Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 171 of 202
Found at i:53344197 original size:7 final size:7
Alignment explanation
Indices: 53344185--53344240 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
53344175 TTTTTGCATG
*
53344185 TAAACCT
1 TAAACCC
53344192 TAAACCC
1 TAAACCC
53344199 TAAACCC
1 TAAACCC
* *
53344206 TAAGTCAC
1 TAA-ACCC
* *
53344214 TGACCCC
1 TAAACCC
53344221 TAAACCC
1 TAAACCC
53344228 TAAACCC
1 TAAACCC
53344235 TAAACC
1 TAAACC
53344241 TTAAGCCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 36 0.90
8 4 0.10
ACGTcount: A:0.39, C:0.39, G:0.04, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:53344225 original size:36 final size:36
Alignment explanation
Indices: 53344185--53344271 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
53344175 TTTTTGCATG
*
53344185 TAAACCTTAAACCCTAAACCCTAAGTCACTGACCCC
1 TAAACCTTAAACCCTAAACCCTAAGCCACTGACCCC
* * *
53344221 TAAACCCTAAACCCTAAACCTTAAGCCATTGACCCC
1 TAAACCTTAAACCCTAAACCCTAAGCCACTGACCCC
53344257 TAAACCTTAAACCCT
1 TAAACCTTAAACCCT
53344272 TAACAAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.37, C:0.38, G:0.05, T:0.21
Consensus pattern (36 bp):
TAAACCTTAAACCCTAAACCCTAAGCCACTGACCCC
Found at i:53344446 original size:21 final size:22
Alignment explanation
Indices: 53344417--53344458 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
53344407 CTTAAATACT
53344417 AAACTTTAAACCCTAAACCCTC
1 AAACTTTAAACCCTAAACCCTC
*
53344439 AAAC-TTAAACTCTAAACCCT
1 AAACTTTAAACCCTAAACCCT
53344459 AAATACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACTTTAAACCCTAAACCCTC
Found at i:53344468 original size:21 final size:20
Alignment explanation
Indices: 53344423--53344489 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
53344413 TACTAAACTT
* *
53344423 TAAACCCTAAACCCTCAAAC
1 TAAACTCTAAACCCTAAAAC
53344443 TTAAACTCTAAACCCTAAATAC
1 -TAAACTCTAAACCCTAAA-AC
*
53344465 TAAA-TCATAAACTCTAAACAC
1 TAAACTC-TAAACCCTAAA-AC
53344486 TAAA
1 TAAA
53344490 AGTAATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAACTCTAAACCCTAAAAC
Found at i:53344475 original size:28 final size:28
Alignment explanation
Indices: 53344416--53344489 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
53344406 TCTTAAATAC
* * *
53344416 TAAACTTTAAACCCTAAACCCTCAAACT
1 TAAACTCTAAACCCTAAACACTCAAACA
*
53344444 TAAACTCTAAACCCTAAATACT-AAATCA
1 TAAACTCTAAACCCTAAACACTCAAA-CA
*
53344472 TAAACTCTAAACACTAAA
1 TAAACTCTAAACCCTAAA
53344490 AGTAATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 3 0.08
28 37 0.93
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAACTCTAAACCCTAAACACTCAAACA
Found at i:53344481 original size:14 final size:14
Alignment explanation
Indices: 53344416--53344483 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
53344406 TCTTAAATAC
* *
53344416 TAAACTTTAAACCC
1 TAAACTCTAAACCA
* *
53344430 TAAACCCTCAAA-CT
1 TAAACTCT-AAACCA
*
53344444 TAAACTCTAAACCC
1 TAAACTCTAAACCA
*
53344458 TAAA-TACTAAATCA
1 TAAACT-CTAAACCA
53344472 TAAACTCTAAAC
1 TAAACTCTAAAC
53344484 ACTAAAAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 4 0.10
14 34 0.81
15 4 0.10
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACTCTAAACCA
Found at i:53344508 original size:100 final size:100
Alignment explanation
Indices: 53344393--53344589 Score: 288
Period size: 100 Copynumber: 2.0 Consensus size: 100
53344383 AGGGCCAAAA
* * * * *
53344393 AATTAAAAAATAATCTTAAATACTAAACTTTAAACCCTAAACCCTCAAA-CTTAAACTCTAAACC
1 AATTAAAAAAGAATCTTAAATACTAAAATCTAAACCCTAAACCC-CAAACCTCAAACTCTAAAAC
*
53344457 CTAAATACTAAATCATAAACTCTAAACACTAAAAGT
65 CTAAACACTAAATCATAAACTCTAAACACTAAAAGT
*
53344493 AATTAAAAAAGAATCTTAAATACTAAAATCTATACCCTAAACCCCAAACCTCAAACTCTAAAACC
1 AATTAAAAAAGAATCTTAAATACTAAAATCTAAACCCTAAACCCCAAACCTCAAACTCTAAAACC
* * *
53344558 TAAACACTAAATCGTAAATTCTAAATACTAAA
66 TAAACACTAAATCATAAACTCTAAACACTAAA
53344590 CCAAAAACCC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 4 0.05
100 82 0.95
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.25
Consensus pattern (100 bp):
AATTAAAAAAGAATCTTAAATACTAAAATCTAAACCCTAAACCCCAAACCTCAAACTCTAAAACC
TAAACACTAAATCATAAACTCTAAACACTAAAAGT
Found at i:53344536 original size:7 final size:7
Alignment explanation
Indices: 53344526--53344624 Score: 56
Period size: 7 Copynumber: 14.1 Consensus size: 7
53344516 TAAAATCTAT
53344526 ACCCTAA
1 ACCCTAA
*
53344533 ACCCCAA
1 ACCCTAA
53344540 A-CCTCAA
1 ACCCT-AA
*
53344547 ACTCTAA
1 ACCCTAA
*
53344554 AACCTAA
1 ACCCTAA
*
53344561 ACACTAA
1 ACCCTAA
* *
53344568 ATCGTAA
1 ACCCTAA
**
53344575 ATTCTAA
1 ACCCTAA
**
53344582 ATACTAA
1 ACCCTAA
**
53344589 ACCAAAA
1 ACCCTAA
53344596 ACCCTAA
1 ACCCTAA
*
53344603 ATCCTAA
1 ACCCTAA
*
53344610 ACCATAA
1 ACCCTAA
53344617 ACCCTAA
1 ACCCTAA
53344624 A
1 A
53344625 ATAAAACTTA
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
6 2 0.03
7 63 0.94
8 2 0.03
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.18
Consensus pattern (7 bp):
ACCCTAA
Found at i:53344602 original size:21 final size:21
Alignment explanation
Indices: 53344578--53344624 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
53344568 ATCGTAAATT
53344578 CTAAATACTAAACCAAAAACC
1 CTAAATACTAAACCAAAAACC
* *
53344599 CTAAATCCTAAACCATAAACC
1 CTAAATACTAAACCAAAAACC
53344620 CTAAA
1 CTAAA
53344625 ATAAAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (21 bp):
CTAAATACTAAACCAAAAACC
Found at i:53347150 original size:91 final size:91
Alignment explanation
Indices: 53346995--53347210 Score: 281
Period size: 91 Copynumber: 2.4 Consensus size: 91
53346985 TTTTGGAGGT
* * * * *
53346995 TCTGGCGTGTTTTCAGTTGAAAAGCTTTTATGAGTAATTTAGCGTGTTATCAGGAGAGAATATTT
1 TCTGGCGTGTTATCAGTTGGAAAGCTCTTATGAGAAATTTAGCATGTTATCAGGAGAGAATATTT
*
53347060 AGCCTACGAGCTTTGTACTATGTGCA
66 AGCCTACGAGCTTTGGACTATGTGCA
* * * *
53347086 TCTGGTGTGTTATCGGTTGGAAAGCTCTTATGAGAAATTT-GACATGTTATCGGGGGAGAATATT
1 TCTGGCGTGTTATCAGTTGGAAAGCTCTTATGAGAAATTTAG-CATGTTATCAGGAGAGAATATT
* *
53347150 TAGCCTATGGGCTTTGGACTATGTGCA
65 TAGCCTACGAGCTTTGGACTATGTGCA
* *
53347177 TCTAGCGTGTTATCAGTTGGAATAACTCTTATGA
1 TCTGGCGTGTTATCAGTTGGAA-AGCTCTTATGA
53347211 TCAAACTGGT
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
90 1 0.01
91 96 0.90
92 10 0.09
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.37
Consensus pattern (91 bp):
TCTGGCGTGTTATCAGTTGGAAAGCTCTTATGAGAAATTTAGCATGTTATCAGGAGAGAATATTT
AGCCTACGAGCTTTGGACTATGTGCA
Found at i:53352082 original size:18 final size:17
Alignment explanation
Indices: 53352043--53352084 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
53352033 TAATTTTAAA
*
53352043 ATATATT-TACAAATTC
1 ATATATTATAAAAATTC
*
53352059 AAATATTATAAAAATTAC
1 ATATATTATAAAAATT-C
53352077 ATATATTA
1 ATATATTA
53352085 AACCCCATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.29
17 7 0.33
18 8 0.38
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATTATAAAAATTC
Found at i:53352579 original size:18 final size:18
Alignment explanation
Indices: 53352513--53352579 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 18
53352503 AAATTATAAA
* *
53352513 AATAAAAATACCAAAATA
1 AATAAAAATATCAAAATT
*
53352531 AAT-CAAA-ATCAAAATT
1 AATAAAAATATCAAAATT
*
53352547 AA-AAAAATATAAAAAGTT
1 AATAAAAATATCAAAA-TT
53352565 AATAAAAAT-TCAAAA
1 AATAAAAATATCAAAA
53352580 AAAAAATTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 12 0.31
17 9 0.23
18 12 0.31
19 6 0.15
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.21
Consensus pattern (18 bp):
AATAAAAATATCAAAATT
Found at i:53354020 original size:25 final size:25
Alignment explanation
Indices: 53353973--53354025 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
53353963 TACATTAATC
*
53353973 AAAGTTTAAGTGGGAAACTAAAAAT
1 AAAGTTTAAGTGGGAAACGAAAAAT
* *
53353998 AAAGTTTAATTGGGAGAA-GAAAAGT
1 AAAGTTTAAGTGGGA-AACGAAAAAT
53354023 AAA
1 AAA
53354026 AAAATACGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAGTTTAAGTGGGAAACGAAAAAT
Found at i:53358815 original size:25 final size:25
Alignment explanation
Indices: 53358781--53358830 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53358771 NNNAATGAAA
*
53358781 TCGGGGAATCAGCACTTAGCAACCC
1 TCGGGGAATCAGCACATAGCAACCC
53358806 TCGGGGAATCAGCACATAGCAACCC
1 TCGGGGAATCAGCACATAGCAACCC
53358831 CCTTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (25 bp):
TCGGGGAATCAGCACATAGCAACCC
Found at i:53359271 original size:29 final size:29
Alignment explanation
Indices: 53359238--53359301 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
53359228 TAATCCACCA
53359238 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
53359267 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
53359297 CCCAA
1 CCCAA
53359302 GCTCAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:53359275 original size:30 final size:30
Alignment explanation
Indices: 53359245--53359301 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53359235 CCACCCAACT
53359245 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
53359274 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
53359302 GCTCAGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:53402332 original size:18 final size:18
Alignment explanation
Indices: 53402309--53402343 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53402299 ATAAAAAAGA
*
53402309 AAAATATTTTTAATAATG
1 AAAATATATTTAATAATG
*
53402327 AAAATATATTTGATAAT
1 AAAATATATTTAATAAT
53402344 TATTATTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAAATATATTTAATAATG
Found at i:53403890 original size:20 final size:20
Alignment explanation
Indices: 53403846--53403883 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53403836 GCGATTCAAT
53403846 ATATATAATAATTATTTAAC
1 ATATATAATAATTATTTAAC
53403866 ATATATAATTAATT-TTTA
1 ATATATAA-TAATTATTTA
53403884 TAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATAATAATTATTTAAC
Found at i:53406803 original size:14 final size:14
Alignment explanation
Indices: 53406768--53406833 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 14
53406758 TCAAAACTCT
* *
53406768 AACCTTAAATCCCG
1 AACCTTAAATCTCA
53406782 AA-CTTAAATCTCA
1 AACCTTAAATCTCA
* *
53406795 AACCTTAAACCTTA
1 AACCTTAAATCTCA
** * *
53406809 AATTTTAAATTTTA
1 AACCTTAAATCTCA
53406823 AACCTTAAATC
1 AACCTTAAATC
53406834 AAGTTTAGGA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
13 11 0.28
14 29 0.73
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (14 bp):
AACCTTAAATCTCA
Found at i:53406810 original size:21 final size:21
Alignment explanation
Indices: 53406784--53406833 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
53406774 AAATCCCGAA
53406784 CTTAAATCTCAAACCTTAAAC
1 CTTAAATCTCAAACCTTAAAC
* * **
53406805 CTTAAATTTTAAATTTTAAAC
1 CTTAAATCTCAAACCTTAAAC
53406826 CTTAAATC
1 CTTAAATC
53406834 AAGTTTAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (21 bp):
CTTAAATCTCAAACCTTAAAC
Found at i:53410347 original size:10 final size:10
Alignment explanation
Indices: 53410332--53410366 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
53410322 TGAAATGAAA
53410332 TAGAAAATTT
1 TAGAAAATTT
*
53410342 TAGAAAAATT
1 TAGAAAATTT
53410352 TA-AAAATTT
1 TAGAAAATTT
53410361 TAGAAA
1 TAGAAA
53410367 CAAAGGTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (10 bp):
TAGAAAATTT
Found at i:53417609 original size:20 final size:20
Alignment explanation
Indices: 53417562--53417610 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
53417552 TTATAAAAAA
* **
53417562 TAAAAAAATTATTAAAATTT
1 TAAAAAAATCATTAAAATCG
**
53417582 TATTAAAATCATTAAAATCG
1 TAAAAAAATCATTAAAATCG
53417602 TAAAAAAAT
1 TAAAAAAAT
53417611 TATAAAATGT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAAAAATCATTAAAATCG
Found at i:53417920 original size:19 final size:18
Alignment explanation
Indices: 53417898--53418027 Score: 74
Period size: 19 Copynumber: 7.2 Consensus size: 18
53417888 TTTTGTTGCA
53417898 TTTTATTATTTTTATAATT
1 TTTTATTATTTTTATAA-T
* **
53417917 TTTTATAATTTTTACGA-
1 TTTTATTATTTTTATAAT
* *
53417934 TTTTATAATTTTTAATAAA
1 TTTTATTATTTTT-ATAAT
* *
53417953 TTTTAGATATTTTTAATAAAA
1 TTTTA-TTATTTTT-AT-AAT
* * *
53417974 TTTAATCATTTTTATAAC
1 TTTTATTATTTTTATAAT
53417992 TTTTATTAATTTTTAT--T
1 TTTTATT-ATTTTTATAAT
53418009 TTTTA-TA-TTTTAT-AT
1 TTTTATTATTTTTATAAT
53418024 TTTT
1 TTTT
53418028 TTGCCTCATC
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
14 6 0.07
15 6 0.07
16 1 0.01
17 18 0.20
18 9 0.10
19 29 0.32
20 15 0.16
21 7 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATTATTTTTATAAT
Found at i:53417966 original size:20 final size:20
Alignment explanation
Indices: 53417941--53418006 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
53417931 CGATTTTATA
53417941 ATTTTTAATAAATTTTAGAT-
1 ATTTTTAATAAATTTTA-ATC
*
53417961 ATTTTTAATAAAATTTAATC
1 ATTTTTAATAAATTTTAATC
* * *
53417981 ATTTTT-ATAACTTTTATTA
1 ATTTTTAATAAATTTTAATC
53418000 ATTTTTA
1 ATTTTTA
53418007 TTTTTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTAATAAATTTTAATC
Found at i:53417974 original size:21 final size:19
Alignment explanation
Indices: 53417933--53417977 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
53417923 AATTTTTACG
*
53417933 ATTTTATAATTTTTAATAA
1 ATTTTAGAATTTTTAATAA
53417952 ATTTTAGATATTTTTAATAA
1 ATTTTAGA-ATTTTTAATAA
*
53417972 AATTTA
1 ATTTTA
53417978 ATCATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTAGAATTTTTAATAA
Found at i:53418007 original size:10 final size:9
Alignment explanation
Indices: 53417898--53418027 Score: 83
Period size: 9 Copynumber: 14.4 Consensus size: 9
53417888 TTTTGTTGCA
*
53417898 TTTTATTAT
1 TTTTATAAT
53417907 TTTTATAATT
1 TTTTATAA-T
53417917 TTTTATAAT
1 TTTTATAAT
**
53417926 TTTTACGA-
1 TTTTATAAT
53417934 TTTTATAAT
1 TTTTATAAT
*
53417943 TTTTAATAAA
1 TTTT-ATAAT
*
53417953 TTTTAGATAT
1 TTTTATA-AT
*
53417963 TTTTAATAAAA
1 TTTT-AT-AAT
* *
53417974 TTTAATCAT
1 TTTTATAAT
*
53417983 TTTTATAAC
1 TTTTATAAT
53417992 TTTTATTAAT
1 TTTTA-TAAT
53418002 TTTTAT--T
1 TTTTATAAT
53418009 TTTTAT-A-
1 TTTTATAAT
53418016 TTTTAT-AT
1 TTTTATAAT
53418024 TTTT
1 TTTT
53418028 TTGCCTCATC
Statistics
Matches: 95, Mismatches: 17, Indels: 19
0.73 0.13 0.15
Matches are distributed among these distances:
7 14 0.15
8 10 0.11
9 33 0.35
10 32 0.34
11 5 0.05
12 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53435309 original size:131 final size:131
Alignment explanation
Indices: 53435076--53435377 Score: 519
Period size: 131 Copynumber: 2.4 Consensus size: 131
53435066 TTGATTTACA
*
53435076 AACGTAA-CATATTGAATTTTCCAATTAA---TCATACAATCATAATCAAATCAGAGTTTGTTCA
1 AACGTAATCA-ATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCA
*
53435137 AATATAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAATTCCTTAAAAATAATTA
65 AATATAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAAATCCTTAAAAATAATTA
53435202 TG
130 TG
53435204 AACGTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAA
1 AACGTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAA
*
53435269 ATATAAACCCAAAACTCATGTACTCATTTCTTGAATTATGAACATAAATCCTTAAAAATAATTAT
66 ATATAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAAATCCTTAAAAATAATTAT
53435334 G
131 G
53435335 AACGTAATCAATTGAATTATCCAATTAATTG---TACAATCATAAT
1 AACGTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAAT
53435378 TTTACAGTTG
Statistics
Matches: 167, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
128 36 0.22
129 2 0.01
131 129 0.77
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (131 bp):
AACGTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAA
ATATAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAAATCCTTAAAAATAATTAT
G
Found at i:53435510 original size:110 final size:110
Alignment explanation
Indices: 53435339--53435586 Score: 270
Period size: 110 Copynumber: 2.3 Consensus size: 110
53435329 ATTATGAACG
** *
53435339 TAATCAATTGAATTATCCAATTAATTGTACAATCATAATTTTACAGTTGGAACATAATTTGTTTG
1 TAATCAATTGAATTATCCAATTAATTGTACAATCATAAACTTACAGTTGGAACATAATTTGTTCG
53435404 AATATAAACCCTAAACACATATACACGTGTCTCGAATTACTAACA
66 AATATAAACCCTAAACACATATACACGTGTCTCGAATTACTAACA
* * * * *
53435449 TAATCGATTGAATTA-CTCAATTGATTGTACACTCATAAACTTATAGTT-GAATCGA-ATTTTGT
1 TAATCAATTGAATTATC-CAATTAATTGTACAATCATAAACTTACAGTTGGAA-C-ATAATTTGT
* * ** * *
53435511 TCGAATATAAACCCTAAACTCATATATAAATGTCTCAAATTACGAA-A
63 TCGAATATAAACCCTAAACACATATACACGTGTCTCGAATTACTAACA
* * * *
53435558 GTAACCAGTTGAATGATCAAATTAATTGT
1 -TAATCAATTGAATTATCCAATTAATTGT
53435587 TTCAATTGAA
Statistics
Matches: 113, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
109 5 0.04
110 106 0.94
111 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (110 bp):
TAATCAATTGAATTATCCAATTAATTGTACAATCATAAACTTACAGTTGGAACATAATTTGTTCG
AATATAAACCCTAAACACATATACACGTGTCTCGAATTACTAACA
Found at i:53435834 original size:132 final size:131
Alignment explanation
Indices: 53435665--53435907 Score: 317
Period size: 132 Copynumber: 1.8 Consensus size: 131
53435655 ATTGATTGCA
* * *
53435665 TTATTCAATTAATCTATAATCACAAAGTTACAATTGAATCGAAAGTTGTT-AAAGTGTAAACCCT
1 TTATCCAATTAATCTATAATCACAAAGTTACAATTGAATCAAAAGTTGTTCAAA-TATAAACCCT
* * ** * *
53435729 ACACTCATATCCGCATGTCTTGAATTATGAACGTAACCGATTGAATTTTAATTAATTGTACAATC
65 AAACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATTTTAATTAATTGTACAATC
53435794 AT
130 AT
** * * *
53435796 TTATCCAATTAATCGTATAATCATGAATTTACAATTGAATCAAAATTTGTTCAAATATGAACCCT
1 TTATCCAATTAATC-TATAATCACAAAGTTACAATTGAATCAAAAGTTGTTCAAATATAAACCCT
* *
53435861 AAACTCATATGCACATGTCTCAAATTTTGAACATAACCAATTGAATT
65 AAACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATT
53435908 ATCCAATTAA
Statistics
Matches: 94, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
131 13 0.14
132 78 0.83
133 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (131 bp):
TTATCCAATTAATCTATAATCACAAAGTTACAATTGAATCAAAAGTTGTTCAAATATAAACCCTA
AACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATTTTAATTAATTGTACAATCA
T
Found at i:53436562 original size:24 final size:24
Alignment explanation
Indices: 53436533--53436579 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
53436523 TTCAAAGATT
53436533 ATGAAATTATAAGTTAATATAATG
1 ATGAAATTATAAGTTAATATAATG
* *
53436557 ATGAAATTGTAATTTAATATAAT
1 ATGAAATTATAAGTTAATATAAT
53436580 AATAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (24 bp):
ATGAAATTATAAGTTAATATAATG
Found at i:53437969 original size:31 final size:31
Alignment explanation
Indices: 53437920--53437983 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
53437910 TGTCATTAGA
53437920 GTCTAAAAAGCAACAGGTA-CTCTGTATCGGT
1 GTCTAAAAAGCAACAGGTACCTC-GTATCGGT
* ** *
53437951 GTCTAAAAAGTATTAGGTACCTCGTATTGGT
1 GTCTAAAAAGCAACAGGTACCTCGTATCGGT
53437982 GT
1 GT
53437984 TGGATGCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (31 bp):
GTCTAAAAAGCAACAGGTACCTCGTATCGGT
Found at i:53441114 original size:37 final size:37
Alignment explanation
Indices: 53441072--53441338 Score: 358
Period size: 37 Copynumber: 7.0 Consensus size: 37
53441062 GGTAGTTTTA
53441072 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
**
53441109 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* **
53441146 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
53441183 GTTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* *
53441219 GCTAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAA---GT-G
53441260 CTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 -----GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
53441301 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
53441338 G
1 G
53441339 TAGCCTAGCT
Statistics
Matches: 208, Mismatches: 11, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
36 66 0.32
37 106 0.51
39 2 0.01
43 2 0.01
46 32 0.15
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:53441328 original size:82 final size:81
Alignment explanation
Indices: 53441185--53441379 Score: 322
Period size: 82 Copynumber: 2.4 Consensus size: 81
53441175 GATAAGTGGT
53441185 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
*
53441250 TAAGTGGTAGCTTTAGC
66 TAAGTGGTAGC-CTAGC
* * *
53441267 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTACACTTATCTGATCAAGTGGCAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
53441332 TAAGTGGTAGCCTAGC
66 TAAGTGGTAGCCTAGC
*
53441348 TACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGT
53441380 AATCATACGT
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
79 11 0.10
80 5 0.05
81 19 0.18
82 73 0.68
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (81 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
TAAGTGGTAGCCTAGC
Found at i:53445743 original size:20 final size:20
Alignment explanation
Indices: 53445705--53445743 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53445695 GGTAAGTATA
**
53445705 CATATGAAACGGTTCATGAT
1 CATATGAAAAAGTTCATGAT
*
53445725 CATATGAAAAAGTTGATGA
1 CATATGAAAAAGTTCATGA
53445744 ATTAAATGAT
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:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (20 bp):
CATATGAAAAAGTTCATGAT
Found at i:53448387 original size:2 final size:2
Alignment explanation
Indices: 53448380--53448407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53448370 TCAATTAAAG
53448380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53448408 CAAATTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53452528 original size:114 final size:114
Alignment explanation
Indices: 53452328--53452558 Score: 408
Period size: 114 Copynumber: 2.0 Consensus size: 114
53452318 TGCAAATTTG
* *
53452328 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCTAAAATTGGTGCCACAAGGGCGGCC
1 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGATGCCACAAGGGCGGCC
* *
53452393 ATACGGCCGTATGAGATACACAGGCTAGAGGTACGATCGTGTTCTTATT
66 ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
*
53452442 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGATGCCACAAGGGTGGCC
1 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGATGCCACAAGGGCGGCC
*
53452507 ATACGGCCGTGTGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
66 ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
53452556 TGT
1 TGT
53452559 AAATTTTTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (114 bp):
TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGATGCCACAAGGGCGGCC
ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
Found at i:53456452 original size:40 final size:39
Alignment explanation
Indices: 53456408--53456490 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
53456398 GCCCAGCCCG
*
53456408 AATA-TAAT-AAATATATATTTTTTATTTTTTTTATTTTTAA
1 AATATTAATAAAATA-AT-TTTTTTA-TTTTTTTACTTTTAA
**
53456448 AATATTTTTAAAATAATTTTTTTATTTTTTTACTTTTAA
1 AATATTAATAAAATAATTTTTTTATTTTTTTACTTTTAA
53456487 AATA
1 AATA
53456491 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 18 0.47
40 11 0.29
41 4 0.11
42 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (39 bp):
AATATTAATAAAATAATTTTTTTATTTTTTTACTTTTAA
Found at i:53456466 original size:12 final size:11
Alignment explanation
Indices: 53456439--53456468 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
53456429 TTATTTTTTT
53456439 TATTTTTAAAA
1 TATTTTTAAAA
53456450 TATTTTTAAAA
1 TATTTTTAAAA
53456461 TAATTTTT
1 T-ATTTTT
53456469 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:53461085 original size:3 final size:3
Alignment explanation
Indices: 53461077--53461141 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
53461067 CATTTGACCC
53461077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53461125 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
53461142 CCATCATCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53461149 original size:3 final size:3
Alignment explanation
Indices: 53461143--53461180 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53461133 TTATTATTAC
53461143 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
53461181 AAACTAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:53467033 original size:29 final size:30
Alignment explanation
Indices: 53466974--53467031 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53466964 TCCGAGCCTT
*
53466974 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
53467004 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
53467032 AGAGTCGAGG
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:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:53467431 original size:50 final size:50
Alignment explanation
Indices: 53467356--53467489 Score: 268
Period size: 50 Copynumber: 2.7 Consensus size: 50
53467346 ATTTGGGTAA
53467356 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
53467406 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
53467456 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
53467490 TCCCATGTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:53467492 original size:29 final size:29
Alignment explanation
Indices: 53467459--53467518 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
53467449 CGAGATGAGA
53467459 GGTCCCATGTAAGACCATGTCTGGGACAT
1 GGTCCCATGTAAGACCATGTCTGGGACAT
53467488 GGTCCCATGTAAGACCATGTCTGGGACAT
1 GGTCCCATGTAAGACCATGTCTGGGACAT
53467517 GG
1 GG
53467519 CGTTGGCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (29 bp):
GGTCCCATGTAAGACCATGTCTGGGACAT
Found at i:53467540 original size:79 final size:79
Alignment explanation
Indices: 53467409--53467568 Score: 293
Period size: 79 Copynumber: 2.0 Consensus size: 79
53467399 CGAGATGAGA
*
53467409 GGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGAC
1 GGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGTAAGAC
53467474 CATGTCTGGGACAT
66 CATGTCTGGGACAT
* *
53467488 GGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGAC
1 GGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGTAAGAC
53467553 CATGTCTGGGACAT
66 CATGTCTGGGACAT
53467567 GG
1 GG
53467569 CTTTGGCATG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (79 bp):
GGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGTAAGAC
CATGTCTGGGACAT
Found at i:53472639 original size:12 final size:12
Alignment explanation
Indices: 53472624--53472659 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
53472614 CCAAAAATAG
53472624 AAATGGAAATGA
1 AAATGGAAATGA
* *
53472636 AAATGAAAATAA
1 AAATGGAAATGA
53472648 AAATGGAAATGA
1 AAATGGAAATGA
53472660 TCCATTTGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (12 bp):
AAATGGAAATGA
Found at i:53472878 original size:26 final size:26
Alignment explanation
Indices: 53472822--53472878 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
53472812 TACCAGGAGC
*
53472822 AAAATCGTCAAAATTTTATTAGAGGT
1 AAAATCGTCAAAATTTTACTAGAGGT
* * * *
53472848 TAAATTGTCAAAATTTTGCTAGGGGT
1 AAAATCGTCAAAATTTTACTAGAGGT
53472874 AAAAT
1 AAAAT
53472879 AGGGATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (26 bp):
AAAATCGTCAAAATTTTACTAGAGGT
Found at i:53484720 original size:104 final size:103
Alignment explanation
Indices: 53484526--53484844 Score: 351
Period size: 102 Copynumber: 3.0 Consensus size: 103
53484516 GGAAAAAAAA
* *
53484526 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCA--ACAGTAATAAAAAATTTAAATTTTTTTCGT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACA--AAT--AAAA---AAATATATTTCGT
* *
53484589 GTCAGAATCAGATATCAATATACGAAAAAAGTTAAAAAAATATTTTT
59 GTCAGAATCAGATATCAGTATACGAAAAAAG-TAAAAAAA-ATTTAT
*
53484636 TTTGGGTGCTGGCCTGTCAATGGTCGGCACCCCA-TACAAATTAAAAAAA-A-ATTTCGTGTCAG
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCA-CCCAGTACAAA-TAAAAAAATATATTTCGTGTCAG
* ***
53484698 AATCAGATATCAGTATAAGAAAAAAGTAAAAAAAAAACAT
64 AATCAGATATCAGTATACGAAAAAAGTAAAAAAAATTTAT
* *
53484738 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATAAAAAAATTATTTTTTTTCGTGTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATAAAAAAA-TA---TATTTCGTGTC
*
53484803 AGAATCAGATATCAGTATACCAAAAAAGTAAAAAAAAATTTA
62 AGAATCAGATATCAGTATACGAAAAAAGT-AAAAAAAATTTA
53484845 AAAAGTAAAA
Statistics
Matches: 181, Mismatches: 17, Indels: 24
0.82 0.08 0.11
Matches are distributed among these distances:
101 12 0.07
102 36 0.20
103 9 0.05
104 35 0.19
106 3 0.02
107 35 0.19
108 9 0.05
109 4 0.02
110 30 0.17
111 5 0.03
112 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (103 bp):
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATAAAAAAATATATTTCGTGTCAGAA
TCAGATATCAGTATACGAAAAAAGTAAAAAAAATTTAT
Found at i:53484766 original size:102 final size:99
Alignment explanation
Indices: 53484518--53484840 Score: 353
Period size: 107 Copynumber: 3.1 Consensus size: 99
53484508 AAAAAAAAGG
53484518 AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCA-ACAGTAATAAAAAATTTAAATT
1 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCATACA--AATAAAAAA---AAA--
*
53484581 TTTTTCGTGTCAGAATCAGATATCAATATACGAAAAAAGTTAAA
59 --TTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAG-TAAA
*** *
53484625 AAAATATTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCCCATACAAATTAAAAAAAAATTT
1 AAAA-A-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCA-CCCATACAAA-TAAAAAAAAATTT
*
53484690 CGTGTCAGAATCAGATATCAGTATAAGAAAAAAGTAAA
62 CGTGTCAGAATCAGATATCAGTATACGAAAAAAGTAAA
53484728 AAAAAAACATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATAAAAAAATTATTTT
1 AAAAAAA-ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCA-TACAAATAAAAAAA--A----
* * *
53484793 TTTTCGTGTTAGAATCAGATATCAGTATACCAAAAAAGTAAA
58 ATTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAGTAAA
53484835 AAAAAA
1 AAAAAA
53484841 TTTAAAAAGT
Statistics
Matches: 188, Mismatches: 14, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
101 12 0.06
102 36 0.19
103 9 0.05
104 35 0.19
107 48 0.26
108 4 0.02
110 30 0.16
111 11 0.06
112 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (99 bp):
AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCATACAAATAAAAAAAAATTTCGTG
TCAGAATCAGATATCAGTATACGAAAAAAGTAAA
Found at i:53485709 original size:89 final size:88
Alignment explanation
Indices: 53485600--53485781 Score: 251
Period size: 89 Copynumber: 2.0 Consensus size: 88
53485590 GAGGTTTTGT
* *
53485600 TTTTTTCTTTACTCATTTGGGTACTTGAACTTTCAAAATGTATCAAAAAAAGCCTTCAAACCTTT
1 TTTTTTCTTTACTCAATTGGGTACTTGAACTTTCAAAATGTATCAAAAAAA-CCCTCAAA-CTTT
*
53485665 TCCAAAAA-AGCAATTAAGCCCCTAC
64 TCCAAAAAGA-CAATTAAGACCCTAC
* * *
53485690 TTTTTT-TTTACTTAATTGGGTACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAAACTTTTT
1 TTTTTTCTTTACTCAATTGGGTACTTGAACTTTCAAAATGTATCAAAAAAACCCTCAAACTTTTC
*
53485754 CAAAAAGTACAATTAAGACCCTGC
66 CAAAAAG-ACAATTAAGACCCTAC
53485778 TTTT
1 TTTT
53485782 ATTAAAAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
87 11 0.13
88 24 0.29
89 42 0.51
90 6 0.07
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (88 bp):
TTTTTTCTTTACTCAATTGGGTACTTGAACTTTCAAAATGTATCAAAAAAACCCTCAAACTTTTC
CAAAAAGACAATTAAGACCCTAC
Found at i:53485873 original size:21 final size:20
Alignment explanation
Indices: 53485848--53485889 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53485838 TAAACAATTC
*
53485848 AAATATTAAAAATTAGAAAAA
1 AAATA-TAAAAATCAGAAAAA
*
53485869 AAATATAAAAATCATAAAAA
1 AAATATAAAAATCAGAAAAA
53485889 A
1 A
53485890 TTATAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAATATAAAAATCAGAAAAA
Found at i:53485878 original size:8 final size:8
Alignment explanation
Indices: 53485867--53485915 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
53485857 AAATTAGAAA
53485867 AAAAATAT
1 AAAAATAT
53485875 AAAAATCAT
1 AAAAAT-AT
53485884 AAAAAATTAT
1 -AAAAA-TAT
53485894 AAAACATAT
1 AAAA-ATAT
*
53485903 AGAAATAT
1 AAAAATAT
53485911 AAAAA
1 AAAAA
53485916 AATTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 14 0.40
9 12 0.34
10 8 0.23
11 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:53485887 original size:19 final size:18
Alignment explanation
Indices: 53485865--53485915 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
53485855 AAAAATTAGA
53485865 AAAAAAATATAAAAATCAT
1 AAAAAAATATAAAAA-CAT
*
53485884 AAAAAATTAT-AAAACAT
1 AAAAAAATATAAAAACAT
* *
53485901 ATAGAAATATAAAAA
1 AAAAAAATATAAAAA
53485916 AATTATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 8 0.30
19 9 0.33
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAAATATAAAAACAT
Found at i:53485902 original size:28 final size:28
Alignment explanation
Indices: 53485866--53485925 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
53485856 AAAATTAGAA
53485866 AAAAAATATAAAAATCAT-AAAAAATTAT
1 AAAAAATATAAAAAT-ATAAAAAAATTAT
* *
53485894 AAAACATATAGAAATATAAAAAAATTAT
1 AAAAAATATAAAAATATAAAAAAATTAT
53485922 AAAA
1 AAAA
53485926 TTTTATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAAAATATAAAAATATAAAAAAATTAT
Found at i:53485916 original size:19 final size:18
Alignment explanation
Indices: 53485866--53485916 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
53485856 AAAATTAGAA
*
53485866 AAAAAATATAAAAATCAT
1 AAAAAATATAAAAAACAT
*
53485884 AAAAAAT-TATAAAACAT
1 AAAAAATATAAAAAACAT
*
53485901 ATAGAAATATAAAAAA
1 A-AAAAATATAAAAAA
53485917 ATTATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.33
18 12 0.44
19 6 0.22
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAATATAAAAAACAT
Found at i:53486230 original size:18 final size:19
Alignment explanation
Indices: 53486188--53486232 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
53486178 ATTTTTTATG
53486188 ATTTTTATAAAAAATTTGTA
1 ATTTTT-TAAAAAATTTGTA
*
53486208 A-TTTTTAATAAA-TTGTA
1 ATTTTTTAAAAAATTTGTA
53486225 ATTTTTTA
1 ATTTTTTA
53486233 TATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 4 0.17
20 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTTTTAAAAAATTTGTA
Found at i:53486260 original size:47 final size:44
Alignment explanation
Indices: 53486178--53486290 Score: 111
Period size: 47 Copynumber: 2.4 Consensus size: 44
53486168 AAATTTTTTT
*
53486178 ATTTTTTATGATTTTTATAAAAAATTTGTAATTTTTAATAAATTGTA
1 ATTTTTTAT-ATTTTTATAAAAAATTTATAATTTTTAA-AAATT-TA
* *
53486225 ATTTTTTATATTTTTAT-TAAAATTTAATAATTTTTTTAAAATTTA
1 ATTTTTTATATTTTTATAAAAAATTT-ATAA-TTTTTAAAAATTTA
* *
53486270 TTTTTATTTTATTTTTTATAA
1 ATTTT-TTATA-TTTTTATAA
53486291 TTTTTTTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
45 13 0.24
46 20 0.36
47 22 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (44 bp):
ATTTTTTATATTTTTATAAAAAATTTATAATTTTTAAAAATTTA
Found at i:53486267 original size:46 final size:45
Alignment explanation
Indices: 53486178--53486290 Score: 113
Period size: 46 Copynumber: 2.4 Consensus size: 45
53486168 AAATTTTTTT
*
53486178 ATTTTTTATGATTTTTATAAAAAATTTGTAATTTTTAATAAATTGTA
1 ATTTTTTAT-ATTTTTATAAAAAATTTATAATTTTTAATAAATT-TA
* *
53486225 ATTTTTTATATTTTTAT-TAAAATTTAATAATTTTT-TTAAAATTTA
1 ATTTTTTATATTTTTATAAAAAATTT-ATAATTTTTAAT-AAATTTA
* *
53486270 TTTTTATTTTATTTTTTATAA
1 ATTTT-TTATA-TTTTTATAA
53486291 TTTTTTTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
45 14 0.25
46 25 0.45
47 16 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (45 bp):
ATTTTTTATATTTTTATAAAAAATTTATAATTTTTAATAAATTTA
Found at i:53487237 original size:82 final size:82
Alignment explanation
Indices: 53487100--53487261 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
53487090 CACTTTCGCC
* *
53487100 ACCAAGAAATCGGTTCGGTTTAATTTAAGTAAGTTCTTTGTTTTTGTATCATGTCTAAGAGCTAG
1 ACCAAGAAATCGGTTCAGTTCAATTTAAGTAAGTTCTTTGTTTTTGTATCATGTCTAAGAGCTAG
*
53487165 TTTAATAATGCTTTTCA
66 TTTAACAATGCTTTTCA
* * *
53487182 ACCAAGAGATCGGTTCAGTTCAATTTGATTAAGTT-TGTTGTTTTTGTATCATGTCTAAGAGCTA
1 ACCAAGAAATCGGTTCAGTTCAATTTAAGTAAGTTCT-TTGTTTTTGTATCATGTCTAAGAGCTA
*
53487246 GTTTAGCAATGCTTTT
65 GTTTAACAATGCTTTT
53487262 TAAAAGTGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 1 0.01
82 71 0.99
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.43
Consensus pattern (82 bp):
ACCAAGAAATCGGTTCAGTTCAATTTAAGTAAGTTCTTTGTTTTTGTATCATGTCTAAGAGCTAG
TTTAACAATGCTTTTCA
Found at i:53489018 original size:13 final size:13
Alignment explanation
Indices: 53489000--53489040 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
53488990 CAAAACTAAT
*
53489000 AGAAAAGGAAGAA
1 AGAAAAGAAAGAA
*
53489013 AGAAAAGAAAGGA
1 AGAAAAGAAAGAA
*
53489026 AGACAAGAAAGAA
1 AGAAAAGAAAGAA
53489039 AG
1 AG
53489041 GGGCGCACGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:53489025 original size:17 final size:17
Alignment explanation
Indices: 53489003--53489041 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
53488993 AACTAATAGA
53489003 AAAGGAAGA-AAGAAAAG
1 AAAGGAAGACAAG-AAAG
53489020 AAAGGAAGACAAGAAAG
1 AAAGGAAGACAAGAAAG
53489037 AAAGG
1 AAAGG
53489042 GGCGCACGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGGAAGACAAGAAAG
Found at i:53490156 original size:14 final size:15
Alignment explanation
Indices: 53490134--53490210 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53490124 CAATCAAACA
53490134 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
53490148 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
53490163 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
53490183 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
53490197 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
53490211 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:53490175 original size:20 final size:20
Alignment explanation
Indices: 53490150--53490189 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53490140 AATATTTTCC
*
53490150 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
53490170 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
53490190 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:53490195 original size:34 final size:35
Alignment explanation
Indices: 53490138--53490204 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53490128 CAAACACCAG
*
53490138 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
53490173 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53490205 TATTTTACTG
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:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53490780 original size:18 final size:18
Alignment explanation
Indices: 53490757--53490849 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 18
53490747 GAAATGACCA
53490757 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
53490775 AGATGAGAAATATTGAAT-TGG
1 AGATGAG-AA-A-TGAATAT-G
* *
53490796 CAAAAATGAGAAATGAATATA
1 ---AGATGAGAAATGAATATG
*
53490817 AGATGAGAAATGTGATATG
1 AGATGAGAAATG-AATATG
*
53490836 AAATGATGAAATGA
1 AGATGA-GAAATGA
53490850 GATGTGAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
18 18 0.31
19 11 0.19
20 8 0.14
21 11 0.19
22 2 0.03
23 2 0.03
24 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.25, T:0.24
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:53490848 original size:20 final size:18
Alignment explanation
Indices: 53490799--53490858 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
53490789 GAATTGGCAA
*
53490799 AAATGAGAAATGAATAT-
1 AAATGAGAAATGGATATG
53490816 AAGATGAGAAATGTGATATG
1 AA-ATGAGAAATG-GATATG
*
53490836 AAATGATGAAATGAGATGTG
1 AAATGA-GAAATG-GATATG
53490856 AAA
1 AAA
53490859 CTTGAAACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.06
18 10 0.28
19 8 0.22
20 16 0.44
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (18 bp):
AAATGAGAAATGGATATG
Found at i:53491064 original size:18 final size:18
Alignment explanation
Indices: 53491041--53491079 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
53491031 ATAATATTTC
53491041 TTGTTGCATTCTCACATT
1 TTGTTGCATTCTCACATT
53491059 TTGTTGCATTCTCACATT
1 TTGTTGCATTCTCACATT
53491077 TTG
1 TTG
53491080 ATTACTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (18 bp):
TTGTTGCATTCTCACATT
Found at i:53494759 original size:37 final size:37
Alignment explanation
Indices: 53494718--53494792 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
53494708 ATCTATTTTC
* *
53494718 ATTTTCTTTCTTCTATCTTTTTCCCTGGTCTGTTGGT
1 ATTTTCTTTCTTCTATCTTTTTCCCTGGCCTGCTGGT
*
53494755 ATTTTTTTTCTTCTATCTTTTTCCCTGGCCTGCTGGT
1 ATTTTCTTTCTTCTATCTTTTTCCCTGGCCTGCTGGT
53494792 A
1 A
53494793 AAGAAGATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.07, C:0.23, G:0.13, T:0.57
Consensus pattern (37 bp):
ATTTTCTTTCTTCTATCTTTTTCCCTGGCCTGCTGGT
Found at i:53507684 original size:6 final size:6
Alignment explanation
Indices: 53507673--53507711 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
53507663 TCAATGTAAA
*
53507673 AAAAAC AAAAAC AAAAA- AAACA- AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
53507712 GAACCTCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:53507689 original size:7 final size:7
Alignment explanation
Indices: 53507672--53507711 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
53507662 TTCAATGTAA
53507672 AAAAAAC
1 AAAAAAC
*
53507679 AAAAACAA
1 AAAAA-AC
53507687 AAAAAAC
1 AAAAAAC
53507694 AAAAAAC
1 AAAAAAC
53507701 -AAAAAC
1 AAAAAAC
53507707 AAAAA
1 AAAAA
53507712 GAACCTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:53507690 original size:15 final size:16
Alignment explanation
Indices: 53507670--53507705 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
53507660 GATTCAATGT
53507670 AAAAAAAAC-AAAAAC
1 AAAAAAAACAAAAAAC
53507685 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
53507701 AAAAA
1 AAAAA
53507706 CAAAAAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:53508233 original size:23 final size:23
Alignment explanation
Indices: 53508201--53508250 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
53508191 AAAAAAGAAA
*
53508201 AAAAAGATGAGAAATGAAAAAGT
1 AAAAAGATGAAAAATGAAAAAGT
*
53508224 GAAAAA-ATGAAAAATGGAAAAGT
1 -AAAAAGATGAAAAATGAAAAAGT
53508247 AAAA
1 AAAA
53508251 TAGAGAGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (23 bp):
AAAAAGATGAAAAATGAAAAAGT
Found at i:53509815 original size:132 final size:132
Alignment explanation
Indices: 53509671--53510610 Score: 1123
Period size: 132 Copynumber: 7.1 Consensus size: 132
53509661 ACAGAGAAGC
* * * *
53509671 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGTAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTT
* *
53509736 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGGCAGCAGCGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
53509801 AT
131 AT
* * * * *
53509803 AGATTGAAGATTTTAGATCTTACCTTCCT--GCA-TAGACAGCGAAGCAGATCGAAGATGGCGGA
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG--TG-G-AGCAGATCGAAGATGGCAGA
* *
53509865 TTTTACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGTA
62 TTTTACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCA
53509929 GTGGAAT
126 GTGGAAT
* * *
53509936 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTT
* *
53510001 ACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
53510066 AT
131 AT
* * * * * *
53510068 AGATTGAAGATTTTAGATCTTACCTTCCT--GCA-TAGACAGCAAAGCAGATCGAAGATGGCGGA
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG--TG--GAGCAGATCGAAGATGGCAGA
* * * ***
53510130 TTTTACCTCCCTGTGATTATAGTGGAGTACATTGAAGCC-GTAATTCTA-TCTCCTTGGTTGGCA
62 TTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCA
*
53510193 GTTGAAT
126 GTGGAAT
* * * *
53510200 AGATTGAAGATTACAGATCTTATCTCCCT-AGACATTAATGGAGTAGATCGAAGATGGCAGATTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAGATGGCAGATTT
* *
53510264 TACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTG
65 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTG
53510328 GAAT
129 GAAT
* * * *
53510332 AGATTGAAGATTTCAGATCTTATCTCCCTAGGAATTAGTGGAGTAGATCGAAGAAAGATGGCAGA
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---G-AAGATGGCAGA
* * * * *
53510397 TTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCCGGAAATTCTA-TCTCCCTTGGCAGCA
62 TTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCA
53510461 GTGGAAT
126 GTGGAAT
* * * * *
53510468 AGATTGAAGATTACAGATCTTATCTCCCTAGGCATTAGTGGAGTAGATTGAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTT
* * *
53510533 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTTACTTCCCTGGTAG-TGTAGT
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC-TACTTCCCTGG--GCAGCAGT
53510597 GGAAT
128 GGAAT
53510602 AGATTGAAG
1 AGATTGAAG
53510611 TCATGACGGC
Statistics
Matches: 704, Mismatches: 77, Indels: 52
0.85 0.09 0.06
Matches are distributed among these distances:
129 6 0.01
130 5 0.01
131 58 0.08
132 308 0.44
133 172 0.24
134 22 0.03
135 7 0.01
136 126 0.18
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTT
ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
AT
Found at i:53510024 original size:265 final size:263
Alignment explanation
Indices: 53509671--53510610 Score: 1264
Period size: 265 Copynumber: 3.5 Consensus size: 263
53509661 ACAGAGAAGC
* * * *
53509671 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGTAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
53509736 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGGCAGCAGCGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
53509801 ATAGATTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCGGAT
131 ATAGATTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCGGAT
*
53509866 TTTACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGACAGTA
196 TTTACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATC-TCCCTGG-CAGCA
53509929 GTGGAAT
257 GTGGAAT
* * *
53509936 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
53510001 ACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
*
53510066 ATAGATTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCAAAGCAGATCGAAGATGGCGGAT
131 ATAGATTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCGGAT
* * * ** *
53510131 TTTACCTCCCTGTGATTATAGTGGAGTACATTGAAGCCGTAATTCTATCTCCTTGGTTGGCAGTT
196 TTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCGTAATTCTATCTCCCTGG-CAGCAGTG
53510196 GAAT
260 GAAT
* * * *
53510200 AGATTGAAGATTACAGATCTTATCTCCCT-AGACATTAATGGAGTAGATCGAAGATGGCAGATTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCAAAGATGGCAGATTT
*
53510264 TACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTG
* * * * ** * * *
53510328 GAATAGATTGAAGATTTCAGATCTTATCTCCCTAGGA-A-TTAGTGGAGTAGATCGAAGAAAGAT
129 GAATAGATTGAAGATTTTAGATCTTACCTTCCT-GCATAGACAGCGAAGCAGATC---G-AAGAT
* * * *
53510391 GGCAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCCGGAAATTCTATCTCCCTTGG
189 GGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATCTCCC-TGG
53510456 CAGCAGTGGAAT
252 CAGCAGTGGAAT
* * * **
53510468 AGATTGAAGATTACAGATCTTATCTCCCTAGGCATTAGTGGAGTAGATTGAAGATGGCAGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* *
53510533 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTTACTTCCCTGGTAG-TGTAGT
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC-TACTTCCCTGG--GCAGCAGT
53510597 GGAATAGATTGAAG
128 GGAATAGATTGAAG
53510611 TCATGACGGC
Statistics
Matches: 608, Mismatches: 51, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
263 12 0.02
264 166 0.27
265 224 0.37
266 4 0.01
267 45 0.07
268 124 0.20
269 13 0.02
270 19 0.03
271 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (263 bp):
AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
ATAGATTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCGGAT
TTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCGTAATTCTATCTCCCTGGCAGCAGTGG
AAT
Found at i:53510247 original size:44 final size:44
Alignment explanation
Indices: 53510199--53510540 Score: 155
Period size: 44 Copynumber: 7.7 Consensus size: 44
53510189 GGCAGTTGAA
* *
53510199 TAGATTGAAGATTACAGATCTTATCTCCCTAGACATTAATGGAG
1 TAGATTGAAGATGACAGATCTTATCTCCCTAGACATTAGTGGAG
* * * * **
53510243 TAGATCGAAGATGGCAGATTTTACCTCCCT-GAGGTTATAGTGGAG
1 TAGATTGAAGATGACAGATCTTATCTCCCTAGA-CAT-TAGTGGAG
* * * * ** *
53510288 TACATTG-A-A-GCCAGTAAT-TCTATCTCCCTGGGCAGCAGTGGAA
1 TAGATTGAAGATGACAG--ATCT-TATCTCCCTAGACATTAGTGGAG
**
53510331 TAGATTGAAGATTTCAGATCTTATCTCCCTAGGA-ATTAGTGGAG
1 TAGATTGAAGATGACAGATCTTATCTCCCTA-GACATTAGTGGAG
* * * * ** *
53510375 TAGATCGAAGAAAGATGGCAGATTTTACCTCCCT-GAGGTTACAATGGAG
1 TAGAT---TG-AAGATGACAGATCTTATCTCCCTAGACATT--AGTGGAG
* ** * * ** *
53510424 TACATTGAAGCCGGA-A-AT-TCTATCTCCCTTGGCAGCAGTGGAA
1 TAGATTGAAG-ATGACAGATCT-TATCTCCCTAGACATTAGTGGAG
* *
53510467 TAGATTGAAGATTACAGATCTTATCTCCCTAGGCATTAGTGGAG
1 TAGATTGAAGATGACAGATCTTATCTCCCTAGACATTAGTGGAG
* * *
53510511 TAGATTGAAGATGGCAGATTTTACCTCCCT
1 TAGATTGAAGATGACAGATCTTATCTCCCT
53510541 GAGGTTACAG
Statistics
Matches: 216, Mismatches: 58, Indels: 48
0.67 0.18 0.15
Matches are distributed among these distances:
42 5 0.02
43 32 0.15
44 118 0.55
45 22 0.10
46 7 0.03
47 3 0.01
48 19 0.09
49 10 0.05
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
TAGATTGAAGATGACAGATCTTATCTCCCTAGACATTAGTGGAG
Found at i:53514838 original size:24 final size:24
Alignment explanation
Indices: 53514811--53514856 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53514801 AGAACAATCC
* *
53514811 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
53514835 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
53514857 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:53519579 original size:132 final size:132
Alignment explanation
Indices: 53518802--53519564 Score: 1253
Period size: 132 Copynumber: 5.8 Consensus size: 132
53518792 TTGACAGCGA
** *
53518802 AGCAGATCGAAGATGGCGGATTTTACCTCATTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
53518867 TCTACTTCCCTGAACAACAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53518932 GG
131 GG
* * **
53518934 AGCAGATCGAAGATGACGGATTTTACCTTCCTGTGGTTATTGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53518999 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53519064 GG
131 GG
* * *
53519066 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTGCATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
53519131 TCTACTTCCCTGGGCAACAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53519196 GG
131 GG
53519198 AGCAGATCGAA-ATTGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCGAAGA-TGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
** *
53519262 TTCTACTTCCCTAAACAACAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAAGCAGTAG
65 TTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
53519327 TGG
130 TGG
* * *
53519330 AGCAGATCGAAGATGGCTGATTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53519395 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTTGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53519460 GG
131 GG
53519462 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
53519526 TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
53519565 GTAAGTCCTA
Statistics
Matches: 588, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 4 0.01
132 583 0.99
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:53519916 original size:19 final size:19
Alignment explanation
Indices: 53519892--53520002 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
53519882 AATCTTCAGG
53519892 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
53519911 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
* ** *
53519930 AATATATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
53519949 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
53519968 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53519987 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
53520003 AGATATGATT
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 78 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53520001 original size:38 final size:38
Alignment explanation
Indices: 53519899--53520002 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
53519889 AGGGATATGC
*
53519899 AATCTTAGATATGATATGCAATCTTAAATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
* *
53519937 AATTTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
53519975 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
53520003 AGATATGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:53520028 original size:22 final size:21
Alignment explanation
Indices: 53519892--53520028 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
53519882 AATCTTCAGG
*
53519892 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
53519911 GATATGCAATCTTA-A-ATAT
1 GATATGTAATCTTAGAGATAT
* * *
53519930 AATATATAAT-TT-TAGATAT
1 GATATGTAATCTTAGAGATAT
*
53519949 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
53519968 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
53519987 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
53520009 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
53520029 TTAATTTATA
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
18 3 0.03
19 69 0.70
20 3 0.03
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:53521665 original size:2 final size:2
Alignment explanation
Indices: 53521660--53521684 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53521650 TGGTTTCTAC
53521660 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53521685 CACACACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53533857 original size:18 final size:18
Alignment explanation
Indices: 53533836--53533873 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53533826 ATCTAATTCT
53533836 AATAACTATTAGAATTTA
1 AATAACTATTAGAATTTA
53533854 AATAACTATTAGAATTTA
1 AATAACTATTAGAATTTA
53533872 AA
1 AA
53533874 GTACATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAACTATTAGAATTTA
Found at i:53533970 original size:23 final size:23
Alignment explanation
Indices: 53533940--53533985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53533930 ACACTCCCCC
53533940 TTGGATGTCCATTGATAGATACT
1 TTGGATGTCCATTGATAGATACT
53533963 TTGGATGTCCATTGATAGATACT
1 TTGGATGTCCATTGATAGATACT
53533986 GTGTCTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
TTGGATGTCCATTGATAGATACT
Found at i:53537881 original size:24 final size:24
Alignment explanation
Indices: 53537854--53537899 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53537844 AACCTAATTC
53537854 TAATCAAA-GTCAAATATATTATGT
1 TAAT-AAATGTCAAATATATTATGT
*
53537878 TAATAAATGTTAAATATATTAT
1 TAATAAATGTCAAATATATTAT
53537900 ACTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
TAATAAATGTCAAATATATTATGT
Found at i:53537915 original size:24 final size:24
Alignment explanation
Indices: 53537865--53537916 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
53537855 AATCAAAGTC
** **
53537865 AAATATATTATGTTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
53537889 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
53537913 AAAT
1 AAAT
53537917 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:53542308 original size:24 final size:24
Alignment explanation
Indices: 53542276--53542327 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53542266 GATCAAAGTC
*
53542276 AAATATATTATGT-TAATAAATGCT
1 AAATATATTAT-TCTAATAAATACT
*
53542300 AAATATATTATTCTCATAAATACT
1 AAATATATTATTCTAATAAATACT
53542324 AAAT
1 AAAT
53542328 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATTCTAATAAATACT
Found at i:53542988 original size:20 final size:20
Alignment explanation
Indices: 53542946--53542989 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
53542936 TCTCAATAAT
* **
53542946 TAAATGCATGAAAGGTTTTA
1 TAAATGCATGAAACGTTAAA
53542966 TAAATGCATGAAACGTTAAA
1 TAAATGCATGAAACGTTAAA
53542986 TAAA
1 TAAA
53542990 AGAAACTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.30
Consensus pattern (20 bp):
TAAATGCATGAAACGTTAAA
Found at i:53543401 original size:20 final size:21
Alignment explanation
Indices: 53543368--53543409 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
53543358 CTTTTTTCTC
53543368 GTGTGATGCACAAGTGTAATGT
1 GTGTGATG-ACAAGTGTAATGT
53543390 GTGTGATG-CAAGTGTAATGT
1 GTGTGATGACAAGTGTAATGT
53543410 ATGTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (21 bp):
GTGTGATGACAAGTGTAATGT
Found at i:53544682 original size:20 final size:20
Alignment explanation
Indices: 53544646--53544683 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53544636 GTTTGTTATT
*
53544646 TTAATTATTCTATTACTAAA
1 TTAATTATTCTAATACTAAA
*
53544666 TTAATTATTTTAATACTA
1 TTAATTATTCTAATACTA
53544684 TTATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTATTCTAATACTAAA
Found at i:53545191 original size:4 final size:4
Alignment explanation
Indices: 53545182--53545214 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
53545172 TGTTTTATCT
53545182 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
53545215 GTGTTCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:53545884 original size:107 final size:108
Alignment explanation
Indices: 53545758--53546064 Score: 519
Period size: 108 Copynumber: 2.9 Consensus size: 108
53545748 AAATAATAAG
* * *
53545758 TAAGGCAATGTTTTGCGTTTGG-AAATTCGAGAAAACATACCGTAATGTGTTGGGTTTCTATTTT
1 TAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
53545822 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
* *
53545865 TAAGGCAATGTTTTGCGTTTGGAAAATTTGAGAAAACGTACCCTAATGTGTTGGGTTTCGATCTT
1 TAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
53545930 TTCGTTCGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
*
53545973 TAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTACCCTAATGTGCTGGGTTTCGA-TTT
1 TAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
* *
53546037 CTCGTTGGACCAAATAGCCAAATATCCT
66 TTCGTTCGACCAAATAGCCAAATATCCT
53546065 CTTGAATCTT
Statistics
Matches: 187, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
107 49 0.26
108 138 0.74
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (108 bp):
TAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
Found at i:53550915 original size:29 final size:29
Alignment explanation
Indices: 53550865--53550933 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
53550855 AATTTTATCA
*
53550865 ATTTTTTAATAAAAATTAAAT-ATTTCTTAT
1 ATTTTTT-ATTAAAATTAAATAATTT-TTAT
53550895 ATTTTTTATTAAAATCT-AATAATTTTTAT
1 ATTTTTTATTAAAAT-TAAATAATTTTTAT
**
53550924 AAATTTTATT
1 ATTTTTTATT
53550934 TTTTATCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTTTTATTAAAATTAAATAATTTTTAT
Found at i:53558426 original size:2 final size:2
Alignment explanation
Indices: 53558419--53558469 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
53558409 GCAACATAGC
53558419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53558461 AT AT AT AT A
1 AT AT AT AT A
53558470 CTTTCACAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53559035 original size:34 final size:36
Alignment explanation
Indices: 53558955--53559035 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
53558945 CAATATTAAA
* * * *
53558955 TGTGAGCCCAGCTCTAGTTGGATGAACTAACGGTAT
1 TGTGTGCCCAGCGCTAGTCGGATAAACTAACGGTAT
*
53558991 T-TGTGCCCAGCGCTAGTCGGATAAATTAAC-G-AT
1 TGTGTGCCCAGCGCTAGTCGGATAAACTAACGGTAT
53559024 TGTGTGCCCAGC
1 TGTGTGCCCAGC
53559036 ACTAATCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 3 0.08
34 11 0.28
35 24 0.62
36 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (36 bp):
TGTGTGCCCAGCGCTAGTCGGATAAACTAACGGTAT
Found at i:53559293 original size:15 final size:15
Alignment explanation
Indices: 53559275--53559313 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
53559265 AACATTAATT
53559275 TATTCCTTAATGTCA
1 TATTCCTTAATGTCA
*
53559290 TATTCTTTAATGTCA
1 TATTCCTTAATGTCA
53559305 TATTTCCTT
1 TA-TTCCTT
53559314 CTAATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (15 bp):
TATTCCTTAATGTCA
Found at i:53573627 original size:19 final size:19
Alignment explanation
Indices: 53573603--53573717 Score: 167
Period size: 19 Copynumber: 5.8 Consensus size: 19
53573593 AATTTTTGAG
53573603 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
53573622 GATATGAAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
53573641 GATATATGGAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
53573662 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
53573681 GATAAGTGCAATCTTGGATAT
1 GAT-A-TGCAATCTTAGATAT
53573702 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
53573718 AGATATGATT
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
19 50 0.57
20 2 0.02
21 35 0.40
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53573648 original size:40 final size:40
Alignment explanation
Indices: 53573604--53573717 Score: 185
Period size: 40 Copynumber: 2.9 Consensus size: 40
53573594 ATTTTTGAGG
*
53573604 ATATGCAATCTTAGATATGATATGAAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
*
53573644 ATATGGAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
*
53573684 A-AGTGCAATCTTGGATATGATATGCAATCTTAGA
1 ATA-TGCAATCTTAGATATGATATGCAATCTTAGA
53573718 AGATATGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.01
40 68 0.99
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
Found at i:53573707 original size:59 final size:56
Alignment explanation
Indices: 53573603--53573724 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 56
53573593 AATTTTTGAG
*
53573603 GATATGCAATCTTAGATATGATATGAAATCTTAGATATGATATATGGAATCTTAGATA
1 GATATGCAATCTTAGATATGATATGAAATCTTAGATATGA-ATATGCAATCTTAGA-A
* *
53573661 TGATATGCAATCTTAGATATGATAAGTGCAATCTTGGATATG-ATATGCAATCTTAGAA
1 -GATATGCAATCTTAGATATGAT-A-TGAAATCTTAGATATGAATATGCAATCTTAGAA
53573719 GATATG
1 GATATG
53573725 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
57 6 0.10
58 1 0.02
59 36 0.62
60 1 0.02
61 14 0.24
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (56 bp):
GATATGCAATCTTAGATATGATATGAAATCTTAGATATGAATATGCAATCTTAGAA
Found at i:53574659 original size:8 final size:8
Alignment explanation
Indices: 53574648--53574696 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
53574638 GCTTTGCGTG
*
53574648 TTATTGAT
1 TTATTTAT
53574656 TTATCTTTAT
1 TTAT--TTAT
53574666 TTATTTAT
1 TTATTTAT
53574674 TTATTTAT
1 TTATTTAT
*
53574682 TTGTTTAT
1 TTATTTAT
53574690 ATTATTT
1 -TTATTT
53574697 CTATGCCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 23 0.66
9 5 0.14
10 7 0.20
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (8 bp):
TTATTTAT
Found at i:53574670 original size:4 final size:4
Alignment explanation
Indices: 53574661--53574696 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
53574651 TTGATTTATC
*
53574661 TTTA TTTA TTTA TTTA TTTA TTTG TTTA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
53574697 CTATGCCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:53592065 original size:3 final size:3
Alignment explanation
Indices: 53592057--53592105 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
53592047 CAAGCTTAAG
53592057 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53592105 T
1 T
53592106 GATGATGATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53596007 original size:21 final size:21
Alignment explanation
Indices: 53595951--53596008 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
53595941 CACTTGGGCC
* *
53595951 GAATGCTACTGGGCCACTTAT
1 GAATGCTACTGGGTCGCTTAT
* *
53595972 AAATGCTGCTGGGTCGCTTAT
1 GAATGCTACTGGGTCGCTTAT
*
53595993 GAATGCTACTAGGTCG
1 GAATGCTACTGGGTCG
53596009 TCAGCTGTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (21 bp):
GAATGCTACTGGGTCGCTTAT
Found at i:53619132 original size:57 final size:57
Alignment explanation
Indices: 53619064--53619179 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
53619054 TGCCTAGAGT
53619064 TCTCGACTGTCATGCATCTAATTTCTCGAATTCTACCATGTCTAATGCTAATGCAAC
1 TCTCGACTGTCATGCATCTAATTTCTCGAATTCTACCATGTCTAATGCTAATGCAAC
53619121 TCTCGACTGTCATGCATCTAATTTCTCGAATTCTACCATGTCTAATGCTAATGCAAC
1 TCTCGACTGTCATGCATCTAATTTCTCGAATTCTACCATGTCTAATGCTAATGCAAC
53619178 TC
1 TC
53619180 ATTTTGGGTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (57 bp):
TCTCGACTGTCATGCATCTAATTTCTCGAATTCTACCATGTCTAATGCTAATGCAAC
Found at i:53625944 original size:30 final size:31
Alignment explanation
Indices: 53625889--53625946 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
53625879 ACCCTTAAAA
** *
53625889 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTTTG
53625920 TATTTACACT-TTAATCCCTCAAATTTT
1 TATTTACACTATTAATCCCTCAAATTTT
53625947 GAGTTTTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTTTG
Found at i:53627744 original size:50 final size:50
Alignment explanation
Indices: 53627669--53628049 Score: 344
Period size: 50 Copynumber: 7.6 Consensus size: 50
53627659 TTTCTGTACA
* * * *
53627669 GCCAATGACATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGT
* ** * * *
53627719 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGT
* * * *
53627769 GCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGT
* * * * * *
53627819 GCCAACGCCATGTCCCAAATATGGTCTTACATGAGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGT
* *
53627869 GCCAACGCCATGTCCCAGACATGGTCTTACATGGG-GCCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCAT-A--TC---GGT
* * * *
53627925 GCCAATGCCATGTCCCAGACATGGTCTTACACT--G-GCTCACACACCGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGAGCTCTCATATCGGT
* * * *
53627973 GTCGATGCCATGTCCCAGACATGGTCTTACACT---AGCTCACATATCGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGAGCTCTCATATCGGT
* *
53628021 GTCGATGCCATGTCCCAGACATGGTCTTA
1 GCCAATGCCATGTCCCAGACATGGTCTTA
53628050 TACGAGATCG
Statistics
Matches: 288, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
48 75 0.26
50 169 0.59
51 1 0.00
53 3 0.01
54 5 0.02
55 2 0.01
56 32 0.11
57 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGT
Found at i:53627984 original size:48 final size:48
Alignment explanation
Indices: 53627929--53628049 Score: 215
Period size: 48 Copynumber: 2.5 Consensus size: 48
53627919 AATGATGCCA
*
53627929 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACACCGATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACACACCGATGTCG
* *
53627977 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACACACCGATGTCG
53628025 ATGCCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
53628050 TACGAGATCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACACACCGATGTCG
Found at i:53628784 original size:22 final size:22
Alignment explanation
Indices: 53628753--53628825 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
53628743 TAATTTAAAA
*
53628753 TGAAATCCCAATTTGTCGTAAT
1 TGAAAGCCCAATTTGTCGTAAT
*
53628775 TGAAAGCCCAA-TT-AC--AA-
1 TGAAAGCCCAATTTGTCGTAAT
**
53628792 -GAAATTCCAATTTGTCGTAAT
1 TGAAAGCCCAATTTGTCGTAAT
53628813 TGAAAGCCCAATT
1 TGAAAGCCCAATT
53628826 ACAAGAAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
16 8 0.21
17 2 0.05
18 3 0.08
20 3 0.08
21 2 0.05
22 20 0.53
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
TGAAAGCCCAATTTGTCGTAAT
Found at i:53628796 original size:38 final size:38
Alignment explanation
Indices: 53628754--53628846 Score: 177
Period size: 38 Copynumber: 2.4 Consensus size: 38
53628744 AATTTAAAAT
53628754 GAAATCCCAATTTGTCGTAATTGAAAGCCCAATTACAA
1 GAAATCCCAATTTGTCGTAATTGAAAGCCCAATTACAA
*
53628792 GAAATTCCAATTTGTCGTAATTGAAAGCCCAATTACAA
1 GAAATCCCAATTTGTCGTAATTGAAAGCCCAATTACAA
53628830 GAAATCCCAATTTGTCG
1 GAAATCCCAATTTGTCG
53628847 AATCCATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (38 bp):
GAAATCCCAATTTGTCGTAATTGAAAGCCCAATTACAA
Found at i:53631652 original size:29 final size:29
Alignment explanation
Indices: 53631595--53631653 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
53631585 CAATGTTTAC
* *
53631595 TTTTCAAAATGGATCATTTACGTACATAA
1 TTTTCAAAATGGATCATTTACATAAATAA
* *
53631624 TTTTCAAAGTGGATCATTTTCATAAATAA
1 TTTTCAAAATGGATCATTTACATAAATAA
53631653 T
1 T
53631654 CAAAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (29 bp):
TTTTCAAAATGGATCATTTACATAAATAA
Found at i:53642174 original size:11 final size:10
Alignment explanation
Indices: 53642153--53642177 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53642143 CCCCCCCCCC
53642153 AAAACAAAAA
1 AAAACAAAAA
53642163 AAAACAAAAA
1 AAAACAAAAA
53642173 AAAAC
1 AAAAC
53642178 TACGTCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:53650224 original size:22 final size:23
Alignment explanation
Indices: 53650193--53650241 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
53650183 CTTTATGAAA
53650193 TTTTCAAAAAATTTAACTAATT-
1 TTTTCAAAAAATTTAACTAATTC
* *
53650215 TTTTCTAAAATTTTAACTAATTC
1 TTTTCAAAAAATTTAACTAATTC
53650238 TTTT
1 TTTT
53650242 ATATTTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTCAAAAAATTTAACTAATTC
Found at i:53650362 original size:21 final size:22
Alignment explanation
Indices: 53650338--53650383 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
53650328 AATATTTTTC
*
53650338 TAAGATATAT-GTT-TTATTAAA
1 TAAGATAT-TGGTTATTATAAAA
53650359 TAAGATATTGGTTATTATAAAA
1 TAAGATATTGGTTATTATAAAA
53650381 TAA
1 TAA
53650384 TTTTTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 11 0.50
22 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (22 bp):
TAAGATATTGGTTATTATAAAA
Found at i:53650523 original size:2 final size:2
Alignment explanation
Indices: 53650516--53650544 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53650506 ATTTCATTCC
53650516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53650545 AACACATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53651014 original size:15 final size:15
Alignment explanation
Indices: 53650980--53651011 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
53650970 TATATACATT
53650980 ACCATATAAATACTA
1 ACCATATAAATACTA
53650995 ACCATA-AAATACTA
1 ACCATATAAATACTA
53651009 ACC
1 ACC
53651012 CATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:53652725 original size:12 final size:12
Alignment explanation
Indices: 53652708--53652737 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53652698 TATTAACCTT
53652708 TATATAAATATA
1 TATATAAATATA
*
53652720 TATATACATATA
1 TATATAAATATA
53652732 TATATA
1 TATATA
53652738 TAAGGCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAAATATA
Found at i:53653803 original size:15 final size:16
Alignment explanation
Indices: 53653777--53653806 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53653767 GATTCAGTTG
53653777 ATTTTGAATTGGATCC
1 ATTTTGAATTGGATCC
53653793 ATTTT-AATTGGATC
1 ATTTTGAATTGGATC
53653807 AACATAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTTTGAATTGGATCC
Found at i:53655467 original size:14 final size:13
Alignment explanation
Indices: 53655438--53655472 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
53655428 AATTCTCTCT
*
53655438 TAAAATTTTTTAC
1 TAAATTTTTTTAC
53655451 TAAATTTTTTTATC
1 TAAATTTTTTTA-C
53655465 TAAATTTT
1 TAAATTTT
53655473 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTTTTTTAC
Found at i:53658884 original size:19 final size:18
Alignment explanation
Indices: 53658836--53658884 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
53658826 GATAGTGACA
53658836 ATTACAAACC-AAAGAAT
1 ATTACAAACCAAAAGAAT
* * *
53658853 ATAAAAAAGCAAACAGAAT
1 ATTACAAACCAAA-AGAAT
53658872 ATTACAAACCAAA
1 ATTACAAACCAAA
53658885 TAATATCGGT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 7 0.29
18 2 0.08
19 15 0.62
ACGTcount: A:0.63, C:0.16, G:0.06, T:0.14
Consensus pattern (18 bp):
ATTACAAACCAAAAGAAT
Found at i:53662929 original size:18 final size:17
Alignment explanation
Indices: 53662896--53662934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53662886 TTTTATAAAT
53662896 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53662914 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53662931 TGTG
1 TGTG
53662935 GAAGAAAAAT
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:53663190 original size:23 final size:23
Alignment explanation
Indices: 53663160--53663303 Score: 182
Period size: 23 Copynumber: 6.3 Consensus size: 23
53663150 AGTGTTATGG
* *
53663160 ATCAGTGGTATCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * *
53663183 TTCTGTGGTAGCTACTGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
53663206 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
53663229 -TCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTACGGCTACAT
*
53663251 ATCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
*
53663274 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
53663297 ATCAGTG
1 ATCAGTG
53663304 TGGCACTTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 18 0.17
23 85 0.83
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:53665068 original size:16 final size:17
Alignment explanation
Indices: 53665047--53665079 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53665037 TAATAGGAAA
53665047 AATATG-ATGATACGAG
1 AATATGAATGATACGAG
53665063 AATATGAAATGATACGA
1 AATATG-AATGATACGA
53665080 ATCAATTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (17 bp):
AATATGAATGATACGAG
Done.