Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 156 of 175
Found at i:47060975 original size:30 final size:30
Alignment explanation
Indices: 47060901--47060976 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
47060891 GGTGACAACC
**
47060901 ATCAAATTATGAAAAGAGATAGTTTCGCCT
1 ATCAAATTATGAAAAGAGATAACTTCGCCT
* **
47060931 GTCGAAA-TATGAAAAGAGATAACTTCGGTT
1 ATC-AAATTATGAAAAGAGATAACTTCGCCT
*
47060961 ATCAAATTACGAAAAG
1 ATCAAATTATGAAAAG
47060977 GGATGTGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.08
30 31 0.84
31 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (30 bp):
ATCAAATTATGAAAAGAGATAACTTCGCCT
Found at i:47066435 original size:21 final size:20
Alignment explanation
Indices: 47066411--47066483 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
47066401 ATTTTATCCA
47066411 TTTTTATTTAATTAGT-TTAT
1 TTTTTATTTAATTA-TATTAT
47066431 TTTTTATTCTAATTATATTAT
1 TTTTTATT-TAATTATATTAT
*
47066452 TTTTATTTTTAAGGTT-TATTACT
1 TTTT-TATTTAA--TTATATTA-T
47066475 TTTTTATTT
1 TTTTTATTT
47066484 TTTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 9 0.20
21 17 0.38
22 12 0.27
23 7 0.16
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTATTTAATTATATTAT
Found at i:47066436 original size:20 final size:19
Alignment explanation
Indices: 47066410--47066459 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
47066400 TATTTTATCC
47066410 ATTTTTATTTAATTAGT-TT
1 ATTTTTATTTAATTA-TATT
47066429 ATTTTTTATTCTAATTATATT
1 A-TTTTTATT-TAATTATATT
47066450 ATTTTTATTT
1 ATTTTTATTT
47066460 TTAAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTATTTAATTATATT
Found at i:47068471 original size:33 final size:33
Alignment explanation
Indices: 47068428--47068492 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
47068418 TGTATGTGTG
*
47068428 TGTGTGTTGATTTCTATAACATTTTTCTTTGTA
1 TGTGCGTTGATTTCTATAACATTTTTCTTTGTA
*
47068461 TGTGCGTTGATTTTTATAACATTTTTCTTTGT
1 TGTGCGTTGATTTCTATAACATTTTTCTTTGT
47068493 TAAATATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.09, G:0.15, T:0.58
Consensus pattern (33 bp):
TGTGCGTTGATTTCTATAACATTTTTCTTTGTA
Found at i:47071857 original size:21 final size:21
Alignment explanation
Indices: 47071822--47071881 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
47071812 ATAAACATAT
* *
47071822 AAAAATACAAAAAT-ATTTTCA
1 AAAAATATAAAAATAAATTT-A
*
47071843 AAAAATATAATAATAAATTTA
1 AAAAATATAAAAATAAATTTA
*
47071864 AAAATATATAAAGATAAA
1 AAAA-ATATAAAAATAAA
47071882 AAATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAATATAAAAATAAATTTA
Found at i:47071927 original size:54 final size:50
Alignment explanation
Indices: 47071813--47071933 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 50
47071803 TAAAATTAAA
*
47071813 TAAACATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAA-TT
1 TAAAAATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAATTT
* *
47071862 TAAAAATATATAAAGATA-AAAAATAATTATTGACAAAATAATAATAGATAAATTTT
1 TAAAAATATA-AAA-ATACAAAAAT-ATT-TTCAAAAAAT-ATAATA-ATAAA-TTT
*
47071918 TAAAAATATATAAATA
1 TAAAAATATAAAAATA
47071934 TACGTAAACA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
49 9 0.15
50 9 0.15
51 6 0.10
52 8 0.13
53 6 0.10
54 8 0.13
55 2 0.03
56 12 0.20
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (50 bp):
TAAAAATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAATTT
Found at i:47084748 original size:24 final size:24
Alignment explanation
Indices: 47084712--47084760 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
47084702 CCAGCAAAGA
* *
47084712 CTTCCAACTGATTCGCCTGAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
*
47084736 CTTCCAACAGATTCTCCTAAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
47084760 C
1 C
47084761 CGAGGGAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (24 bp):
CTTCCAACAGATTCGCCTAAGAGG
Found at i:47085418 original size:6 final size:6
Alignment explanation
Indices: 47085407--47085438 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
47085397 TCTACATATG
*
47085407 TACATA TACATA TACATA TATATA TACATA TA
1 TACATA TACATA TACATA TACATA TACATA TA
47085439 TAATTGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (6 bp):
TACATA
Found at i:47085439 original size:12 final size:12
Alignment explanation
Indices: 47085402--47085440 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
47085392 TTGCTTCTAC
*
47085402 ATATGTACATAT
1 ATATATACATAT
*
47085414 ACATATACATAT
1 ATATATACATAT
47085426 ATATATACATAT
1 ATATATACATAT
47085438 ATA
1 ATA
47085441 ATTGGTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (12 bp):
ATATATACATAT
Found at i:47089189 original size:9 final size:9
Alignment explanation
Indices: 47089109--47089336 Score: 54
Period size: 10 Copynumber: 24.0 Consensus size: 9
47089099 TAATCTATTT
47089109 TTATAAAAA
1 TTATAAAAA
*
47089118 CGTATAAAAA
1 -TTATAAAAA
*
47089128 TTCTTAAAAA
1 TT-ATAAAAA
*
47089138 CTTATAAAAG
1 -TTATAAAAA
*
47089148 TCATTAAAAA
1 TTA-TAAAAA
47089158 -TA-AAAAA
1 TTATAAAAA
* * *
47089165 TAATATACAC
1 TTATA-AAAA
47089175 TTATAAAAA
1 TTATAAAAA
*
47089184 TTATAATAA
1 TTATAAAAA
*
47089193 -TATAATAA
1 TTATAAAAA
*
47089201 TATGTAAAAA
1 T-TATAAAAA
* *
47089211 ATAT-AAAT
1 TTATAAAAA
**
47089219 TTAATGAAATGT
1 TT-AT-AAA-AA
* *
47089231 TTTTAAAATT
1 TTATAAAA-A
47089241 TTATAAAAA
1 TTATAAAAA
47089250 CTTATAAAAAA
1 -TTAT-AAAAA
** *
47089261 TTCCCAAAAT
1 TT-ATAAAAA
47089271 TTATAAATAA
1 TTATAAA-AA
47089281 -TATAAAAAA
1 TTAT-AAAAA
* *
47089290 TTCTAATAAG
1 TTATAA-AAA
47089300 TTATATAGAAA
1 TTATA-A-AAA
47089311 TTATAAAAA
1 TTATAAAAA
47089320 TT-TAAAAA
1 TTATAAAAA
*
47089328 TTTTAAAAA
1 TTATAAAAA
47089337 ATAATCATTT
Statistics
Matches: 159, Mismatches: 37, Indels: 45
0.66 0.15 0.19
Matches are distributed among these distances:
7 5 0.03
8 21 0.13
9 40 0.25
10 72 0.45
11 18 0.11
12 3 0.02
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:47089288 original size:29 final size:30
Alignment explanation
Indices: 47089235--47089292 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
47089225 AAATGTTTTT
47089235 AAAATTTTATAAAAACTTATAAAAAATTCCC
1 AAAATTTTATAAAAAC-TATAAAAAATTCCC
47089266 AAAA-TTTATAAATAA-TATAAAAAATTC
1 AAAATTTTATAAA-AACTATAAAAAATTC
47089293 TAATAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAATTTTATAAAAACTATAAAAAATTCCC
Found at i:47089459 original size:14 final size:15
Alignment explanation
Indices: 47089440--47089475 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
47089430 GTTCCTCTCT
47089440 TTTTTATTTAT-AAA
1 TTTTTATTTATAAAA
*
47089454 TTTTTATTTTTAAAA
1 TTTTTATTTATAAAA
47089469 TTTTTAT
1 TTTTTAT
47089476 CTCCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATTTATAAAA
Found at i:47089891 original size:10 final size:10
Alignment explanation
Indices: 47089876--47090066 Score: 58
Period size: 10 Copynumber: 19.4 Consensus size: 10
47089866 CCAGTTGAAG
*
47089876 TTTTTATGAT
1 TTTTTATAAT
47089886 TTTTTATAAT
1 TTTTTATAAT
*
47089896 TTTTTA-AAG
1 TTTTTATAAT
* *
47089905 TTTATATTATT
1 TTTTTA-TAAT
*
47089916 TTTTTATGAT
1 TTTTTATAAT
* *
47089926 TTTTTAAGAAA
1 TTTTT-ATAAT
*
47089937 CTTTTAT-AT
1 TTTTTATAAT
*
47089946 GTTTTTATAAA
1 -TTTTTATAAT
* *
47089957 ATTTTAAACAT
1 TTTTTATA-AT
*
47089968 GTTTTATTAA-
1 TTTTTA-TAAT
47089978 -TTTTATAAT
1 TTTTTATAAT
* *
47089987 TTATTAGAAT
1 TTTTTATAAT
** *
47089997 TTACTA-GA-
1 TTTTTATAAT
47090005 TTTTTAT-A-
1 TTTTTATAAT
47090013 TTTTTATAA-
1 TTTTTATAAT
** *
47090022 CATTTATAAG
1 TTTTTATAAT
*
47090032 TTTTTATTAT
1 TTTTTATAAT
47090042 TTTTTATAAAT
1 TTTTTAT-AAT
* *
47090053 TTTATATCAT
1 TTTTTATAAT
47090063 TTTT
1 TTTT
47090067 AATATCTTTA
Statistics
Matches: 131, Mismatches: 37, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
8 15 0.11
9 22 0.17
10 65 0.50
11 28 0.21
12 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:47089916 original size:29 final size:30
Alignment explanation
Indices: 47089873--47089932 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
47089863 GGTCCAGTTG
*
47089873 AAGTTTTTATGA-TTTTTTATAATTTTTTA
1 AAGTTTATATGATTTTTTTATAATTTTTTA
* *
47089902 AAGTTTATATTATTTTTTTATGATTTTTTA
1 AAGTTTATATGATTTTTTTATAATTTTTTA
47089932 A
1 A
47089933 GAAACTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (30 bp):
AAGTTTATATGATTTTTTTATAATTTTTTA
Found at i:47090017 original size:9 final size:9
Alignment explanation
Indices: 47089969--47090058 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
47089959 TTTAAACATG
47089969 TTTTATTAA-
1 TTTTA-TAAT
47089978 TTTTATAAT
1 TTTTATAAT
*
47089987 TTATTAGAA-
1 TT-TTATAAT
47089996 -TTTACTAGAT
1 TTTTA-TA-AT
47090006 TTTTAT-AT
1 TTTTATAAT
*
47090014 TTTTATAAC
1 TTTTATAAT
*
47090023 ATTTATAAGT
1 TTTTATAA-T
*
47090033 TTTTATTATT
1 TTTTA-TAAT
*
47090043 TTTTATAAA
1 TTTTATAAT
47090052 TTTTATA
1 TTTTATA
47090059 TCATTTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.05
8 13 0.21
9 25 0.40
10 16 0.25
11 6 0.10
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:47090026 original size:19 final size:19
Alignment explanation
Indices: 47090004--47090067 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
47089994 AATTTACTAG
47090004 ATTTTTATATTTTTATAAC
1 ATTTTTATATTTTTATAAC
* *
47090023 ATTTATA-AGTTTTTATTA-
1 ATTTTTATA-TTTTTATAAC
* * *
47090041 TTTTTTATAAATTTTATATC
1 ATTTTTAT-ATTTTTATAAC
47090061 ATTTTTA
1 ATTTTTA
47090068 ATATCTTTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTTTATAAC
Found at i:47090709 original size:15 final size:16
Alignment explanation
Indices: 47090674--47090708 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47090664 GACATAATTT
47090674 AAAATGAATATTATAA
1 AAAATGAATATTATAA
* *
47090690 AAAATGTATATTACAA
1 AAAATGAATATTATAA
47090706 AAA
1 AAA
47090709 TCTTGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATGAATATTATAA
Found at i:47093178 original size:19 final size:21
Alignment explanation
Indices: 47093154--47093197 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
47093144 CATCGTTTTT
* *
47093154 AGAAGC-C-TGAAGGCTGAAC
1 AGAAGCTCATGAAAGCTAAAC
47093173 AGAAGCTCATGAAAGCTAAAC
1 AGAAGCTCATGAAAGCTAAAC
47093194 AGAA
1 AGAA
47093198 ACCCATAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.11
Consensus pattern (21 bp):
AGAAGCTCATGAAAGCTAAAC
Found at i:47093237 original size:42 final size:42
Alignment explanation
Indices: 47093170--47093305 Score: 134
Period size: 42 Copynumber: 3.2 Consensus size: 42
47093160 CTGAAGGCTG
* * *
47093170 AACAGAAGCTCATGAA-AGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCA-AAAGAGCTGAACAGAAACCCATAAGGGTTA
**
47093212 AAC-GAAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAG-AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* * * *
47093254 AACAGAAGCTCAAAAGGGCTGAACGGAAACTCATATA-AGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATA-AGGGTTA
*
47093296 AATAGAAGCT
1 AACAGAAGCT
47093306 AGTGAGAGCT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 3 0.04
42 74 0.94
43 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:47093248 original size:21 final size:21
Alignment explanation
Indices: 47093166--47093248 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
47093156 AAGCCTGAAG
* *
47093166 GCTGAACAGAAGCTCATGAA-A
1 GCTGAACAGAAACCCAT-AAGA
* *
47093187 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAACCCATAAGA
* * *
47093208 GTTGAAC-GAAAGCTCGTAAGA
1 GCTGAACAGAAA-CCCATAAGA
47093229 GCTGAACAGAAACCCATAAG
1 GCTGAACAGAAACCCATAAG
47093249 GGTTAAACAG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
20 6 0.13
21 37 0.79
22 4 0.09
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (21 bp):
GCTGAACAGAAACCCATAAGA
Found at i:47093257 original size:21 final size:21
Alignment explanation
Indices: 47093189--47093260 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
47093179 TCATGAAAGC
47093189 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * *
47093210 TGAAC-GAAAGCTCGTAAGAGC
1 TAAACAGAAA-CCCATAAGGGT
*
47093231 TGAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
47093252 TAAACAGAA
1 TAAACAGAA
47093261 GCTCAAAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 4 0.10
21 31 0.79
22 4 0.10
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:47093286 original size:21 final size:21
Alignment explanation
Indices: 47093165--47093286 Score: 70
Period size: 21 Copynumber: 5.8 Consensus size: 21
47093155 GAAGCCTGAA
*
47093165 GGCTGAACAGAAGCTCATGAAA-
1 GGCTGAACAGAAACTCA--AAAG
* * *
47093187 -GCTAAACAGAAACCCATAAG
1 GGCTGAACAGAAACTCAAAAG
* **
47093207 GGTTGAAC-GAAAGCTCGTAAG
1 GGCTGAACAGAAA-CTCAAAAG
* * *
47093228 AGCTGAACAGAAACCCATAAG
1 GGCTGAACAGAAACTCAAAAG
* * *
47093249 GGTTAAACAGAAGCTCAAAAG
1 GGCTGAACAGAAACTCAAAAG
*
47093270 GGCTGAACGGAAACTCA
1 GGCTGAACAGAAACTCA
47093287 TATAAGTTAA
Statistics
Matches: 74, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
19 2 0.03
20 4 0.05
21 64 0.86
22 4 0.05
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.13
Consensus pattern (21 bp):
GGCTGAACAGAAACTCAAAAG
Found at i:47102376 original size:24 final size:23
Alignment explanation
Indices: 47102335--47102390 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
47102325 CTTGTTTAAG
* *
47102335 TTTATCTATTTATTTTTAT-TTTT
1 TTTAT-TAGTTATTTTTATATATT
47102358 ATTTATTAGTTATTATTTATATATT
1 -TTTATTAGTTATT-TTTATATATT
47102383 TTTATTAG
1 TTTATTAG
47102391 AATTATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTATTAGTTATTTTTATATATT
Found at i:47104001 original size:19 final size:20
Alignment explanation
Indices: 47103974--47104011 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
47103964 TTGTGATAAT
*
47103974 TATATTTTA-ATAGTTAAAA
1 TATAATTTATATAGTTAAAA
*
47103993 TATAATTTATATATTTAAA
1 TATAATTTATATAGTTAAA
47104012 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAATTTATATAGTTAAAA
Found at i:47104015 original size:25 final size:25
Alignment explanation
Indices: 47103969--47104017 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
47103959 TGAATTTGTG
47103969 ATAATTATATTTTAATAGTTAAAAT
1 ATAATTATATTTTAATAGTTAAAAT
47103994 ATAATTTATATATTTAA-A-TTAAAA
1 ATAA-TTATAT-TTTAATAGTTAAAA
47104018 ATTTACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAATTATATTTTAATAGTTAAAAT
Found at i:47104570 original size:19 final size:18
Alignment explanation
Indices: 47104548--47104601 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
47104538 ATTTTATGTT
47104548 ATTTTTTAAATTTTTATGA
1 ATTTTTTAAATTTTTAT-A
47104567 ATTTTTTATATATTTTT-TA
1 ATTTTTTA-A-ATTTTTATA
*
47104586 A-TTTTTAAATATTTAT
1 ATTTTTTAAATTTTTAT
47104602 TAACATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 6 0.19
19 10 0.32
20 2 0.06
21 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTTAAATTTTTATA
Found at i:47104590 original size:18 final size:18
Alignment explanation
Indices: 47104550--47104604 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
47104540 TTTATGTTAT
* *
47104550 TTTTTAAATTTTTATGAA
1 TTTTTAAATATTTATTAA
* *
47104568 TTTTTTATATATTTTTTAA
1 -TTTTTAAATATTTATTAA
47104587 TTTTTAAATATTTATTAA
1 TTTTTAAATATTTATTAA
47104605 CATTACATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTAAATATTTATTAA
Found at i:47109798 original size:24 final size:24
Alignment explanation
Indices: 47109770--47109821 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47109760 TTCGTAGGCC
* *
47109770 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
47109794 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
47109818 AAAT
1 AAAT
47109822 GTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:47110976 original size:16 final size:15
Alignment explanation
Indices: 47110934--47110968 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
47110924 GCCCATTAAA
47110934 CAAATAAATAAAACC
1 CAAATAAATAAAACC
*
47110949 TAAATAAATAAAACC
1 CAAATAAATAAAACC
47110964 CAAAT
1 CAAAT
47110969 CCAATAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAATAAATAAAACC
Found at i:47112041 original size:9 final size:9
Alignment explanation
Indices: 47112027--47112059 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
47112017 CCTAAAGTTA
47112027 ATATTATTT
1 ATATTATTT
47112036 ATATTATTT
1 ATATTATTT
47112045 ATA-TATTT
1 ATATTATTT
47112053 AT-TTATT
1 ATATTATT
47112060 ATTCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.48
9 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATATTATTT
Found at i:47112061 original size:15 final size:15
Alignment explanation
Indices: 47112028--47112074 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
47112018 CTAAAGTTAA
47112028 TATTATTTATATTATT
1 TATTATTTAT-TTATT
47112044 TATATATTTATTTA-T
1 TAT-TATTTATTTATT
*
47112059 TATTCTTTATTT-TT
1 TATTATTTATTTATT
47112073 TA
1 TA
47112075 AATGCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 11 0.39
15 4 0.14
16 6 0.21
17 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTATTTATT
Found at i:47112173 original size:4 final size:4
Alignment explanation
Indices: 47112164--47112221 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
47112154 ATATGCTTGT
* * *
47112164 TTTA TTTA TTTA CTTA TTTA TTTA TTTA TTCA TTCA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
47112212 -TTA TTT- TTTA
1 TTTA TTTA TTTA
47112222 AAATATTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 6 0.12
4 42 0.88
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:47114610 original size:20 final size:20
Alignment explanation
Indices: 47114585--47114624 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47114575 CGTAAAATGA
*
47114585 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
47114605 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
47114625 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:47114614 original size:34 final size:35
Alignment explanation
Indices: 47114570--47114636 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
47114560 CAGTAAAATA
*
47114570 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
47114604 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
47114637 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:47114640 original size:14 final size:15
Alignment explanation
Indices: 47114564--47114640 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
47114554 GATTGCCAGT
* *
47114564 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
47114578 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
47114592 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
47114612 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
47114627 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
47114641 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:47115572 original size:29 final size:30
Alignment explanation
Indices: 47115540--47115596 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
47115530 ATTGTAAAGA
*
47115540 TTAATAGA-AAATATTATT-AATAATATTTG
1 TTAATA-ACAAATATTATTGAAAAATATTTG
47115569 TTAATAACAAATATTATTGAAAAATATT
1 TTAATAACAAATATTATTGAAAAATATT
47115597 AAAATGCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
TTAATAACAAATATTATTGAAAAATATTTG
Found at i:47127620 original size:16 final size:16
Alignment explanation
Indices: 47127601--47127638 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
47127591 AAAATTTTCA
*
47127601 AAATTTAAAATAATTT
1 AAATTTAAAATAACTT
*
47127617 AAATTCAAAATAACTT
1 AAATTTAAAATAACTT
47127633 AAATTT
1 AAATTT
47127639 CAACCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAAAATAACTT
Found at i:47131501 original size:3 final size:3
Alignment explanation
Indices: 47131493--47131530 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
47131483 TTACTTCCTA
*
47131493 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47131531 AAATTTATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47133919 original size:3 final size:3
Alignment explanation
Indices: 47133911--47133945 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
47133901 TTTGAGACAC
*
47133911 TCT TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
47133946 AACATGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:47134052 original size:2 final size:2
Alignment explanation
Indices: 47134047--47134072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47134037 TCTTTTTTTT
47134047 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
47134073 AAGCCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47137298 original size:20 final size:20
Alignment explanation
Indices: 47137273--47137337 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
47137263 ACATGGGCTA
47137273 TATTAATAAAATTGCACATT
1 TATTAATAAAATTGCACATT
* * **
47137293 TATTAA-GAAAGTGTTC-TT
1 TATTAATAAAATTGCACATT
47137311 ATATTAATAAAATTGCACATT
1 -TATTAATAAAATTGCACATT
47137332 TATTAA
1 TATTAA
47137338 GAAAGTGTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.35
20 18 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
TATTAATAAAATTGCACATT
Found at i:47137314 original size:39 final size:39
Alignment explanation
Indices: 47137271--47137359 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
47137261 CAACATGGGC
47137271 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
1 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
47137310 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
1 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
*
47137349 TAT-TTAGTAAA
1 TATATTAATAAA
47137360 TTTTTAGTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 7 0.14
39 42 0.86
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (39 bp):
TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
Found at i:47137317 original size:19 final size:19
Alignment explanation
Indices: 47137293--47137351 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
47137283 ATTGCACATT
47137293 TATTAAGAAAGTGTTCTTA
1 TATTAAGAAAGTGTTCTTA
* * **
47137312 TATTAATAAAATTGCACATT-
1 TATTAA-GAAAGTGTTC-TTA
47137332 TATTAAGAAAGTGTTCTTA
1 TATTAAGAAAGTGTTCTTA
47137351 T
1 T
47137352 TTAGTAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 12 0.41
21 2 0.07
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (19 bp):
TATTAAGAAAGTGTTCTTA
Found at i:47143895 original size:161 final size:161
Alignment explanation
Indices: 47143708--47144035 Score: 647
Period size: 161 Copynumber: 2.0 Consensus size: 161
47143698 CTCTCTTGAT
47143708 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
1 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
*
47143773 CTACTGAATGTTTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
66 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
47143838 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
131 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
47143869 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
1 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
47143934 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
66 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
47143999 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
131 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
47144030 TTATGG
1 TTATGG
47144036 TCGCATGAGT
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 166 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (161 bp):
TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
GGGAGTGTTACTTTTTGTTGTTCACTGATGA
Found at i:47147510 original size:6 final size:6
Alignment explanation
Indices: 47147478--47147527 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
47147468 ACAGCACCTA
* *
47147478 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
47147527 A
1 A
47147528 TTCAACACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:47147848 original size:40 final size:40
Alignment explanation
Indices: 47147802--47147888 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
47147792 AATTCATTAC
* *
47147802 TTCAGTAA-TCTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACT-TCACAATTCAATGCAGTACACAAAACAATA
* *
47147842 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
47147882 TTCAGTA
1 TTCAGTA
47147889 TTCCATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:47149430 original size:11 final size:11
Alignment explanation
Indices: 47149414--47149438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47149404 ACTCAAGGTC
47149414 GAAGTATCCCT
1 GAAGTATCCCT
47149425 GAAGTATCCCT
1 GAAGTATCCCT
47149436 GAA
1 GAA
47149439 CTCTTCCAAT
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (11 bp):
GAAGTATCCCT
Found at i:47150554 original size:13 final size:13
Alignment explanation
Indices: 47150532--47150637 Score: 52
Period size: 13 Copynumber: 7.7 Consensus size: 13
47150522 CAAATTTTCC
*
47150532 TCTTTTTTTTCTT
1 TCTTTCTTTTCTT
*
47150545 TCTTTCTTTTTCCT
1 TCTTTC-TTTTCTT
* *
47150559 TCTTTCCTTTCTC
1 TCTTTCTTTTCTT
* *
47150572 TGTTTCGTTCTACTT
1 TCTTTC-TT-TTCTT
47150587 CTCTGTTCTTTTTCTT
1 -TCT-TTC-TTTTCTT
* *
47150603 TCTTT-ATTTCAT
1 TCTTTCTTTTCTT
* *
47150615 TGTTTCTTTTATT
1 TCTTTCTTTTCTT
47150628 TCTTTACTTT
1 TCTTT-CTTT
47150638 ATATTATAAT
Statistics
Matches: 67, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
12 9 0.13
13 22 0.33
14 19 0.28
15 6 0.09
16 6 0.09
17 5 0.07
ACGTcount: A:0.05, C:0.22, G:0.04, T:0.70
Consensus pattern (13 bp):
TCTTTCTTTTCTT
Found at i:47150824 original size:18 final size:19
Alignment explanation
Indices: 47150803--47150838 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
47150793 ATTATTTATC
47150803 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
47150821 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
47150839 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:47154182 original size:10 final size:10
Alignment explanation
Indices: 47154164--47154241 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
47154154 CCAAATTTTC
47154164 CTTTTTCTTT
1 CTTTTTCTTT
47154174 -TTCTTTCTTT
1 CTT-TTTCTTT
*
47154184 CTTTTTCCTT
1 CTTTTTCTTT
*
47154194 C-TTTCCTTT
1 CTTTTTCTTT
*
47154203 CTCTGTTTCGTT
1 CT-T-TTTCTTT
*
47154215 CTACTTCTCTGTT
1 CT--TTTTCT-TT
47154228 CTTTTTCTTT
1 CTTTTTCTTT
47154238 CTTT
1 CTTT
47154242 ATTTCATTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
9 9 0.17
10 20 0.38
11 8 0.15
12 10 0.19
13 6 0.11
ACGTcount: A:0.01, C:0.26, G:0.04, T:0.69
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:47154188 original size:13 final size:14
Alignment explanation
Indices: 47154167--47154241 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
47154157 AATTTTCCTT
47154167 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
*
47154181 TTTCTTTTTCCTTC
1 TTTCTTTTTCTTTC
* * *
47154195 TTTC-CTTTCTCTG
1 TTTCTTTTTCTTTC
* *
47154208 TTTCGTTCTACTTCTC
1 TTTC-TTTTTCTT-TC
47154224 TGTTCTTTTTCTTTC
1 T-TTCTTTTTCTTTC
47154239 TTT
1 TTT
47154242 ATTTCATTGT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
13 9 0.20
14 19 0.42
15 6 0.13
16 8 0.18
17 3 0.07
ACGTcount: A:0.01, C:0.25, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:47154211 original size:27 final size:27
Alignment explanation
Indices: 47154159--47154211 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
47154149 GACAACCAAA
* *
47154159 TTTTCCTTTTTCTTTTTCTTTCTTTCT
1 TTTTCCTTTTTCTCTTTCTCTCTTTCT
*
47154186 TTTTCCTTCTTTC-CTTTCTCTGTTTC
1 TTTTCCTT-TTTCTCTTTCTCTCTTTC
47154212 GTTCTACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTCCTTTTTCTCTTTCTCTCTTTCT
Found at i:47154455 original size:18 final size:19
Alignment explanation
Indices: 47154432--47154467 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
47154422 ATTATCTATC
47154432 TAATAAATATCT-TTTAAA
1 TAATAAATATCTGTTTAAA
47154450 TAATAAATATCTGTTTAA
1 TAATAAATATCTGTTTAA
47154468 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTGTTTAAA
Found at i:47155352 original size:17 final size:17
Alignment explanation
Indices: 47155330--47155364 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47155320 TTCGAATAGC
* *
47155330 TGTTTCTTTTCTTCTTT
1 TGTTTCATTTATTCTTT
47155347 TGTTTCATTTATTCTTT
1 TGTTTCATTTATTCTTT
47155364 T
1 T
47155365 ATTTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCATTTATTCTTT
Found at i:47158578 original size:30 final size:30
Alignment explanation
Indices: 47158542--47158601 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
47158532 CAATATGATC
47158542 CTATTTTATCTCATGGTAACCATTAAATCT
1 CTATTTTATCTCATGGTAACCATTAAATCT
47158572 CTATTTTATCTCATGGTAACCATTAAATCT
1 CTATTTTATCTCATGGTAACCATTAAATCT
47158602 TTCTTCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
CTATTTTATCTCATGGTAACCATTAAATCT
Found at i:47161121 original size:18 final size:18
Alignment explanation
Indices: 47161100--47161150 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
47161090 CTATTTTTGT
*
47161100 TATGATTTTCTGTTGAGA
1 TATGATTTTCTATTGAGA
*
47161118 TATGATTTCCTATTGAGA
1 TATGATTTTCTATTGAGA
47161136 TATGATTTTCTATTG
1 TATGATTTTCTATTG
47161151 GGATTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.51
Consensus pattern (18 bp):
TATGATTTTCTATTGAGA
Found at i:47165429 original size:18 final size:18
Alignment explanation
Indices: 47165408--47165462 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
47165398 CTATTTTTGT
47165408 TATGATTTTCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
47165426 TATGATTTCCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
47165444 TATGATTTTCTATTGAGA
1 TATGATTTTCTGTTGAGA
47165462 T
1 T
47165463 TTGTTGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTGTTGAGA
Found at i:47165818 original size:17 final size:17
Alignment explanation
Indices: 47165780--47165828 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
47165770 TTAGCTATAA
47165780 ATATTTTTAT-AT-TTT
1 ATATTTTTATAATATTT
47165795 ATATTTTATATAA-ATTT
1 ATATTTT-TATAATATTT
*
47165812 ATTTTTTTATAATATTT
1 ATATTTTTATAATATTT
47165829 TAATTAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTTTTATAATATTT
Found at i:47165830 original size:18 final size:19
Alignment explanation
Indices: 47165788--47165830 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
47165778 AAATATTTTT
47165788 ATATTTTATATTTTATATA
1 ATATTTTATATTTTATATA
*
47165807 A-A-TTTAT-TTTTTTATA
1 ATATTTTATATTTTATATA
47165823 ATATTTTA
1 ATATTTTA
47165831 ATTAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 5 0.24
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTTATATTTTATATA
Found at i:47171211 original size:92 final size:92
Alignment explanation
Indices: 47171054--47171237 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
47171044 TTAATTCAGG
47171054 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
47171119 ACCGGAATGGGTCATTTTCCCCGAAAT
66 ACCGGAATGGGTCATTTTCCCCGAAAT
47171146 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
47171211 ACCGGAATGGGTCATTTTCCCCGAAAT
66 ACCGGAATGGGTCATTTTCCCCGAAAT
47171238 CACGTCCACG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (92 bp):
ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
ACCGGAATGGGTCATTTTCCCCGAAAT
Found at i:47177517 original size:25 final size:25
Alignment explanation
Indices: 47177473--47177563 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
47177463 CTCTTTTATG
*
47177473 AGCTTCCCGATAT-TGGCTCACATA
1 AGCTTCCCGTTATATGGCTCACATA
** *
47177497 ATTTTCCCGTTATATGGCTCACATG
1 AGCTTCCCGTTATATGGCTCACATA
*
47177522 AGCTTCTCGTTATATGGCTCGA-A-A
1 AGCTTCCCGTTATATGGCTC-ACATA
47177546 GAGCTTCCCGTTTATATG
1 -AGCTTCCCG-TTATATG
47177564 CTTGTATGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 10 0.19
25 36 0.67
26 8 0.15
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCACATA
Found at i:47177574 original size:25 final size:25
Alignment explanation
Indices: 47177470--47177581 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
47177460 AGGCTCTTTT
*
47177470 ATGAGCTTCCCGATAT-TGGCTC-A
1 ATGAGCTTCCCGTTATATGGCTCGA
* **
47177493 CATAATTTTCCCGTTATATGGCTC-A
1 -ATGAGCTTCCCGTTATATGGCTCGA
*
47177518 CATGAGCTTCTCGTTATATGGCTCGA
1 -ATGAGCTTCCCGTTATATGGCTCGA
* * *
47177544 AAGAGCTTCCCGTTTATAT-GCTTGT
1 ATGAGCTTCCCG-TTATATGGCTCGA
47177569 ATGAGCATTCCCG
1 ATGAGC-TTCCCG
47177582 AATATGAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
24 12 0.17
25 46 0.65
26 13 0.18
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCGA
Found at i:47178252 original size:14 final size:15
Alignment explanation
Indices: 47178220--47178252 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47178210 TATGATAATG
*
47178220 TATGATTTGAGATAA
1 TATGATTGGAGATAA
47178235 TATGATTGGAGA-AA
1 TATGATTGGAGATAA
47178249 TATG
1 TATG
47178253 CATATAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (15 bp):
TATGATTGGAGATAA
Found at i:47184906 original size:13 final size:13
Alignment explanation
Indices: 47184888--47184912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47184878 GTGAATATTT
47184888 CTGTGATTTTGAC
1 CTGTGATTTTGAC
47184901 CTGTGATTTTGA
1 CTGTGATTTTGA
47184913 GTATATTCAT
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:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
CTGTGATTTTGAC
Found at i:47189751 original size:25 final size:23
Alignment explanation
Indices: 47189721--47189772 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
47189711 GAAATTATTG
47189721 ATTTAATCTACTTAAATAAAATTAA
1 ATTTAATCTA-TTAAAT-AAATTAA
* *
47189746 ATTTAATCTATTATATAAATTGA
1 ATTTAATCTATTAAATAAATTAA
47189769 ATTT
1 ATTT
47189773 CGGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAATCTATTAAATAAATTAA
Found at i:47209436 original size:17 final size:19
Alignment explanation
Indices: 47209409--47209444 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
47209399 CAATTTAAAG
47209409 TTAAGAATTCCA-AACAAT
1 TTAAGAATTCCATAACAAT
47209427 TTAA-AATTCCATAACAAT
1 TTAAGAATTCCATAACAAT
47209445 CTGAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (19 bp):
TTAAGAATTCCATAACAAT
Found at i:47209778 original size:147 final size:147
Alignment explanation
Indices: 47209484--47209768 Score: 326
Period size: 147 Copynumber: 1.9 Consensus size: 147
47209474 AATTTGTACA
* * **
47209484 TATTATAATTTACCATAAAGTCAGTTACACATTTAAGGTTTAAGGTTATGTATCATTAATATAAA
1 TATTATAATTTACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATAT-AA
* ** * *
47209549 AAAATGTACATTATAATGTCATAATTGTAGATAAGGTGACATATAATTAATAATCTATCTTAACT
65 AAAATATACATTATAATAACATAATTGTA-ATAAGGTGACATATAATTAATAATCTACCTAAACT
47209614 ATATAATGGTAACTGTATG
129 ATATAATGGTAACTGTATG
* * ** *
47209633 TATTATAATTTGA-CATAAAGTTAATTGCATGTTTAGGGTTTAAGCTTACATATCATTAATAT-A
1 TATTATAATTT-ACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATATAA
* * *
47209696 AAAATATACATTATAATAACATAGTTGT-AT-AGAGTGATACATATCATTAATTATCTACCTAAA
65 AAAATATACATTATAATAACATAATTGTAATAAG-GTG--ACATATAATTAATAATCTACCTAAA
*
47209759 TTATATAATG
127 CTATATAATG
47209769 TCAATTGTAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
144 2 0.02
145 5 0.04
147 55 0.48
149 51 0.45
150 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (147 bp):
TATTATAATTTACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATATAAA
AAATATACATTATAATAACATAATTGTAATAAGGTGACATATAATTAATAATCTACCTAAACTAT
ATAATGGTAACTGTATG
Found at i:47215197 original size:15 final size:16
Alignment explanation
Indices: 47215177--47215210 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
47215167 AATTATTGTT
47215177 TAAATAAATTTTTA-A
1 TAAATAAATTTTTACA
*
47215192 TAAATATATTTTTACA
1 TAAATAAATTTTTACA
47215208 TAA
1 TAA
47215211 TTTTTTCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAAATTTTTACA
Found at i:47220898 original size:16 final size:17
Alignment explanation
Indices: 47220877--47220909 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47220867 ATCAATCTAA
47220877 TATTTAT-TTAAAATAT
1 TATTTATATTAAAATAT
*
47220893 TATTTATATTAACATAT
1 TATTTATATTAAAATAT
47220910 ATGAAAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATATTAAAATAT
Found at i:47221786 original size:14 final size:14
Alignment explanation
Indices: 47221764--47221793 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47221754 TCTCTACCGA
*
47221764 AAAATTTTGTACCC
1 AAAACTTTGTACCC
47221778 AAAACTTTGTACCC
1 AAAACTTTGTACCC
47221792 AA
1 AA
47221794 CGGTTGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAACTTTGTACCC
Found at i:47238986 original size:16 final size:17
Alignment explanation
Indices: 47238965--47238999 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47238955 TAAATTTTAA
47238965 ATTTTTTTA-AAATAAT
1 ATTTTTTTAGAAATAAT
*
47238981 ATTTTTTTAGAATTAAT
1 ATTTTTTTAGAAATAAT
47238998 AT
1 AT
47239000 CTACTCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTTTTAGAAATAAT
Found at i:47238997 original size:17 final size:16
Alignment explanation
Indices: 47238961--47238999 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
47238951 ATACTAAATT
47238961 TTAA-ATTTTTTTAAA
1 TTAATATTTTTTTAAA
*
47238976 ATAATATTTTTTTAGAA
1 TTAATATTTTTTTA-AA
47238993 TTAATAT
1 TTAATAT
47239000 CTACTCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAATATTTTTTTAAA
Found at i:47242380 original size:32 final size:32
Alignment explanation
Indices: 47242320--47242380 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
47242310 TGTATAATTA
47242320 TATTAAATTATTTAAATATTATCTAAAATATT
1 TATTAAATTATTTAAATATTATCTAAAATATT
*
47242352 TATTTAATT-TTT-AATATTATGTCTAAAAT
1 TATTAAATTATTTAAATATTA--TCTAAAAT
47242381 GAACATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 3 0.12
32 16 0.62
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (32 bp):
TATTAAATTATTTAAATATTATCTAAAATATT
Found at i:47248565 original size:18 final size:18
Alignment explanation
Indices: 47248539--47248581 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
47248529 AAAAGCTGTT
*
47248539 TTTACATATATCAATAAA
1 TTTATATATATCAATAAA
*
47248557 TTTATATATATTAATAAA
1 TTTATATATATCAATAAA
47248575 TTTATAT
1 TTTATAT
47248582 TTTAAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATCAATAAA
Found at i:47249846 original size:32 final size:32
Alignment explanation
Indices: 47249805--47249865 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
47249795 TGTCAGTCAT
47249805 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
47249837 TTCAATATCCAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
47249866 CAATATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:47249872 original size:27 final size:30
Alignment explanation
Indices: 47249805--47249878 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
47249795 TGTCAGTCAT
47249805 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
47249837 TTCAATATCCAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
47249865 -TCAATATCTAACAA
1 TTCAATATCCAACAA
47249879 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 13 0.32
28 2 0.05
29 2 0.05
32 24 0.59
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:47253360 original size:17 final size:17
Alignment explanation
Indices: 47253338--47253390 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
47253328 TCTTCAACAG
47253338 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
47253355 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
*
47253368 ACATATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
47253385 ACAGAT
1 ACAGAT
47253391 TCTTCAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.29
15 6 0.21
17 14 0.50
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:47253376 original size:30 final size:30
Alignment explanation
Indices: 47253333--47253391 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47253323 AAGATTCTTC
*
47253333 AACAGACAGATGCAAAATCCAAACAGATTA
1 AACAAACAGATGCAAAATCCAAACAGATTA
*
47253363 AACAAACATATGCAAAATCCAAACAGATT
1 AACAAACAGATGCAAAATCCAAACAGATT
47253392 CTTCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.15
Consensus pattern (30 bp):
AACAAACAGATGCAAAATCCAAACAGATTA
Found at i:47259207 original size:31 final size:32
Alignment explanation
Indices: 47259135--47259211 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
47259125 ACTGAGCTCT
* * * * * *
47259135 CAAAAATTTTGAAAAATTTTCATTAGGCTCTT
1 CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
47259167 CAAAATTTTTGGAAAATCTT-ATTAAGCCCTC
1 CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
47259198 CAAAATTTTTGGAA
1 CAAAATTTTTGGAA
47259212 TATTCTCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (32 bp):
CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
Found at i:47260084 original size:2 final size:2
Alignment explanation
Indices: 47260077--47260114 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
47260067 AAAAAGAAAA
47260077 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
47260115 CACCTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47280503 original size:30 final size:31
Alignment explanation
Indices: 47280441--47280540 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
47280431 AAGTCAAGAG
* *
47280441 TTTCAAGTC-AGGTCATCTCGGATTT-AGGTCA
1 TTTCAAGTCTAGGTCAT-TTGG-TTTCGGGTCA
* *
47280472 TTTCACGTTTA-GTCATTTGGGTTT-GGGTCA
1 TTTCAAGTCTAGGTCATTT-GGTTTCGGGTCA
* *
47280502 TTCCAAGTCTAGGTCATTTGGTTTCGAGTCA
1 TTTCAAGTCTAGGTCATTTGGTTTCGGGTCA
*
47280533 TTTTAAGT
1 TTTCAAGT
47280541 TTGTTAGGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
30 22 0.40
31 32 0.58
32 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (31 bp):
TTTCAAGTCTAGGTCATTTGGTTTCGGGTCA
Found at i:47280520 original size:31 final size:31
Alignment explanation
Indices: 47280444--47280522 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 31
47280434 TCAAGAGTTT
* *
47280444 CAAGTC-AGGTCATCTCGGATTTAGGTCATTT
1 CAAGTCTAGGTCAT-TTGGATTTAGGTCATTC
* * * *
47280475 CACGTTTA-GTCATTTGGGTTTGGGTCATTC
1 CAAGTCTAGGTCATTTGGATTTAGGTCATTC
47280505 CAAGTCTAGGTCATTTGG
1 CAAGTCTAGGTCATTTGG
47280523 TTTCGAGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 19 0.50
31 18 0.47
32 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (31 bp):
CAAGTCTAGGTCATTTGGATTTAGGTCATTC
Found at i:47286067 original size:22 final size:23
Alignment explanation
Indices: 47286026--47286071 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
47286016 AAACCCGCCC
47286026 ATATTATTATTTTTTAAATATTT
1 ATATTATTATTTTTTAAATATTT
47286049 ATATTA-TATTATTTT-AATATTT
1 ATATTATTATT-TTTTAAATATTT
47286071 A
1 A
47286072 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTATTTTTTAAATATTT
Found at i:47289822 original size:33 final size:34
Alignment explanation
Indices: 47289719--47289823 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
47289709 AAACTCATGT
* * * *
47289719 TAAGCAAGTTTATTGCTACTGTAATGATTTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
* * *
47289753 TAAGCATGATGATT-CTTACCATATTGATTTGCTA
1 TAAGCATGATTATTGC-TACCGTATTGATTTGTTA
*
47289787 TAAGCATG-TTATTGCTACCGTATTGATCTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
47289820 TAAG
1 TAAG
47289824 TATGTCATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
33 24 0.41
34 34 0.59
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (34 bp):
TAAGCATGATTATTGCTACCGTATTGATTTGTTA
Found at i:47294834 original size:22 final size:22
Alignment explanation
Indices: 47294809--47294853 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47294799 CCCATTGAAA
47294809 GTTAATAAAAATTCCATTATGT
1 GTTAATAAAAATTCCATTATGT
* *
47294831 GTTAATAAAATTTTCATTATGT
1 GTTAATAAAAATTCCATTATGT
47294853 G
1 G
47294854 CACTTGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (22 bp):
GTTAATAAAAATTCCATTATGT
Found at i:47299133 original size:14 final size:14
Alignment explanation
Indices: 47299114--47299141 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47299104 CATTAAAGAT
47299114 GCCACTTAGGAACC
1 GCCACTTAGGAACC
47299128 GCCACTTAGGAACC
1 GCCACTTAGGAACC
47299142 CGAAGAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (14 bp):
GCCACTTAGGAACC
Found at i:47300526 original size:34 final size:34
Alignment explanation
Indices: 47300487--47300552 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
47300477 AGTATGAAAG
*
47300487 TATAAATAAAACATATGTACGATATATGAATACA
1 TATAAATAAAACATATGGACGATATATGAATACA
** *
47300521 TATAAATAAAATGTATGGATGATATATGAATA
1 TATAAATAAAACATATGGACGATATATGAATA
47300553 AATGTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.32
Consensus pattern (34 bp):
TATAAATAAAACATATGGACGATATATGAATACA
Found at i:47303376 original size:41 final size:40
Alignment explanation
Indices: 47303326--47303405 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
47303316 AAACTAGCAG
**
47303326 TTTAACAATTTATATGCAAGGAACTAGCAAAAAATCAACAA
1 TTTAACAATTTATATGCAACAAACTAGC-AAAAATCAACAA
* *
47303367 TTTAGCAATTTATATGCAACAAATTAGCAAAAATCAACA
1 TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACA
47303406 CGAAATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (40 bp):
TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACAA
Found at i:47305702 original size:15 final size:15
Alignment explanation
Indices: 47305682--47305718 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
47305672 GAAGTAAATG
47305682 TGATAACATTAGGAT
1 TGATAACATTAGGAT
47305697 TGATAACATTAGGAT
1 TGATAACATTAGGAT
47305712 TGATAAC
1 TGATAAC
47305719 GACACATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (15 bp):
TGATAACATTAGGAT
Found at i:47316263 original size:22 final size:22
Alignment explanation
Indices: 47316237--47316304 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
47316227 ATATCTAAAC
*
47316237 AATAACAACAAAATAGTAGCTA
1 AATAACAACAAAATAGTAGCAA
* * * *
47316259 TATAATAGCAAAATGGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* *
47316281 AACAACAACAAAATAGTAGAAA
1 AATAACAACAAAATAGTAGCAA
47316303 AA
1 AA
47316305 AATTTAGACA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:47319675 original size:4 final size:4
Alignment explanation
Indices: 47319658--47319688 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
47319648 GAAGATGAAA
*
47319658 GAGG GAGT GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
47319689 AACGTGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.71, T:0.03
Consensus pattern (4 bp):
GAGG
Found at i:47322964 original size:11 final size:10
Alignment explanation
Indices: 47322925--47322983 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
47322915 AATTCGATTT
47322925 ATTTAAATTCG
1 ATTTAAATT-G
47322936 AGTTTAAATTG
1 A-TTTAAATTG
47322947 ATTTAAATTG
1 ATTTAAATTG
***
47322957 ATTTTAAAACA
1 A-TTTAAATTG
*
47322968 ATTTAAATTT
1 ATTTAAATTG
47322978 ATTTAA
1 ATTTAA
47322984 GATAAAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 22 0.55
11 10 0.25
12 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (10 bp):
ATTTAAATTG
Found at i:47324744 original size:24 final size:24
Alignment explanation
Indices: 47324716--47324762 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
47324706 ATGAAATAAT
*
47324716 TAAAATTTTAAAAATTATTAAAAA
1 TAAAATATTAAAAATTATTAAAAA
* *
47324740 TAAAATATTGATAATTATTAAAA
1 TAAAATATTAAAAATTATTAAAA
47324763 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATATTAAAAATTATTAAAAA
Found at i:47324746 original size:33 final size:33
Alignment explanation
Indices: 47324709--47324772 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
47324699 AAAATGTATG
47324709 AAATAATT-AAAATT-TTAAAAATTATTAAAAATA
1 AAAT-ATTGAAAATTATT-AAAATTATTAAAAATA
* *
47324742 AAATATTGATAATTATTAAAATTATTTAAAA
1 AAATATTGAAAATTATTAAAATTATTAAAAA
47324773 CATATACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 22 0.81
34 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
AAATATTGAAAATTATTAAAATTATTAAAAATA
Found at i:47326063 original size:32 final size:31
Alignment explanation
Indices: 47326027--47326135 Score: 102
Period size: 32 Copynumber: 3.6 Consensus size: 31
47326017 TATGATTCAC
47326027 ATTTATTAAATTTTATAAATATCGAGAGTTAA
1 ATTTATTAAATTTT-TAAATATCGAGAGTTAA
*
47326059 ATTTATTAAATTTTTAGAAT-CCGA-A-TTAA
1 ATTTATTAAATTTTTA-AATATCGAGAGTTAA
* ** *
47326088 ATTGA-T-AATTTTATAAATATTAAGGGTTAA
1 ATTTATTAAATTTT-TAAATATCGAGAGTTAA
*
47326118 ATTTATTGAATTTTTAAA
1 ATTTATTAAATTTTTAAA
47326136 ATTCGAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.14
28 4 0.06
29 8 0.13
30 9 0.14
31 10 0.16
32 23 0.37
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (31 bp):
ATTTATTAAATTTTTAAATATCGAGAGTTAA
Found at i:47326105 original size:59 final size:60
Alignment explanation
Indices: 47326035--47326164 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 60
47326025 ACATTTATTA
* * *
47326035 AATTTTATAAATATCGAGAGTTAAATTTATTAAATTTTTAGAATCCGAATTAAATTGA-T
1 AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
* * * *
47326094 AATTTTATAAATATTAAGGGTTAAATTTATTGAATTTTTAAAATTCGAATTAAAATGATT
1 AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
*
47326154 AATTTTGTAAA
1 AATTTTATAAA
47326165 CATTGAGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
59 51 0.82
60 11 0.18
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (60 bp):
AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
Found at i:47326178 original size:59 final size:59
Alignment explanation
Indices: 47326056--47326180 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
47326046 TATCGAGAGT
* * * **
47326056 TAAATTTATTAAATTTTTAGAATCCGAATTAAATTGATAATTTTATAAATATTAAGGGT
1 TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATAATTTTATAAACATTAAGGAA
* * * *
47326115 TAAATTTATTGAATTTTTAAAATTCGAATTAAAATGATTAATTTTGTAAACATTGA-GAA
1 TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGA-TAATTTTATAAACATTAAGGAA
47326174 TAAATTT
1 TAAATTT
47326181 GTTGTTTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 41 0.73
60 15 0.27
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (59 bp):
TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATAATTTTATAAACATTAAGGAA
Found at i:47333121 original size:23 final size:23
Alignment explanation
Indices: 47333066--47333110 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47333056 AAGCGTGTTC
* * *
47333066 ATATTATTTTTTATTTTTTTAAA
1 ATATTATATTATATTATTTTAAA
47333089 ATATTATATTATATTATTTTAA
1 ATATTATATTATATTATTTTAA
47333111 TATTTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTATATTATATTATTTTAAA
Found at i:47333134 original size:26 final size:29
Alignment explanation
Indices: 47333097--47333157 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 29
47333087 AAATATTATA
*
47333097 TTATAT-TATTTTAATAT-TTGATA-TTT
1 TTATATATATTTTAATATATTGAAATTTT
* *
47333123 TTATATAT-TTTTTATTTATTGAAATTTT
1 TTATATATATTTTAATATATTGAAATTTT
47333151 TTATATA
1 TTATATA
47333158 GTCATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 13 0.45
27 6 0.21
28 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (29 bp):
TTATATATATTTTAATATATTGAAATTTT
Found at i:47333142 original size:28 final size:28
Alignment explanation
Indices: 47333070--47333157 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
47333060 GTGTTCATAT
* * *
47333070 TATTTTTTATTTTTTTAAAATATTATATTA
1 TATTTTTTATTTATTTGAAAT-TTTTA-TA
* *
47333100 TATTATTTTA-ATATTTGATATTTTTATA
1 TATT-TTTTATTTATTTGAAATTTTTATA
47333128 TATTTTTTATTTA-TTGAAATTTTTTATA
1 TATTTTTTATTTATTTGAAA-TTTTTATA
47333156 TA
1 TA
47333158 GTCATCTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.21
28 18 0.38
29 4 0.08
30 11 0.23
31 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TATTTTTTATTTATTTGAAATTTTTATA
Found at i:47333415 original size:6 final size:6
Alignment explanation
Indices: 47333404--47333430 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47333394 CAATACATCT
47333404 AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AAT
47333431 CGATTGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:47336057 original size:17 final size:18
Alignment explanation
Indices: 47336024--47336057 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47336014 TCATAACAGT
*
47336024 TTTTATAATTTTTAAAAC
1 TTTTATAATTTTAAAAAC
47336042 TTTTA-AATTTTAAAAA
1 TTTTATAATTTTAAAAA
47336058 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATAATTTTAAAAAC
Found at i:47343222 original size:14 final size:14
Alignment explanation
Indices: 47343189--47343221 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
47343179 CGTTGATTAA
*
47343189 AATTTTATTAAATT
1 AATTTTAATAAATT
47343203 AATTTTAATAAATT
1 AATTTTAATAAATT
47343217 -ATTTT
1 AATTTT
47343222 TTTTTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTAATAAATT
Found at i:47365833 original size:92 final size:95
Alignment explanation
Indices: 47365589--47365857 Score: 257
Period size: 92 Copynumber: 2.9 Consensus size: 95
47365579 GATCCAACAG
* ** ** * * *
47365589 AAATCTATCATAGTAAATATTATTTCCCTAAAGTTGTAGTTGAGCAGATTGAAGCTA-AAAATCC
1 AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTCC
47365653 TATACCCTTGAAGTTGCAGTAGGTCAGATT
66 TATACCCTTGAAGTTGCAGTAGGTCAGATT
* * * *
47365683 AAATCTACCATAGCGAATCTTATCCCCCTGAAGTTGCAGTGGAGCAAGA-TAAAACTACAAATTC
1 AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGC-AGATTGAAGCTACAAATTC
* * *
47365747 C-ATTCCC-TGAAGTTGCAGTGGGT-TGATT
65 CTATACCCTTGAAGTTGCAGTAGGTCAGATT
** * * *
47365775 GAAA-CTACGGTGGTGAATATTATCCCCCTAAAGTTACAGTGGAGCAGATTGAAGCTACAAA-TC
1 -AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTC
* *
47365838 TTAT-CTCCTTAAAGTTGCAG
65 CTATAC-CCTTGAAGTTGCAG
47365858 GGGAGCAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
91 6 0.04
92 52 0.37
93 28 0.20
94 47 0.33
95 9 0.06
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (95 bp):
AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTCC
TATACCCTTGAAGTTGCAGTAGGTCAGATT
Found at i:47366015 original size:44 final size:44
Alignment explanation
Indices: 47365795--47366037 Score: 193
Period size: 44 Copynumber: 5.5 Consensus size: 44
47365785 TGGTGAATAT
* * * *
47365795 TATCCCCCTAAAGTTACAGTGGAGC-AGATTGAAGCTACAAATCT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGA-TGAAGCTACAAATCC
* * * * * * * *
47365839 TATCTCCTTAAAGTTGCAGGGGAGCAA-ATTAAAGCTACAAGTCT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGA-TGAAGCTACAAATCC
* * * **
47365883 TATCTCCTTGAAGTTGCAGTGGAACAAGATGAAGCTACAAGTTT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
**
47365927 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACTGATCC
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
* * * * * *
47365971 TATGCCCCTGAGGTTGCAGTGGAGCAAGACGAGGATACAAATCC
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
** * *
47366015 TATATCCTTGAAGTTACAGTGGA
1 TATCCCCCTGAAGTTGCAGTGGA
47366038 TTGGATTGAA
Statistics
Matches: 166, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
44 164 0.99
45 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
Found at i:47366439 original size:22 final size:22
Alignment explanation
Indices: 47366412--47366453 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
47366402 CCCACTTGCT
47366412 AAACCTAATA-CCCAATAACCCG
1 AAACCTAATAGCCC-ATAACCCG
47366434 AAACCTAATAGCCCATAACC
1 AAACCTAATAGCCCATAACC
47366454 TAAACTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (22 bp):
AAACCTAATAGCCCATAACCCG
Found at i:47367796 original size:3 final size:3
Alignment explanation
Indices: 47367751--47367778 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47367741 TTGCCTTTAC
47367751 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
47367779 TATCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:47374494 original size:17 final size:17
Alignment explanation
Indices: 47374472--47374506 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47374462 ATAAAGAAGA
47374472 AAAATATGCATATATAT
1 AAAATATGCATATATAT
*
47374489 AAAATATGTATATATAT
1 AAAATATGCATATATAT
47374506 A
1 A
47374507 TATATAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAATATGCATATATAT
Found at i:47374775 original size:36 final size:36
Alignment explanation
Indices: 47374735--47374814 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
47374725 ATACATATAA
* *
47374735 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATACGT
* *
47374771 ATATAGATATATATAAAAAGAAATATGAGTATACGT
1 ATATATATATATATAAAAAGAAAAATGAGTATACGT
47374807 ATATATAT
1 ATATATAT
47374815 TAAACAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATACGT
Found at i:47374956 original size:3 final size:3
Alignment explanation
Indices: 47374945--47375023 Score: 106
Period size: 3 Copynumber: 26.3 Consensus size: 3
47374935 CAATAATACC
* * * *
47374945 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
47374990 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47375024 GCAAAAGTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.02
3 65 0.98
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:47377309 original size:88 final size:88
Alignment explanation
Indices: 47377087--47377763 Score: 999
Period size: 88 Copynumber: 7.7 Consensus size: 88
47377077 AGCTCCAATG
** * * *
47377087 CAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
** * * * *
47377150 TGCT-TCTTTAACTAGCTCCA-CTG
65 TTTTGTCTTCAACCAGCTCTATC-A
* ** * * * *
47377173 CAATCGATGGATGCAAGGCTTTGT-T-TTCGAACTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
47377236 TTTTGTCTTCAACCAGCTCTATCA
65 TTTTGTCTTCAACCAGCTCTATCA
*
47377260 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
47377325 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
47377348 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
47377413 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* *
47377436 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
47377501 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
* *
47377524 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA-AAAAGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
47377588 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
47377611 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
47377676 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * * *
47377699 CAACCGAAAGAGGCAAGGTTTATGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
47377764 GTAACTTCAT
Statistics
Matches: 555, Mismatches: 31, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
86 64 0.12
87 114 0.21
88 377 0.68
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:47382547 original size:19 final size:20
Alignment explanation
Indices: 47382513--47382566 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
47382503 AGGGTCACTT
* *
47382513 CATGAAAATCTAATGCATATG
1 CATG-AAATGTAATGCAAATG
*
47382534 -ATGCAATGTAATGCAAATG
1 CATGAAATGTAATGCAAATG
47382553 CATGAAATG-AATGC
1 CATGAAATGTAATGC
47382567 CTAAAGAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (20 bp):
CATGAAATGTAATGCAAATG
Found at i:47384627 original size:17 final size:17
Alignment explanation
Indices: 47384605--47384639 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47384595 ATAAAGAAGA
47384605 AAAATATGCATATATAT
1 AAAATATGCATATATAT
*
47384622 AAAATATGTATATATAT
1 AAAATATGCATATATAT
47384639 A
1 A
47384640 TATAGGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAATATGCATATATAT
Found at i:47384906 original size:36 final size:36
Alignment explanation
Indices: 47384866--47384945 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
47384856 ATACATATAA
* *
47384866 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATACGT
* *
47384902 ATATAGATATATATAAAAAGAAATATGAGTATACGT
1 ATATATATATATATAAAAAGAAAAATGAGTATACGT
47384938 ATATATAT
1 ATATATAT
47384946 TAAACAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATACGT
Found at i:47385087 original size:3 final size:3
Alignment explanation
Indices: 47385076--47385139 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
47385066 CAATAATACC
* * * *
47385076 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
47385121 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
47385140 GCAAAAGTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.98
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:47385102 original size:18 final size:18
Alignment explanation
Indices: 47385067--47385139 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
47385057 AAGTAACAAC
* *
47385067 AATAATACCAATACTAAT
1 AATAATAACAATAATAAT
* *
47385085 AATAGTAA-AGATGATAAT
1 AATAATAACA-ATAATAAT
47385103 AATAATAACAATAATAAT
1 AATAATAACAATAATAAT
*
47385121 AATAATAATAATAATAAT
1 AATAATAACAATAATAAT
47385139 A
1 A
47385140 GCAAAAGTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
17 1 0.02
18 44 0.96
19 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (18 bp):
AATAATAACAATAATAAT
Found at i:47396319 original size:18 final size:19
Alignment explanation
Indices: 47396280--47396320 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47396270 TATAATTTGA
* *
47396280 TAAATTAAAAATTTATGAC
1 TAAAATAAAAATTGATGAC
47396299 TAAAATAAAAATTGATG-C
1 TAAAATAAAAATTGATGAC
47396317 TAAA
1 TAAA
47396321 TTAAGTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATAAAAATTGATGAC
Found at i:47397653 original size:13 final size:13
Alignment explanation
Indices: 47397635--47397664 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
47397625 AATGGGTGAT
47397635 GGCATATGAGGCA
1 GGCATATGAGGCA
47397648 GGCATATGAGGCA
1 GGCATATGAGGCA
47397661 GGCA
1 GGCA
47397665 GTCCCTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.40, T:0.13
Consensus pattern (13 bp):
GGCATATGAGGCA
Found at i:47400119 original size:27 final size:30
Alignment explanation
Indices: 47400083--47400147 Score: 100
Period size: 27 Copynumber: 2.3 Consensus size: 30
47400073 AAAAAATAAT
47400083 TAAAATATTATAATT-T-TTT-TTATTTAC
1 TAAAATATTATAATTATATTTATTATTTAC
*
47400110 TAAAATATTATAATTATATTTATTATTTAT
1 TAAAATATTATAATTATATTTATTATTTAC
47400140 TAAAATAT
1 TAAAATAT
47400148 ATCAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 15 0.44
28 1 0.03
29 3 0.09
30 15 0.44
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAAATATTATAATTATATTTATTATTTAC
Found at i:47400148 original size:27 final size:27
Alignment explanation
Indices: 47400081--47400148 Score: 64
Period size: 30 Copynumber: 2.4 Consensus size: 27
47400071 ATAAAAAATA
* * *
47400081 ATTAAAATATTATAATTTTTTTTATTT
1 ATTAAAATATAATAATATTTATTATTT
* *
47400108 ACTAAAATATTATAATTATATTTATTATTT
1 A-TTAAA-A-TATAATAATATTTATTATTT
47400138 ATTAAAATATA
1 ATTAAAATATA
47400149 TCAAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
27 5 0.16
28 5 0.16
29 5 0.16
30 17 0.53
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTAAAATATAATAATATTTATTATTT
Done.