Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 147 of 279
Found at i:47796076 original size:40 final size:39
Alignment explanation
Indices: 47796017--47796165 Score: 131
Period size: 41 Copynumber: 3.7 Consensus size: 39
47796007 ATACACGAGA
* *
47796017 CTTCGGCTATTTATTGCACTTAGTGTGCGATTTGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGATTT-GAATAG
**
47796057 CTTCGGCTATATATGGCACTTAGTGTGCGAGACTGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGA-TTTGA-ATAG
* * * *
47796098 CTTCGGTTATGTAAGGCACTTAGTGTATGAGATTAT-AATAG
1 CTTCGGCTATATATGGCACTTAGTG--TGCGATT-TGAATAG
*
47796139 CTTCGGCTATGCA-ATGGCAATTAGTGT
1 CTTCGGCTAT--ATATGGCACTTAGTGT
47796166 ACAAAACATT
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
40 31 0.35
41 40 0.45
42 12 0.14
43 5 0.06
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (39 bp):
CTTCGGCTATATATGGCACTTAGTGTGCGATTTGAATAG
Found at i:47796116 original size:41 final size:40
Alignment explanation
Indices: 47796017--47796123 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
47796007 ATACACGAGA
* ** **
47796017 CTTCGGCTATTTATTGCACTTAGTGTGCGATTTGGAATAG
1 CTTCGGCTATATAAGGCACTTAGTGTGCGAACTGGAATAG
*
47796057 CTTCGGCTATATATGGCACTTAGTGTGCGAGACT-GAGATAG
1 CTTCGGCTATATAAGGCACTTAGTGTGCGA-ACTGGA-ATAG
* *
47796098 CTTCGGTTATGTAAGGCACTTAGTGT
1 CTTCGGCTATATAAGGCACTTAGTGT
47796124 ATGAGATTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
40 30 0.52
41 28 0.48
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (40 bp):
CTTCGGCTATATAAGGCACTTAGTGTGCGAACTGGAATAG
Found at i:47796696 original size:18 final size:18
Alignment explanation
Indices: 47796673--47796710 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47796663 TGTTATATAG
47796673 TATATAATTGTGTGATAA
1 TATATAATTGTGTGATAA
47796691 TATATAATTGTGTGATAA
1 TATATAATTGTGTGATAA
47796709 TA
1 TA
47796711 AAGATGTCCA
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:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (18 bp):
TATATAATTGTGTGATAA
Found at i:47796911 original size:46 final size:46
Alignment explanation
Indices: 47796858--47797123 Score: 271
Period size: 46 Copynumber: 5.7 Consensus size: 46
47796848 ATATGTTATG
*
47796858 ATGCTGTCTAATTTGA-GCATATTAATGCTGTCCAATTTGATG-TA-TA
1 ATGCTGTCCAATTTGATG--TATTAATGCTGTCCAATTTGA-GATATTA
* *
47796904 ATGCTGTCCATTTTGA-GCATATTGATGCTGTCCAATTTGATG-TA-TA
1 ATGCTGTCCAATTTGATG--TATTAATGCTGTCCAATTTGA-GATATTA
*
47796950 ATGCTGTCCAATTTGA-GCATATTAAAGCTGTCCAATTTGAGCATATTA
1 ATGCTGTCCAATTTGATG--TATTAATGCTGTCCAATTTGAG-ATATTA
* * *
47796998 AAGCTGTCCAATTTGATGTA-TAATGCTGTCCATTTTGAGCATATTG
1 ATGCTGTCCAATTTGATGTATTAATGCTGTCCAATTTGAG-ATATTA
* * *
47797044 ATGCTGTCTAATTTGATGTA-TAATGCTATCCATTTTGAGCATATTA
1 ATGCTGTCCAATTTGATGTATTAATGCTGTCCAATTTGAG-ATATTA
*
47797090 ATGCTGTCCAATTTGATGTATAAATGCTGTCCAA
1 ATGCTGTCCAATTTGATGTATTAATGCTGTCCAA
47797124 AACAGGGTAG
Statistics
Matches: 197, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 164 0.83
47 14 0.07
48 17 0.09
49 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (46 bp):
ATGCTGTCCAATTTGATGTATTAATGCTGTCCAATTTGAGATATTA
Found at i:47796980 original size:70 final size:70
Alignment explanation
Indices: 47796856--47797123 Score: 277
Period size: 70 Copynumber: 3.8 Consensus size: 70
47796846 TTATATGTTA
* *
47796856 TGATGCTGTCTAATTTGA-GCATATTAATGCTGTCCAATTTGATG--TA-TAATGCTGTCCATTT
1 TGATGCTGTCCAATTTGATG--TA-TAATGCTGTCCAATTTGA-GCATATTAATGCTGTCCAATT
47796917 TGAGCATAT
62 TGAGCATAT
*
47796926 TGATGCTGTCCAATTTGATGTATAATGCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGAG
1 TGATGCTGTCCAATTTGATGTATAATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGAG
47796991 CATAT
66 CATAT
* * * * *
47796996 TAAAGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATATTGATGCTGTCTAATTTGAT
1 TGATGCTGTCCAATTTGATGTATAATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGA-
47797061 G--TA-
65 GCATAT
* * * *
47797064 TAATGCTATCCATTTTGA-GCATATTAATGCTGTCCAATTTGATG--TATAAATGCTGTCCAA
1 TGATGCTGTCCAATTTGATG--TA-TAATGCTGTCCAATTTGA-GCATATTAATGCTGTCCAA
47797124 AACAGGGTAG
Statistics
Matches: 173, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
67 2 0.01
68 33 0.19
69 21 0.12
70 114 0.66
71 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (70 bp):
TGATGCTGTCCAATTTGATGTATAATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGAG
CATAT
Found at i:47797064 original size:116 final size:116
Alignment explanation
Indices: 47796860--47797105 Score: 438
Period size: 116 Copynumber: 2.1 Consensus size: 116
47796850 ATGTTATGAT
* *
47796860 GCTGTCTAATTTGAGCATATTAATGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATA
1 GCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATA
*
47796925 TTGATGCTGTCCAATTTGATGTATAATGCTGTCCAATTTGAGCATATTAAA
66 TTGATGCTGTCCAATTTGATGTATAATGCTATCCAATTTGAGCATATTAAA
47796976 GCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATA
1 GCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATA
* * *
47797041 TTGATGCTGTCTAATTTGATGTATAATGCTATCCATTTTGAGCATATTAAT
66 TTGATGCTGTCCAATTTGATGTATAATGCTATCCAATTTGAGCATATTAAA
47797092 GCTGTCCAATTTGA
1 GCTGTCCAATTTGA
47797106 TGTATAAATG
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 124 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (116 bp):
GCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGATGTATAATGCTGTCCATTTTGAGCATA
TTGATGCTGTCCAATTTGATGTATAATGCTATCCAATTTGAGCATATTAAA
Found at i:47799824 original size:20 final size:20
Alignment explanation
Indices: 47799795--47799847 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
47799785 TAGTTTTAGG
* *
47799795 GTCTCAAGACAAGTGG-CTTT
1 GTCTCGAGACAAG-GGTCATT
47799815 GTCTCGAGACATAGGGTCATT
1 GTCTCGAGACA-AGGGTCATT
*
47799836 ATCTCGAGACAA
1 GTCTCGAGACAA
47799848 TCGACAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (20 bp):
GTCTCGAGACAAGGGTCATT
Found at i:47805270 original size:116 final size:116
Alignment explanation
Indices: 47805058--47805290 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 116
47805048 TGATCTTAAA
* *
47805058 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAAACTTAACAATATCAGTTATGATCTTAAAT
1 TCGAATGAACTTAGGTTACAATATTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
* ** * *
47805123 CAGCGAGCTGTTTGGAGTTAGGATTTGAGATCAACTAACTCAAATAAAATT
66 CAGCGAGCTATTCAGAGTTAGGATCTAAGATCAACTAACTCAAATAAAATT
* * * * * *
47805174 TCGAATGAGCTTAGGTTACGATCTTAAATCATCGAACCTTAACAATATTAGCTATGATCTTAAAT
1 TCGAATGAACTTAGGTTACAATATTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
* * *
47805239 TAGTGAGTTATTCAGAGTT-GCGATCTAAGATCAACTAACTCAAATAAAATT
66 CAGCGAGCTATTCAGAGTTAG-GATCTAAGATCAACTAACTCAAATAAAATT
47805290 T
1 T
47805291 GTTCACAATC
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
115 1 0.01
116 99 0.99
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (116 bp):
TCGAATGAACTTAGGTTACAATATTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
CAGCGAGCTATTCAGAGTTAGGATCTAAGATCAACTAACTCAAATAAAATT
Found at i:47805348 original size:132 final size:132
Alignment explanation
Indices: 47805174--47805692 Score: 621
Period size: 132 Copynumber: 3.9 Consensus size: 132
47805164 AAATAAAATT
* * * * * * * *
47805174 TCGAATGAGCTTAGGTTACGATCTTAAATCATCGAACCTTAACAATATTAGCTATGATCTTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGTGATATTAAAT
** * **
47805239 TAGTGAGTTATTCAGAGTTGCGATCTAAGATCAACTAACTCAAATAAAATTTGTTCACAATCTTA
66 TAGCAAGTTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
47805304 AA
131 AA
* * * *
47805306 TTGAATGAACTTAGGTTGCGATATTAAATCAGCTAACCTTAACAACATCAGCTGTGATATTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGTGATATTAAAT
* * *
47805371 TAGCAAGTTGTTCGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGGTCTTA
66 TAGCAAGTTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
47805436 AA
131 AA
* * * * *
47805438 TCGAATGAACTTAGGTTGCAATCTTAAATCAGTGAACCTTAACAATATCAGTTGCGATCTTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGTGATATTAAAT
* *
47805503 TAGCAAGCTGT-TTGA-AGTTGCGATCTTG-GATCAACTAACTCAAATAAAATTTGTTCTTGATC
66 TAGCAAG-T-TATTCAGAGTTGCGATC-TGAGATCAACTAACTCAAATAAAATTTGTTCATGATC
47805565 TTAAA
128 TTAAA
* * * * ** *
47805570 CCGAATGAACTTAGGTTGCAATATTAAATTAACGAACCTTAACAATATCAGTTGCAATATTAAAC
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGTGATATTAAAT
* * * * * * *
47805635 CAGCGAGCTATTAAGAGTTGCAATATGAGATCAGCTAACTCAAATAAAATTTGTTCAT
66 TAGCAAGTTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCAT
47805693 AAAATAAAGT
Statistics
Matches: 334, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
130 1 0.00
131 5 0.01
132 322 0.96
133 5 0.01
134 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (132 bp):
TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGTGATATTAAAT
TAGCAAGTTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
AA
Found at i:47808247 original size:48 final size:48
Alignment explanation
Indices: 47808163--47808256 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
47808153 TTTCTTGGCT
* *
47808163 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAAAGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
47808211 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
47808257 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:47809922 original size:20 final size:19
Alignment explanation
Indices: 47809882--47809939 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
47809872 TTTCTAAACC
*
47809882 ATTTCATTGCATTTTATTTA
1 ATTTCATTGCA-TTTAGTTA
47809902 ATTTCATTGCATTTAGGTTA
1 ATTTCATTGCATTTA-GTTA
*
47809922 A-TTCATTTGCATATAGTT
1 ATTTCA-TTGCATTTAGTT
47809940 TATTAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.32
20 23 0.68
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (19 bp):
ATTTCATTGCATTTAGTTA
Found at i:47814145 original size:18 final size:18
Alignment explanation
Indices: 47814122--47814162 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
47814112 CTTAACTAAC
47814122 AATAAG-AACATGAAGAAA
1 AATAAGCAA-ATGAAGAAA
*
47814140 AATAAGCAAATGTAGAAA
1 AATAAGCAAATGAAGAAA
47814158 AATAA
1 AATAA
47814163 ACTCTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (18 bp):
AATAAGCAAATGAAGAAA
Found at i:47818059 original size:17 final size:17
Alignment explanation
Indices: 47818039--47818085 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
47818029 AATTATGTAT
47818039 AAAAATAAATAAAATAA
1 AAAAATAAATAAAATAA
* *
47818056 AAAATTAAATTAAATTAA
1 AAAAATAAA-TAAAATAA
47818074 AAAAATAAATAA
1 AAAAATAAATAA
47818086 CTAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATAAATAAAATAA
Found at i:47819332 original size:21 final size:21
Alignment explanation
Indices: 47819291--47819332 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47819281 TCGTCTCAGA
* *
47819291 TTATTGGGTTTTGCTTTTTAT
1 TTATTGGGTTATGCTTGTTAT
47819312 TTATTGGGTTAATGC-TGTTAT
1 TTATTGGGTT-ATGCTTGTTAT
47819333 CTTTAAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.14, C:0.05, G:0.21, T:0.60
Consensus pattern (21 bp):
TTATTGGGTTATGCTTGTTAT
Found at i:47822759 original size:32 final size:30
Alignment explanation
Indices: 47822714--47822774 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
47822704 CATTTACTAA
47822714 ATTTTTTTAATTTTAAAA-ATATTTAAAAAT
1 ATTTTTTTAATTTTAAAATA-ATTTAAAAAT
47822744 ATTTTTTTATGATTTTAAAATAATTTAAAAA
1 ATTTTTTTA--ATTTTAAAATAATTTAAAAA
47822775 ATTAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 9 0.32
32 18 0.64
33 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTTTTTAATTTTAAAATAATTTAAAAAT
Found at i:47827652 original size:2 final size:2
Alignment explanation
Indices: 47827645--47827674 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47827635 TCTGCAACTT
47827645 TA TA TA TA TA TA TA -A 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
47827675 TGGAACCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47827664 original size:13 final size:13
Alignment explanation
Indices: 47827646--47827671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47827636 CTGCAACTTT
47827646 ATATATATATATA
1 ATATATATATATA
47827659 ATATATATATATA
1 ATATATATATATA
47827672 TATTGGAACC
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:47827665 original size:15 final size:15
Alignment explanation
Indices: 47827645--47827673 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47827635 TCTGCAACTT
47827645 TATATATATATATAA
1 TATATATATATATAA
47827660 TATATATATATATA
1 TATATATATATATA
47827674 TTGGAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:47838483 original size:26 final size:27
Alignment explanation
Indices: 47838406--47838492 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 27
47838396 AGCCAATATT
*
47838406 GGGAAGCTC-CGGAGAGCCAT-TAATC
1 GGGAAGCTCACGAAGAGCCATATAATC
** * *
47838431 AAGAAGCTCACAAAGAGCC-TTTAATC
1 GGGAAGCTCACGAAGAGCCATATAATC
47838457 GGGAAGCTCACGAAGAGCCATAT-ATC
1 GGGAAGCTCACGAAGAGCCATATAATC
*
47838483 GGGATGCTCA
1 GGGAAGCTCA
47838493 TAAGAACTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 8 0.16
26 40 0.80
27 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.17
Consensus pattern (27 bp):
GGGAAGCTCACGAAGAGCCATATAATC
Found at i:47839521 original size:13 final size:13
Alignment explanation
Indices: 47839505--47839532 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47839495 TTTTATTTTA
47839505 TTATTTTTCATCT
1 TTATTTTTCATCT
47839518 TTATTTTTCATCT
1 TTATTTTTCATCT
47839531 TT
1 TT
47839533 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTCATCT
Found at i:47845203 original size:21 final size:21
Alignment explanation
Indices: 47845179--47845223 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
47845169 TTTTTTGTAA
47845179 TTTTT-AT-ATTATTTTAGAAT
1 TTTTTAATGATTA-TTTAGAAT
*
47845199 TTTTTAATGATTATTTATAAT
1 TTTTTAATGATTATTTAGAAT
47845220 TTTT
1 TTTT
47845224 CTATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTTAATGATTATTTAGAAT
Found at i:47846495 original size:21 final size:22
Alignment explanation
Indices: 47846462--47846503 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
47846452 CGATAATTAA
* *
47846462 TATATTTTTCTATTA-ATTCTG
1 TATATCTTCCTATTATATTCTG
47846483 TATATCTTCCTATTATATTCT
1 TATATCTTCCTATTATATTCT
47846504 TACGAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.60
Consensus pattern (22 bp):
TATATCTTCCTATTATATTCTG
Found at i:47852525 original size:18 final size:17
Alignment explanation
Indices: 47852502--47852536 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47852492 GAATGTTAGA
47852502 GTATTTTATAAAATTATT
1 GTATTTTA-AAAATTATT
*
47852520 GTATTTTAAAATTTATT
1 GTATTTTAAAAATTATT
47852537 TAGAAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
GTATTTTAAAAATTATT
Found at i:47862762 original size:18 final size:18
Alignment explanation
Indices: 47862741--47862775 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47862731 CAAAAAATAA
*
47862741 AAAATACATAAAATTTAG
1 AAAACACATAAAATTTAG
*
47862759 AAAACATATAAAATTTA
1 AAAACACATAAAATTTA
47862776 TTCCACCATG
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:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACACATAAAATTTAG
Found at i:47873021 original size:19 final size:20
Alignment explanation
Indices: 47872999--47873060 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
47872989 TAAGATGACT
47872999 ATATAAAAAATTTTAAAA-A
1 ATATAAAAAATTTTAAAATA
*
47873018 ATATAAAATATTAAATTAAAATA
1 ATATAAAAAATT---TTAAAATA
*
47873041 ATAATAATAAATTTTAAAAT
1 AT-ATAAAAAATTTTAAAAT
47873061 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 11 0.31
21 7 0.20
22 6 0.17
23 3 0.09
24 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAAAAATTTTAAAATA
Found at i:47876380 original size:21 final size:21
Alignment explanation
Indices: 47876354--47876394 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47876344 AGACGAGCAA
* *
47876354 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
47876375 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
47876395 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:47879591 original size:21 final size:21
Alignment explanation
Indices: 47879566--47879627 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
47879556 AATAATTAAC
47879566 TTTAAATAAATTCAAAATAAA
1 TTTAAATAAATTCAAAATAAA
** * *
47879587 TTTAAATTTATTCAATAATCAT
1 TTTAAATAAATTCAA-AATAAA
* *
47879609 TTTAAATAACTTAAAAATA
1 TTTAAATAAATTCAAAATA
47879628 CTATACAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAATAAATTCAAAATAAA
Found at i:47882421 original size:53 final size:54
Alignment explanation
Indices: 47882207--47882421 Score: 235
Period size: 53 Copynumber: 4.0 Consensus size: 54
47882197 ACCCCTCAAA
* **
47882207 TCCTTTTACTTTTTCCCTAAAAAATTTACTTCCCCCAAATCCCCAAAAACTTTTT
1 TCCTTTTACTTTCTCCCTAAAACTTTTACTTCCCCCAAA-CCCCAAAAACTTTTT
* *** *
47882262 TTCTTTTTGATT-TCCCTCAAAAGTTTTACTTCCCCCAAACCCCTAAAAA--TTTT
1 TCCTTTTACTTTCTCCCT-AAAACTTTTACTTCCCCCAAACCCC-AAAAACTTTTT
**
47882315 TCCTTTTACTTTCTCCCTAAAACTTTTACTT-CCCCAAACTCCC-AAATTTTTTT
1 TCCTTTTACTTTCTCCCTAAAACTTTTACTTCCCCCAAAC-CCCAAAAACTTTTT
* * *
47882368 TCCTTTTGCTTTCTCCC-AAAACTTTTACTTCCTCCGAACCCCAAAAACTTTTT
1 TCCTTTTACTTTCTCCCTAAAACTTTTACTTCCCCCAAACCCCAAAAACTTTTT
47882421 T
1 T
47882422 TTCAAATTTA
Statistics
Matches: 135, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
51 3 0.02
52 24 0.18
53 62 0.46
54 14 0.10
55 32 0.24
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (54 bp):
TCCTTTTACTTTCTCCCTAAAACTTTTACTTCCCCCAAACCCCAAAAACTTTTT
Found at i:47890070 original size:31 final size:33
Alignment explanation
Indices: 47890005--47890070 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 33
47889995 CAACTCAATA
* * *
47890005 ACTTAAATAAAAACAATTTTTGAATAGTTTAGTG
1 ACTTAAAT-AAAACAATTTTTAAATAATTCAGTG
47890039 ACTTAAAT-AAA-AATTTTTAAATAATTCAGTG
1 ACTTAAATAAAACAATTTTTAAATAATTCAGTG
47890070 A
1 A
47890071 TCAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 18 0.62
32 3 0.10
34 8 0.28
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (33 bp):
ACTTAAATAAAACAATTTTTAAATAATTCAGTG
Found at i:47896395 original size:20 final size:20
Alignment explanation
Indices: 47896370--47896413 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
47896360 AAAAACACTT
47896370 ATGCTGGATTGAAAGAACTC
1 ATGCTGGATTGAAAGAACTC
47896390 ATGCTGGATTGAAAGAACTC
1 ATGCTGGATTGAAAGAACTC
47896410 ATGC
1 ATGC
47896414 CTACGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (20 bp):
ATGCTGGATTGAAAGAACTC
Found at i:47900487 original size:26 final size:25
Alignment explanation
Indices: 47900446--47900495 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
47900436 CTGGAACATA
*
47900446 CATCCTTCCCATAAATCGAAGTTTGC
1 CATCCTTCCCATAAAT-AAAGTTTGC
47900472 CATCCTTTCCCA-AAATAAAGTTTG
1 CATCC-TTCCCATAAATAAAGTTTG
47900496 TAGTATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (25 bp):
CATCCTTCCCATAAATAAAGTTTGC
Found at i:47916057 original size:77 final size:77
Alignment explanation
Indices: 47915962--47916117 Score: 242
Period size: 77 Copynumber: 2.0 Consensus size: 77
47915952 TCATTTGTGC
* * *
47915962 ATGGCGAGACTCAAATATAGACTATGAAAGTTACG-GGGCCTTAATCTTGTAAACACAACTAATG
1 ATGGCGAGACTCAAATATAGACTATGAAAGTT-CGAGGGCCTTAACCTTGTAAACACAACCAAGG
47916026 CATCATTGATAAA
65 CATCATTGATAAA
* *
47916039 ATGGCGAGCCTCAAATATAGACTATGAAAGTTTGAGGGCCTTAACCTTGTAAACACAACCAAGGC
1 ATGGCGAGACTCAAATATAGACTATGAAAGTTCGAGGGCCTTAACCTTGTAAACACAACCAAGGC
*
47916104 TTCATTGATAAA
66 ATCATTGATAAA
47916116 AT
1 AT
47916118 TAAATTATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 71 0.99
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (77 bp):
ATGGCGAGACTCAAATATAGACTATGAAAGTTCGAGGGCCTTAACCTTGTAAACACAACCAAGGC
ATCATTGATAAA
Found at i:47917556 original size:6 final size:6
Alignment explanation
Indices: 47917545--47917573 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
47917535 GGAGGACATA
47917545 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
47917574 ACTATGGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:47920620 original size:3 final size:3
Alignment explanation
Indices: 47920612--47920641 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
47920602 AGTTTCAACT
47920612 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
47920642 GATTTCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:47923748 original size:61 final size:59
Alignment explanation
Indices: 47923614--47923753 Score: 174
Period size: 61 Copynumber: 2.3 Consensus size: 59
47923604 ATTAAATTGT
* * * *
47923614 ATAATAAATAATAAATAATTTAATTATATTTTAATATAATTATTATTAAATAAAATTTA
1 ATAATATATAATATATAATTTAATAACATTTTAATATAATTATTATTAAATAAAATTTA
* * *
47923673 ATAACAATAAAATATATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TTA
1 ATAA-TATATAATATATAATTTAATAACATT-TTAATATAATTATTATT-AAATA-AAATTTA
47923735 ATAATATATAATATATAAT
1 ATAATATATAATATATAAT
47923754 ATTAGAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.06
60 20 0.29
61 30 0.44
62 12 0.18
63 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (59 bp):
ATAATATATAATATATAATTTAATAACATTTTAATATAATTATTATTAAATAAAATTTA
Found at i:47934682 original size:44 final size:44
Alignment explanation
Indices: 47934633--47934833 Score: 192
Period size: 45 Copynumber: 4.5 Consensus size: 44
47934623 CGAAATGAGA
* **
47934633 AAGACTATAGTTGAAAGATACTATGATATTAAATCGGAATGAAT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATCGGAATGAAT
* * * **
47934677 AAGACTATAGTTGAAAGATACTACGGCACTAAA-CTGGAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATC-GG-AATGAAT
* * *
47934722 AAGACCGTAGTTGAAAGATACTATGGCATTAAATCTGATACGAAT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATCGGA-ATGAAT
* * *
47934767 AAGACCATAGTTGAAAGATATTATGGCATCACAT-GGATAATG-AT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATCGG--AATGAAT
*
47934811 CAATACCATAGTTGAAAGATACT
1 -AAGACCATAGTTGAAAGATACT
47934834 GTGACACTAC
Statistics
Matches: 128, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
43 1 0.01
44 35 0.27
45 90 0.70
46 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (44 bp):
AAGACCATAGTTGAAAGATACTATGGCATTAAATCGGAATGAAT
Found at i:47934823 original size:90 final size:89
Alignment explanation
Indices: 47934624--47934839 Score: 240
Period size: 90 Copynumber: 2.4 Consensus size: 89
47934614 CATCTTACCC
* * * * * *
47934624 GAAATGAGAAAGACTATAGTTGAAAGATACTATGATATTAAATCGGAATGAATAAGACTATAGTT
1 GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGAACGAATAAGACCATAGTT
47934689 GAAAGATACTACGGCACTAAACTG
66 GAAAGATACTACGGCACTAAACTG
* * * *
47934713 GAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCATTAAATCTGATACGAATAAGACCATAGT
1 GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGA-ACGAATAAGACCATAGT
* * *
47934778 TGAAAGATATTATGGCA-T-CACATG
65 TGAAAGATACTACGGCACTAAAC-TG
* *
47934802 GATAATGAT-CAATACCATAGTTGAAAGATACTGTGACA
1 GA-AATG-TGCAAGACCATAGTTGAAAGATACTATGACA
47934840 CTACTTCAGA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.02
89 45 0.42
90 58 0.55
91 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (89 bp):
GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGAACGAATAAGACCATAGTT
GAAAGATACTACGGCACTAAACTG
Found at i:47939615 original size:16 final size:16
Alignment explanation
Indices: 47939594--47939627 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
47939584 TGTGACTTTC
47939594 AAAAATCCAATCTTCA
1 AAAAATCCAATCTTCA
47939610 AAAAATCCAATCTTCA
1 AAAAATCCAATCTTCA
47939626 AA
1 AA
47939628 GGGAAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATCCAATCTTCA
Found at i:47939999 original size:36 final size:36
Alignment explanation
Indices: 47939951--47940021 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
47939941 ATCAAGGGCT
*
47939951 ACAATTAAAAGCTGTATACAATTTGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
* *
47939987 ACAATTAGAAGCTGTATACAATTAGAACTTTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
47940022 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:47940009 original size:17 final size:17
Alignment explanation
Indices: 47939950--47940013 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
47939940 CATCAAGGGC
*
47939950 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
* *
47939967 TACAATTTGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
47939986 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
47940003 TACAATTAGAA
1 TACAATTAGAA
47940014 CTTTAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.56
19 10 0.28
20 3 0.08
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:47944026 original size:21 final size:21
Alignment explanation
Indices: 47944000--47944040 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47943990 ATCTGCTCAA
* *
47944000 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
47944021 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
47944041 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:47948509 original size:19 final size:19
Alignment explanation
Indices: 47948473--47948509 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47948463 CACATGTCAT
*
47948473 GTATCACTATCTAGTCCAC
1 GTATCACTATCTAATCCAC
*
47948492 GTATCACTATTTAATCCA
1 GTATCACTATCTAATCCA
47948510 TGTTAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (19 bp):
GTATCACTATCTAATCCAC
Found at i:47948918 original size:21 final size:20
Alignment explanation
Indices: 47948889--47948929 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
47948879 ACATATGAAA
*
47948889 TATAAATTTGGAATATAATTT
1 TATAAATTTGAAATA-AATTT
*
47948910 TATATATTTGAAATAAATTT
1 TATAAATTTGAAATAAATTT
47948930 CAATAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TATAAATTTGAAATAAATTT
Found at i:47950122 original size:14 final size:14
Alignment explanation
Indices: 47950103--47950132 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47950093 GGATATGCCT
47950103 ATTAGAAAATGAGA
1 ATTAGAAAATGAGA
47950117 ATTAGAAAATGAGA
1 ATTAGAAAATGAGA
47950131 AT
1 AT
47950133 GAAGGTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (14 bp):
ATTAGAAAATGAGA
Found at i:47956117 original size:42 final size:43
Alignment explanation
Indices: 47956071--47956176 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 43
47956061 GGAAACCTGC
* *
47956071 AAGGGTTAAACGGAAGCTCATAAA-AGCTGAAC-GAAAACCCAT
1 AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTG-AAACCCAG
*
47956113 AAGGGTTAAACTGCAGCTCA-AAATAGCTGAACTGAAACCCAG
1 AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCAG
*
47956155 AAGGGTTAAACTGAAACTCATA
1 AAGGGTTAAACTGAAGCTCATA
47956177 TGAGATAACT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.05
42 51 0.91
43 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (43 bp):
AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCAG
Found at i:47956188 original size:20 final size:20
Alignment explanation
Indices: 47956163--47956204 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
47956153 AGAAGGGTTA
47956163 AACTGAAACTCAT-ATGAGAT
1 AACTGAAACTCATGA-GAGAT
*
47956183 AACTGAAGCTCATGAGAGAT
1 AACTGAAACTCATGAGAGAT
47956203 AA
1 AA
47956205 ACGGAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (20 bp):
AACTGAAACTCATGAGAGAT
Found at i:47958623 original size:20 final size:20
Alignment explanation
Indices: 47958590--47958639 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
47958580 GTTGATGAGA
* * *
47958590 AAAAAATAATTATAAGTTAT
1 AAAAATTAAATATAAATTAT
*
47958610 AAAAATTAAATATAAATTTT
1 AAAAATTAAATATAAATTAT
*
47958630 AAAAGTTAAA
1 AAAAATTAAA
47958640 AGTTTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAAATTAAATATAAATTAT
Found at i:47965597 original size:29 final size:30
Alignment explanation
Indices: 47965555--47965632 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
47965545 ATTAAGAATA
*
47965555 CAATCAATTAAGCCCCTAATTGAAAATT-G
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
** *
47965584 CAATCAATTGAGCCATTAATTGAAAGTTGG
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
*
47965614 CAATCAATTGAGCTCCTAA
1 CAATCAATTGAGCCCCTAA
47965633 AATATAGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (30 bp):
CAATCAATTGAGCCCCTAATTGAAAATTGG
Found at i:47967696 original size:85 final size:86
Alignment explanation
Indices: 47967542--47967702 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
47967532 AGATAAAAAC
* * *
47967542 ATTTGCAGTTACTGCCACTTGTTATGAGTGCACAACATGGTTTCAGATTAAACAAACTGCCACTA
1 ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTA
47967607 GG-TTTGTGGACGAACCACAT
66 GGTTTTGTGGACGAACCACAT
* * * *
47967627 ATTTACAGTTATTGTCACTTGTTGTGAGTGCACAACAT-ATTCGCAGATTAAACAAACTGTCACT
1 ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATT-GCAGATTAAACAAACTGCCACT
*
47967691 GGGTTTTGTGGA
65 AGGTTTTGTGGA
47967703 TGGGCAACTA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 2 0.03
85 56 0.85
86 8 0.12
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (86 bp):
ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTA
GGTTTTGTGGACGAACCACAT
Found at i:47970204 original size:16 final size:16
Alignment explanation
Indices: 47970179--47970214 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
47970169 TTTAACATAT
47970179 AAAAATTATATATAAA
1 AAAAATTATATATAAA
47970195 GAAAAA-TATATATAAA
1 -AAAAATTATATATAAA
47970211 AAAA
1 AAAA
47970215 TTTGTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAAATTATATATAAA
Found at i:47974259 original size:18 final size:19
Alignment explanation
Indices: 47974233--47974269 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
47974223 TTATTATATC
47974233 TTATCATTTT-TTAGATTAA
1 TTATCATTTTATT-GATTAA
47974252 TTAT-ATTTTATTGATTAA
1 TTATCATTTTATTGATTAA
47974270 ATACCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATCATTTTATTGATTAA
Found at i:47974528 original size:24 final size:26
Alignment explanation
Indices: 47974476--47974541 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
47974466 TATAGAGGTA
47974476 AACAT-AGTAATAAATAATTTATAAT
1 AACATAAGTAATAAATAATTTATAAT
47974501 -ACATAAGTAA-AAAT-A-TTATGAAT
1 AACATAAGTAATAAATAATTTAT-AAT
*
47974524 AACATAA-AAATAAATAAT
1 AACATAAGTAATAAATAAT
47974542 GATAATAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 18 0.53
25 6 0.18
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AACATAAGTAATAAATAATTTATAAT
Found at i:47977251 original size:11 final size:11
Alignment explanation
Indices: 47977235--47977261 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47977225 AAAATAATCT
47977235 GGGCCAAGCTC
1 GGGCCAAGCTC
47977246 GGGCCAAGCTC
1 GGGCCAAGCTC
47977257 GGGCC
1 GGGCC
47977262 TTGAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.37, G:0.41, T:0.07
Consensus pattern (11 bp):
GGGCCAAGCTC
Found at i:47979708 original size:627 final size:627
Alignment explanation
Indices: 47978515--47979761 Score: 2395
Period size: 627 Copynumber: 2.0 Consensus size: 627
47978505 TCAAAGCTAT
47978515 AGGGGACACACGGCCGTGTGGCCAGGCCGTGTGGGCATTCGAAATAGGGACACACGGCCGTGTCC
1 AGGGGACACACGGCCGTGTGGCCAGGCCGTGTGGGCATTCGAAATAGGGACACACGGCCGTGTCC
* *
47978580 CAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTGGGTCACATGACCAAGTCACACACCTATGT
66 CAGCCCGTGTCCGTGCCCGTGTAACTCTCTAACTTGGGTCACACGACCAAGTCACACACCTATGT
*
47978645 GCTAGGCCGTGTTGAGCATACTAACTTGTGCAATTTTAAAGATACAGGGAACACACAGCCATGTC
131 GCTAGGCCGTGTTGAGCATACTAACTTGTGCAATTTTAAAGATACAGGGAACACACAGCCATGCC
*
47978710 ACCTGGCCGTGTGTCACACACGGCTGAGACGCACGCCCGTGTCTTTGCCCATTTGGATGAAAATA
196 ACCTGGCCGTGTGTCACACACGGCTGAGACGCACGCCCATGTCTTTGCCCATTTGGATGAAAATA
* *
47978775 GGTCATTTTCCAAGCCACATTTCTCACCCAATTTGGTACCAACCTAAACAGAACAATTTGCACAT
261 AGTCATTTTCCAAGCCACATTTCTCACCCAATTCGGTACCAACCTAAACAGAACAATTTGCACAT
47978840 CAACAAGCCATAACTAGGCATCCAAATCAAGCTAAAATCAAGTCTTAAACATGTATTATCACAAC
326 CAACAAGCCATAACTAGGCATCCAAATCAAGCTAAAATCAAGTCTTAAACATGTATTATCACAAC
47978905 ATATAACCAATATGCCCTTAGGCACCTCAAATGACAAATTAATAACATGTCAACCAAATATCCAT
391 ATATAACCAATATGCCCTTAGGCACCTCAAATGACAAATTAATAACATGTCAACCAAATATCCAT
47978970 ATTTACCTAGATAACCAAATGCATATATGCTTAATGGTACCAAATATACCTATAATTTTTCCATC
456 ATTTACCTAGATAACCAAATGCATATATGCTTAATGGTACCAAATATACCTATAATTTTTCCATC
47979035 ATTCAACCATATCAAATACACATTAAATATGATAAGGCCACATATATAAACACATCAAAATATAC
521 ATTCAACCATATCAAATACACATTAAATATGATAAGGCCACATATATAAACACATCAAAATATAC
47979100 CAAACACAAGTCATTCAAGTGGCTAGTATCAACAAGTCATTC
586 CAAACACAAGTCATTCAAGTGGCTAGTATCAACAAGTCATTC
*
47979142 AGGGGACACACGGTCGTGTGGCCAGGCCGTGTGGGCATTCGAAATAGGGACACACGGCCGTGTCC
1 AGGGGACACACGGCCGTGTGGCCAGGCCGTGTGGGCATTCGAAATAGGGACACACGGCCGTGTCC
*
47979207 CAGCCCGTGTCCTTGCCCGTGTAACTCTCTAACTTGGGTCACACGACCAAGTCACACACCTATGT
66 CAGCCCGTGTCCGTGCCCGTGTAACTCTCTAACTTGGGTCACACGACCAAGTCACACACCTATGT
*
47979272 GCTAGGCCGTGTTGAGCATACTGACTTGTGCAATTTTAAAGATACAGGGAACACACAGCCATGCC
131 GCTAGGCCGTGTTGAGCATACTAACTTGTGCAATTTTAAAGATACAGGGAACACACAGCCATGCC
*
47979337 ACCTGGCCGTGTGTCACACACGGCTGAGACGCATGCCCATGTCTTTGCCCATTTGGATGAAAATA
196 ACCTGGCCGTGTGTCACACACGGCTGAGACGCACGCCCATGTCTTTGCCCATTTGGATGAAAATA
47979402 AGTCATTTTCCAAGCCACATTTCTCACCCAATTCGGTACCAACCTAAACAGAACAATTTGCACAT
261 AGTCATTTTCCAAGCCACATTTCTCACCCAATTCGGTACCAACCTAAACAGAACAATTTGCACAT
47979467 CAACAAGCCATAACTAGGCATCCAAATCAAGCTAAAATCAAGTCTTAAACATGTATTATCACAAC
326 CAACAAGCCATAACTAGGCATCCAAATCAAGCTAAAATCAAGTCTTAAACATGTATTATCACAAC
*
47979532 ATATAACCAATATGCCCTTAGGCACCTCAAATGACAAATTAATAACGTGTCAACCAAATATCCAT
391 ATATAACCAATATGCCCTTAGGCACCTCAAATGACAAATTAATAACATGTCAACCAAATATCCAT
47979597 ATTTACCTAGATAACCAAATGCATATATGCTTAATGGTACCAAATATACCTATAATTTTTCCATC
456 ATTTACCTAGATAACCAAATGCATATATGCTTAATGGTACCAAATATACCTATAATTTTTCCATC
47979662 ATTCAACCATATCAAATACACATTAAATATGATAAGGCCACATATATAAACACATCAAAATATAC
521 ATTCAACCATATCAAATACACATTAAATATGATAAGGCCACATATATAAACACATCAAAATATAC
47979727 CAAACACAAGTCATTCAAGTGGCTAGTATCAACAA
586 CAAACACAAGTCATTCAAGTGGCTAGTATCAACAA
47979762 AACAATTATA
Statistics
Matches: 609, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
627 609 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (627 bp):
AGGGGACACACGGCCGTGTGGCCAGGCCGTGTGGGCATTCGAAATAGGGACACACGGCCGTGTCC
CAGCCCGTGTCCGTGCCCGTGTAACTCTCTAACTTGGGTCACACGACCAAGTCACACACCTATGT
GCTAGGCCGTGTTGAGCATACTAACTTGTGCAATTTTAAAGATACAGGGAACACACAGCCATGCC
ACCTGGCCGTGTGTCACACACGGCTGAGACGCACGCCCATGTCTTTGCCCATTTGGATGAAAATA
AGTCATTTTCCAAGCCACATTTCTCACCCAATTCGGTACCAACCTAAACAGAACAATTTGCACAT
CAACAAGCCATAACTAGGCATCCAAATCAAGCTAAAATCAAGTCTTAAACATGTATTATCACAAC
ATATAACCAATATGCCCTTAGGCACCTCAAATGACAAATTAATAACATGTCAACCAAATATCCAT
ATTTACCTAGATAACCAAATGCATATATGCTTAATGGTACCAAATATACCTATAATTTTTCCATC
ATTCAACCATATCAAATACACATTAAATATGATAAGGCCACATATATAAACACATCAAAATATAC
CAAACACAAGTCATTCAAGTGGCTAGTATCAACAAGTCATTC
Found at i:47980329 original size:25 final size:25
Alignment explanation
Indices: 47980301--47980371 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
47980291 CTCTTCAGAG
47980301 CTGAATAACGGGAAGCTCATACGAC
1 CTGAATAACGGGAAGCTCATACGAC
* * *
47980326 CTGAGTAACGGGAAGCTCATGCGAG
1 CTGAATAACGGGAAGCTCATACGAC
* *
47980351 CTGTATAACGAGAAGCTCATA
1 CTGAATAACGGGAAGCTCATA
47980372 TAAGTTGTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
CTGAATAACGGGAAGCTCATACGAC
Found at i:47980706 original size:15 final size:16
Alignment explanation
Indices: 47980686--47980715 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47980676 CGAATGAATT
47980686 TAACTCA-ATTCAATA
1 TAACTCATATTCAATA
47980701 TAACTCATATTCAAT
1 TAACTCATATTCAAT
47980716 TTAGTCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (16 bp):
TAACTCATATTCAATA
Found at i:47983551 original size:41 final size:41
Alignment explanation
Indices: 47983504--47983731 Score: 390
Period size: 41 Copynumber: 5.6 Consensus size: 41
47983494 CAGACGTTAC
* *
47983504 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATAT
47983545 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
47983586 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
47983627 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
47983668 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
47983709 GTCTAGCAGGC-TAAGTGCCGGTG
1 GTCTAGCAGGCTTAA-TGCCGGTG
47983732 TACTGAATCA
Statistics
Matches: 182, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 175 0.96
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
Found at i:47983756 original size:123 final size:122
Alignment explanation
Indices: 47983506--47983773 Score: 373
Period size: 123 Copynumber: 2.2 Consensus size: 122
47983496 GACGTTACGT
*
47983506 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATA
1 CTAGCAGGCTTAATGCCGGTG-AGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGATA
* * *
47983571 CATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGT
65 CATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTATAAGC
*
47983629 CTAGCAGGCTTAATGCCGGTGA-TACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGAT
1 CTAGCAGGCTTAATGCCGGTGAGTA-A-TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAT
* *
47983693 ACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGC
64 ACATTTCAGACTATATGTCTAGCAGGCTTAA-TGCCGGTGATACAT--ATCAGACTATAAGC
**
47983752 CTAGCAGGCAAAATGCCGGTGA
1 CTAGCAGGCTTAATGCCGGTGA
47983774 ATCTGTTTAA
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
121 3 0.02
122 8 0.06
123 120 0.92
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (122 bp):
CTAGCAGGCTTAATGCCGGTGAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGATAC
ATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTATAAGC
Found at i:47992392 original size:41 final size:39
Alignment explanation
Indices: 47992329--47992532 Score: 214
Period size: 41 Copynumber: 5.0 Consensus size: 39
47992319 GTGATTGAAT
* * *
47992329 ATAATACAGACGTTACGTCTAGCAGGCTTAATGCCGGTG
1 ATAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
*
47992368 AAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG
1 -A-TAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
47992409 ATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
1 ATA-A-TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
* *
47992450 ATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 ATA-A-TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
* * **
47992491 TACTGAA-TCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTG
1 -A-T-AATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
47992532 A
1 A
47992533 ATCTGTTTAA
Statistics
Matches: 144, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.01
40 7 0.05
41 129 0.90
42 3 0.02
43 2 0.01
44 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (39 bp):
ATAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
Found at i:47992440 original size:82 final size:82
Alignment explanation
Indices: 47992330--47992534 Score: 247
Period size: 82 Copynumber: 2.5 Consensus size: 82
47992320 TGATTGAATA
* * *
47992330 TAATACAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAAGTCTAGC
1 TAAT-CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAA-TACATTTCAGACTATAAGTCTAGC
47992393 AGGCTAAATGCCGGTGATAC
64 AGGCTAAATGCCGGTG-TAC
* *
47992413 -ATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGTCTAGCA
1 TA-ATCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTATAAGTCTAGCA
*
47992476 GGCTAAGTGCCGGTGTAC
65 GGCTAAATGCCGGTGTAC
* * **
47992494 TGAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGAAT
1 T-AATCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAT
47992535 CTGTTTAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
80 2 0.02
81 5 0.05
82 94 0.90
83 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (82 bp):
TAATCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTATAAGTCTAGCAG
GCTAAATGCCGGTGTAC
Found at i:47996459 original size:17 final size:17
Alignment explanation
Indices: 47996433--47996472 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
47996423 TCGTACGCTC
*
47996433 AATTAAGGCTCAAATTT
1 AATTACGGCTCAAATTT
47996450 AATTACGGCTCAAATTT
1 AATTACGGCTCAAATTT
47996467 AATTAC
1 AATTAC
47996473 ATTTCATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (17 bp):
AATTACGGCTCAAATTT
Found at i:47996686 original size:15 final size:18
Alignment explanation
Indices: 47996649--47996689 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
47996639 TGTTTAACTT
47996649 TTAATTAATCATAATTAAC
1 TTAATTAATCAT-ATTAAC
47996668 TTAATTAATC-T-TTAA-
1 TTAATTAATCATATTAAC
47996683 TTAATTA
1 TTAATTA
47996690 GTTTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
18 1 0.05
19 10 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAATCATATTAAC
Found at i:47998082 original size:5 final size:5
Alignment explanation
Indices: 47998072--47998119 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
47998062 TTGATTATTA
47998072 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
47998120 GAAAATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:48001338 original size:5 final size:5
Alignment explanation
Indices: 48001328--48001359 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
48001318 TCTTGTAAAA
48001328 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT
48001360 GTAATCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (5 bp):
ATTTG
Found at i:48002025 original size:17 final size:18
Alignment explanation
Indices: 48001993--48002026 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48001983 TCAAAAAATT
48001993 ATTTAAAAAATAATAAAG
1 ATTTAAAAAATAATAAAG
48002011 ATTTAAAAAAT-ATAAA
1 ATTTAAAAAATAATAAA
48002027 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTTAAAAAATAATAAAG
Found at i:48002033 original size:17 final size:18
Alignment explanation
Indices: 48001995--48002033 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
48001985 AAAAAATTAT
* *
48001995 TTAAAAAATAATAAAGAT
1 TTAAAAAATAATAAAAAA
48002013 TTAAAAAAT-ATAAAAAA
1 TTAAAAAATAATAAAAAA
48002030 TTAA
1 TTAA
48002034 TTAATTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAATAATAAAAAA
Found at i:48006120 original size:19 final size:19
Alignment explanation
Indices: 48006096--48006133 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48006086 TATAGAGTGG
48006096 TGATGGATTCAATAACATC
1 TGATGGATTCAATAACATC
*
48006115 TGATGGATTTAATAACATC
1 TGATGGATTCAATAACATC
48006134 CACTCTCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
TGATGGATTCAATAACATC
Found at i:48008893 original size:21 final size:22
Alignment explanation
Indices: 48008868--48008909 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
48008858 TAATTTCTAA
48008868 AAATATTAAAATA-TTAATATC
1 AAATATTAAAATATTTAATATC
*
48008889 AAATATTATAATATTTAATAT
1 AAATATTAAAATATTTAATAT
48008910 TATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATTAAAATATTTAATATC
Found at i:48009284 original size:16 final size:17
Alignment explanation
Indices: 48009268--48009303 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
48009258 AAGGTATTAA
48009268 TTATTATAAAATATAATC
1 TTATTATAAAATATAA-C
48009286 TTATTATAAAATA-AAC
1 TTATTATAAAATATAAC
48009302 TT
1 TT
48009304 TGATTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 2 0.11
18 13 0.72
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTATAAAATATAAC
Found at i:48009598 original size:31 final size:30
Alignment explanation
Indices: 48009563--48009627 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
48009553 ACATTAGCAA
48009563 TCACCCAACTATTAGTAAATT-TCTTTTTTGG
1 TCACCCAACTATT--TAAATTATCTTTTTTGG
* *
48009594 TCACCTAACTATTTAATTTCATCTTTTTTGG
1 TCACCCAACTATTTAAATT-ATCTTTTTTGG
48009625 TCA
1 TCA
48009628 TCGGGCGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
31 25 0.83
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.48
Consensus pattern (30 bp):
TCACCCAACTATTTAAATTATCTTTTTTGG
Found at i:48012346 original size:29 final size:30
Alignment explanation
Indices: 48012300--48012366 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
48012290 ATATGTGTCA
* *
48012300 TCAACAAATAAATTAAAACTTT-TAAAAAT
1 TCAAAAAATAAATAAAAACTTTATAAAAAT
* *
48012329 TCAAAAAATATATAAAAAGTTTATAAAAAT
1 TCAAAAAATAAATAAAAACTTTATAAAAAT
48012359 TCAAAAAA
1 TCAAAAAA
48012367 AAAAGTAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.28
Consensus pattern (30 bp):
TCAAAAAATAAATAAAAACTTTATAAAAAT
Found at i:48020054 original size:21 final size:19
Alignment explanation
Indices: 48020023--48020064 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
48020013 CTTTTTACCA
*
48020023 TTTTTATATTTCTAATATT
1 TTTTTATATTTCTAAAATT
48020042 TTTTTAATAATTTCTAAAATT
1 TTTTT-AT-ATTTCTAAAATT
48020063 TT
1 TT
48020065 ATATTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTATATTTCTAAAATT
Found at i:48023083 original size:17 final size:18
Alignment explanation
Indices: 48023061--48023095 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48023051 GTTTTTATAC
*
48023061 CTTTTT-AATAATTTTTA
1 CTTTTTAAATAAATTTTA
48023078 CTTTTTAAATAAATTTTA
1 CTTTTTAAATAAATTTTA
48023096 TAAATTTTTA
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:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTTTTAAATAAATTTTA
Found at i:48032861 original size:32 final size:32
Alignment explanation
Indices: 48032825--48032893 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
48032815 TACGAATTTG
48032825 ATTTTCATTTGGAATTTAAGAGAAATTATTCT
1 ATTTTCATTTGGAATTTAAGAGAAATTATTCT
48032857 ATTTTCATTTGGAATTTAAGAGAAATTATTCT
1 ATTTTCATTTGGAATTTAAGAGAAATTATTCT
48032889 -TTTTC
1 ATTTTC
48032894 TTCCAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.14
32 32 0.86
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (32 bp):
ATTTTCATTTGGAATTTAAGAGAAATTATTCT
Found at i:48043604 original size:14 final size:14
Alignment explanation
Indices: 48043585--48043622 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
48043575 GTTTGCCAGT
*
48043585 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
48043599 AAAATGATTTCTGG
1 AAAATGATTTCCGG
48043613 AAAATGATTT
1 AAAATGATTT
48043623 ACTTTTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:48043638 original size:19 final size:19
Alignment explanation
Indices: 48043614--48043651 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48043604 GATTTCTGGA
48043614 AAATGATTTACTTTTCTAG
1 AAATGATTTACTTTTCTAG
*
48043633 AAATGATTTATTTTTCTAG
1 AAATGATTTACTTTTCTAG
48043652 TGTTTGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (19 bp):
AAATGATTTACTTTTCTAG
Found at i:48046811 original size:11 final size:11
Alignment explanation
Indices: 48046797--48046822 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48046787 ATTTTTTTAA
48046797 TTTTAAAATAC
1 TTTTAAAATAC
48046808 TTTTAAAATAC
1 TTTTAAAATAC
48046819 TTTT
1 TTTT
48046823 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:48046832 original size:41 final size:42
Alignment explanation
Indices: 48046779--48046895 Score: 186
Period size: 41 Copynumber: 2.8 Consensus size: 42
48046769 TAAATATTTA
48046779 TTTTTTTT--ATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAATAC
**
48046819 -TTTTTTTAAATTTTTTTAATTTTAAAATTTTTTTAAAATAC
1 TTTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAATAC
48046860 TTTTTTTTAAATTTTTTTTAATTTTAAAATACTTTT
1 TTTTTTTTAAA-TTTTTTTAATTTTAAAATACTTTT
48046896 TTTAATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
39 7 0.10
41 30 0.43
42 10 0.14
43 22 0.32
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (42 bp):
TTTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAATAC
Found at i:48046843 original size:16 final size:17
Alignment explanation
Indices: 48046821--48046854 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48046811 TAAAATACTT
*
48046821 TTTTTAAATTTTTTTAA
1 TTTTAAAATTTTTTTAA
48046838 TTTTAAAATTTTTTTAA
1 TTTTAAAATTTTTTTAA
48046855 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAAATTTTTTTAA
Found at i:48046905 original size:41 final size:41
Alignment explanation
Indices: 48046788--48046917 Score: 133
Period size: 41 Copynumber: 3.1 Consensus size: 41
48046778 ATTTTTTTTA
**
48046788 TTTTTTTAATTTTAAAATAC-TTTTAAAATACTTTTTTTAAA-
1 TTTTTTTAATTTTAAAATACTTTTTTTAAT--TTTTTTTAAAT
*
48046829 TTTTTTTAATTTTAAAAT--TTTTTTAAAATACTTTTTTTTAAAT
1 TTTTTTTAATTTTAAAATACTTTTTT----TAATTTTTTTTAAAT
*
48046872 TTTTTTTAATTTTAAAATACTTTTTTTAATTTTTATTTTAAT
1 TTTTTTTAATTTTAAAATACTTTTTTTAATTTTT-TTTAAAT
48046914 TTTT
1 TTTT
48046918 AAAAAAAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
40 4 0.05
41 25 0.33
42 20 0.27
43 18 0.24
44 2 0.03
45 6 0.08
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (41 bp):
TTTTTTTAATTTTAAAATACTTTTTTTAATTTTTTTTAAAT
Found at i:48049596 original size:15 final size:15
Alignment explanation
Indices: 48049564--48049595 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
48049554 AAATTTACTC
48049564 TTTTATATTTATATT
1 TTTTATATTTATATT
48049579 TTTTA-ATTTA-ATT
1 TTTTATATTTATATT
48049592 TTTT
1 TTTT
48049596 TAAAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATATTTATATT
Found at i:48050204 original size:31 final size:32
Alignment explanation
Indices: 48050139--48050205 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
48050129 TAACGAAAAC
**
48050139 AATTCAACTCTTTTTAAAAAGGCTGGTGGTCA
1 AATTCAACTCTTTTTAAAAAGGCTGAAGGTCA
* * *
48050171 AATTCAAGTCTTTTT-AAAATGTTGAAGGTCA
1 AATTCAACTCTTTTTAAAAAGGCTGAAGGTCA
48050202 AATT
1 AATT
48050206 TAACAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.53
32 14 0.47
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
AATTCAACTCTTTTTAAAAAGGCTGAAGGTCA
Found at i:48050233 original size:20 final size:21
Alignment explanation
Indices: 48050200--48050239 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
48050190 TGTTGAAGGT
*
48050200 CAAATTTAACAAAATAAAGTC
1 CAAATTTAACAAAAAAAAGTC
*
48050221 CAAA-TTAAGAAAAAAAAGT
1 CAAATTTAACAAAAAAAAGT
48050240 AAATGTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (21 bp):
CAAATTTAACAAAAAAAAGTC
Found at i:48053276 original size:30 final size:32
Alignment explanation
Indices: 48053212--48053278 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
48053202 TAATTTATGC
***
48053212 AAAATAAATATTAAATATATAGTTTATTTTAA
1 AAAATAAATATTAAATATATAGTTTATACAAA
*
48053244 AAAATATATATTAAATATATA-TTTA-ACAAA
1 AAAATAAATATTAAATATATAGTTTATACAAA
48053274 AAAAT
1 AAAAT
48053279 TGCATTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.23
31 4 0.13
32 20 0.65
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (32 bp):
AAAATAAATATTAAATATATAGTTTATACAAA
Found at i:48056129 original size:14 final size:14
Alignment explanation
Indices: 48056093--48056134 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
48056083 TTATGTTATA
48056093 AAATAATATTATATT
1 AAATAATA-TATATT
* *
48056108 -AATTATATATGTT
1 AAATAATATATATT
48056121 AAATAATATATATT
1 AAATAATATATATT
48056135 TATATTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AAATAATATATATT
Found at i:48056437 original size:14 final size:15
Alignment explanation
Indices: 48056418--48056446 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48056408 ATTATATATG
48056418 TAATTTTAAA-AAAA
1 TAATTTTAAATAAAA
48056432 TAATTTTAAATAAAA
1 TAATTTTAAATAAAA
48056447 ATTAATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTTTAAATAAAA
Found at i:48057651 original size:27 final size:27
Alignment explanation
Indices: 48057601--48057664 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
48057591 TGCTAATTTT
* *
48057601 AATTTTTAATATTTTATATTTTTTAAA
1 AATTTTTAAAATTTAATATTTTTTAAA
* *
48057628 AATTTTTAAAATTTGAAT-TTTTTTTAT
1 AATTTTTAAAATTT-AATATTTTTTAAA
48057655 AATTTTTAAA
1 AATTTTTAAA
48057665 TTATTTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
AATTTTTAAAATTTAATATTTTTTAAA
Found at i:48065484 original size:31 final size:30
Alignment explanation
Indices: 48065443--48065508 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
48065433 TAAAATTTAC
**
48065443 TATTAAAATAAA-ATTTTAATATTGAATAATT
1 TATTAAAATAAATAAATT-ATATT-AATAATT
*
48065474 TATTACAATAAATAAATTATATTAATAATT
1 TATTAAAATAAATAAATTATATTAATAATT
48065504 TATTA
1 TATTA
48065509 TATTATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.39
31 16 0.52
32 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
TATTAAAATAAATAAATTATATTAATAATT
Found at i:48065599 original size:22 final size:22
Alignment explanation
Indices: 48065547--48065600 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
48065537 ATGTTTAATA
*
48065547 ATATTAAAAATTATAATATTTT
1 ATATTAAAATTTATAATATTTT
*
48065569 ATATT-AAATTTTTAATATTTT
1 ATATTAAAATTTATAATATTTT
48065590 -TAATTAAAATT
1 AT-ATTAAAATT
48065601 AAAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTAAAATTTATAATATTTT
Found at i:48073456 original size:50 final size:48
Alignment explanation
Indices: 48073334--48073461 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 48
48073324 TAATAACATG
* *
48073334 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTTTAAACTA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCTAAACTA
* * *
48073383 CCAATGCCATATCCCAGATATGGTCTTACATGGGA-G-TTCTAATATCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTAA-A-C--TA
*
48073433 CCCATGCCATGTCCCAGACATGGTCTTAC
1 CCAATGCCATGTCCCAGACATGGTCTTAC
48073462 GGGGGACCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
46 5 0.07
47 1 0.01
48 2 0.03
49 32 0.48
50 27 0.40
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTAAACTA
Found at i:48085517 original size:13 final size:13
Alignment explanation
Indices: 48085498--48085532 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
48085488 GCCCAAACTT
48085498 CGAAATTTTTGAA
1 CGAAATTTTTGAA
* *
48085511 TGAAATTTTTTAA
1 CGAAATTTTTGAA
48085524 CGAAATTTT
1 CGAAATTTT
48085533 CACAAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (13 bp):
CGAAATTTTTGAA
Found at i:48087298 original size:12 final size:12
Alignment explanation
Indices: 48087281--48087310 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
48087271 TACACTTGCT
48087281 GAGTTTAATATA
1 GAGTTTAATATA
48087293 GAGTTTAATATA
1 GAGTTTAATATA
*
48087305 GCGTTT
1 GAGTTT
48087311 CCTTTATCTC
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:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (12 bp):
GAGTTTAATATA
Found at i:48087410 original size:20 final size:20
Alignment explanation
Indices: 48087385--48087428 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
48087375 TATGGATGAT
48087385 TTTTTTCTACTTGGCCCTTC
1 TTTTTTCTACTTGGCCCTTC
48087405 TTTTTTCTACTTGGCCCTTC
1 TTTTTTCTACTTGGCCCTTC
48087425 TTTT
1 TTTT
48087429 GTGTTCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.27, G:0.09, T:0.59
Consensus pattern (20 bp):
TTTTTTCTACTTGGCCCTTC
Found at i:48088855 original size:16 final size:16
Alignment explanation
Indices: 48088834--48088867 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
48088824 TCAATTATAT
48088834 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
48088850 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
48088866 TT
1 TT
48088868 CCAATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:48089033 original size:30 final size:30
Alignment explanation
Indices: 48088997--48089065 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
48088987 GGTGCAATTG
*
48088997 TATAAATATAAAT-TTAATTTTAATTCAAT
1 TATAAATATAAATCTTAATTTTAACTCAAT
* *
48089026 ATATAAAT-GAAATCTTAATTTTAGCTCAAT
1 -TATAAATATAAATCTTAATTTTAACTCAAT
*
48089056 TATACATATA
1 TATAAATATA
48089066 CCTACAAAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
TATAAATATAAATCTTAATTTTAACTCAAT
Found at i:48089647 original size:19 final size:19
Alignment explanation
Indices: 48089623--48089695 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
48089613 AATCTTCAAG
48089623 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
48089642 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* * *
48089661 GACATGCAATCCTAGATAC
1 GATATGCAATCTTAGATAT
48089680 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48089696 AGATATGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48089945 original size:23 final size:23
Alignment explanation
Indices: 48089901--48089945 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
48089891 TCGTATTTTG
* *
48089901 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
48089924 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
48089946 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:48096797 original size:44 final size:44
Alignment explanation
Indices: 48096749--48097063 Score: 143
Period size: 44 Copynumber: 7.2 Consensus size: 44
48096739 AATAGCAGAT
*
48096749 CTTGCCTTCTTGCGTCGACAACGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * ** * *** *
48096793 CTTGCCTCCCTGGGTTG-CAGCGGAGCA-AGTTAAAAATTGCAGAT
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGA-TCGAAGACACCAG-C
* * **
48096837 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * * ** * * * *
48096881 CTTGCCTTTTTGGGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAG-C
* **
48096925 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * * ** * * * *
48096969 CTTGCCTTTTTGGGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAG-C
** *
48097013 CTTGCCTTCTTGCACCGACAACGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAGC
48097057 CTTGCCT
1 CTTGCCT
48097064 CCCTAGGTTG
Statistics
Matches: 175, Mismatches: 88, Indels: 16
0.63 0.32 0.06
Matches are distributed among these distances:
42 1 0.01
43 49 0.28
44 75 0.43
45 49 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCTTGCGTCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:48097349 original size:88 final size:88
Alignment explanation
Indices: 48096656--48097319 Score: 999
Period size: 88 Copynumber: 7.6 Consensus size: 88
48096646 GTGAAGATAA
* * * *
48096656 CAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGTTCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
48096721 GTAGTGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* ** *
48096744 CAGATCTTGCCTTCTTGCGTCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
48096809 GCAGCGGAGCAAGTTAAAAATTG
66 GTAGCGGAGCAGGTTAAAAATAG
* ***
48096832 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTTTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
48096897 GTAGCGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
***
48096920 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTTTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
48096985 GTAGCGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* * *
48097008 CAGATCTTGCCTTCTTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
48097073 GCAGCGGAGCAAGTTAAAAATTG
66 GTAGCGGAGCAGGTTAAAAATAG
* *
48097096 CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACA--AACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
48097159 GTAGCGGAGTAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* *
48097182 CAGATCTTGCCTTCCTGCACCGACAGCGAACCGGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
48097247 GCAGCGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* * * *
48097270 CAGATCTTGCCTTCCTGCATCGACAGCGAAGCAAATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
48097320 CTATCTCCCT
Statistics
Matches: 520, Mismatches: 54, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
86 77 0.15
88 443 0.85
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GTAGCGGAGCAGGTTAAAAATAG
Found at i:48097369 original size:44 final size:44
Alignment explanation
Indices: 48097319--48097427 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
48097309 TGACCCCAGC
** *
48097319 CCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTAGACAACAGTAGAATAGGTTGAAGATTGTGAA-T
* *
48097363 CCTATCTCCCTGGTCAACAGTAGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTAGACAACAGTAGAATAGGTTGAAGATTGTGAAT
48097407 CCTATCTCCCT-GAGCAACAGT
1 CCTATCTCCCTAGA-CAACAGT
48097428 GGAGTAGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 54 0.95
45 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTAGACAACAGTAGAATAGGTTGAAGATTGTGAAT
Found at i:48097863 original size:44 final size:44
Alignment explanation
Indices: 48097803--48098039 Score: 245
Period size: 44 Copynumber: 5.5 Consensus size: 44
48097793 GAAGATGGCG
48097803 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * **
48097847 AATCCTATCTCTCTGAAGTCGCAGTGGAGCGGATTAAAATCACAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * *
48097892 -ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CG-CATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
48097931 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * ** **
48097975 AATCCTATCTCCCTGAAATTGCAGTGGAGTGGATTAAAATC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
*
48098018 AGATCTTATCTCTCTGAAGTTG
1 A-ATCTTATCTCCCTGAAGTTG
48098040 TAGAGAACAG
Statistics
Matches: 158, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.02
40 22 0.14
41 7 0.04
42 2 0.01
43 9 0.06
44 111 0.70
45 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:48098031 original size:128 final size:128
Alignment explanation
Indices: 48097801--48098091 Score: 483
Period size: 128 Copynumber: 2.3 Consensus size: 128
48097791 CTGAAGATGG
* *
48097801 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCTCTGAAGT
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAAT
* *
48097866 CGCAGTGGAGCGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCAT
66 CGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCAT
*
48097929 CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAAT
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAAT
* * * *
48097994 TGCAGTGGAGTGGATTAAAATCATAGATCTTATCTCTCTGAAGTTGTAGAGAACAGATCGCAT
66 CGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCAT
**
48098057 CGGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
48098092 CCCAAGAAAG
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 151 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (128 bp):
CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAAT
CGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCAT
Found at i:48098124 original size:45 final size:45
Alignment explanation
Indices: 48098060--48098181 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
48098050 ATCGCATCGG
*
48098060 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* * *
48098105 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTCAAGAAATCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* * *
48098150 GTCTTATC-CCCTAAAATTGCAGTGGGGCAGAC
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
48098182 TAAATAAACA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
44 20 0.29
45 49 0.71
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
Found at i:48098279 original size:135 final size:135
Alignment explanation
Indices: 48098124--48098394 Score: 542
Period size: 135 Copynumber: 2.0 Consensus size: 135
48098114 CCCTGAAGTT
48098124 GTAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCTAAAATTGCAGTGGGGCAGACTAAATAA
1 GTAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCTAAAATTGCAGTGGGGCAGACTAAATAA
48098189 ACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTAGATTAGAATCTCTCTGAAATTACAGTAGAGT
66 ACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTAGATTAGAATCTCTCTGAAATTACAGTAGAGT
48098254 AGATC
131 AGATC
48098259 GTAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCTAAAATTGCAGTGGGGCAGACTAAATAA
1 GTAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCTAAAATTGCAGTGGGGCAGACTAAATAA
48098324 ACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTAGATTAGAATCTCTCTGAAATTACAGTAGAGT
66 ACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTAGATTAGAATCTCTCTGAAATTACAGTAGAGT
48098389 AGATC
131 AGATC
48098394 G
1 G
48098395 CATCAAATTC
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (135 bp):
GTAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCTAAAATTGCAGTGGGGCAGACTAAATAA
ACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTAGATTAGAATCTCTCTGAAATTACAGTAGAGT
AGATC
Found at i:48098891 original size:19 final size:19
Alignment explanation
Indices: 48098867--48098920 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
48098857 AATCTTTAAG
48098867 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
48098886 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48098905 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48098921 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48098911 original size:38 final size:40
Alignment explanation
Indices: 48098867--48098943 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
48098857 AATCTTTAAG
48098867 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
48098905 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
48098944 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:48099170 original size:23 final size:23
Alignment explanation
Indices: 48099126--48099170 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
48099116 TCTTATTTTG
* *
48099126 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
48099149 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
48099171 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:48102116 original size:49 final size:49
Alignment explanation
Indices: 48102059--48102162 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
48102049 TCATGTGTTA
* * *
48102059 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
48102108 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
48102157 TAATTT
1 TAATTT
48102163 GTTTTTTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:48102853 original size:15 final size:15
Alignment explanation
Indices: 48102833--48102867 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
48102823 GATGTTTCTG
48102833 CGAATTCTATGACTA
1 CGAATTCTATGACTA
*
48102848 CGAATTCTATGACTG
1 CGAATTCTATGACTA
48102863 CGAAT
1 CGAAT
48102868 CTGATGTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (15 bp):
CGAATTCTATGACTA
Found at i:48103188 original size:21 final size:21
Alignment explanation
Indices: 48103147--48103189 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
48103137 AATAAAGTAG
*
48103147 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
48103168 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
48103189 A
1 A
48103190 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:48103231 original size:17 final size:18
Alignment explanation
Indices: 48103206--48103251 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
48103196 TATAAGAATA
*
48103206 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
48103223 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
48103241 ATTAAATTATA
1 ATTAAATTATA
48103252 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:48103294 original size:119 final size:119
Alignment explanation
Indices: 48103154--48103392 Score: 444
Period size: 120 Copynumber: 2.0 Consensus size: 119
48103144 TAGATTATAT
48103154 ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATTAAGA
1 ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATTAAGA
*
48103218 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
*
48103272 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATTAAG
48103337 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
65 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
48103392 A
1 A
48103393 ATATGATTAA
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
118 5 0.04
119 49 0.42
120 63 0.54
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (119 bp):
ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATTAAGA
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:48103632 original size:16 final size:16
Alignment explanation
Indices: 48103613--48103645 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48103603 ACTATTACGC
48103613 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
*
48103629 CTCTATTCTATTACAG
1 CTCTATTCCATTACAG
48103645 C
1 C
48103646 GAACCAAACG
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:0.24, C:0.30, G:0.06, T:0.39
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:48104274 original size:21 final size:21
Alignment explanation
Indices: 48104232--48104294 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
48104222 TTTTTCTAAA
* * *
48104232 AATTTTCTA-AAATTTTTTAT
1 AATTTTTTATAAATTTATAAT
48104252 AATTTTTTATAAATTTATAAT
1 AATTTTTTATAAATTTATAAT
* *
48104273 AAGTTTTTATGAATTTTATAAT
1 AATTTTTTAT-AAATTTATAAT
48104295 TTATATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 8 0.22
21 18 0.50
22 10 0.28
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTTTTATAAATTTATAAT
Found at i:48113135 original size:77 final size:77
Alignment explanation
Indices: 48112947--48113351 Score: 413
Period size: 77 Copynumber: 5.3 Consensus size: 77
48112937 CTATCATGAT
** *
48112947 CTTCGATATTCTAATAGTTCGCTTGATTTAATACAGCGGTTGTCATTTTTACGGTTCGCTTGATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCGGTTGTCATTTTTACGGTTCGCTT-AAT
48113012 TTAAGATCGCGAC
65 TTAAGATCGCGAC
** * * * *
48113025 CTTCGATATTCTAGCAGTTCGCTTGATTCAATATTGCGATTGTCATTTTTACGGTCCACTTAATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCGGTTGTCATTTTTACGGTTCGCTTAATT
*
48113090 TAAGATTGCGAC
66 TAAGATCGCGAC
* * * * * **
48113102 CTTTGATATTCTAATAGTTTGCTCGATTTAATATTGTGGCTGTCATTTTTACGGTTCGCTCGATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCGGTTGTCATTTTTACGGTTCGCTTAATT
48113167 TAAGATCGCGAC
66 TAAGATCGCGAC
* * * * ** * * * *
48113179 CTTCAATATTTTAACAATTCAATTGATTTAATATCGCAGCTGTCATTTTTACGGTTCG-TTACAC
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCGGTTGTCATTTTTACGGTTCGCTTA-AT
*
48113243 TTAAGATCGCAAC
65 TTAAGATCGCGAC
* * * * * * *
48113256 CTTCGATATTTTAACAGTTCACTTGATTTAATA-T-CGTTTCTATAATTTTTACGGTTCG-TTGA
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCG-GT-TGTCATTTTTACGGTTCGCTTAA
*
48113318 TTTAAGATCGCAAC
64 TTTAAGATCGCGAC
*
48113332 CTTCGATATTCTAACAGTTC
1 CTTCGATATTCTAATAGTTC
48113352 ACTAATTTCT
Statistics
Matches: 272, Mismatches: 52, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
75 1 0.00
76 34 0.12
77 184 0.68
78 53 0.19
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (77 bp):
CTTCGATATTCTAATAGTTCGCTTGATTTAATATTGCGGTTGTCATTTTTACGGTTCGCTTAATT
TAAGATCGCGAC
Found at i:48113207 original size:40 final size:38
Alignment explanation
Indices: 48113163--48113352 Score: 115
Period size: 40 Copynumber: 4.9 Consensus size: 38
48113153 CGGTTCGCTC
*
48113163 GATTTAAGATCGCGACCTTCAATATTTTAACAATTCAATT
1 GATTTAAGATCGC-ACCTTC-ATATTTTAACAGTTCAATT
* * * *
48113203 GATTTAATATCGCAGCTGTCAT-TTTT-ACGGTTC-GTT
1 GATTTAAGATCGCACCT-TCATATTTTAACAGTTCAATT
* * *
48113239 ACACTTAAGATCGCAACCTTCGATATTTTAACAGTTCACTT
1 -GATTTAAGATCGC-ACCTTC-ATATTTTAACAGTTCAATT
* * * * *
48113280 GATTTAATATCG---TTTCTATAATTTTTACGGTTC-GTT
1 GATTTAAGATCGCACCTTC-AT-ATTTTAACAGTTCAATT
*
48113316 GATTTAAGATCGCAACCTTCGATATTCTAACAGTTCA
1 GATTTAAGATCGC-ACCTTC-ATATTTTAACAGTTCA
48113353 CTAATTTCTT
Statistics
Matches: 112, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
36 20 0.18
37 28 0.25
38 9 0.08
39 19 0.17
40 34 0.30
41 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (38 bp):
GATTTAAGATCGCACCTTCATATTTTAACAGTTCAATT
Found at i:48113247 original size:154 final size:154
Alignment explanation
Indices: 48112947--48113352 Score: 485
Period size: 154 Copynumber: 2.6 Consensus size: 154
48112937 CTATCATGAT
* * *
48112947 CTTCGATATTCTAATAGTTCGCTTGATTTAATACAGCGGTTGTCATTTTTACGGTTCGCTTGATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATAGTGGCTGTCATTTTTACGGTTCGCTTGA-T
* ** * *
48113012 TTAAGATCGCGACCTTCGATATTCTAGCAGTTCGCTTGATTCAATATTGCGATTGTCATTTTTAC
65 TTAAGATCGCGACCTTCGATATTCTAACAGTTCAATTGATTCAATATCGCGACTGTCATTTTTAC
* * *
48113077 GGTCCACTTAATTTAAGATTGCGAC
130 GGTCCACTTAACTTAAGATCGCAAC
* * * * *
48113102 CTTTGATATTCTAATAGTTTGCTCGATTTAATATTGTGGCTGTCATTTTTACGGTTCGCTCGATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATAGTGGCTGTCATTTTTACGGTTCGCTTGATT
* * * *
48113167 TAAGATCGCGACCTTCAATATTTTAACAATTCAATTGATTTAATATCGC-AGCTGTCATTTTTAC
66 TAAGATCGCGACCTTCGATATTCTAACAGTTCAATTGATTCAATATCGCGA-CTGTCATTTTTAC
* *
48113231 GGTTC-GTTACACTTAAGATCGCAAC
130 GGTCCACTTA-ACTTAAGATCGCAAC
* * * * ** * *
48113256 CTTCGATATTTTAACAGTTCACTTGATTTAATATCGTTTCTATAATTTTTACGGTTCG-TTGATT
1 CTTCGATATTCTAATAGTTCGCTTGATTTAATATAGTGGCTGTCATTTTTACGGTTCGCTTGATT
*
48113320 TAAGATCGCAACCTTCGATATTCTAACAGTTCA
66 TAAGATCGCGACCTTCGATATTCTAACAGTTCA
48113353 CTAATTTCTT
Statistics
Matches: 211, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
153 38 0.18
154 118 0.56
155 55 0.26
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (154 bp):
CTTCGATATTCTAATAGTTCGCTTGATTTAATATAGTGGCTGTCATTTTTACGGTTCGCTTGATT
TAAGATCGCGACCTTCGATATTCTAACAGTTCAATTGATTCAATATCGCGACTGTCATTTTTACG
GTCCACTTAACTTAAGATCGCAAC
Found at i:48121839 original size:26 final size:24
Alignment explanation
Indices: 48121809--48121869 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 24
48121799 AGCCATGATT
48121809 GGTAAGCTCAT-TCCGAGCTGAAAAAC
1 GGTAAGCTCATAT-CGAGCT--AAAAC
48121835 GGTAAGCTC-TATCGAGCTAAAAC
1 GGTAAGCTCATATCGAGCTAAAAC
48121858 GGTAAGCTCATA
1 GGTAAGCTCATA
48121870 AGAGCTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.42
24 2 0.06
25 7 0.21
26 10 0.30
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (24 bp):
GGTAAGCTCATATCGAGCTAAAAC
Found at i:48121874 original size:23 final size:23
Alignment explanation
Indices: 48121830--48121901 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
48121820 TCCGAGCTGA
*
48121830 AAAACGGTAAGCTCTATCGAGCT
1 AAAACGGTAAGCTCTATAGAGCT
48121853 AAAACGGTAAGCTC-ATAAGAGCT
1 AAAACGGTAAGCTCTAT-AGAGCT
*
48121876 GATATATCGGTAAGCT-TATATGAGCT
1 -A-A-AACGGTAAGCTCTATA-GAGCT
48121902 GTGGTGAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 2 0.05
23 19 0.46
24 1 0.02
25 2 0.05
26 17 0.41
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (23 bp):
AAAACGGTAAGCTCTATAGAGCT
Found at i:48124221 original size:45 final size:45
Alignment explanation
Indices: 48124129--48124246 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 45
48124119 ACTTAATCAT
* ** *
48124129 TTTAATATTAAATTAATACAATACTTATCAAGATAATTATTAGATTAAA
1 TTTAATATTAAATTAATA-AA-A--TACCAAGATAAGAATTAAATTAAA
48124178 TTTAATATTAAATTAATAAAATACCAAGATAAGAATTAAATTAAA
1 TTTAATATTAAATTAATAAAATACCAAGATAAGAATTAAATTAAA
* *
48124223 TTAAATATTAAAATTATTAAAATA
1 TTTAATATT-AAATTAATAAAATA
48124247 ATATTATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 28 0.45
46 13 0.21
47 1 0.02
48 2 0.03
49 18 0.29
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (45 bp):
TTTAATATTAAATTAATAAAATACCAAGATAAGAATTAAATTAAA
Done.