATC
44755334 AGTATCCTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
42 83 0.89
43 10 0.11
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
Found at i:44756065 original size:11 final size:11
Alignment explanation
Indices: 44756051--44756076 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44756041 AAATACTCAC
44756051 CAAATAAAGCA
1 CAAATAAAGCA
44756062 CAAATAAAGCA
1 CAAATAAAGCA
44756073 CAAA
1 CAAA
44756077 ACTTGGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (11 bp):
CAAATAAAGCA
Found at i:44757019 original size:18 final size:17
Alignment explanation
Indices: 44756986--44757024 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
44756976 TTTTATAAAT
44756986 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
44757004 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
44757021 TGTG
1 TGTG
44757025 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:44757281 original size:23 final size:23
Alignment explanation
Indices: 44757250--44757302 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44757240 AGTGTTATTG
*
44757250 ATCAGTGGTAG-TTTCGGCTACAT
1 ATCAGTGGTAGCTTT-AGCTACAT
*
44757273 TTCAGTGGTAGCTTTAGCTACAT
1 ATCAGTGGTAGCTTTAGCTACAT
44757296 ATCAGTG
1 ATCAGTG
44757303 TGGCACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (23 bp):
ATCAGTGGTAGCTTTAGCTACAT
Found at i:44759966 original size:71 final size:71
Alignment explanation
Indices: 44759843--44760044 Score: 226
Period size: 71 Copynumber: 2.8 Consensus size: 71
44759833 TGCAAGTTTT
* * * ** *
44759843 ATTCGATGCTGCTCACTCAAGCTGTTGAGGA-TCTGCAACCTATGTTGGATCTCAACCATTGATA
1 ATTCGATGCTGCTCACTCAAGCTGTTGAGAATTC-GCAACATATGCTAAATCTCAACCATCGATA
*
44759907 AAGAATG
65 AAAAATG
* * *
44759914 ATTCGATGCTGCTCACTCAAGCTATCGAGAATTCGCAACATGTGCTAAATCTCAACCATCGATAA
1 ATTCGATGCTGCTCACTCAAGCTGTTGAGAATTCGCAACATATGCTAAATCTCAACCATCGATAA
44759979 AAAATG
66 AAAATG
* * * * * * * *
44759985 ATTTGATGATACTCACTCAAGCTGTTGAGAATCCGCAACACATGTTAGATCTCAGCCATC
1 ATTCGATGCTGCTCACTCAAGCTGTTGAGAATTCGCAACATATGCTAAATCTCAACCATC
44760045 AAATTAATTC
Statistics
Matches: 109, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
71 107 0.98
72 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (71 bp):
ATTCGATGCTGCTCACTCAAGCTGTTGAGAATTCGCAACATATGCTAAATCTCAACCATCGATAA
AAAATG
Found at i:44764635 original size:28 final size:30
Alignment explanation
Indices: 44764595--44764652 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
44764585 ATAAGAGAAG
44764595 AGAATGAAGGAAAAATGATAAA-GAAAGGAA
1 AGAATGAAGGAAAAATGA-AAAGGAAAGGAA
*
44764625 AGAAT-AA-GAAAAATTAAAAGGAAAGGAA
1 AGAATGAAGGAAAAATGAAAAGGAAAGGAA
44764653 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 2 0.08
30 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.10
Consensus pattern (30 bp):
AGAATGAAGGAAAAATGAAAAGGAAAGGAA
Found at i:44779729 original size:23 final size:23
Alignment explanation
Indices: 44779670--44779737 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
44779660 AAATCAAATT
* * *
44779670 AATATAAATTAATCTAATTAAAC
1 AATAAAAAATAATCCAATTAAAC
44779693 --T-AAAAATCAA-CCAATTAAAC
1 AATAAAAAAT-AATCCAATTAAAC
*
44779713 AATAAAAAATAATCCAATAAAAC
1 AATAAAAAATAATCCAATTAAAC
44779736 AA
1 AA
44779738 GAAGAGCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
22 3 0.08
23 17 0.47
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
AATAAAAAATAATCCAATTAAAC
Found at i:44786419 original size:36 final size:36
Alignment explanation
Indices: 44786372--44786443 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
44786362 TAGGCTTGTT
*
44786372 TATTTGATAAGACTTGAGTTGGATTCTCATTCTTGA
1 TATTTGATAAGACTTGAGTTGGATTCTCATACTTGA
44786408 TATTTGATAAGACTTGAGTTGGATTCTCATACTTGA
1 TATTTGATAAGACTTGAGTTGGATTCTCATACTTGA
44786444 CATCATGCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (36 bp):
TATTTGATAAGACTTGAGTTGGATTCTCATACTTGA
Found at i:44786495 original size:6 final size:6
Alignment explanation
Indices: 44786486--44786523 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
44786476 TTCAAACTCA
* *
44786486 AATTGG AATTGG AATTAG AATTAG AATTAG AATT-G AAT
1 AATTAG AATTAG AATTAG AATTAG AATTAG AATTAG AAT
44786524 ATATTTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (6 bp):
AATTAG
Found at i:44786693 original size:51 final size:51
Alignment explanation
Indices: 44786613--44786716 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
44786603 CTGTAGCGCA
44786613 ATTAATGTATTGTTATTGTATTCACGTATATATCATATCAAGTTCTTGTTC
1 ATTAATGTATTGTTATTGTATTCACGTATATATCATATCAAGTTCTTGTTC
*
44786664 ATTAATGTATTGTTATTGTATTCATGTATATATCATATCAAGTTCTTGTTC
1 ATTAATGTATTGTTATTGTATTCACGTATATATCATATCAAGTTCTTGTTC
44786715 AT
1 AT
44786717 CAATTTAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.50
Consensus pattern (51 bp):
ATTAATGTATTGTTATTGTATTCACGTATATATCATATCAAGTTCTTGTTC
Found at i:44792605 original size:3 final size:3
Alignment explanation
Indices: 44792587--44792637 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
44792577 TCAAATATCC
* * * * *
44792587 TTA TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44792634 TTA T
1 TTA T
44792638 GTACTAGTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:44792769 original size:3 final size:3
Alignment explanation
Indices: 44792761--44792787 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44792751 TATTCCAATG
44792761 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
44792788 GTTTATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44815127 original size:296 final size:296
Alignment explanation
Indices: 44814593--44815177 Score: 1152
Period size: 296 Copynumber: 2.0 Consensus size: 296
44814583 GTCTAAATTG
44814593 CATCTATTTCTTTAGGTTTTCTGTCAAAGGTACTGGCTGAACAAGAAGGCATCAGTGATAGAACC
1 CATCTATTTCTTTAGGTTTTCTGTCAAAGGTACTGGCTGAACAAGAAGGCATCAGTGATAGAACC
44814658 TTGATGAACAATGAGGAATGACAACCTAAGCATTAAAAATGGATCATTCTCATGACATTCTACAA
66 TTGATGAACAATGAGGAATGACAACCTAAGCATTAAAAATGGATCATTCTCATGACATTCTACAA
44814723 ATATAATACATACACATCTAGTTAGGAGCATTTGATTCATTCTGATCATGTCATCCTAAACACTA
131 ATATAATACATACACATCTAGTTAGGAGCATTTGATTCATTCTGATCATGTCATCCTAAACACTA
44814788 GGCGTAAATAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTC
196 GGCGTAAATAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTC
44814853 CCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGAT
261 CCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGAT
44814889 CATCTATTTCTTTAGGTTTTCTGTCAAAGGTACTGGCTGAACAAGAAGGCATCAGTGATAGAACC
1 CATCTATTTCTTTAGGTTTTCTGTCAAAGGTACTGGCTGAACAAGAAGGCATCAGTGATAGAACC
44814954 TTGATGAACAATGAGGAATGACAACCTAAGCATTAAAAATGGATCATTCTCATGACATTCTACAA
66 TTGATGAACAATGAGGAATGACAACCTAAGCATTAAAAATGGATCATTCTCATGACATTCTACAA
44815019 ATATAATACATACACATCTAGTTAGGAGCATTTGATTCATTCTGATCATGTCATCCTAAACACTA
131 ATATAATACATACACATCTAGTTAGGAGCATTTGATTCATTCTGATCATGTCATCCTAAACACTA
*
44815084 GGCGTAAATAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
196 GGCGTAAATAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTC
*
44815149 CCATATTGGTGGCGAAGTAGATCGCAGAA
261 CCATATTGGTGGCGAAGTAGATCGAAGAA
44815178 GGTAGATCTT
Statistics
Matches: 287, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
296 287 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (296 bp):
CATCTATTTCTTTAGGTTTTCTGTCAAAGGTACTGGCTGAACAAGAAGGCATCAGTGATAGAACC
TTGATGAACAATGAGGAATGACAACCTAAGCATTAAAAATGGATCATTCTCATGACATTCTACAA
ATATAATACATACACATCTAGTTAGGAGCATTTGATTCATTCTGATCATGTCATCCTAAACACTA
GGCGTAAATAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTC
CCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGAT
Found at i:44815332 original size:132 final size:132
Alignment explanation
Indices: 44815093--44815413 Score: 507
Period size: 132 Copynumber: 2.4 Consensus size: 132
44815083 AGGCGTAAAT
*
44815093 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
** * * * * *
44815158 TGGCGAAGTAGATCGCAGAAGGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGATA
66 TGGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGTGAAGTAGATCGAAGATA
44815223 GC
131 GC
*
44815225 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTTCCATATTGG
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
*
44815290 TGGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGTGAAGTAGATCGAAGATG
66 TGGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGTGAAGTAGATCGAAGATA
44815355 GC
131 GC
* * * *
44815357 TGGTCCTGTCTTCCTATATTGATAGGAAGTGGATCTAAGATGTAGATCCTTGTCTTC
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGAT-CTTGTCTTC
44815414 ATGTATTGGC
Statistics
Matches: 173, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
132 165 0.95
133 8 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (132 bp):
AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
TGGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGTGAAGTAGATCGAAGATA
GC
Found at i:44815342 original size:88 final size:88
Alignment explanation
Indices: 44815250--44815485 Score: 237
Period size: 88 Copynumber: 2.7 Consensus size: 88
44815240 ATATTGATAG
* * * *
44815250 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTTCC-ATATTGGTGGCGAAGTAGATCAAAGAAAGA
1 GAAGTAGATCGAAGATGGCAGATCCTGTC-TTCCTATATTGATAG-GAAGTAGATCAAAG-AAGA
44815313 AGAT-CTTATCTTCACGTATTGGCGT
63 AGATCCTTATCTTCACGTATTGGCGT
* * * * * *
44815338 GAAGTAGATCGAAGATGGCTGGTCCTGTCTTCCTATATTGATAGGAAGTGGATCTAAGATGTAGA
1 GAAGTAGATCGAAGATGGCAGATCCTGTCTTCCTATATTGATAGGAAGTAGATCAAAGAAGAAGA
* *
44815403 TCCTTGTCTTCATGTATTGGCGT
66 TCCTTATCTTCACGTATTGGCGT
** * * * * *
44815426 GAAGTAGATCGAAGATAACATG-TCCTGTCTCCCTATATTGGTAGGGAGTGGATCGAAGAA
1 GAAGTAGATCGAAGATGGCA-GATCCTGTCTTCCTATATTGATAGGAAGTAGATCAAAGAA
44815486 AGCAAATCTT
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
87 6 0.05
88 100 0.81
89 18 0.15
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (88 bp):
GAAGTAGATCGAAGATGGCAGATCCTGTCTTCCTATATTGATAGGAAGTAGATCAAAGAAGAAGA
TCCTTATCTTCACGTATTGGCGT
Found at i:44815441 original size:44 final size:43
Alignment explanation
Indices: 44815101--44815441 Score: 213
Period size: 44 Copynumber: 7.8 Consensus size: 43
44815091 ATAGGTCCTA
* * *
44815101 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCATATATTGG-CGTGAAGTAGATCGAAGATGCAGATCTTG
** * * * * *
44815144 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAGGTAGATCTTG
1 TCTTCATATATTGG-CGTGAAGTAGATCGAAG-ATGCAGATCTTG
* * * * *
44815189 TCTTCATGTATTGGCGTGAAGTAGATTGAAGATAGCAGGTCCTA
1 TCTTCATATATTGGCGTGAAGTAGATCGAAGAT-GCAGATCTTG
* ** *
44815233 TCTTCCTATATTGATAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCATATATTG-GCGTGAAGTAGATCGAAGATGCAGATCTTG
* * * * * * *
44815276 TCTTTC-CATATTGGTGGCGAAGTAGATCAAAGAAAGAAGATCTTA
1 TC-TTCATATATTGG-CGTGAAGTAGATCGAAG-ATGCAGATCTTG
** * * *
44815321 TCTTCACGTATTGGCGTGAAGTAGATCGAAGATGGCTGGTCCTG
1 TCTTCATATATTGGCGTGAAGTAGATCGAAGAT-GCAGATCTTG
* ** * * *
44815365 TCTTCCTATATTGATAG-GAAGTGGATCTAAGATGTAGATCCTTG
1 TCTTCATATATTG-GCGTGAAGTAGATCGAAGATGCAGAT-CTTG
*
44815409 TCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 TCTTCATATATTGGCGTGAAGTAGATCGAAGAT
44815442 AACATGTCCT
Statistics
Matches: 223, Mismatches: 62, Indels: 25
0.72 0.20 0.08
Matches are distributed among these distances:
43 37 0.17
44 145 0.65
45 41 0.18
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
TCTTCATATATTGGCGTGAAGTAGATCGAAGATGCAGATCTTG
Found at i:44815455 original size:44 final size:44
Alignment explanation
Indices: 44815118--44815506 Score: 195
Period size: 44 Copynumber: 8.8 Consensus size: 44
44815108 ATATTGGTAG
* * *** * *
44815118 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTATTGG-CGT
* * *
44815162 GAAGTAGATCGCAGA-AGGTAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGATA-GCAGATCCTGTCTTCATGTATTGGCGT
* * * * * **
44815206 GAAGTAGATTGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-
1 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTATTG-GCGT
* * * *
44815250 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTTCCA--TATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCCTGTC-TT-CATGTATTGG-CGT
* * * * * *
44815294 GAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGT
1 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTATTGGCGT
* * * * * **
44815338 GAAGTAGATCGAAGATGGCTGGTCCTGTCTTCCTATATTGATAG-
1 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTATTG-GCGT
* * *
44815382 GAAGTGGATCTAAGAT-GTAGATCCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGATAGCAGATCC-TGTCTTCATGTATTGGCGT
* * * * *
44815426 GAAGTAGATCGAAGATAACATG-TCCTGTCTCCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCA-GATCCTGTCTTCATGTATTGG-CGT
* * * * *
44815470 GGAGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTA
1 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTA
44815507 CTAGCAGTAG
Statistics
Matches: 255, Mismatches: 72, Indels: 36
0.70 0.20 0.10
Matches are distributed among these distances:
43 23 0.09
44 186 0.73
45 45 0.18
46 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (44 bp):
GAAGTAGATCGAAGATAGCAGATCCTGTCTTCATGTATTGGCGT
Found at i:44815484 original size:132 final size:130
Alignment explanation
Indices: 44815093--44815466 Score: 450
Period size: 132 Copynumber: 2.8 Consensus size: 130
44815083 AGGCGTAAAT
*
44815093 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTT--CATATTGG
* * * * *
44815158 TGGCGAAGTAGATCGCAG-AAGGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGAT
64 TGGCGAAGTAGATCGAAGAAAGAT-GATCTTGTCTCCCTGTATTGGCGTGAAGTAGATCGAAGAT
44815222 AGC
128 AGC
44815225 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTTCCATATTGG
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTC-TT-CATATTGG
* * * *
44815290 TGGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCAC-GTATTGGCGTGAAGTAGATCGAAGAT
64 TGGCGAAGTAGATCGAAGAAAGATGATCTTGTC-TCCCTGTATTGGCGTGAAGTAGATCGAAGAT
*
44815354 GGC
128 AGC
* * * *
44815357 TGGTCCTGTCTTCCTATATTGATAGGAAGTGGATCTAAGATGTAGATCCTTGTCTTCATGTATTG
1 AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGAT-CTTGTCTTCA--TATTG
* * * * *
44815422 G-CGTGAAGTAGATCGAAGATAACATG-TCCTGTCTCCCTATATTGG
63 GTGGCGAAGTAGATCGAAGA-AAGATGATCTTGTCTCCCTGTATTGG
44815467 TAGGGAGTGG
Statistics
Matches: 210, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
131 5 0.02
132 183 0.87
133 22 0.10
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (130 bp):
AGGTCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCATATTGGTG
GCGAAGTAGATCGAAGAAAGATGATCTTGTCTCCCTGTATTGGCGTGAAGTAGATCGAAGATAGC
Found at i:44815497 original size:88 final size:87
Alignment explanation
Indices: 44815283--44815506 Score: 256
Period size: 88 Copynumber: 2.5 Consensus size: 87
44815273 TTGTCTTTCC
* * *
44815283 ATATTGGT-GGCGAAGTAGATCAAAGAAAGAAGATCTTATCTTCACGTATTGGCGTGAAGTAGAT
1 ATATTGGTAGG-G-AGTGGATCAAAGAAAGAA-ATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
** *
44815347 CGAAGATGGCTGGTCCTGTCTTCCT
63 CGAAGATAACTGGTCCTGTCTCCCT
* * * * *
44815372 ATATTGATAGGAAGTGGATCTAAG-ATGTAGATCCTTGTCTTCATGTATTGGCGTGAAGTAGATC
1 ATATTGGTAGGGAGTGGATCAAAGAAAG-AAAT-CTTGTCTTCATGTATTGGCGTGAAGTAGATC
44815436 GAAGATAACAT-GTCCTGTCTCCCT
64 GAAGATAAC-TGGTCCTGTCTCCCT
*
44815460 ATATTGGTAGGGAGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTA
1 ATATTGGTAGGGAGTGGATCAAAGAAAG-AAATCTTGTCTTCATGTA
44815507 CTAGCAGTAG
Statistics
Matches: 113, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
87 4 0.04
88 94 0.83
89 13 0.12
90 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (87 bp):
ATATTGGTAGGGAGTGGATCAAAGAAAGAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
AGATAACTGGTCCTGTCTCCCT
Found at i:44819808 original size:30 final size:30
Alignment explanation
Indices: 44819772--44819829 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
44819762 CGGGTAACCT
*
44819772 TGATATAATGTCAGCTTGTGTGAGCAATCC
1 TGATATAATATCAGCTTGTGTGAGCAATCC
* *
44819802 TGATATACTATTAGCTTGTGTGAGCAAT
1 TGATATAATATCAGCTTGTGTGAGCAAT
44819830 TTATTCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (30 bp):
TGATATAATATCAGCTTGTGTGAGCAATCC
Found at i:44824743 original size:15 final size:15
Alignment explanation
Indices: 44824715--44824755 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
44824705 TTATCCAATC
44824715 AAATAAAG-AAAAAT
1 AAATAAAGCAAAAAT
44824729 AAATAAAGCAAAAAT
1 AAATAAAGCAAAAAT
* *
44824744 GAATAAAACAAA
1 AAATAAAGCAAA
44824756 GAAGCTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (15 bp):
AAATAAAGCAAAAAT
Found at i:44825529 original size:26 final size:26
Alignment explanation
Indices: 44825485--44825559 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
44825475 AAATTAAACC
44825485 TAAACCCAAGTT-ACC-AGCCCAAAAT
1 TAAACCCAA-TTAACCTAGCCCAAAAT
*
44825510 CT-AACCCAATTAACCTAGCCCAAACT
1 -TAAACCCAATTAACCTAGCCCAAAAT
* *
44825536 TAAACCCAACTACATCTAGCCCAA
1 TAAACCCAATTA-ACCTAGCCCAA
44825560 CTATCATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 19 0.45
27 10 0.24
ACGTcount: A:0.41, C:0.36, G:0.05, T:0.17
Consensus pattern (26 bp):
TAAACCCAATTAACCTAGCCCAAAAT
Found at i:44825800 original size:28 final size:26
Alignment explanation
Indices: 44825755--44825806 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
44825745 ACAGAGGACA
* *
44825755 GACAAACAAAAAGAAAAGCAAAAATC
1 GACAAAAAAAAAGAAAAGAAAAAATC
44825781 GACAAAAAATAAAGGAAAAGAAAAAA
1 GACAAAAAA-AAA-GAAAAGAAAAAA
44825807 GAAAAGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 3 0.14
28 11 0.50
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.04
Consensus pattern (26 bp):
GACAAAAAAAAAGAAAAGAAAAAATC
Found at i:44826869 original size:47 final size:47
Alignment explanation
Indices: 44826817--44826912 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
44826807 ACTTAATTTA
* * * * *
44826817 TTCATTAATACATATTTTTGATGGTTTGATATAATTTATATGTATAT
1 TTCATTAATACATAATTTTGAAGATTTGACATAATTTACATGTATAT
44826864 TTCATTAATACATAATTTTGAAGATTTGACATAATTTACATGTATAT
1 TTCATTAATACATAATTTTGAAGATTTGACATAATTTACATGTATAT
44826911 TT
1 TT
44826913 TGATGTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (47 bp):
TTCATTAATACATAATTTTGAAGATTTGACATAATTTACATGTATAT
Found at i:44829412 original size:16 final size:16
Alignment explanation
Indices: 44829393--44829423 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44829383 TTATTTTTAA
44829393 ATAAATCTAATTAAAT
1 ATAAATCTAATTAAAT
44829409 ATAAATCTAATTAAA
1 ATAAATCTAATTAAA
44829424 AGATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATCTAATTAAAT
Found at i:44830878 original size:16 final size:17
Alignment explanation
Indices: 44830857--44830898 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
44830847 TAAAGAACAT
*
44830857 AAACAAGAAGATAAA-C
1 AAACAAGAAGAAAAACC
*
44830873 AAACAAAAAGAAAAACC
1 AAACAAGAAGAAAAACC
44830890 AAACCAAGA
1 AAA-CAAGA
44830899 TCAATAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 4 0.19
18 4 0.19
ACGTcount: A:0.71, C:0.17, G:0.10, T:0.02
Consensus pattern (17 bp):
AAACAAGAAGAAAAACC
Found at i:44832125 original size:126 final size:126
Alignment explanation
Indices: 44831920--44832214 Score: 441
Period size: 126 Copynumber: 2.4 Consensus size: 126
44831910 AGTGTTAATT
* * * * *
44831920 TAAAA-AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCT-CTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
* * * * *
44831983 ACGTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGCAGGATGCTTTGTTAGGAAAAATAC
66 ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
* * *
44832044 TGAAAGAAGCTCTCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
*
44832109 ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAGTAC
66 ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
*
44832170 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGTTCCT
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCT
44832215 GTTTGGCCTG
Statistics
Matches: 152, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
124 4 0.03
125 32 0.21
126 116 0.76
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
Found at i:44832773 original size:14 final size:14
Alignment explanation
Indices: 44832754--44832784 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44832744 TATGGAATAC
44832754 ACATCCCCTACACG
1 ACATCCCCTACACG
*
44832768 ACATCCCCTACCCG
1 ACATCCCCTACACG
44832782 ACA
1 ACA
44832785 CTCTGTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.06, T:0.13
Consensus pattern (14 bp):
ACATCCCCTACACG
Found at i:44835482 original size:34 final size:36
Alignment explanation
Indices: 44835404--44835500 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 36
44835394 ATTTAAAAGA
* *
44835404 ATTTCTATTATATTAAA-AATGTAAAAGTAAATTTCT
1 ATTT-TATTACATTAAATAATATAAAAGTAAATTTCT
44835440 ATTTTATTACATTAAATAATATAAAAG-AAATTT-T
1 ATTTTATTACATTAAATAATATAAAAGTAAATTTCT
*
44835474 ATTTTATTACATCAAATAATATCAAAA
1 ATTTTATTACATTAAATAATAT-AAAA
44835501 TATTCAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
34 22 0.39
35 21 0.38
36 13 0.23
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (36 bp):
ATTTTATTACATTAAATAATATAAAAGTAAATTTCT
Found at i:44835945 original size:18 final size:18
Alignment explanation
Indices: 44835919--44835961 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44835909 GACTAGAAAA
* * *
44835919 AGGAAACATAGAAGGGTT
1 AGGATACATAAAAGGGCT
44835937 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
44835955 AGGATAC
1 AGGATAC
44835962 GCACCTGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:44836596 original size:7 final size:7
Alignment explanation
Indices: 44836586--44836610 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44836576 CATAATACAT
44836586 AATACTA
1 AATACTA
44836593 AATACTA
1 AATACTA
44836600 AATACTA
1 AATACTA
44836607 AATA
1 AATA
44836611 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:44837611 original size:28 final size:29
Alignment explanation
Indices: 44837567--44837629 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
44837557 AAAAATTATT
*
44837567 TAAAAATTATAAGAAATT-TAT-AATAAAA
1 TAAAAATTATAAGAAATTGCATAAAT-AAA
*
44837595 TAAAAATTATTTA-AAATTGCATAAATAAA
1 TAAAAATTA-TAAGAAATTGCATAAATAAA
44837624 TAAAAA
1 TAAAAA
44837630 ATCTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 14 0.47
29 13 0.43
30 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAAAATTATAAGAAATTGCATAAATAAA
Found at i:44837856 original size:22 final size:22
Alignment explanation
Indices: 44837831--44837873 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44837821 TTAAGAGGAA
*
44837831 ATTGAA-AGGAAATTGAGAGAAT
1 ATTGAAGA-GAAATTGAAAGAAT
*
44837853 ATTGGAGAGAAATTGAAAGAA
1 ATTGAAGAGAAATTGAAAGAA
44837874 AGGATTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (22 bp):
ATTGAAGAGAAATTGAAAGAAT
Found at i:44838556 original size:54 final size:52
Alignment explanation
Indices: 44838468--44838578 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 52
44838458 CCTCTGGTTT
44838468 TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATT-TATAA
1 TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATTCT-TAA
* * * *
44838520 TTTTGTTTCAAAATTTTGAA-TTTGATTGATGCATCTTAAAATTCGAATTCTTAA
1 TTTTG-TTCAAAA-TTTAAATTTTG-TTGAGGAATCTTAAAATTCAAATTCTTAA
44838574 TTTTG
1 TTTTG
44838579 ATTTTATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
52 5 0.10
53 11 0.22
54 34 0.67
55 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (52 bp):
TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATTCTTAA
Found at i:44841887 original size:7 final size:7
Alignment explanation
Indices: 44841875--44841899 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44841865 GAACATGTGT
44841875 GTTATGG
1 GTTATGG
44841882 GTTATGG
1 GTTATGG
44841889 GTTATGG
1 GTTATGG
44841896 GTTA
1 GTTA
44841900 ACATTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (7 bp):
GTTATGG
Found at i:44842781 original size:20 final size:20
Alignment explanation
Indices: 44842755--44842793 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44842745 AACACAACTA
*
44842755 AAAAAAAGTAAAAGTAAAAGT
1 AAAAAAA-TAAAAATAAAAGT
44842776 AAAAAAATAAAAATAAAA
1 AAAAAAATAAAAATAAAA
44842794 ATAATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAAAATAAAAATAAAAGT
Found at i:44842799 original size:15 final size:14
Alignment explanation
Indices: 44842735--44842799 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
44842725 GAAGTCTAAG
*
44842735 AAATAAAAATAACAC
1 AAATAAAAATAA-AA
*
44842750 AACTAAAAA-AAAGTA
1 AAATAAAAATAAA--A
*
44842765 AAAGTAAAAGTAAAA
1 AAA-TAAAAATAAAA
44842780 AAATAAAAATAAAA
1 AAATAAAAATAAAA
44842794 ATAATA
1 A-AATA
44842800 TTGAAAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.03
14 13 0.32
15 18 0.45
16 5 0.12
17 3 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:44844450 original size:16 final size:16
Alignment explanation
Indices: 44844385--44844448 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
44844375 GAATAACAAT
*
44844385 AATAAGAATAAGAATAA
1 AATAAAAATAA-AATAA
44844402 ATACTAAAAATAAAATAA
1 A-A-TAAAAATAAAATAA
* *
44844420 AAGAAAGATAAAATAA
1 AATAAAAATAAAATAA
44844436 AATAAGAAATAAA
1 AATAA-AAATAAA
44844449 TAGATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 16 0.41
17 8 0.21
18 7 0.18
19 8 0.21
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:44844456 original size:25 final size:25
Alignment explanation
Indices: 44844385--44844457 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
44844375 GAATAACAAT
*
44844385 AATAAGAATAAG-AATAAATA-CTAAA
1 AATAA-AATAAGAAATAAATAGAT-AA
*
44844410 AATAAAAT-A-AAA-GAA-AGATAA
1 AATAAAATAAGAAATAAATAGATAA
44844431 AATAAAATAAGAAATAAATAGATAA
1 AATAAAATAAGAAATAAATAGATAA
44844456 AA
1 AA
44844458 AGGGTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
21 11 0.28
22 4 0.10
23 6 0.15
24 5 0.13
25 13 0.33
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (25 bp):
AATAAAATAAGAAATAAATAGATAA
Found at i:44846437 original size:50 final size:50
Alignment explanation
Indices: 44846362--44846487 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 50
44846352 CTTTCTTTAC
* * * **
44846362 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* * ** *
44846412 TGCCCATGCCATGTCCTAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
44846462 TGCCAATGCCATGTCCCAGACATGGT
1 TGCCAATGCCATGTCCCAGACATGGT
44846488 GTAACAGCCC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
Done.