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 162 of 175
Found at i:48661555 original size:21 final size:19
Alignment explanation
Indices: 48661531--48661581 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
48661521 TTTATTTAAA
48661531 TGAATTTAATTAATTTTCTAC
1 TGAATTTAATT--TTTTCTAC
*
48661552 TGAAATT-ATTTTTTCTAC
1 TGAATTTAATTTTTTCTAC
*
48661570 TCAATTCTAATT
1 TGAATT-TAATT
48661582 CCGTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 12 0.48
19 1 0.04
20 6 0.24
21 6 0.24
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (19 bp):
TGAATTTAATTTTTTCTAC
Found at i:48663015 original size:20 final size:19
Alignment explanation
Indices: 48662990--48663048 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
48662980 CTCCGACCAG
48662990 CTCAATTGAGCTCATTTCAA
1 CTCAATTGAGCTCATTT-AA
* *
48663010 CTCAATCGAGCTCAATTTAG
1 CTCAATTGAGCTC-ATTTAA
*
48663030 CTACAATTCAGCTCATTTA
1 CT-CAATTGAGCTCATTTA
48663049 TTTTATTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (19 bp):
CTCAATTGAGCTCATTTAA
Found at i:48663042 original size:11 final size:10
Alignment explanation
Indices: 48662987--48663044 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
48662977 CAACTCCGAC
48662987 CAGCTCAATT
1 CAGCTCAATT
* *
48662997 GAGCTCATTT
1 CAGCTCAATT
*
48663007 CAACTCAA-T
1 CAGCTCAATT
48663016 CGAGCTCAATT
1 C-AGCTCAATT
*
48663027 TAGCTACAATT
1 CAGCT-CAATT
48663038 CAGCTCA
1 CAGCTCA
48663045 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:48664558 original size:46 final size:46
Alignment explanation
Indices: 48664508--48664643 Score: 166
Period size: 46 Copynumber: 3.0 Consensus size: 46
48664498 GCTTCCTAGC
** *
48664508 TTCCAAGCTTTTGCATATGTTGTGGACTCGAGAATGCA-AGAATAGG
1 TTCCAAGCTCCTGCATATGTTGTGGACTCGAGAATACATA-AATAGG
* * **
48664554 TTCCAAACTCCTGCATATGTTGCGGACTCGAGAATACATATTTAGG
1 TTCCAAGCTCCTGCATATGTTGTGGACTCGAGAATACATAAATAGG
* * *
48664600 TTCCGAGCTCCTACATATGTTGTGGACTCGAGAATACAGAAATA
1 TTCCAAGCTCCTGCATATGTTGTGGACTCGAGAATACATAAATA
48664644 TTAAGCCCTG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
46 74 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (46 bp):
TTCCAAGCTCCTGCATATGTTGTGGACTCGAGAATACATAAATAGG
Found at i:48670906 original size:19 final size:19
Alignment explanation
Indices: 48670876--48670930 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
48670866 TATATATATT
48670876 TTTTGAAATTTTTATAAATA
1 TTTTG-AATTTTTATAAATA
* *
48670896 TTTTGAATTTTAAAAAATA
1 TTTTGAATTTTTATAAATA
48670915 TTTTGAATTTTT-TAAA
1 TTTTGAATTTTTATAAA
48670931 ATTAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 3 0.10
19 23 0.74
20 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTGAATTTTTATAAATA
Found at i:48670939 original size:20 final size:19
Alignment explanation
Indices: 48670876--48670943 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
48670866 TATATATATT
*
48670876 TTTTGAAATTTTTATAAATA
1 TTTTGAATTTTTTA-AAATA
**
48670896 TTTTGAATTTTAAAAAATA
1 TTTTGAATTTTTTAAAATA
48670915 TTTTGAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAA-TA
*
48670935 ATTTGAATT
1 TTTTGAATT
48670944 ATATTATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 20 0.49
20 21 0.51
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTGAATTTTTTAAAATA
Found at i:48670958 original size:39 final size:39
Alignment explanation
Indices: 48670863--48670958 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
48670853 TTAACTTTCT
* *
48670863 TTATATATATATTTTTTGAAATTTTTATAAATATTTTGAA
1 TTATAT-TATAATTTTTGAAATTTTTATAAATAATTTGAA
* * * *
48670903 TTTTA-AAAAATATTTTGAATTTTTTA-AAATTAATTTGAA
1 TTATATTATAAT-TTTTGAAATTTTTATAAA-TAATTTGAA
48670942 TTATATTATAATTTTTG
1 TTATATTATAATTTTTG
48670959 TTGAGAGTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
38 6 0.14
39 30 0.68
40 8 0.18
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (39 bp):
TTATATTATAATTTTTGAAATTTTTATAAATAATTTGAA
Found at i:48673618 original size:21 final size:24
Alignment explanation
Indices: 48673563--48673626 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
48673553 GGTGATCAAC
*
48673563 AACAGCAGGAGCTGCAATATGAGG
1 AACAGCAGCAGCTGCAATATGAGG
48673587 AACAGCAGCAGCTGCAATATGAGG
1 AACAGCAGCAGCTGCAATATGAGG
48673611 AACAGCAGCAGCTGCA
1 AACAGCAGCAGCTGCA
48673627 TCAGCAACAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.11
Consensus pattern (24 bp):
AACAGCAGCAGCTGCAATATGAGG
Found at i:48676347 original size:53 final size:53
Alignment explanation
Indices: 48676267--48676425 Score: 291
Period size: 53 Copynumber: 3.0 Consensus size: 53
48676257 TATTGTAGCG
* *
48676267 TAAGACAAAAAGTAAGCTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
1 TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
48676320 TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
1 TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
*
48676373 TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTGCCCATCCAAAC
1 TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
48676426 CCATCCTTAG
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.18
Consensus pattern (53 bp):
TAAGATAAAAAGTAAGTTAAATGCACGCACCGCACTCAATTACCCATCCAAAC
Found at i:48676875 original size:3 final size:3
Alignment explanation
Indices: 48676867--48676902 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
48676857 ACAAGCGGGG
*
48676867 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GTA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
48676903 ACCTTGGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:48685117 original size:46 final size:45
Alignment explanation
Indices: 48685050--48685293 Score: 285
Period size: 46 Copynumber: 5.6 Consensus size: 45
48685040 TTTGAGTACT
**
48685050 TCTGATCAAGTGATGAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
48685096 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
48685132 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
48685178 TCTGATCCAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
48685224 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
48685269 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
48685294 ATCATATGTA
Statistics
Matches: 173, Mismatches: 15, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
36 28 0.16
38 1 0.01
39 1 0.01
40 3 0.02
41 1 0.01
42 4 0.02
43 15 0.09
44 3 0.02
45 19 0.11
46 98 0.57
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:48685132 original size:36 final size:36
Alignment explanation
Indices: 48685086--48685158 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
48685076 GGTAGCTTTA
48685086 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
48685122 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
48685158 G
1 G
48685159 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:48685144 original size:82 final size:84
Alignment explanation
Indices: 48685050--48685293 Score: 300
Period size: 82 Copynumber: 2.8 Consensus size: 84
48685040 TTTGAGTACT
**
48685050 TCTGATCAAGTGATGAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC-AGTGAAAAAGT
48685115 GATAAGTG-C-TA-TA-CTTA
64 GATAAGTGCCTTACTACCTTA
* *
48685132 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCCAGTGAGAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGAT-CAGTGAAAAAGT
48685197 GATAAGTGGTAGCCTTAGCTACTCTTA
64 GATAA---GT-GCCTTA-CTAC-CTTA
* * *
48685224 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAG-GGACAAGTGA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGAAAAAGTGA
48685288 TAAGTG
66 TAAGTG
48685294 ATCATATGTA
Statistics
Matches: 141, Mismatches: 9, Indels: 21
0.82 0.05 0.12
Matches are distributed among these distances:
82 62 0.44
83 2 0.01
85 3 0.02
86 3 0.02
87 1 0.01
88 2 0.01
89 10 0.07
90 5 0.04
91 19 0.13
92 34 0.24
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (84 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGAAAAAGTGA
TAAGTGCCTTACTACCTTA
Found at i:48686405 original size:26 final size:26
Alignment explanation
Indices: 48686335--48686405 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
48686325 AAGTTTAAGT
*
48686335 GAGCCATAT-T-GGGAAGCTC-CGGA
1 GAGCCATATATCGGGAAGCTCACGAA
* *
48686358 GAGCCAT-TAATCAGGAAACTCACGAA
1 GAGCCATAT-ATCGGGAAGCTCACGAA
*
48686384 GAGCCATATATCGGGACGCTCA
1 GAGCCATATATCGGGAAGCTCA
48686406 TAAGAGTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
22 1 0.03
23 7 0.19
24 1 0.03
25 7 0.19
26 20 0.54
27 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (26 bp):
GAGCCATATATCGGGAAGCTCACGAA
Found at i:48688745 original size:35 final size:35
Alignment explanation
Indices: 48688699--48688768 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
48688689 TCATGAAGTT
48688699 GTAACAGTGCGACTTCGTGCTTCACCTTGTCGCAA
1 GTAACAGTGCGACTTCGTGCTTCACCTTGTCGCAA
48688734 GTAACAGTGCGACTTCGTGCTTCACCTTGTCGCAA
1 GTAACAGTGCGACTTCGTGCTTCACCTTGTCGCAA
48688769 CCTCATTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (35 bp):
GTAACAGTGCGACTTCGTGCTTCACCTTGTCGCAA
Found at i:48697037 original size:16 final size:18
Alignment explanation
Indices: 48697018--48697058 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
48697008 TGTATGTATA
48697018 TAATATTTATTA-AA-AT
1 TAATATTTATTATAATAT
*
48697034 TAATAATTATTATAATAT
1 TAATATTTATTATAATAT
48697052 TAATATT
1 TAATATT
48697059 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATTTATTATAATAT
Found at i:48697059 original size:24 final size:22
Alignment explanation
Indices: 48697025--48697081 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
48697015 ATATAATATT
*
48697025 TATTAAAATTAATAATTATTATAA
1 TATTAAAATTAA-AATT-TAATAA
*
48697049 TATTAATATTAAAATTTAATAA
1 TATTAAAATTAAAATTTAATAA
48697071 TAATATAAAAT
1 T-AT-TAAAAT
48697082 ATATAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 6 0.21
23 6 0.21
24 16 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAAAATTAAAATTTAATAA
Found at i:48697074 original size:19 final size:18
Alignment explanation
Indices: 48697046--48697081 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48697036 ATAATTATTA
*
48697046 TAATATTAATATTAAAATT
1 TAATAATAATA-TAAAATT
48697065 TAATAATAATATAAAAT
1 TAATAATAATATAAAAT
48697082 ATATAATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATATAAAATT
Found at i:48697078 original size:30 final size:28
Alignment explanation
Indices: 48697015--48697078 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
48697005 TTCTGTATGT
48697015 ATATAATATTTATTAAAATTAATAATTA
1 ATATAATATTTATTAAAATTAATAATTA
*
48697043 TTATAATATTAATATTAAAATTTAATAA-TA
1 ATATAATATT--TATTAAAA-TTAATAATTA
48697073 ATATAA
1 ATATAA
48697079 AATATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.29
30 15 0.48
31 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAATATTTATTAAAATTAATAATTA
Found at i:48698221 original size:16 final size:16
Alignment explanation
Indices: 48698192--48698228 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48698182 TTTATGTTCG
*
48698192 AAATT-AAAATATTTA
1 AAATTAAAAAAATTTA
48698207 AAATTAAAAAAATTTA
1 AAATTAAAAAAATTTA
48698223 AAATTA
1 AAATTA
48698229 TTTGAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAAAAAATTTA
Found at i:48699705 original size:39 final size:39
Alignment explanation
Indices: 48699651--48699728 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
48699641 GACCTAACTA
48699651 ATATTCCTATTTCAGACTATGAAAAAACCATAAACGATT
1 ATATTCCTATTTCAGACTATGAAAAAACCATAAACGATT
48699690 ATATTCCTATTTCAGACTATGAAAAAACCATAAACGATT
1 ATATTCCTATTTCAGACTATGAAAAAACCATAAACGATT
48699729 GGGCACAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (39 bp):
ATATTCCTATTTCAGACTATGAAAAAACCATAAACGATT
Found at i:48701275 original size:33 final size:33
Alignment explanation
Indices: 48701233--48701298 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
48701223 CAGACAAAAA
48701233 ATTTTGATATTAATGATCTAGCAGAAGATCAAG
1 ATTTTGATATTAATGATCTAGCAGAAGATCAAG
48701266 ATTTTGATATTAATGATCTAGCAGAAGATCAAG
1 ATTTTGATATTAATGATCTAGCAGAAGATCAAG
48701299 CAATAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (33 bp):
ATTTTGATATTAATGATCTAGCAGAAGATCAAG
Found at i:48702624 original size:26 final size:27
Alignment explanation
Indices: 48702583--48702635 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
48702573 AGATCTTTCT
48702583 AAAATAAAAGATTTTTATAATCCTGGA
1 AAAATAAAAGATTTTTATAATCCTGGA
48702610 AAAATAAAAGATTTTTATAATCCTGG
1 AAAATAAAAGATTTTTATAATCCTGG
48702636 TTTATCACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (27 bp):
AAAATAAAAGATTTTTATAATCCTGGA
Found at i:48708785 original size:26 final size:24
Alignment explanation
Indices: 48708734--48708788 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
48708724 AATTTTAAAA
* *
48708734 TATTTTTAAAATGTTTTTATTTTT
1 TATTTTTAAAATGTTTTTAATGTT
*
48708758 TATTTTTAAAATAATTTTTTAATGTT
1 TATTTTTAAAAT--GTTTTTAATGTT
48708784 TATTT
1 TATTT
48708789 AAAAATGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 12 0.46
26 14 0.54
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTTTTAAAATGTTTTTAATGTT
Found at i:48713058 original size:23 final size:23
Alignment explanation
Indices: 48713032--48713129 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48713022 ATAAGTGCCA
48713032 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48713055 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48713078 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48713100 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48713123 CACTGAT
1 CACTGAT
48713130 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48713097 original size:45 final size:45
Alignment explanation
Indices: 48713039--48713127 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
48713029 CCACACTGAT
* *
48713039 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
48713084 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
48713128 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:48716111 original size:14 final size:14
Alignment explanation
Indices: 48716092--48716136 Score: 90
Period size: 14 Copynumber: 3.2 Consensus size: 14
48716082 CAAATCACCA
48716092 GGCCAGTTTGGTTG
1 GGCCAGTTTGGTTG
48716106 GGCCAGTTTGGTTG
1 GGCCAGTTTGGTTG
48716120 GGCCAGTTTGGTTG
1 GGCCAGTTTGGTTG
48716134 GGC
1 GGC
48716137 TAAATGACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.07, C:0.16, G:0.44, T:0.33
Consensus pattern (14 bp):
GGCCAGTTTGGTTG
Found at i:48719994 original size:24 final size:26
Alignment explanation
Indices: 48719942--48719997 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
48719932 AACAACCAAC
* *
48719942 AAATTTTTAAAGAATAAAAAAATAGA
1 AAATATTTAAAGAATAAAAAAATAAA
48719968 AAATATTTAAA-AAT-AAAAAATAAA
1 AAATATTTAAAGAATAAAAAAATAAA
48719992 AAATAT
1 AAATAT
48719998 AATTTGTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.54
25 3 0.11
26 10 0.36
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (26 bp):
AAATATTTAAAGAATAAAAAAATAAA
Found at i:48728725 original size:5 final size:5
Alignment explanation
Indices: 48728715--48728744 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
48728705 TTATGTTCAC
48728715 GGGAA GGGAA GGGAA GGGAA GGG-A GGGAA G
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA G
48728745 AATACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:48730046 original size:5 final size:5
Alignment explanation
Indices: 48730036--48730060 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
48730026 ATCCATCCAA
48730036 ACCCC ACCCC ACCCC ACCCC ACCCC
1 ACCCC ACCCC ACCCC ACCCC ACCCC
48730061 CCACACACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCC
Found at i:48739906 original size:195 final size:193
Alignment explanation
Indices: 48739575--48739952 Score: 463
Period size: 195 Copynumber: 1.9 Consensus size: 193
48739565 TTACGTACTC
* * *
48739575 TGTAACACCCTAGGAAAATTCCATATCGGTAAAGCATGGGAGAGACCTGCGTATATAAAAGGGTA
1 TGTAACACCCTAGGAAAATTCCACATCGGTAAAACACGGGAGAGACCTGCGTATATAAAAGGGTA
* * * * ****
48739640 GTAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTGTATGACCTATTCTAAGAACAAGGTTATGAG
66 GCAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTGTATGACCGATCCCAAGAACAAAACCATGAG
* * * * **
48739705 GGCCATGTGCGCTCAAGGCAGATAATATCTTACTGGGATGGGTGTTGGCTATGAAATTTATCAA
131 GGCCATGTGCACCCAAAGCAGACAATAT-TTACCAGGATGGGTGTTGGCTATGAAATTTATCAA
* * *
48739769 TGTAACACCCTAGGTAAA-TCGCACATCGGTAAAACACGGGAGGGACCTGGGCTATAT-AAAGGA
1 TGTAACACCCTAGGAAAATTC-CACATCGGTAAAACACGGGAGAGACCTGCG-TATATAAAAGG-
* * ** *
48739832 GTAGCAACACTTTAGTGGAAAGAGGCCTTTTGGGGGTGTATGGGCGCTCCCAAGAACAAAACCAT
63 GTAGCAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTGTATGACCGATCCCAAGAACAAAACCAT
* *
48739897 GAGGGCCATGTGCACCCAAAGCGGACAATATTTACCAGGCTGGGTGTTGGCTATGA
128 GAGGGCCATGTGCACCCAAAGCAGACAATATTTACCAGGATGGGTGTTGGCTATGA
48739953 CATACGCCAT
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
193 2 0.01
194 69 0.45
195 83 0.54
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (193 bp):
TGTAACACCCTAGGAAAATTCCACATCGGTAAAACACGGGAGAGACCTGCGTATATAAAAGGGTA
GCAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTGTATGACCGATCCCAAGAACAAAACCATGAG
GGCCATGTGCACCCAAAGCAGACAATATTTACCAGGATGGGTGTTGGCTATGAAATTTATCAA
Found at i:48749658 original size:31 final size:31
Alignment explanation
Indices: 48749619--48749698 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
48749609 TTATTGTAAG
*
48749619 GCATGGAAATTGAAGCAATAA-GGAGGTATAA
1 GCATGGAAATTGAAGCAATAACGG-GGAATAA
*
48749650 TCATGGAAATTGAAGCAATAACGGGGAATAA
1 GCATGGAAATTGAAGCAATAACGGGGAATAA
*
48749681 GCATAGAAATTGAAGCAA
1 GCATGGAAATTGAAGCAA
48749699 CTGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (31 bp):
GCATGGAAATTGAAGCAATAACGGGGAATAA
Found at i:48752034 original size:6 final size:6
Alignment explanation
Indices: 48751936--48752033 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
48751926 TCGGCGTCGG
* * * * ** *
48751936 CTTCGT CTTCGT CTTCGT CTTCTT CTTCAT CATCCTCAT CTTCAT CCCCAC
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C-T--TCAT CTTCAT CTTCAT
* * *
48751987 CTCCAT CCTCAT CTTCA- CTTTCAT CTTCAT CTTCAT CTTCAG CTTCA
1 CTTCAT CTTCAT CTTCAT C-TTCAT CTTCAT CTTCAT CTTCAT CTTCA
48752034 GGCTCAGTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
5 1 0.01
6 67 0.88
7 2 0.03
8 1 0.01
9 5 0.07
ACGTcount: A:0.13, C:0.40, G:0.04, T:0.43
Consensus pattern (6 bp):
CTTCAT
Found at i:48757749 original size:21 final size:22
Alignment explanation
Indices: 48757715--48757755 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48757705 AAAACCTAGA
*
48757715 AAAATACGAAGATTTTTTTTTT
1 AAAATACGAAGATTTATTTTTT
*
48757737 AAAAT-CGTAGATTTATTTT
1 AAAATACGAAGATTTATTTT
48757756 CATGCCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
AAAATACGAAGATTTATTTTTT
Found at i:48758474 original size:19 final size:18
Alignment explanation
Indices: 48758438--48758491 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
48758428 AAAAAAAAAT
* **
48758438 TATTTTAAAATTCAATAA
1 TATTTTAAATTTTTATAA
48758456 T-TTTTATAACTTTTTATAA
1 TATTTTA-AA-TTTTTATAA
48758475 TATTTTAAATTTTTATA
1 TATTTTAAATTTTTATA
48758492 TGTTTGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.17
18 11 0.37
19 9 0.30
20 5 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTAAATTTTTATAA
Found at i:48758501 original size:28 final size:29
Alignment explanation
Indices: 48758454--48758512 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
48758444 AAAATTCAAT
*
48758454 AATTTTTATAACTTTTTAT-AATATTTTA
1 AATTTTTATAACTTTGTATAAATATTTTA
**
48758482 AATTTTTATATGTTTGTATAAAATATTTTA
1 AATTTTTATAACTTTGTAT-AAATATTTTA
48758512 A
1 A
48758513 TAATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 16 0.62
30 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
AATTTTTATAACTTTGTATAAATATTTTA
Found at i:48758565 original size:9 final size:9
Alignment explanation
Indices: 48758452--48758594 Score: 71
Period size: 9 Copynumber: 15.2 Consensus size: 9
48758442 TTAAAATTCA
48758452 ATAATTTTT
1 ATAATTTTT
48758461 ATAACTTTTT
1 ATAA-TTTTT
48758471 ATAATATTTT
1 ATAAT-TTTT
48758481 A-AATTTTT
1 ATAATTTTT
48758489 AT-ATGTTTGT
1 ATAAT-TTT-T
48758499 ATAAAATATTTT
1 AT--AAT-TTTT
*
48758511 AATAATATTT
1 -ATAATTTTT
*
48758521 ATGATTGTTT
1 ATAATT-TTT
48758531 AT-ATCTTTT
1 ATAAT-TTTT
* *
48758540 ACAATCTCTT
1 ATAAT-TTTT
*
48758550 ATGATTTTT
1 ATAATTTTT
48758559 ATAATTTTT
1 ATAATTTTT
***
48758568 -TAA-AAAT
1 ATAATTTTT
*
48758575 ATAATTTTC
1 ATAATTTTT
48758584 ATAATTTTT
1 ATAATTTTT
48758593 AT
1 AT
48758595 GACCTTTATA
Statistics
Matches: 102, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
7 1 0.01
8 13 0.13
9 42 0.41
10 35 0.34
11 3 0.03
12 1 0.01
13 7 0.07
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.57
Consensus pattern (9 bp):
ATAATTTTT
Found at i:48758637 original size:24 final size:24
Alignment explanation
Indices: 48758586--48758637 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48758576 TAATTTTCAT
* *
48758586 AATTTTTATGACCTTTATATATAC
1 AATTTTTATGACCTTTATAGATAA
*
48758610 AATTTTTATGACTTTTACTAGA-AA
1 AATTTTTATGACCTTTA-TAGATAA
48758634 AATT
1 AATT
48758638 CATGATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (24 bp):
AATTTTTATGACCTTTATAGATAA
Found at i:48762139 original size:11 final size:11
Alignment explanation
Indices: 48762123--48762161 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
48762113 ATTTATATTT
48762123 ATTTAAAACTC
1 ATTTAAAACTC
*
48762134 ATTTAACAAATC
1 ATTTAA-AACTC
*
48762146 ATTTAAAACTT
1 ATTTAAAACTC
48762157 ATTTA
1 ATTTA
48762162 TTGTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAAAACTC
Found at i:48762253 original size:21 final size:21
Alignment explanation
Indices: 48762209--48762247 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
48762199 ATATGTGTTT
48762209 TATTTATAATATAATTATTAA
1 TATTTATAATATAATTATTAA
*
48762230 TATTTAT-ATTTAATTATT
1 TATTTATAATATAATTATT
48762248 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATAATATAATTATTAA
Found at i:48773486 original size:51 final size:52
Alignment explanation
Indices: 48773424--48773530 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 52
48773414 TTATAAAACT
* * *
48773424 TATATATATATAAAAAACA-TAATGCATTTATGAAAACAATGAAA-ATATAAA
1 TATATACATATAAAAAACATTAATGCATTTA-CAAAAAAATGAAATATATAAA
* * * *
48773475 TATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATATATAAG
1 TATATACATATAAAAAACATTAATGCATTTACAAAAAAATGAAATATATAAA
48773527 TATA
1 TATA
48773531 ATATAAAACG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
51 27 0.57
52 20 0.43
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.32
Consensus pattern (52 bp):
TATATACATATAAAAAACATTAATGCATTTACAAAAAAATGAAATATATAAA
Found at i:48773805 original size:3 final size:3
Alignment explanation
Indices: 48773797--48773833 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
48773787 ATACGTAGGT
48773797 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
48773834 CAAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:48773843 original size:24 final size:24
Alignment explanation
Indices: 48773797--48773849 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
48773787 ATACGTAGGT
* *
48773797 ATAATAATAATATATAATATAATA
1 ATAATAATAATACAAAATATAATA
48773821 ATAATAATAATAACAAAAT-TAATA
1 ATAATAATAAT-ACAAAATATAATA
48773845 A-AATA
1 ATAATA
48773850 GACTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 17 0.65
25 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAATAATAATACAAAATATAATA
Found at i:48774319 original size:21 final size:21
Alignment explanation
Indices: 48774293--48774347 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
48774283 AATCATATAT
48774293 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
48774314 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
*
48774333 TCTAAAATTGTATAT
1 TCTAAGATTGTATAT
48774348 CCTCGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:48793454 original size:12 final size:13
Alignment explanation
Indices: 48793437--48793466 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
48793427 AATTTGAATT
48793437 TTATTT-TTAGGA
1 TTATTTGTTAGGA
48793449 TTATTTGTTAGGA
1 TTATTTGTTAGGA
48793462 TTATT
1 TTATT
48793467 ATATTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (13 bp):
TTATTTGTTAGGA
Found at i:48798493 original size:8 final size:8
Alignment explanation
Indices: 48798474--48798503 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
48798464 CTAACTAGAA
48798474 TAAATA-T
1 TAAATATT
48798481 TAAATATT
1 TAAATATT
48798489 TAAATATT
1 TAAATATT
48798497 TAAATAT
1 TAAATAT
48798504 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATATT
Found at i:48800193 original size:18 final size:19
Alignment explanation
Indices: 48800150--48800194 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
48800140 TTTTAAAAAT
*
48800150 TATATTTTATATTTTTAAA
1 TATATTTTACATTTTTAAA
48800169 -ATGATTTT-CATTTTTAAA
1 TAT-ATTTTACATTTTTAAA
48800187 TATATTTT
1 TATATTTT
48800195 TATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATTTTACATTTTTAAA
Found at i:48812096 original size:2 final size:2
Alignment explanation
Indices: 48812084--48812114 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
48812074 CTATGTCTCA
*
48812084 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
48812115 CAGATGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (2 bp):
GT
Found at i:48813221 original size:59 final size:60
Alignment explanation
Indices: 48813148--48813280 Score: 207
Period size: 59 Copynumber: 2.2 Consensus size: 60
48813138 TTCAGAATGC
* *
48813148 TTTAATGCTTAAGTAAATGAAACATTAGAATCTATTG-AAATTTGACCTTTGGAACTCGT
1 TTTAATGCTTAAGTAAATGAAACATTAGAACCTATTGAAAATTTGACCTTTGGAACTCGA
* *
48813207 TTTAATG-TTGAAGTAAATGAAATATTAGAACCTATTGAAAATTTGACTTTTGGAACTCGA
1 TTTAATGCTT-AAGTAAATGAAACATTAGAACCTATTGAAAATTTGACCTTTGGAACTCGA
48813267 TTTAATGCTTAAGT
1 TTTAATGCTTAAGT
48813281 TAATCTCCGA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
58 2 0.03
59 32 0.48
60 31 0.46
61 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (60 bp):
TTTAATGCTTAAGTAAATGAAACATTAGAACCTATTGAAAATTTGACCTTTGGAACTCGA
Found at i:48826102 original size:13 final size:13
Alignment explanation
Indices: 48826084--48826108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48826074 AGAGAATCCT
48826084 CCAACATTGCTTG
1 CCAACATTGCTTG
48826097 CCAACATTGCTT
1 CCAACATTGCTT
48826109 TTAGGCACCA
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:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (13 bp):
CCAACATTGCTTG
Found at i:48827232 original size:11 final size:11
Alignment explanation
Indices: 48827213--48827262 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
48827203 ATTATACCAA
48827213 CATTC-AAAC-
1 CATTCAAAACT
48827222 CAGTTCAAAACT
1 CA-TTCAAAACT
48827234 CATTC-AAAC-
1 CATTCAAAACT
48827243 CAGTTCAAAACT
1 CA-TTCAAAACT
48827255 CATTCAAA
1 CATTCAAA
48827263 CATACCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.11
10 10 0.29
11 17 0.49
12 4 0.11
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.24
Consensus pattern (11 bp):
CATTCAAAACT
Found at i:48827239 original size:21 final size:21
Alignment explanation
Indices: 48827213--48827263 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
48827203 ATTATACCAA
48827213 CATTCAAACCAGTTCAAAACT
1 CATTCAAACCAGTTCAAAACT
48827234 CATTCAAACCAGTTCAAAACT
1 CATTCAAACCAGTTCAAAACT
48827255 CATTCAAAC
1 CATTCAAAC
48827264 ATACCAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.24
Consensus pattern (21 bp):
CATTCAAACCAGTTCAAAACT
Found at i:48829481 original size:20 final size:20
Alignment explanation
Indices: 48829458--48829502 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
48829448 AGAATTTTAC
48829458 CGATACTTGATTAAAGGTAT
1 CGATACTTGATTAAAGGTAT
** *
48829478 CGATACTTTTTTATAGGTAT
1 CGATACTTGATTAAAGGTAT
48829498 CGATA
1 CGATA
48829503 TTCGAACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (20 bp):
CGATACTTGATTAAAGGTAT
Found at i:48835133 original size:16 final size:18
Alignment explanation
Indices: 48835111--48835151 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
48835101 CGTAGACTTA
*
48835111 AATAAAATTAACT-AAAT
1 AATAAAATAAACTGAAAT
48835128 -ATAAAATAAACTGAAAT
1 AATAAAATAAACTGAAAT
48835145 AATAAAA
1 AATAAAA
48835152 GAAAATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.52
17 4 0.19
18 6 0.29
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAAACTGAAAT
Found at i:48838528 original size:19 final size:18
Alignment explanation
Indices: 48838504--48838544 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
48838494 TTTAATACTT
48838504 TAAACT-AAATAATATAAAA
1 TAAACTGAAATAA-A-AAAA
48838523 TAAACTGAAATAAAAAAA
1 TAAACTGAAATAAAAAAA
48838541 TAAA
1 TAAA
48838545 ATATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (18 bp):
TAAACTGAAATAAAAAAA
Found at i:48842332 original size:20 final size:20
Alignment explanation
Indices: 48842296--48842333 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48842286 TGGGTGATGT
*
48842296 ATTAAATATATTTATAAAAA
1 ATTAAATATATTAATAAAAA
48842316 ATTAAA-ATGATTAATAAA
1 ATTAAATAT-ATTAATAAA
48842334 TGTTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTAAATATATTAATAAAAA
Found at i:48845602 original size:3 final size:3
Alignment explanation
Indices: 48845596--48845631 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
48845586 TCTTTTACTT
48845596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48845632 AAAAAACTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48853532 original size:16 final size:17
Alignment explanation
Indices: 48853500--48853534 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
48853490 AATTTAGTTG
48853500 AAGTATAAACGATGTAT
1 AAGTATAAACGATGTAT
*
48853517 AAGTATATAC-ATGTAT
1 AAGTATAAACGATGTAT
48853533 AA
1 AA
48853535 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
AAGTATAAACGATGTAT
Found at i:48854246 original size:41 final size:41
Alignment explanation
Indices: 48854184--48854341 Score: 228
Period size: 41 Copynumber: 3.9 Consensus size: 41
48854174 TGAAAATAAG
* *
48854184 ATGTTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGTGAA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
48854225 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
*
48854266 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
* * * * *
48854307 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCC
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCC
48854342 AGTGTTTTAT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 105 0.97
42 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (41 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
Found at i:48858454 original size:182 final size:182
Alignment explanation
Indices: 48858147--48858513 Score: 716
Period size: 182 Copynumber: 2.0 Consensus size: 182
48858137 TTCAACCCGA
48858147 ATCGGGTAAAGAGTTTGTTATCTATAGTGATGCATCTTTAAATGGTTTGAGCTGTGTTTTGATGC
1 ATCGGGTAAAGAGTTTGTTATCTATAGTGATGCATCTTTAAATGGTTTGAGCTGTGTTTTGATGC
48858212 AGGAAGGCAAAGTTGTAGCCTATGCCTCGAGACAGTTAAAGCCGCATGAAAAGAACTATCCGACG
66 AGGAAGGCAAAGTTGTAGCCTATGCCTCGAGACAGTTAAAGCCGCATGAAAAGAACTATCCGACG
48858277 CATGATTTGGAATTGGCCGCTATTGTATTTGCGTTAAAAATATGGCGTCACT
131 CATGATTTGGAATTGGCCGCTATTGTATTTGCGTTAAAAATATGGCGTCACT
* *
48858329 ATCGGGTAAAGAGTTTGTTATCTATAGTGATGCATCTTTAAATGGTTTGAGTTGTTTTTTGATGC
1 ATCGGGTAAAGAGTTTGTTATCTATAGTGATGCATCTTTAAATGGTTTGAGCTGTGTTTTGATGC
48858394 AGGAAGGCAAAGTTGTAGCCTATGCCTCGAGACAGTTAAAGCCGCATGAAAAGAACTATCCGACG
66 AGGAAGGCAAAGTTGTAGCCTATGCCTCGAGACAGTTAAAGCCGCATGAAAAGAACTATCCGACG
48858459 CATGATTTGGAATTGGCCGCTATTGTATTTGCGTTAAAAATATGGCGTCACT
131 CATGATTTGGAATTGGCCGCTATTGTATTTGCGTTAAAAATATGGCGTCACT
48858511 ATC
1 ATC
48858514 TATTTGGCGA
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (182 bp):
ATCGGGTAAAGAGTTTGTTATCTATAGTGATGCATCTTTAAATGGTTTGAGCTGTGTTTTGATGC
AGGAAGGCAAAGTTGTAGCCTATGCCTCGAGACAGTTAAAGCCGCATGAAAAGAACTATCCGACG
CATGATTTGGAATTGGCCGCTATTGTATTTGCGTTAAAAATATGGCGTCACT
Found at i:48861495 original size:16 final size:17
Alignment explanation
Indices: 48861463--48861497 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
48861453 AATTTAGTTG
48861463 AAGTATAAACGATGTAT
1 AAGTATAAACGATGTAT
*
48861480 AAGTATATAC-ATGTAT
1 AAGTATAAACGATGTAT
48861496 AA
1 AA
48861498 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
AAGTATAAACGATGTAT
Found at i:48862209 original size:41 final size:41
Alignment explanation
Indices: 48862147--48862308 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
48862137 TGAAAATAAG
* *
48862147 ATGTTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGTGAA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
48862188 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
*
48862229 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
* * * * *
48862270 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTG
48862309 TTTTATACAA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 109 0.97
42 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAA
Found at i:48863695 original size:17 final size:16
Alignment explanation
Indices: 48863666--48863704 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
48863656 AAGTATACTG
48863666 AATTAATTTATAAATA
1 AATTAATTTATAAATA
48863682 AATTAATATTATAAATA
1 AATTAAT-TTATAAATA
*
48863699 AGTTAA
1 AATTAA
48863705 AATATTAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATTTATAAATA
Found at i:48867208 original size:3 final size:3
Alignment explanation
Indices: 48867202--48867233 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48867192 ACAACAAAGC
48867202 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48867234 ACAGAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48871020 original size:21 final size:22
Alignment explanation
Indices: 48870996--48871051 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
48870986 GAGGTGCAAA
48870996 GTCTCGAGACATAGA-CTAAAT
1 GTCTCGAGACATAGATCTAAAT
* **
48871017 GTCTCGAGCCAT-GATCTGTAT
1 GTCTCGAGACATAGATCTAAAT
*
48871038 GTCTTGAGACATAG
1 GTCTCGAGACATAG
48871052 CCTCCAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (22 bp):
GTCTCGAGACATAGATCTAAAT
Found at i:48873848 original size:25 final size:25
Alignment explanation
Indices: 48873820--48873879 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
48873810 GGGTTTTTCT
*
48873820 TTTTCTTTTTTATTTTTAGATTAGA
1 TTTTCTTTTTTATTTTTAGAATAGA
* * *
48873845 TTTTCTCTTTTCTTTTTAGAATATA
1 TTTTCTTTTTTATTTTTAGAATAGA
48873870 TTTTCTTTTT
1 TTTTCTTTTT
48873880 GTTGTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (25 bp):
TTTTCTTTTTTATTTTTAGAATAGA
Found at i:48879102 original size:2 final size:2
Alignment explanation
Indices: 48879095--48879125 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48879085 TTATATCTTT
48879095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48879126 GTTTTGATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48879377 original size:12 final size:12
Alignment explanation
Indices: 48879360--48879384 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48879350 CTTATGTGTA
48879360 ATTTATTTTTTT
1 ATTTATTTTTTT
48879372 ATTTATTTTTTT
1 ATTTATTTTTTT
48879384 A
1 A
48879385 AAAAACTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:48882011 original size:16 final size:16
Alignment explanation
Indices: 48881998--48882030 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48881988 AGTAATTATT
48881998 TTAAATATTAATTAAA
1 TTAAATATTAATTAAA
*
48882014 TTAATTATTAATTAAA
1 TTAAATATTAATTAAA
48882030 T
1 T
48882031 AATTTCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATATTAATTAAA
Found at i:48885382 original size:79 final size:79
Alignment explanation
Indices: 48885259--48885404 Score: 256
Period size: 79 Copynumber: 1.8 Consensus size: 79
48885249 CGAATATACG
* *
48885259 AATAGCATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTCTGATATGTTTTATCTGCAT
1 AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
48885324 ATAGGTAATATGCC
66 ATAGGTAATATGCC
* *
48885338 AATAACATGTTTTGATCTGTTAATTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
1 AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
48885403 AT
66 AT
48885405 GGGCACGTCT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (79 bp):
AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
ATAGGTAATATGCC
Found at i:48887551 original size:24 final size:24
Alignment explanation
Indices: 48887519--48887575 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
48887509 ATTTTAGGTA
*
48887519 CACACGGCCTGAAACAGAGACTGT
1 CACACGGCCTGAAACACAGACTGT
*
48887543 CACACGGCCTGAGACACAGACTGT
1 CACACGGCCTGAAACACAGACTGT
*
48887567 CACATGGCC
1 CACACGGCC
48887576 GTATATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.25, T:0.12
Consensus pattern (24 bp):
CACACGGCCTGAAACACAGACTGT
Found at i:48888540 original size:36 final size:35
Alignment explanation
Indices: 48888493--48888564 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 35
48888483 TGATGGCTAG
48888493 GTTCCATTTATTGATCAATTCATTAATTTCTAATTA
1 GTTCCATTTATTGATCAATTCATTAATTTCT-ATTA
48888529 GTTCCATTTATTGATCAATTCATTAATTTCTATTA
1 GTTCCATTTATTGATCAATTCATTAATTTCTATTA
48888564 G
1 G
48888565 GTTGTCGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 5 0.14
36 31 0.86
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (35 bp):
GTTCCATTTATTGATCAATTCATTAATTTCTATTA
Found at i:48889426 original size:18 final size:17
Alignment explanation
Indices: 48889391--48889429 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
48889381 TTCTATTGCA
*
48889391 ATTTTATTTTGGTTTTT
1 ATTTGATTTTGGTTTTT
*
48889408 ATTTGATTTTTGTTATTT
1 ATTTGATTTTGGTT-TTT
48889426 ATTT
1 ATTT
48889430 TATATTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (17 bp):
ATTTGATTTTGGTTTTT
Found at i:48897511 original size:8 final size:7
Alignment explanation
Indices: 48897491--48897531 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
48897481 AATAAATATA
48897491 TATTTTT
1 TATTTTT
48897498 TATTTTT
1 TATTTTT
48897505 TATTTTT
1 TATTTTT
48897512 TATTTTT
1 TATTTTT
*
48897519 TAATTTT
1 TATTTTT
*
48897526 AATTTT
1 TATTTT
48897532 AAAATACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:48897590 original size:26 final size:26
Alignment explanation
Indices: 48897539--48897592 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
48897529 TTTAAAATAC
* * *
48897539 TTTTAAAATATTTTTTTATTTTTTTA
1 TTTTAAAATAATTTTTTATATGTTTA
48897565 TTTTGAAAATAATTTTTTA-ATGTTTA
1 TTTT-AAAATAATTTTTTATATGTTTA
48897591 TT
1 TT
48897593 AAAAATGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTATATGTTTA
Found at i:48904324 original size:101 final size:101
Alignment explanation
Indices: 48904182--48904420 Score: 390
Period size: 101 Copynumber: 2.4 Consensus size: 101
48904172 GAATTGAGGA
* *
48904182 ATAAGACCATAACTAGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAATGTTTA
* *
48904247 TATGTAAGACCGTAGCTGGGCTATGACATTCTGATG
66 TATGTAAGACCATAGCCGGGCTATGACATTCTGATG
* *
48904283 ATAATACCATAACTGGGTTATGGCACTATG-ATCGTAAGACCATGGTTGGATCATGGCAATGTTT
1 ATAAGACCATAACTGGGTTATGGCACTATGAAT-GTAAGACCATGGTTGGACCATGGCAATGTTT
48904347 ATATGTAAGACCATAGCCGGGCTATGACATTCTGATG
65 ATATGTAAGACCATAGCCGGGCTATGACATTCTGATG
**
48904384 ATAAGACCATAACTGGGTTATGGCACTACAAATGTAA
1 ATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
48904421 AGGATGAATT
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 2 0.02
101 123 0.97
102 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAATGTTTA
TATGTAAGACCATAGCCGGGCTATGACATTCTGATG
Found at i:48904325 original size:33 final size:32
Alignment explanation
Indices: 48904183--48904411 Score: 93
Period size: 33 Copynumber: 6.8 Consensus size: 32
48904173 AATTGAGGAA
*
48904183 TAAGACCATAACTAGGTTATGGCACTATGAATG
1 TAAGACCATAACTGGGTTATGGCACTATG-ATG
*** *** *
48904216 TAAGACCATGGTTGGACCATGGCAGTGTTTAT-ATG
1 TAAGACCATAACTGGGTTATGGCA----CTATGATG
* * * * * *
48904251 TAAGACCGTAGCTGGGCTATGACATTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTATGATG
*
48904283 ATAATACCATAACTGGGTTATGGCACTATGATCG
1 -TAAGACCATAACTGGGTTATGGCACTATGAT-G
*** * * *
48904317 TAAGACCATGGTTGGATCATGGCAATGTTTAT-ATG
1 TAAGACCATAACTGGGTTATGGC-A---CTATGATG
* * * * * *
48904352 TAAGACCATAGCCGGGCTATGACATTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTATGATG
48904384 ATAAGACCATAACTGGGTTATGGCACTA
1 -TAAGACCATAACTGGGTTATGGCACTA
48904412 CAAATGTAAA
Statistics
Matches: 140, Mismatches: 43, Indels: 26
0.67 0.21 0.12
Matches are distributed among these distances:
31 6 0.04
32 6 0.04
33 79 0.56
34 3 0.02
35 38 0.27
36 2 0.01
37 6 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (32 bp):
TAAGACCATAACTGGGTTATGGCACTATGATG
Found at i:48904452 original size:26 final size:26
Alignment explanation
Indices: 48904413--48904465 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
48904403 ATGGCACTAC
48904413 AAATGTAAAGGATGAATTGACGAAAA
1 AAATGTAAAGGATGAATTGACGAAAA
* *
48904439 AAATGTAAATGATGAATTGACGGAAA
1 AAATGTAAAGGATGAATTGACGAAAA
48904465 A
1 A
48904466 TTACCCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.21
Consensus pattern (26 bp):
AAATGTAAAGGATGAATTGACGAAAA
Found at i:48912416 original size:27 final size:29
Alignment explanation
Indices: 48912366--48912428 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
48912356 AAAAATTTAT
* *
48912366 TTTTAAAGTTAAAAAAAAT-TAAAAAGTA
1 TTTTAAAATTAAAAAAAATAAAAAAAGTA
48912394 TTTTAAAATT-AAAAAAATAAAAAAAGTA
1 TTTTAAAATTAAAAAAAATAAAAAAAGTA
48912422 TTTTAAA
1 TTTTAAA
48912429 CATATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTTAAAATTAAAAAAAATAAAAAAAGTA
Found at i:48915774 original size:3 final size:3
Alignment explanation
Indices: 48915766--48915845 Score: 72
Period size: 3 Copynumber: 25.7 Consensus size: 3
48915756 TTAGTCCCGT
** *
48915766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA AAA TAA TTA GTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
48915811 TTA TTA TTA TTGCA TTTA TCA TTA TAA TTA TTA TT
1 TTA TTA TTA TT--A -TTA TTA TTA TTA TTA TTA TT
48915846 TACCCATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 3 0.05
5 1 0.02
6 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:48916116 original size:26 final size:26
Alignment explanation
Indices: 48916059--48916108 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
48916049 TTTCATAATT
*
48916059 TATATAGATACCTACATACTTTTAGA
1 TATATACATACCTACATACTTTTAGA
*
48916085 TATATACATACCTATAT-CTTTTAG
1 TATATACATACCTACATACTTTTAG
48916109 GCTTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (26 bp):
TATATACATACCTACATACTTTTAGA
Found at i:48922741 original size:19 final size:20
Alignment explanation
Indices: 48922717--48922755 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48922707 AATATCCTAT
48922717 TAATTTAA-TGAATAAAAAA
1 TAATTTAATTGAATAAAAAA
*
48922736 TAATTTAATTTAATAAAAAA
1 TAATTTAATTGAATAAAAAA
48922756 AATCTATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAATTTAATTGAATAAAAAA
Found at i:48934668 original size:39 final size:39
Alignment explanation
Indices: 48934614--48934693 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
48934604 CGCCACTTGA
*
48934614 TAGTGTCCTGATTGATGTATATGTTTAATAGCAATTCGG
1 TAGTGCCCTGATTGATGTATATGTTTAATAGCAATTCGG
*
48934653 TAGTGCCCTGATTGATGTATATGTTTAATAGCAATTTGG
1 TAGTGCCCTGATTGATGTATATGTTTAATAGCAATTCGG
48934692 TA
1 TA
48934694 ATTGTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (39 bp):
TAGTGCCCTGATTGATGTATATGTTTAATAGCAATTCGG
Found at i:48951813 original size:20 final size:19
Alignment explanation
Indices: 48951776--48951817 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
48951766 TTAAAATAAT
48951776 TAAAAAAATTAAAGAATTCA
1 TAAAAAAATTAAAGAATT-A
*
48951796 TAAAAAATATTACA-AATTA
1 TAAAAAA-ATTAAAGAATTA
48951815 TAA
1 TAA
48951818 GTTTCTTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAAAAATTAAAGAATTA
Found at i:48952438 original size:26 final size:28
Alignment explanation
Indices: 48952404--48952457 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
48952394 AATATATAAT
48952404 TTATAATA-TATTTATTTTTA-AAAAAA
1 TTATAATATTATTTATTTTTACAAAAAA
48952430 TTATAATATTATTTATTTTTACAAAAAA
1 TTATAATATTATTTATTTTTACAAAAAA
48952458 ATTTAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 8 0.31
27 12 0.46
28 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAATATTATTTATTTTTACAAAAAA
Found at i:48952466 original size:29 final size:27
Alignment explanation
Indices: 48952401--48952466 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
48952391 TTAAATATAT
48952401 AATTTATAATATATTTATTTTTAAAAA
1 AATTTATAATATATTTATTTTTAAAAA
48952428 AA-TTATAATATTATTTATTTTTACAAAAA
1 AATTTATAATA-TATTTATTTTT--AAAAA
48952457 AATTTA-AATA
1 AATTTATAATA
48952467 GTTTTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.23
27 13 0.37
29 11 0.31
30 3 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTATAATATATTTATTTTTAAAAA
Found at i:48952885 original size:12 final size:11
Alignment explanation
Indices: 48952858--48952887 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
48952848 TTATTTTTTT
48952858 TATTTTTAAAA
1 TATTTTTAAAA
48952869 TATTTTTAAAA
1 TATTTTTAAAA
48952880 TAATTTTT
1 T-ATTTTT
48952888 TTATTTATTT
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:48952890 original size:31 final size:31
Alignment explanation
Indices: 48952852--48952913 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
48952842 AAATTTTTAT
48952852 TTTTTTTATTT-TTAAAATATTTTTAAAATAA
1 TTTTTTTATTTATT-AAATATTTTTAAAATAA
* *
48952883 TTTTTTTATTTATTTATTATTTTTAAAATAA
1 TTTTTTTATTTATTAAATATTTTTAAAATAA
48952914 ACTTTTGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTTTATTTATTAAATATTTTTAAAATAA
Found at i:48955511 original size:41 final size:40
Alignment explanation
Indices: 48955461--48955635 Score: 156
Period size: 41 Copynumber: 4.3 Consensus size: 40
48955451 ATTTATAGAA
* **
48955461 CATAGAGCCTTGTATAAAACACCGGCATAAAGCCTGCTAGG
1 CATAAAGCC-TGTATAATTCACCGGCATAAAGCCTGCTAGG
* * *
48955502 CACAAAGCCTG-ATACATTTCACCGGCACAAAGCCTGCTAGA
1 CATAAAGCCTGTATA-A-TTCACCGGCATAAAGCCTGCTAGG
* *
48955543 CATAAAGTCTGATATAATTCACCGGCACT-GAGCCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCA-TAAAGCCTGCTAGG
* * * * *
48955584 CATAAAGCCTGATGTAATCCACCGACATCAAGTCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCATAAAGCCTGCTAGG
*
48955625 CATTAAGCCTG
1 CATAAAGCCTG
48955636 AAAATCTCAA
Statistics
Matches: 110, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
39 3 0.03
40 4 0.04
41 99 0.90
42 1 0.01
43 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (40 bp):
CATAAAGCCTGTATAATTCACCGGCATAAAGCCTGCTAGG
Found at i:48958207 original size:51 final size:51
Alignment explanation
Indices: 48958099--48958263 Score: 242
Period size: 51 Copynumber: 3.3 Consensus size: 51
48958089 CTTACATATG
* * * *
48958099 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAACT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
* * *
48958149 ATCACTTGCCACTTGTCACTTATCAGATAAGTATAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
* *
48958200 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTACTACAT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
48958251 ATCACTTGTCACT
1 ATCACTTGTCACT
48958264 GATCAGAAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 32 0.31
51 70 0.69
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
Found at i:48960380 original size:8 final size:8
Alignment explanation
Indices: 48960358--48960388 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
48960348 GATTAGGGGA
48960358 GAGAGAGG
1 GAGAGAGG
48960366 G-GAGAGG
1 GAGAGAGG
48960373 GAGAGAGG
1 GAGAGAGG
48960381 GAGAGAGG
1 GAGAGAGG
48960389 AATAATTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:48971458 original size:19 final size:18
Alignment explanation
Indices: 48971423--48971458 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48971413 TGAATTTTAA
*
48971423 TCAAATTAACTCTAAAAC
1 TCAAATTAACACTAAAAC
48971441 TCAAATTAAACACTAAAA
1 TCAAATT-AACACTAAAA
48971459 AGTTAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (18 bp):
TCAAATTAACACTAAAAC
Found at i:48971872 original size:24 final size:24
Alignment explanation
Indices: 48971824--48971885 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
48971814 ATTGTGGAAG
*
48971824 ACAAATGCCTAAAA-TTTAGTCAA
1 ACAAATCCCTAAAATTTTAGTCAA
48971847 ACAAATCCCTAAAATTTTAG-CTAA
1 ACAAATCCCTAAAATTTTAGTC-AA
48971871 ACAAA-CCCTAAAATT
1 ACAAATCCCTAAAATT
48971886 GTGAAAGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 24 0.67
24 12 0.33
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (24 bp):
ACAAATCCCTAAAATTTTAGTCAA
Found at i:48973643 original size:17 final size:17
Alignment explanation
Indices: 48973621--48973653 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48973611 TAGAATTGGG
48973621 TTGAGATAATT-ATTTAA
1 TTGAGA-AATTAATTTAA
48973638 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
48973654 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:48975595 original size:32 final size:31
Alignment explanation
Indices: 48975550--48975645 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
48975540 CTTAGATAAT
48975550 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48975581 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
48975613 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48975644 TT
1 TT
48975646 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:48976264 original size:57 final size:56
Alignment explanation
Indices: 48976189--48976304 Score: 153
Period size: 55 Copynumber: 2.1 Consensus size: 56
48976179 AAATAAAAGC
48976189 AAAAAAAAGTAAAAAGTAAAAAGCACAAAAACAAAACAAAAAAAAGCAAAAAAGCGCA
1 AAAAAAAAGTAAAAAGTAAAAAGCAC-AAAA-AAAACAAAAAAAAGCAAAAAAGCGCA
* * * * **
48976247 AAAAAAAAG-AGAGAGTAAAAAGCGCAAAAAAAAGAGCAAAAAGCAAAAAAGCGCA
1 AAAAAAAAGTAAAAAGTAAAAAGCACAAAAAAAACAAAAAAAAGCAAAAAAGCGCA
48976302 AAA
1 AAA
48976305 GCTCAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
55 26 0.50
56 4 0.08
57 13 0.25
58 9 0.17
ACGTcount: A:0.72, C:0.11, G:0.15, T:0.03
Consensus pattern (56 bp):
AAAAAAAAGTAAAAAGTAAAAAGCACAAAAAAAACAAAAAAAAGCAAAAAAGCGCA
Found at i:48976289 original size:21 final size:22
Alignment explanation
Indices: 48976226--48976290 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 22
48976216 AAAACAAAAC
48976226 AAAAAAA-AGCAAAAAAGCGCAAAA
1 AAAAAAAGAGC-AAAAAGCGC--AA
*
48976250 AAAAAGAGAGAGTAAAAAGCGC-A
1 AAAAA-A-AGAGCAAAAAGCGCAA
48976273 AAAAAAAGAGCAAAAAGC
1 AAAAAAAGAGCAAAAAGC
48976291 AAAAAAGCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 11 0.31
22 1 0.03
23 6 0.17
24 5 0.14
25 1 0.03
26 10 0.28
27 2 0.06
ACGTcount: A:0.69, C:0.11, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAGCAAAAAGCGCAA
Found at i:48979387 original size:31 final size:31
Alignment explanation
Indices: 48979351--48979443 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
48979341 AGATAATTTT
48979351 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
48979382 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
48979413 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
48979444 TAATTTGCCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:48979754 original size:4 final size:4
Alignment explanation
Indices: 48979745--48979775 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
48979735 ATCTATCCTT
48979745 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
48979776 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:48984582 original size:21 final size:21
Alignment explanation
Indices: 48984556--48984596 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48984546 ATCTGCTCAA
* *
48984556 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
48984577 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
48984597 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:48998499 original size:348 final size:347
Alignment explanation
Indices: 48997856--48998501 Score: 1193
Period size: 348 Copynumber: 1.9 Consensus size: 347
48997846 GACTATTCTA
48997856 ATTTAAAGATCTTTGGGTGTCCTGCGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATCT
1 ATTTAAAGATCTTTGGGTGTCCTGCGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATCT
48997921 ATTAAATATGTTTTTCTTGGTCATAAAGCTAGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAAA
66 ATTAAATATGTTTTTCTTGGTCATAAAGCTAGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAAA
* * * *
48997986 TAGAAAAGTTATAATTAGCAGAGATATTGTTTTTGATGAAATTATTATGCTACCTAATTTATCTC
131 TAGAAAAGTTATAATTAGCAGAGATATTGGTTTTGATGAAACTATTATACTACCTAACTTATCTC
48998051 TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
196 TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
*
48998116 ATAGAGCCGACTCCTCAAGCCAGTATAAAAATTTAGAATAGAGTTACTTTTAATAGATCTTTTTA
261 ATAGAGCCGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTACTTTTAATAGATCTTTTTA
48998181 ATCTACAATAGAACCGAGATCT
326 ATCTACAATAGAACCGAGATCT
*
48998203 ATTTAATAGATCTTTGGGTGTCCTGTGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATC
1 ATTTAA-AGATCTTTGGGTGTCCTGCGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATC
*
48998268 TATTAAATATGTTTTTCTTGGTCATAAAGCTGGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAA
65 TATTAAATATGTTTTTCTTGGTCATAAAGCTAGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAA
* *
48998333 ATAGAAAAGTTATGATTAGTAGAGATATTGGTTTTGATGAAACTATTATACTACCTAACTTATCT
130 ATAGAAAAGTTATAATTAGCAGAGATATTGGTTTTGATGAAACTATTATACTACCTAACTTATCT
48998398 CTTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTAC
195 CTTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTAC
*
48998463 AATAGAGCCGACTCCTCAAGCTAGTACAAAAATTTAGAA
260 AATAGAGCCGACTCCTCAAGCCAGTACAAAAATTTAGAA
48998502 CAAAGTTGCT
Statistics
Matches: 288, Mismatches: 10, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
347 6 0.02
348 282 0.98
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (347 bp):
ATTTAAAGATCTTTGGGTGTCCTGCGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATCT
ATTAAATATGTTTTTCTTGGTCATAAAGCTAGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAAA
TAGAAAAGTTATAATTAGCAGAGATATTGGTTTTGATGAAACTATTATACTACCTAACTTATCTC
TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
ATAGAGCCGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTACTTTTAATAGATCTTTTTA
ATCTACAATAGAACCGAGATCT
Found at i:49003460 original size:45 final size:45
Alignment explanation
Indices: 49003398--49003488 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
49003388 ATAAAATATC
* * *
49003398 TCAAATATCATTATTTTTATACT-TGAAGTATTTCAAATAATTATT
1 TCAAATATAATTATTTTTATA-TGGGAAATATTTCAAATAATTATT
*
49003443 TCAAATATAATTGTTTTTATATGGGAAATATTTCAAATAATTATT
1 TCAAATATAATTATTTTTATATGGGAAATATTTCAAATAATTATT
49003488 T
1 T
49003489 TCAATACACA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (45 bp):
TCAAATATAATTATTTTTATATGGGAAATATTTCAAATAATTATT
Found at i:49004744 original size:54 final size:53
Alignment explanation
Indices: 49004641--49004744 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 53
49004631 TATAAAAAAA
** * *
49004641 TAAATTATACAATGTATAAATATTAAAGATTAATTATTTTTTTAAATCAAGAG
1 TAAATTATACAACATATAAATATTAAAGATTAATAATTTTATTAAATCAAGAG
** *
49004694 TAAATTAATACAACATATAAATATTGGAGATTAA-AATTGTTATTATATCAA
1 TAAATT-ATACAACATATAAATATTAAAGATTAATAATT-TTATTAAATCAA
49004745 ATTTAAAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
53 9 0.21
54 33 0.79
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (53 bp):
TAAATTATACAACATATAAATATTAAAGATTAATAATTTTATTAAATCAAGAG
Found at i:49008631 original size:27 final size:27
Alignment explanation
Indices: 49008600--49008656 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
49008590 GCCCGTCTAA
49008600 AAAAATGGGAAGGTTTGGAGAAAACTC
1 AAAAATGGGAAGGTTTGGAGAAAACTC
49008627 AAAAATGGGAAGGTTTGGAGAAAACTC
1 AAAAATGGGAAGGTTTGGAGAAAACTC
49008654 AAA
1 AAA
49008657 TGGAAACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.18
Consensus pattern (27 bp):
AAAAATGGGAAGGTTTGGAGAAAACTC
Found at i:49009117 original size:19 final size:21
Alignment explanation
Indices: 49009069--49009124 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
49009059 CAATTAATGC
*
49009069 ATATG-TATATATTACTATTA
1 ATATGATATAGATTACTATTA
49009089 ATAT-AGTATAGATTA-TA-TA
1 ATATGA-TATAGATTACTATTA
49009108 ATATGATATAGCATTAC
1 ATATGATATAG-ATTAC
49009125 ATGATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 11 0.37
20 11 0.37
21 8 0.27
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (21 bp):
ATATGATATAGATTACTATTA
Found at i:49013601 original size:6 final size:6
Alignment explanation
Indices: 49013590--49013615 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49013580 TATTAGTATA
49013590 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
49013616 AAGTCTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:49014333 original size:6 final size:6
Alignment explanation
Indices: 49014325--49014358 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
49014315 ATCATCTTAT
*
49014325 TCCTAT TCCTAA TCCTAA TCCTAA TCCTAA TCCT
1 TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA TCCT
49014359 CACAAAAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCTAA
Found at i:49015421 original size:24 final size:24
Alignment explanation
Indices: 49015394--49015440 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
49015384 ACAATGAGAT
49015394 AAAATAAGATCATATTGGGTGAAA
1 AAAATAAGATCATATTGGGTGAAA
* *
49015418 AAAATAGGATTATATTGGGTGAA
1 AAAATAAGATCATATTGGGTGAA
49015441 CGATTTTAAC
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:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAATAAGATCATATTGGGTGAAA
Found at i:49016839 original size:8 final size:8
Alignment explanation
Indices: 49016828--49016858 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
49016818 AAATTTCATA
*
49016828 ATTAAATT
1 ATTACATT
49016836 ATTACATT
1 ATTACATT
49016844 ATTACATT
1 ATTACATT
49016852 ATTACAT
1 ATTACAT
49016859 GTTTATCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTACATT
Found at i:49022816 original size:6 final size:6
Alignment explanation
Indices: 49022805--49022829 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49022795 CTAATCATAA
49022805 CCAACT CCAACT CCAACT CCAACT C
1 CCAACT CCAACT CCAACT CCAACT C
49022830 TTCTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCAACT
Found at i:49025705 original size:13 final size:13
Alignment explanation
Indices: 49025689--49025714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49025679 GCTAAAATAA
49025689 TTTTTATTTTTAT
1 TTTTTATTTTTAT
49025702 TTTTTATTTTTAT
1 TTTTTATTTTTAT
49025715 AAATTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:49027700 original size:2 final size:2
Alignment explanation
Indices: 49027693--49027720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49027683 TATTATTTTA
49027693 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
49027721 GCACATAACA
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:49029231 original size:42 final size:43
Alignment explanation
Indices: 49029087--49029280 Score: 191
Period size: 43 Copynumber: 4.5 Consensus size: 43
49029077 CAATGCTAAC
* * * * *
49029087 GTCCCAGACGTGATCTTACATGTAATCAAATAACGATGTCACT
1 GTCCCAGACGTGGTCTTACACGTAATTAAATAACGATGCCAAT
* *
49029130 GTCCCAGACAG-GGTCTTACATGTAATTAAATAACGATGCCACT
1 GTCCCAGAC-GTGGTCTTACACGTAATTAAATAACGATGCCAAT
* * *
49029173 GTCCCAGATAG-GGTCTTACACGTAATTATAT-ACGACGCCAAT
1 GTCCCAGA-CGTGGTCTTACACGTAATTAAATAACGATGCCAAT
* *
49029215 GTCCCAGACTTGGTCTTACACGTAAATCTCAAAT--TGATGCCAAT
1 GTCCCAGACGTGGTCTTACACGT-AAT-T-AAATAACGATGCCAAT
*
49029259 GTCCCAGACGTGATCTTACACG
1 GTCCCAGACGTGGTCTTACACG
49029281 AAATCACATT
Statistics
Matches: 130, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
42 29 0.22
43 68 0.52
44 30 0.23
45 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACACGTAATTAAATAACGATGCCAAT
Found at i:49033890 original size:16 final size:16
Alignment explanation
Indices: 49033869--49033904 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
49033859 TTTGGTTCGC
49033869 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
49033885 TGTATTGGATTAGATG
1 TGTATTGGATTAGAGG
49033901 TGTA
1 TGTA
49033905 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:49033968 original size:44 final size:44
Alignment explanation
Indices: 49033918--49034019 Score: 204
Period size: 44 Copynumber: 2.3 Consensus size: 44
49033908 GCAAATCAAC
49033918 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
49033962 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
49034006 TGTTTGGTTGAATG
1 TGTTTGGTTGAATG
49034020 GAATAGAGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.38
Consensus pattern (44 bp):
TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
Found at i:49034020 original size:39 final size:42
Alignment explanation
Indices: 49033918--49034036 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 42
49033908 GCAAATCAAC
49033918 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
1 TGTTTGGTT--ATGTAATGGAATAGAGGCGTAATAGTAATCTTG
49033962 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
1 TGTTTGGTT--ATGTAATGGAATAGAGGCGTAATAGTAATCTTG
*
49034006 TGTTTGG-T-TG-AATGGAATAGAGGTGTAATAG
1 TGTTTGGTTATGTAATGGAATAGAGGCGTAATAG
49034037 CATAATGGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
39 20 0.27
40 2 0.03
43 1 0.01
44 51 0.69
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.36
Consensus pattern (42 bp):
TGTTTGGTTATGTAATGGAATAGAGGCGTAATAGTAATCTTG
Found at i:49034205 original size:18 final size:17
Alignment explanation
Indices: 49034184--49034218 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49034174 TTATTATTAA
*
49034184 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
49034202 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49034219 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49034420 original size:18 final size:18
Alignment explanation
Indices: 49034399--49034446 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
49034389 TTATTATTAA
49034399 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
49034417 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
49034434 -TAT-TAATAATTAA
1 ATATATTATAATTAA
49034447 TATTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:49034427 original size:14 final size:15
Alignment explanation
Indices: 49034378--49034429 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
49034368 GTAAAATATA
49034378 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
49034393 TATTAAATATATTAT
1 AATTAAATATATTAT
49034408 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
49034421 AATTTAATA
1 AATTAAATA
49034430 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:49034435 original size:44 final size:43
Alignment explanation
Indices: 49034355--49034438 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
49034345 CTCAAATCAT
* *
49034355 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTATTA
* *
49034398 AATATATTATAAT-TAAAATATATAATTTAATAAAATTATTA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTA
49034439 ATAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 13 0.37
44 13 0.37
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTATTA
Done.