Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 124 of 253
Found at i:39327698 original size:40 final size:40
Alignment explanation
Indices: 39327460--39327684 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
39327450 TCGAATGATG
* * * *
39327460 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39327500 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39327540 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39327579 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39327619 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39327660 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39327685 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39327706 original size:119 final size:119
Alignment explanation
Indices: 39327460--39327717 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
39327450 TCGAATGATG
* *
39327460 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
39327525 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
39327579 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
39327642 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
39327699 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39327718 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:39341528 original size:40 final size:40
Alignment explanation
Indices: 39341447--39341664 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
39341437 CAACCAAGTA
** * *
39341447 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGAAATAG-TAACTCGCACAAATG
** *
39341486 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
* * *
39341526 CCTTCGGGACATAGCCCGGAAATAGCAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
*
39341566 CCTTCGGGACTTAGCCTGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
39341606 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
39341646 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39341665 TTATCATCCG
Statistics
Matches: 161, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.08
40 148 0.92
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
Found at i:39348952 original size:40 final size:40
Alignment explanation
Indices: 39348858--39349002 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
39348848 TACTCGAATG
*
39348858 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
39348899 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
39348939 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
39348979 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
39349003 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:39352981 original size:40 final size:40
Alignment explanation
Indices: 39352937--39353088 Score: 241
Period size: 40 Copynumber: 3.8 Consensus size: 40
39352927 AGATATAGCT
* **
39352937 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
* * *
39352977 ACTCGCACAATTGCCTTCGGAACTTAGCCCGGAAATAGCA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
*
39353017 ACTCGCACAAATGCCTTCGGGATTTAGCCCGGAAATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
39353057 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
39353089 TTATCATCCG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
Found at i:39357814 original size:40 final size:40
Alignment explanation
Indices: 39357759--39357980 Score: 295
Period size: 40 Copynumber: 5.6 Consensus size: 40
39357749 TATTCGAATG
* *
39357759 ATATCCGGGTTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
39357799 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
**
39357839 ATATCCGGGCTAAGTCCTAAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
39357879 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * * *
39357919 ATATCTGGGCTAAGACCCGAAGGCATTTGCGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
*
39357959 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
39357981 TACTTGGGTT
Statistics
Matches: 161, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
39 14 0.09
40 145 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:39361184 original size:44 final size:46
Alignment explanation
Indices: 39360974--39361240 Score: 181
Period size: 47 Copynumber: 5.7 Consensus size: 46
39360964 GATTTGTGCA
* * **
39360974 CCAGTATAAGACTATGTCTGGGACATGGCATCGGCATC-CAGACGAGGG
1 CCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCACAGA-GATAG
* * * *
39361022 CTAGTGTAAGACATGTCTGGGACATGCTTCAGCCAT-ATTATGAG-T-G
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCA-CA-GAGATAG
39361068 CCA-TAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAG
1 CCAGT-GTAAGACATGTCTGGGACATGCATCGGCCTC-ACAGAGATAG
* * * *
39361115 CCAGTGTAAGACGTGTCTGGAACATGCATCGG-CT-A-AGAGTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCACAGAGAT-AG
** * * * * *
39361159 TTAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CACAGA-GATAG
*
39361207 CCAGTATAAGACCATGTCTGGGACATAGCATCGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
39361241 TAATTTATCC
Statistics
Matches: 172, Mismatches: 29, Indels: 34
0.73 0.12 0.14
Matches are distributed among these distances:
43 5 0.03
44 29 0.17
45 6 0.03
46 40 0.23
47 45 0.26
48 24 0.14
49 17 0.10
50 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCACAGAGATAG
Found at i:39370688 original size:71 final size:67
Alignment explanation
Indices: 39370611--39370748 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 67
39370601 TCACCAGATA
* * *
39370611 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
39370676 GGCTGC
62 GGCTGC
* *
39370682 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
39370747 GC
66 GC
39370749 TAGAACGTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
67 37 0.60
71 25 0.40
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:39370730 original size:27 final size:26
Alignment explanation
Indices: 39370682--39370733 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39370672 GCGAGGCTGC
*
39370682 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
39370708 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
39370734 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39378041 original size:27 final size:26
Alignment explanation
Indices: 39377993--39378052 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39377983 GCGAGGCTGC
*
39377993 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
39378020 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
39378046 CAGATAT
1 CAGATAT
39378053 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39378065 original size:33 final size:32
Alignment explanation
Indices: 39378014--39378075 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
39378004 ACGAAGTCAC
* *
39378014 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
39378046 CAGATATATATATATGTGGCGAAGCCACCA
1 CAGATACAGATAT-TGTGGCGAAGCCACCA
39378076 AATTGCAGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 11 0.44
33 14 0.56
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:39381740 original size:24 final size:24
Alignment explanation
Indices: 39381713--39381847 Score: 114
Period size: 24 Copynumber: 5.6 Consensus size: 24
39381703 GAAATGACTT
*
39381713 TGGCACTATGTGTGTGAATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
*
39381737 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* * * * *
39381761 CGGGACTATGTGTGCGGATATGTA
1 TGGCACTATGTGTGCGAATTTGAA
*
39381785 TGACACTATGTGTGC-AGATTTGAA
1 TGGCACTATGTGTGCGA-ATTTGAA
* * * *
39381809 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
39381834 -GGCACTATGTGTGC
1 TGGCACTATGTGTGC
39381848 AGGTAAACAT
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
24 83 0.95
25 3 0.03
26 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGAA
Found at i:39386643 original size:10 final size:10
Alignment explanation
Indices: 39386628--39386666 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
39386618 GAAGTCTGAG
39386628 GTTTGAATAA
1 GTTTGAATAA
39386638 GTTTGAATAA
1 GTTTGAATAA
39386648 GTTTGAATAA
1 GTTTGAATAA
39386658 GTTTGAATA
1 GTTTGAATA
39386667 TATTTATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (10 bp):
GTTTGAATAA
Found at i:39388057 original size:17 final size:19
Alignment explanation
Indices: 39388035--39388071 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
39388025 TTGGGTTTAT
39388035 TGGG-CCACACGGG-CGTG
1 TGGGCCCACACGGGCCGTG
*
39388052 TGGGCCCACATGGGCCGTG
1 TGGGCCCACACGGGCCGTG
39388071 T
1 T
39388072 TATGGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16
Consensus pattern (19 bp):
TGGGCCCACACGGGCCGTG
Found at i:39388589 original size:34 final size:32
Alignment explanation
Indices: 39388509--39388592 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 32
39388499 GAATACTGCA
* *
39388509 CTGATTCTGTAATGGGCTTAGGCCCACTGATT
1 CTGATTCTGAAATGGGCTCAGGCCCACTGATT
* *
39388541 CT-ATTACTGGAATGGGCTCAGGCCCACACTGTTT
1 CTGATT-CTGAAATGGGCTCAGG-CC-CACTGATT
*
39388575 CTGATTCAGAAATGGGCT
1 CTGATTCTGAAATGGGCT
39388593 AAGACCCTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 3 0.07
32 16 0.37
33 2 0.05
34 19 0.44
35 3 0.07
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (32 bp):
CTGATTCTGAAATGGGCTCAGGCCCACTGATT
Found at i:39390791 original size:40 final size:40
Alignment explanation
Indices: 39390709--39390915 Score: 253
Period size: 40 Copynumber: 5.2 Consensus size: 40
39390699 CGAAATTTAA
* *
39390709 CCGGATATAGCT-ACTCGCTCAAATGCC-TCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39390748 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39390788 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
39390827 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39390867 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39390908 CCGGATAT
1 CCGGATAT
39390916 CATTCGAATA
Statistics
Matches: 145, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 3 0.02
39 55 0.38
40 56 0.39
41 28 0.19
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:39390827 original size:79 final size:78
Alignment explanation
Indices: 39390705--39390912 Score: 244
Period size: 79 Copynumber: 2.6 Consensus size: 78
39390695 CCTTCGAAAT
* * *
39390705 TTAACCGGATATAGCTACTCGCTCAAATGCC-TCGGGACATAGCCCGG-TTATAGTAACTCGCAC
1 TTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCAC
39390768 AAATGCCTTCGGGA-C
64 AAATGCCTTC-GGATC
* *
39390783 TTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCAC
1 TTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCAC
39390847 AAATGCCTTCGGATC
64 AAATGCCTTCGGATC
* * *
39390862 TTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 TTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
39390913 TATCATTCGA
Statistics
Matches: 111, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
78 8 0.07
79 70 0.63
80 22 0.20
81 11 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (78 bp):
TTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAA
ATGCCTTCGGATC
Found at i:39400768 original size:27 final size:26
Alignment explanation
Indices: 39400720--39400779 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39400710 GCGAGGCTGT
*
39400720 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
39400747 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
39400773 CAGATAT
1 CAGATAT
39400780 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39400824 original size:71 final size:67
Alignment explanation
Indices: 39400747--39400884 Score: 168
Period size: 67 Copynumber: 2.0 Consensus size: 67
39400737 TCACCAGATA
* * * *
39400747 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGAAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAAATTGAAGCGA
39400812 GGCTGC
62 GGCTGC
* * **
39400818 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAAATTGCGGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAAATTGAAGCGAGGCT
39400883 GC
66 GC
39400885 TAGAACGCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 34 0.58
71 25 0.42
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAAATTGAAGCGAGGCT
GC
Found at i:39408279 original size:27 final size:26
Alignment explanation
Indices: 39408231--39408282 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39408221 GCGAGGCTGC
*
39408231 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
39408257 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
39408283 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39410603 original size:15 final size:14
Alignment explanation
Indices: 39410580--39410616 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
39410570 AAATAATCCA
*
39410580 AATAAAAATGAATT
1 AATAAAAATGAATG
39410594 AATAAGAAATGAATG
1 AATAA-AAATGAATG
39410609 AATAAAAA
1 AATAAAAA
39410617 AAGAAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
AATAAAAATGAATG
Found at i:39411930 original size:24 final size:24
Alignment explanation
Indices: 39411842--39411929 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
39411832 GAAATGACTT
* * *
39411842 TGGCACTATGTGTACAAATTTGAA
1 TGGCACTATGTGTGCGAATTTGTA
39411866 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
* * *
39411890 CGACACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
39411914 TGGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
39411930 GGTAAACATG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGTA
Found at i:39416940 original size:10 final size:10
Alignment explanation
Indices: 39416925--39416954 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
39416915 AAACACCAAG
39416925 AGTTTGAATA
1 AGTTTGAATA
39416935 AGTTTGAATA
1 AGTTTGAATA
*
39416945 AGTTTAAATA
1 AGTTTGAATA
39416955 TATTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (10 bp):
AGTTTGAATA
Found at i:39426625 original size:10 final size:10
Alignment explanation
Indices: 39426590--39426619 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
39426580 AAACACCAAG
39426590 AGTTTGAATA
1 AGTTTGAATA
39426600 AGTTTGAATA
1 AGTTTGAATA
39426610 AGTTTGAATA
1 AGTTTGAATA
39426620 TATTTGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (10 bp):
AGTTTGAATA
Found at i:39427991 original size:17 final size:19
Alignment explanation
Indices: 39427969--39428005 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
39427959 TTGGGTTTAT
39427969 TGGG-CCACACGGG-CGTG
1 TGGGCCCACACGGGTCGTG
*
39427986 TGGGCCCACATGGGTCGTG
1 TGGGCCCACACGGGTCGTG
39428005 T
1 T
39428006 TATGGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.11, C:0.27, G:0.43, T:0.19
Consensus pattern (19 bp):
TGGGCCCACACGGGTCGTG
Found at i:39443315 original size:55 final size:55
Alignment explanation
Indices: 39443194--39443317 Score: 142
Period size: 55 Copynumber: 2.3 Consensus size: 55
39443184 TGCGATATGG
* * * * *
39443194 CCGTGGTCGAGCTTGCCAAAACAACACGGGCGTGTGACACGCCCGTGTGGAAGAA
1 CCGTGGTCGAACCTGCCAAAACAACACGGACGTGTGACACGCCCGTGTGAAACAA
* * ** *
39443249 CTGTGGGCGAACCTGCCAAAACAACACGGACGT-TCGACACGCTTGTGTGAAACAC
1 CCGTGGTCGAACCTGCCAAAACAACACGGACGTGT-GACACGCCCGTGTGAAACAA
39443304 CCGTGGTCGAACCT
1 CCGTGGTCGAACCT
39443318 ATTAAATTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 1 0.02
55 55 0.98
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (55 bp):
CCGTGGTCGAACCTGCCAAAACAACACGGACGTGTGACACGCCCGTGTGAAACAA
Found at i:39448704 original size:40 final size:40
Alignment explanation
Indices: 39448658--39448882 Score: 231
Period size: 40 Copynumber: 5.6 Consensus size: 40
39448648 CTTGCGCAAG
* * * *
39448658 GCCTTCGGGTATTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTATTAGCCCGGATATAGTCGCTAGCACAAAT
39448698 GCCTTCGGG-ACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTA-TTAGCCCGGATATAGTCGCTAGCACAAAT
* *
39448738 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTATTAGCCCGGATATAGTCGCTAGCACAAAT
* ** * *
39448778 GCCTTCGGGTCTTAGCCCGGATATAG-CAATTCGCACGAAT
1 GCCTTCGGGTATTAGCCCGGATATAGTC-GCTAGCACAAAT
** * * * * *
39448818 GCCTTCGAATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTATTAGCCCGGATATAGTC-GCTAGCACAAAT
39448859 GCCTTCGGG-ACTTAGCCCGGATAT
1 GCCTTCGGGTA-TTAGCCCGGATAT
39448883 CATTCGAATA
Statistics
Matches: 154, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.01
40 125 0.81
41 27 0.18
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTATTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:39448753 original size:80 final size:80
Alignment explanation
Indices: 39448622--39448882 Score: 276
Period size: 80 Copynumber: 3.3 Consensus size: 80
39448612 CTCAAGTAAT
* * * * * * * *
39448622 CTTCGGGATTTAG-CCGGATATAACTACTTGCGC-AAGGCCTTCGGGTATTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTATTAGCCCGGATATAGT
*
39448685 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * *
39448700 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTATTAGCCCGGATATAG
*
39448764 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * ** * * *
39448780 CTTCGGGTCTTAGCCCGGATATAGCAATTCGCACGAATGCCTTCGAATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTATTAGCCCGGATATAGT
*
39448845 CACCTAGCACAAAAGC
66 CA-CTAGCACAAATGC
39448861 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
39448883 CATTCGAATA
Statistics
Matches: 152, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
78 12 0.08
79 15 0.10
80 92 0.61
81 33 0.22
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTATTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:39451822 original size:37 final size:37
Alignment explanation
Indices: 39451765--39451849 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
39451755 CGATCATAAG
* *
39451765 TGTAAGACCATAGTCGGGCTATGGCATCGTAATAGCA
1 TGTAAGACCATAGTCAGGCTATGGCATCGTAATACCA
* * * *
39451802 TGTAAGACCATAG-CTAGGCTATGGCCTTGTGATCCCA
1 TGTAAGACCATAGTC-AGGCTATGGCATCGTAATACCA
39451839 TGTAAGACCAT
1 TGTAAGACCAT
39451850 GTTTGGGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 1 0.02
37 40 0.98
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (37 bp):
TGTAAGACCATAGTCAGGCTATGGCATCGTAATACCA
Found at i:39451890 original size:48 final size:48
Alignment explanation
Indices: 39451829--39452057 Score: 298
Period size: 48 Copynumber: 4.8 Consensus size: 48
39451819 GCTATGGCCT
*
39451829 TGTGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * *
39451877 TGTGATCCTATGTAAGACCATGTCTAGGACATAGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * *
39451925 TGTGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * * *
39451973 TGTGATCCCATATAAGACCATATCTAGGATATAGG-GTTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACAT-GGCATTGGCATCGATA
****
39452021 TGTGATTTTGTGTAAGACCATGTCTGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
39452058 CAATATGAGA
Statistics
Matches: 153, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
47 2 0.01
48 149 0.97
49 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:39451944 original size:96 final size:96
Alignment explanation
Indices: 39451829--39452057 Score: 332
Period size: 96 Copynumber: 2.4 Consensus size: 96
39451819 GCTATGGCCT
* * * *
39451829 TGTGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATATGTGATCCTATGTAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCCATATAAGA
*
39451894 CCATGTCTAGGACATAGCATTGGCATCGATA
66 CCATATCTAGGACATAGCATTGGCATCGATA
* *
39451925 TGTGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCAATATGTGATCCCATATAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCCATATAAGA
* **
39451990 CCATATCTAGGATATAGGGTTGGCATCGATA
66 CCATATCTAGGACATAGCATTGGCATCGATA
****
39452021 TGTGATTTTGTGTAAGACCATGTCTGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
39452058 CAATATGAGA
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 117 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (96 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCCATATAAGA
CCATATCTAGGACATAGCATTGGCATCGATA
Found at i:39452076 original size:42 final size:41
Alignment explanation
Indices: 39452010--39452101 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
39452000 GATATAGGGT
* * * *
39452010 TGGCATCGATATGTGATTTTGTGTAAGACCATGTCTGGGAC-A
1 TGGCATCAATATGAGACTTCGTGTAAGACCATGT-T-GGACTA
* *
39452052 TGGCATCAATATGAGACTTCGTGTAATATCATGTTGGACTA
1 TGGCATCAATATGAGACTTCGTGTAAGACCATGTTGGACTA
39452093 TGGCATCAA
1 TGGCATCAA
39452102 GTAAACAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 4 0.09
41 11 0.26
42 28 0.65
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
TGGCATCAATATGAGACTTCGTGTAAGACCATGTTGGACTA
Found at i:39453949 original size:12 final size:12
Alignment explanation
Indices: 39453932--39453956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39453922 ACTTCGTGTG
39453932 TTTGACGGGAAA
1 TTTGACGGGAAA
39453944 TTTGACGGGAAA
1 TTTGACGGGAAA
39453956 T
1 T
39453957 GTCACGTGCT
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:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (12 bp):
TTTGACGGGAAA
Found at i:39458723 original size:40 final size:40
Alignment explanation
Indices: 39458679--39458845 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
39458669 GGTAGCCTTA
* *
39458679 AATGCACAAATGTGCCCTTGATTGTACTTTAGTAACCCTG
1 AATGCACAAATGTGCCCCTGATTGTACTTTGGTAACCCTG
* * *
39458719 AATGCACATACGTACCCCT-ACTTGTACTTTGGT-ACTCCTG
1 AATGCACAAATGTGCCCCTGA-TTGTACTTTGGTAAC-CCTG
* * * *
39458759 AATGCACATAA-ATGCCCCTGATTGTACTTCGGTACCCCTA
1 AATGCACA-AATGTGCCCCTGATTGTACTTTGGTAACCCTG
* * *
39458799 AATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTG
1 AATGCACAAATGTGCCCCTGATTGTACTTTGGTAACCCTG
39458839 AATGCAC
1 AATGCAC
39458846 TTACATACCC
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
39 4 0.04
40 98 0.93
41 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (40 bp):
AATGCACAAATGTGCCCCTGATTGTACTTTGGTAACCCTG
Found at i:39458775 original size:80 final size:80
Alignment explanation
Indices: 39458691--39458881 Score: 229
Period size: 80 Copynumber: 2.4 Consensus size: 80
39458681 TGCACAAATG
* *
39458691 TGCCCTTGATTGTACTTTAGTAACCCTGAATGCACATACGTACCCCTACTTGTACTTTGGTACTC
1 TGCCCTTGATTGTACTTTAGTAACCCTAAATGCACATACGTACCCCTACTTGTACTTTGGTACCC
39458756 CTGAATGCACATAAA
66 CTGAATGCACATAAA
* ** * * * **
39458771 TGCCCCTGATTGTACTTCGGTACCCCTAAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCC
1 TGCCCTTGATTGTACTTTAGTAACCCTAAATGCACATACGTACCCCTACTTGTACTTTGGTACCC
* *
39458836 CTGAATGCACTTACA
66 CTGAATGCACATAAA
* * * * *
39458851 TACCCTTGTTTATACCTTAGTAACTCTAAAT
1 TGCCCTTGATTGTACTTTAGTAACCCTAAAT
39458882 CATATAGTAT
Statistics
Matches: 90, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (80 bp):
TGCCCTTGATTGTACTTTAGTAACCCTAAATGCACATACGTACCCCTACTTGTACTTTGGTACCC
CTGAATGCACATAAA
Found at i:39458801 original size:120 final size:120
Alignment explanation
Indices: 39458637--39458855 Score: 296
Period size: 120 Copynumber: 1.8 Consensus size: 120
39458627 AATTATTGAA
*** * * * *
39458637 TGAATGCACATGTGTGCCCCTATTTGTAGTGCGGTAGCCTTAAATGCACAAATGTGCCCTTGATT
1 TGAATGCACATAAATGCCCCTATTTGTACTGCGGTACCCCTAAATGCACAAATGTGCCCCTGATT
*
39458702 GTACTTTAGTAACCCTGAATGCACATACGTACCCCTACTTGTACTTTGGTACTCC
66 GTACTTTAGTAACCCTGAATGCACATACATACCCCTACTTGTACTTTGGTACTCC
* * *
39458757 TGAATGCACATAAATGCCCCTGA-TTGTACTTCGGTACCCCTAAATGCACATATGTGCCCCTGTT
1 TGAATGCACATAAATGCCCCT-ATTTGTACTGCGGTACCCCTAAATGCACAAATGTGCCCCTGAT
* * *
39458821 TGTACTTTGGTACCCCTGAATGCACTTACATACCC
65 TGTACTTTAGTAACCCTGAATGCACATACATACCC
39458856 TTGTTTATAC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
120 83 0.99
121 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (120 bp):
TGAATGCACATAAATGCCCCTATTTGTACTGCGGTACCCCTAAATGCACAAATGTGCCCCTGATT
GTACTTTAGTAACCCTGAATGCACATACATACCCCTACTTGTACTTTGGTACTCC
Found at i:39458847 original size:20 final size:20
Alignment explanation
Indices: 39458704--39458847 Score: 58
Period size: 20 Copynumber: 7.2 Consensus size: 20
39458694 CCTTGATTGT
* *
39458704 ACTTTAGTAACCCTGAATGC
1 ACTTTGGTACCCCTGAATGC
* ** * *
39458724 ACATACGTACCCCT-ACTTGT
1 ACTTTGGTACCCCTGA-ATGC
*
39458744 ACTTTGGTACTCCTGAATGC
1 ACTTTGGTACCCCTGAATGC
* *** * * *
39458764 ACATAAATGCCCCTGATTGT
1 ACTTTGGTACCCCTGAATGC
* *
39458784 ACTTCGGTACCCCTAAATGC
1 ACTTTGGTACCCCTGAATGC
* * ** *
39458804 ACATAT-GTGCCCCTGTTTGT
1 AC-TTTGGTACCCCTGAATGC
39458824 ACTTTGGTACCCCTGAATGC
1 ACTTTGGTACCCCTGAATGC
39458844 ACTT
1 ACTT
39458848 ACATACCCTT
Statistics
Matches: 80, Mismatches: 40, Indels: 8
0.62 0.31 0.06
Matches are distributed among these distances:
19 3 0.04
20 75 0.94
21 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (20 bp):
ACTTTGGTACCCCTGAATGC
Found at i:39458861 original size:40 final size:40
Alignment explanation
Indices: 39458697--39458855 Score: 185
Period size: 40 Copynumber: 4.0 Consensus size: 40
39458687 AATGTGCCCT
* * *
39458697 TGATTGTACTTTAGTAACCCTGAATGCACATACGTACCCC
1 TGATTGTACTTTGGTACCCCTGAATGCACATACATACCCC
* * *
39458737 T-ACTTGTACTTTGGTACTCCTGAATGCACATAAATGCCCC
1 TGA-TTGTACTTTGGTACCCCTGAATGCACATACATACCCC
* * ** *
39458777 TGATTGTACTTCGGTACCCCTAAATGCACATATGTGCCCC
1 TGATTGTACTTTGGTACCCCTGAATGCACATACATACCCC
* *
39458817 TGTTTGTACTTTGGTACCCCTGAATGCACTTACATACCC
1 TGATTGTACTTTGGTACCCCTGAATGCACATACATACCC
39458856 TTGTTTATAC
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (40 bp):
TGATTGTACTTTGGTACCCCTGAATGCACATACATACCCC
Found at i:39469648 original size:66 final size:66
Alignment explanation
Indices: 39469529--39469653 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
39469519 ACACAGCATG
* * * *
39469529 TGGCATGGCCGTGTGCTCATGTCAGAGAGTCACACGGGGTCAAACATGACCTGCAGCACTGACTT
1 TGGCATGGCCGTGTGCTCAAGTCAGAGAATCACACGAGGTCAAACACGACCTGCAGCACTGACTT
39469594 A
66 A
* * * *
39469595 TGGCATGGCCGTGTGCTCAAGT-ATATGAATTACACGAGGTCGAACACGGCCTGCAGCAC
1 TGGCATGGCCGTGTGCTCAAGTCAGA-GAATCACACGAGGTCAAACACGACCTGCAGCAC
39469654 GGGAGTGTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
65 2 0.04
66 48 0.96
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.21
Consensus pattern (66 bp):
TGGCATGGCCGTGTGCTCAAGTCAGAGAATCACACGAGGTCAAACACGACCTGCAGCACTGACTT
A
Found at i:39474969 original size:46 final size:45
Alignment explanation
Indices: 39474902--39475119 Score: 215
Period size: 46 Copynumber: 4.7 Consensus size: 45
39474892 TTGAGCATCC
*
39474902 GAACTCGTTGAGTTGATTCCGAGTTCACTTATCGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCAAATGTCT
39474948 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCAAATGTCT
* * * * * *
39474994 GAACTCATTGAGTTGAGTCTGAGTTC-GTGA-GATGTAACTAGTCAT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCAAAT-GTC-T
* * * * * * *
39475039 CCGAACTTGTTCAGTTGAGTCCGAGTTCACTCATAAATGCAAACGCCC
1 --GAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCAAATGTCT
* *
39475087 GAGCTCGTTGAGTTGAGTCCGAGTTCTCTTATG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
39475120 GGCGGGTTAC
Statistics
Matches: 139, Mismatches: 26, Indels: 15
0.77 0.14 0.08
Matches are distributed among these distances:
43 7 0.05
44 3 0.02
45 3 0.02
46 95 0.68
47 22 0.16
48 2 0.01
49 2 0.01
50 5 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCAAATGTCT
Found at i:39478050 original size:15 final size:15
Alignment explanation
Indices: 39478024--39478102 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
39478014 GTATCTTGGG
39478024 TTTCTTTA-TCTGGA
1 TTTCTTTATTCTGGA
*
39478038 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
39478053 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
39478068 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
39478083 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
39478097 TTTCTT
1 TTTCTT
39478103 GTTATCTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
14 17 0.31
15 36 0.65
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:39478083 original size:30 final size:30
Alignment explanation
Indices: 39478015--39478101 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
39478005 CATAGTATCG
* * *
39478015 TATCTTGGGTTTCTTTA-TCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
39478044 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
39478074 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
39478102 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.42
30 27 0.54
31 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:39480547 original size:46 final size:46
Alignment explanation
Indices: 39480492--39480666 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
39480482 GGTTGAGCAT
39480492 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
* * * *
39480538 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATGC
* * *
39480583 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAATGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
* *
39480631 CCGAGCTCGTTGAGTTGAGTCCGAGTTCTCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39480667 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 60 0.56
47 27 0.25
48 5 0.05
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
Found at i:39480647 original size:93 final size:93
Alignment explanation
Indices: 39480488--39480658 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
39480478 GGATGGTTGA
*
39480488 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
39480553 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
39480581 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
39480646 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39480659 TCTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39490464 original size:47 final size:47
Alignment explanation
Indices: 39490408--39490529 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
39490398 GCATTGGCAC
*
39490408 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGTCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGCCATTTGG
39490455 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGCCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGCCATTTGG
* *
39490502 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
39490530 CTATGGCATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGCCATTTGG
Found at i:39490572 original size:54 final size:54
Alignment explanation
Indices: 39490508--39490691 Score: 185
Period size: 54 Copynumber: 3.4 Consensus size: 54
39490498 TTGGTAAGAT
* * *
39490508 AAGGATATCATGTAAGACCATGCTATGGCATGGAATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCTAAGGCATGGAATTGATGAGTTCTATAAGGC
* * * * * *
39490562 AAGGAAATCATATAAGACCATG-TCAAGACATGGTATTGATGAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGCT-AAGGCATGGAATTGATGAGTT-CTATAAGG-C
* * * * * *
39490618 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGATTTC-ATAAAGC
1 AAGGATACCATGTAAGACCATGCTAAGGCATGGAATTGATGAGTTCTATAAGGC
39490670 AAGGATACCATGTAAGACCATG
1 AAGGATACCATGTAAGACCATG
39490692 TCAAGACATG
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
52 4 0.04
53 22 0.21
54 38 0.36
55 38 0.36
56 4 0.04
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCTAAGGCATGGAATTGATGAGTTCTATAAGGC
Found at i:39490730 original size:108 final size:109
Alignment explanation
Indices: 39490516--39490726 Score: 264
Period size: 108 Copynumber: 2.0 Consensus size: 109
39490506 ATAAGGATAT
* * * *
39490516 CATGTAAGACCATGCTATGGCATGGAATTGATAAGTTCTATAAGGCAAGGAAATCATATAAGACC
1 CATGTAAGACCATGCCAAGGCATGGAATTGATAAGTTCTATAAAGCAAGGAAACCATATAAGACC
* * * * *
39490581 ATGTCAAGACATGGTATTGATGAGTTACTATAAGGAAAAGGTCC
66 ATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAAGGTCC
* * * * * *
39490625 CATGTAAGACCATGCCAAGGCATGGCATTGGTGATTTC-ATAAAGCAAGGATACCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGAATTGATAAGTTCTATAAAGCAAGGAAACCATATAAGACC
*
39490689 ATGTCAAGACATGGCAATGGTAAGTT-CAAAAAGGAAAA
66 ATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAA
39490727 AGGTTCCCGA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
107 10 0.12
108 44 0.51
109 32 0.37
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGAATTGATAAGTTCTATAAAGCAAGGAAACCATATAAGACC
ATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAAGGTCC
Found at i:39492057 original size:54 final size:54
Alignment explanation
Indices: 39491989--39492092 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
39491979 GTTGTAGAAC
* *
39491989 TACCGAAATACCCCTATAGGATAGAATTATCGAAATACCCTTGTAGGGTAGAGA
1 TACCGAAATACCCCTATAGGATAGAAATACCGAAATACCCTTGTAGGGTAGAGA
* * * *
39492043 TACCGAAATACCCCTGTAGGGTAGAAATACCGAGATACCCTTGTGGGGTA
1 TACCGAAATACCCCTATAGGATAGAAATACCGAAATACCCTTGTAGGGTA
39492093 AAATTACCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (54 bp):
TACCGAAATACCCCTATAGGATAGAAATACCGAAATACCCTTGTAGGGTAGAGA
Found at i:39492100 original size:27 final size:27
Alignment explanation
Indices: 39491982--39492096 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 27
39491972 TGGATAAGTT
* * *
39491982 GTAGAACTACCGAAATACCCCTATAGG
1 GTAGAAATACCGAAATACCCTTGTAGG
* * *
39492009 ATAGAATTATCGAAATACCCTTGTAGG
1 GTAGAAATACCGAAATACCCTTGTAGG
* *
39492036 GTAGAGATACCGAAATACCCCTGTAGG
1 GTAGAAATACCGAAATACCCTTGTAGG
* *
39492063 GTAGAAATACCGAGATACCCTTGTGGG
1 GTAGAAATACCGAAATACCCTTGTAGG
39492090 GTA-AAAT
1 GTAGAAAT
39492097 TACCATTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 4 0.05
27 70 0.95
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (27 bp):
GTAGAAATACCGAAATACCCTTGTAGG
Found at i:39492759 original size:27 final size:26
Alignment explanation
Indices: 39492715--39492766 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39492705 CTCGTTACAA
*
39492715 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
39492742 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
39492767 GCAACCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:39500036 original size:85 final size:85
Alignment explanation
Indices: 39499893--39500071 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
39499883 GGCCGGCCAT
39499893 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39499958 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
39499978 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39500043 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
39500063 GGGCATGGG
1 GAGCATGGG
39500072 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:39502309 original size:47 final size:47
Alignment explanation
Indices: 39502258--39502791 Score: 717
Period size: 47 Copynumber: 11.1 Consensus size: 47
39502248 TTAGGATTTT
*
39502258 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
39502305 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
39502356 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
39502403 CTGTTATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
39502450 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
*
39502501 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
39502548 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA
39502601 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
39502648 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGGATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
39502695 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
39502742 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
39502789 ATG
1 ATG
39502792 CGAAACGTGT
Statistics
Matches: 433, Mismatches: 40, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
47 301 0.70
48 1 0.00
49 4 0.01
51 85 0.20
52 1 0.00
53 41 0.09
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:39502412 original size:145 final size:144
Alignment explanation
Indices: 39502258--39502791 Score: 774
Period size: 145 Copynumber: 3.7 Consensus size: 144
39502248 TTAGGATTTT
* *
39502258 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
39502323 CGTATATATATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
39502388 AAGGCCGAATGGCCA
130 AAGGCCGAATGGCCA
* * * *
39502403 CTGTTATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
39502468 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
*
39502533 AAGGCCGAATGACCA
130 AAGGCCGAATGGCCA
** *
39502548 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATG
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
***
39502613 TGAA--C-ATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGT
60 TGAACCCGATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGT
*
39502675 GTGATAAGGCCGGATGGCCA
125 GTGATAAGGCCGAATGGCCA
* * *
39502695 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* *
39502760 TGA-ATATATGTG-G-TAAGGCCGAATGGCTAATG
66 CGATATATATGTGTGATAAGGCCGAATGGCCAATG
39502792 CGAAACGTGT
Statistics
Matches: 354, Mismatches: 26, Indels: 22
0.88 0.06 0.05
Matches are distributed among these distances:
141 59 0.17
142 1 0.00
143 6 0.02
144 1 0.00
145 154 0.44
146 2 0.01
147 88 0.25
149 1 0.00
151 42 0.12
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (144 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
CGATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATA
AGGCCGAATGGCCA
Found at i:39502628 original size:23 final size:23
Alignment explanation
Indices: 39502601--39502675 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
39502591 CGAATGGCCA
39502601 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
* * **
39502624 ATGTG-TGATAAG-G-CCGAATGGCCA
1 ATGTGATGA-ATGTGAAC--AT-GCGT
39502648 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
39502671 ATGTG
1 ATGTG
39502676 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 16 0.43
24 11 0.30
25 4 0.11
26 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAACATGCGT
Found at i:39502854 original size:46 final size:46
Alignment explanation
Indices: 39502765--39502855 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
39502755 GAACATGAAT
* * * *
39502765 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
39502811 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
39502856 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:39503145 original size:37 final size:37
Alignment explanation
Indices: 39503000--39503144 Score: 236
Period size: 37 Copynumber: 3.9 Consensus size: 37
39502990 GGAAATATAT
*
39503000 TCCGGGTAAGACCCGATGACTACGTGTAGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
39503037 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
39503074 TCCAGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
39503111 TCCGGGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
39503145 TCGTCTGAGC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 101 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:39504528 original size:31 final size:31
Alignment explanation
Indices: 39504469--39504528 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
39504459 TATACATGAA
* *
39504469 ATACATGGAAATGATGGTACATGATATATTG
1 ATACATGGAAATGATGATAAATGATATATTG
*
39504500 ATACATTGAAATGGATGATAAATG-TATAT
1 ATACATGGAAAT-GATGATAAATGATATAT
39504529 GATGAAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (31 bp):
ATACATGGAAATGATGATAAATGATATATTG
Found at i:39504548 original size:25 final size:24
Alignment explanation
Indices: 39504506--39504553 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
39504496 ATTGATACAT
*
39504506 TGAAATGGATGATAAATGTATATGA
1 TGAAATGGACGATAAATG-ATATGA
39504531 TGAAATGGTACGAT-AATGATATG
1 TGAAATGG-ACGATAAATGATATG
39504554 TATCATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (24 bp):
TGAAATGGACGATAAATGATATGA
Found at i:39510623 original size:39 final size:39
Alignment explanation
Indices: 39510558--39510702 Score: 200
Period size: 39 Copynumber: 3.7 Consensus size: 39
39510548 CCAACATAAT
* **
39510558 TGCCTTCGGGGACTGAGCCCATATATAACACCAGCACGAA
1 TGCCTTC-GGGACTTAGCCCGGATATAACACCAGCACGAA
* * *
39510598 TGCCTTTGGGATTTAGCCCGGATATAACACCAACACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* * *
39510637 TGCCTTCAGGACTTAGGCCGGATATAACACCAGCACGAG
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
39510676 TGCCTTCGGGACTTAGCCCGGATATAA
1 TGCCTTCGGGACTTAGCCCGGATATAA
39510703 ATCTCACACA
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 85 0.93
40 6 0.07
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (39 bp):
TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
Found at i:39516111 original size:16 final size:16
Alignment explanation
Indices: 39516092--39516123 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39516082 GCTAGGCACG
39516092 AAGGCCCAAATACACA
1 AAGGCCCAAATACACA
39516108 AAGGCCCAAATACACA
1 AAGGCCCAAATACACA
39516124 TTACCGGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.12, T:0.06
Consensus pattern (16 bp):
AAGGCCCAAATACACA
Found at i:39516151 original size:59 final size:58
Alignment explanation
Indices: 39516050--39516166 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 58
39516040 GCTAGGCACG
*
39516050 AAGGCCCGAATACACATCACAGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
1 AAGGCCCAAATACACATCACAGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
* * ** *
39516108 AAGGCCCAAATACACATTACCGGCACTCAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 AAGGCCCAAATACACATCA-CAGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
39516167 TCACCGGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 17 0.33
59 35 0.67
ACGTcount: A:0.36, C:0.33, G:0.21, T:0.10
Consensus pattern (58 bp):
AAGGCCCAAATACACATCACAGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
Found at i:39516156 original size:43 final size:43
Alignment explanation
Indices: 39516108--39516205 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
39516098 CAAATACACA
* * * *
39516108 AAGGCCCAAATACACATTACCGGCACTCAGCCTGCTAGGCACG
1 AAGGCCCGAATACACATCACCGGCACTAAGCCTACTAGGCACG
39516151 AAGGCCCGAATACACATCACCGGCACTAAGCCTACTAGGCACG
1 AAGGCCCGAATACACATCACCGGCACTAAGCCTACTAGGCACG
39516194 AAGGCCCGAATA
1 AAGGCCCGAATA
39516206 TAATACCAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.33, C:0.34, G:0.21, T:0.12
Consensus pattern (43 bp):
AAGGCCCGAATACACATCACCGGCACTAAGCCTACTAGGCACG
Found at i:39516263 original size:38 final size:38
Alignment explanation
Indices: 39516198--39516271 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
39516188 GGCACGAAGG
***
39516198 CCCGAATATAATACCAGCACTTGGCCTGCGGGATTTGT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTGT
* *
39516236 CCCGGATATAATACCAGCACGAAGCCTGTGGGATTT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTT
39516272 AACTCGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTGT
Found at i:39522406 original size:55 final size:54
Alignment explanation
Indices: 39522337--39522591 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 54
39522327 ATTAGGGTTT
* *
39522337 AAGGATACCATGTAAGACCTTGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCATAAGGC
* * * * *
39522392 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-TCATAAGGC
* * * * *
39522447 AAAGG-TCCCTTGTAAAACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGC
* * *
39522500 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC--AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGC
* * * * *
39522549 AAGGATACCACGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
39522592 GTACCCGTGT
Statistics
Matches: 165, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
49 38 0.23
52 6 0.04
53 41 0.25
54 12 0.07
55 64 0.39
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGC
Found at i:39522543 original size:108 final size:110
Alignment explanation
Indices: 39522347--39522544 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 110
39522337 AAGGATACCA
* * *
39522347 TGTAAGACCTTGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
39522412 TGTCAAGACATGGCATTGATAAGTTACCATAAGGCAAAGGTCCCT
66 TGTCAAGACATGGCAATGATAAGTTACCATAAGGCAAAGGTCCCT
* *
39522457 TGTAAAACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
* *
39522519 ATGTCGAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
39522545 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 7 0.09
110 22 0.28
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (110 bp):
TGTAAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGCAATGATAAGTTACCATAAGGCAAAGGTCCCT
Found at i:39522686 original size:23 final size:24
Alignment explanation
Indices: 39522660--39522704 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
39522650 AAGGTAAGGT
*
39522660 AAGGTAAGACTAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
39522683 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
39522705 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:39535454 original size:30 final size:31
Alignment explanation
Indices: 39535343--39535456 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
39535333 TTAGTCTTGA
*
39535343 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
39535373 CATATCACTGGGCCGAAGACTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
39535404 TATATCACTGGGCTGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
39535435 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
39535457 ACTGTAAGCG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
30 17 0.22
31 59 0.78
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:39535696 original size:25 final size:25
Alignment explanation
Indices: 39535662--39535745 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
39535652 CTGGAGGCCT
39535662 AGCCTCTTTTTAAT-AACTAGGGCAA
1 AGCC-CTTTTTAATAAACTAGGGCAA
* * *
39535687 AGCCCTTTTTGATAAATTGGGGCAA
1 AGCCCTTTTTAATAAACTAGGGCAA
*** * *
39535712 AGCCCTTTTCGGTAAACTGGGGCAT
1 AGCCCTTTTTAATAAACTAGGGCAA
39535737 AGCCCTTTT
1 AGCCCTTTT
39535746 AGCAGTTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 8 0.16
25 43 0.84
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (25 bp):
AGCCCTTTTTAATAAACTAGGGCAA
Found at i:39536676 original size:27 final size:27
Alignment explanation
Indices: 39536646--39536753 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
39536636 GTAAATCTAC
39536646 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
39536673 AAACCAAAGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* * *
39536699 AGAAAGTCAATGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
39536729 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
39536754 ACAAATTGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
26 1 0.01
27 40 0.60
28 7 0.10
29 18 0.27
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:39536759 original size:27 final size:26
Alignment explanation
Indices: 39536710--39536859 Score: 158
Period size: 27 Copynumber: 5.6 Consensus size: 26
39536700 GAAAGTCAAT
**
39536710 GGTATTTCT-GTAATTTTGTAAATCAGG
1 GGTATTT-TGGTAATTTTACAAA-CAGG
**
39536737 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTGGTAATTTTACAAACAG-G
* * *
39536764 GGTATTTCGGTAATTTCACAAACCAGT
1 GGTATTTTGGTAATTTTACAAA-CAGG
39536791 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAAC-AGG
* *
39536818 CGTATTTTGGTAATTTTACAAACTAAG
1 GGTATTTTGGTAATTTTACAAAC-AGG
39536845 GGTATTTTGGTAATT
1 GGTATTTTGGTAATT
39536860 CTATCCTACA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.03
27 100 0.96
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTACAAACAGG
Found at i:39536795 original size:54 final size:52
Alignment explanation
Indices: 39536625--39536859 Score: 184
Period size: 54 Copynumber: 4.3 Consensus size: 52
39536615 TTATCCTACA
* * * * * **
39536625 AGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACC
1 AGGGTATTTTGGTAATTTTACAAA-CTAGGGTATTTCGGTAATTTTACAAACC
* * * * * * ** *
39536678 AAAGGTATTTCT-ATAATTTTTAGAAAGTCAATGGTATTTCTGTAATTTTGTAAATC
1 -AGGGTATTT-TGGTAA-TTTTACAAA--CTAGGGTATTTCGGTAATTTTACAAACC
* *
39536734 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTCGGTAATTTTACAAACC
* *
39536788 AGTGGTATTTTGGTAATTTTACAAACTAGGCGTATTTTGGTAATTTTACAAACTA
1 AG-GGTATTTTGGTAATTTTACAAACTAGG-GTATTTCGGTAATTTTACAAAC-C
39536843 AGGGTATTTTGGTAATT
1 AGGGTATTTTGGTAATT
39536860 CTATCCTACA
Statistics
Matches: 147, Mismatches: 25, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
53 4 0.03
54 89 0.61
55 19 0.13
56 35 0.24
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (52 bp):
AGGGTATTTTGGTAATTTTACAAACTAGGGTATTTCGGTAATTTTACAAACC
Found at i:39536877 original size:54 final size:54
Alignment explanation
Indices: 39536737--39536892 Score: 165
Period size: 54 Copynumber: 2.9 Consensus size: 54
39536727 GTAAATCAGG
* * * *
39536737 GGTATTTTGGTAATTTTACAAATTGAGG-GTATTTCGGTAATTTCACAAACCAGT
1 GGTATTTTGGTAATTCTACAAACT-AGGAGTATTTTGGTAATTTCACAAACAAGT
* * *
39536791 GGTATTTTGGTAATTTTACAAACTAGGCGTATTTTGGTAATTTTACAAACTAAG-
1 GGTATTTTGGTAATTCTACAAACTAGGAGTATTTTGGTAATTTCACAAAC-AAGT
** * *
39536845 GGTATTTTGGTAATTCTATCCTAC-ATGAGTATTTTAGTAATTTCACAA
1 GGTATTTTGGTAATTCTA-CAAACTAGGAGTATTTTGGTAATTTCACAA
39536893 TCGAGGGTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.03
54 80 0.91
55 5 0.06
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (54 bp):
GGTATTTTGGTAATTCTACAAACTAGGAGTATTTTGGTAATTTCACAAACAAGT
Found at i:39536877 original size:81 final size:81
Alignment explanation
Indices: 39536738--39536892 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
39536728 TAAATCAGGG
* * *
39536738 GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTA
1 GTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAGTA
*
39536803 ATTTTACAAACTAGGC
66 ATTTCACAAACTAGGC
* **
39536819 GTATTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAA-TTCTATCCTA-CA-TGAGTATTTTA
1 GTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTC-A-CAAACCAGTG-GTATTTTA
39536881 GTAATTTCACAA
63 GTAATTTCACAA
39536893 TCGAGGGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
80 5 0.08
81 57 0.89
82 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (81 bp):
GTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAGTA
ATTTCACAAACTAGGC
Found at i:39536928 original size:27 final size:27
Alignment explanation
Indices: 39536891--39537036 Score: 193
Period size: 27 Copynumber: 5.4 Consensus size: 27
39536881 GTAATTTCAC
*
39536891 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * * *
39536918 AATTGAGGGTAAAATGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
39536945 AATCAAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
39536972 AATAGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
39536999 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
39537026 AATCGAGGGTA
1 AATCGAGGGTA
39537037 CTTTGGTAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:39537045 original size:54 final size:54
Alignment explanation
Indices: 39536891--39537050 Score: 221
Period size: 54 Copynumber: 3.0 Consensus size: 54
39536881 GTAATTTCAC
* * * * *
39536891 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTGTAAATAGAGGGTAAAATGGTAATTTTATA
* *
39536945 AATCAAGGGTAAAATGGTAATTCTGTAAATAGAGGGTAAAACGGTAATTTTATA
1 AATCAAGGGTAAAACGGTAATTCTGTAAATAGAGGGTAAAATGGTAATTTTATA
* ***
39536999 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTA
1 AATCAAGGGTAAAACGGTAATTCTGTAAATAGAGGGTAAAATGGTAATTTTA
39537051 CAAGTCGAGG
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (54 bp):
AATCAAGGGTAAAACGGTAATTCTGTAAATAGAGGGTAAAATGGTAATTTTATA
Found at i:39537061 original size:81 final size:80
Alignment explanation
Indices: 39536881--39537061 Score: 220
Period size: 81 Copynumber: 2.2 Consensus size: 80
39536871 GAGTATTTTA
* * ** *
39536881 GTAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTATAA
1 GTAATTTTACAATCGAGGGTAAAACGGTAATTTTATAAATCAAGGGTAAAACGATAATTCTATAA
39536946 ATCAAGGGTAAAATG
66 ATCAAGGGTAAAATG
* * *
39536961 GTAATTCTGTA-AATAGAGGGTAAAACGGTAATTTTATAAATCAAGGGTAAAACGGTAATTCTGT
1 GTAATT-T-TACAATCGAGGGTAAAACGGTAATTTTATAAATCAAGGGTAAAACGATAATTCTAT
* ***
39537025 AAATCGAGGGTACTTTG
64 AAATCAAGGGTAAAATG
39537042 GTAATTTTACAAGTCGAGGG
1 GTAATTTTACAA-TCGAGGG
39537062 CATTTCAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.02
80 9 0.11
81 72 0.86
82 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (80 bp):
GTAATTTTACAATCGAGGGTAAAACGGTAATTTTATAAATCAAGGGTAAAACGATAATTCTATAA
ATCAAGGGTAAAATG
Found at i:39539335 original size:24 final size:23
Alignment explanation
Indices: 39539298--39539348 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
39539288 TTAGTCTTGA
*
39539298 CATATACTGGGCCGAAGCCTTTT
1 CATATACTAGGCCGAAGCCTTTT
39539321 CATATCACTAGGCCGAAGCCTTTT
1 CATAT-ACTAGGCCGAAGCCTTTT
39539345 CATA
1 CATA
39539349 AATCATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (23 bp):
CATATACTAGGCCGAAGCCTTTT
Found at i:39539398 original size:30 final size:31
Alignment explanation
Indices: 39539320--39539404 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
39539310 CGAAGCCTTT
39539320 TCATATCACTAGGCCGAAGCCTTTTCATAAA
1 TCATATCACTAGGCCGAAGCCTTTTCATAAA
*
39539351 TCATATCACTGGGCCGAAGCCTTTTCATAAA
1 TCATATCACTAGGCCGAAGCCTTTTCATAAA
39539382 TCATATCACT-GGCCGAAGCCTTT
1 TCATATCACTAGGCCGAAGCCTTT
39539405 ACTGTAAGCG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 13 0.25
31 40 0.75
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (31 bp):
TCATATCACTAGGCCGAAGCCTTTTCATAAA
Found at i:39539645 original size:25 final size:25
Alignment explanation
Indices: 39539611--39539694 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
39539601 CTGGAGGCCT
39539611 AGCCTCTTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTTAATAAACTGGGGCAA
*
39539636 AGCCCTTTTTGATAAACTGGGGCAA
1 AGCCCTTTTTAATAAACTGGGGCAA
*** **
39539661 AGCCCTTTTCGGTAAACTGGGGCGT
1 AGCCCTTTTTAATAAACTGGGGCAA
39539686 AGCCCTTTT
1 AGCCCTTTT
39539695 AGCACTTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 8 0.15
25 45 0.85
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (25 bp):
AGCCCTTTTTAATAAACTGGGGCAA
Found at i:39546143 original size:45 final size:47
Alignment explanation
Indices: 39546080--39546181 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 47
39546070 GGCTATCCGG
* *
39546080 AGCTCCTTGA-TAATAACTCTTCA-GAGTTACCTGTTAAGCTC-AATA
1 AGCTTCTTGATTAATAACTCTT-ATGAGTTACCTATTAAGCTCGAATA
* * *
39546125 AGTTTCTTGATTAA-AACTCTTATGAGTTTCCTATTTAGCTCGAATA
1 AGCTTCTTGATTAATAACTCTTATGAGTTACCTATTAAGCTCGAATA
*
39546171 AGCTTCCTGAT
1 AGCTTCTTGAT
39546182 ACATGGCTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 1 0.02
45 30 0.64
46 16 0.34
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (47 bp):
AGCTTCTTGATTAATAACTCTTATGAGTTACCTATTAAGCTCGAATA
Found at i:39548541 original size:22 final size:19
Alignment explanation
Indices: 39548516--39548557 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
39548506 TGATAATCAG
39548516 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
39548538 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
39548557 T
1 T
39548558 GAACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:39551668 original size:13 final size:13
Alignment explanation
Indices: 39551650--39551676 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39551640 GTTCAGCAAG
39551650 GACACGCCCGTGT
1 GACACGCCCGTGT
39551663 GACACGCCCGTGT
1 GACACGCCCGTGT
39551676 G
1 G
39551677 CGATTACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:39553752 original size:51 final size:51
Alignment explanation
Indices: 39553663--39553762 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
39553653 TGGATGCGAG
* *
39553663 CATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGATACATGTAA
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAACGGATGCGATACATGTAA
* * * *
39553714 CATCCGAGCTCGTTGAGAGGTCCGAGTTTATTACGGATGTGTTACATGT
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAACGGATGCGATACATGT
39553763 TGTAAGGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAACGGATGCGATACATGTAA
Found at i:39554021 original size:14 final size:14
Alignment explanation
Indices: 39554002--39554032 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39553992 TGGATAGTTG
39554002 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
39554016 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
39554030 AAG
1 AAG
39554033 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:39555881 original size:21 final size:20
Alignment explanation
Indices: 39555843--39555882 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39555833 TGTGTGACTT
*
39555843 TGAAAATCCATTAAAATTTG
1 TGAAAATCAATTAAAATTTG
*
39555863 TGAAAATCTAATTAGAATTT
1 TGAAAATC-AATTAAAATTT
39555883 AATGAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TGAAAATCAATTAAAATTTG
Found at i:39559957 original size:47 final size:47
Alignment explanation
Indices: 39559903--39560643 Score: 1103
Period size: 47 Copynumber: 15.6 Consensus size: 47
39559893 TATTTGAATA
*
39559903 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39559950 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39559999 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39560046 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39560093 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39560142 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39560189 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39560238 AATGTGAAAGTGTATATATGTAATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39560284 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39560331 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39560380 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39560427 AATGTGAAAGTGTATATATATGTGATAAGGTCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* ** * *
39560476 AATGTGAACA-TGTGTACGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39560523 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCC-ATTGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGA-TGTGATG
* *
39560570 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39560617 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39560644 TCCCGAAGGG
Statistics
Matches: 647, Mismatches: 32, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
46 47 0.07
47 372 0.57
48 1 0.00
49 226 0.35
50 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39560011 original size:96 final size:94
Alignment explanation
Indices: 39559903--39560643 Score: 1103
Period size: 96 Copynumber: 7.8 Consensus size: 94
39559893 TATTTGAATA
39559903 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATA
39559968 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39559999 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
39560064 TGTGATAAGGCCTAATGGCCGACGTGATG
66 TGTGATAAGGCCTAATGGCCGATGTGATG
*
39560093 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
* * *
39560158 TATGTGATAAGGCCGAATGACCAATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
39560189 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
39560254 TATGTAATAAGGCCTAAT-GCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
39560284 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATA
39560349 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39560380 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATA
* * *
39560445 TATGTGATAAGGTCGAATGGCCAATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* ** * *
39560476 AATGTGAACA-TGTGTACGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCATA
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTGTATA
* *
39560539 TATGAGATAAGGCCGAATGGCC-ATTGTGATG
64 TATGTGATAAGGCCTAATGGCCGA-TGTGATG
* * * *
39560570 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAAGTGTATAAA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
39560635 TGTGATAAG
66 TGTGATAAG
39560644 TCCCGAAGGG
Statistics
Matches: 601, Mismatches: 34, Indels: 22
0.91 0.05 0.03
Matches are distributed among these distances:
93 50 0.08
94 138 0.23
95 43 0.07
96 368 0.61
97 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39560161 original size:143 final size:141
Alignment explanation
Indices: 39559903--39560643 Score: 1121
Period size: 143 Copynumber: 5.2 Consensus size: 141
39559893 TATTTGAATA
*
39559903 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
*
39559968 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT
* *
39560033 AGCCGATGTGATG
129 GGCCAATGTGATG
*
39560046 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
39560111 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT
*
39560176 GACCAATGTGATG
129 GGCCAATGTGATG
39560189 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
39560254 TATGTAATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT
*
39560318 GGCCGATGTGATG
129 GGCCAATGTGATG
39560331 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * *
39560396 TATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTCGA
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGA
39560461 ATGGCCAATGTGATG
127 ATGGCCAATGTGATG
* ** * * *
39560476 AATGTGAACA-TGTGTACGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCATA
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTGTATA
* *
39560539 TATGAGATAAGGCCGAATGGCC-ATTGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
64 TATGTGATAAGGCCTAATGGCCGA-TGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
39560603 TGGCCAATGTGATG
128 TGGCCAATGTGATG
* * *
39560617 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39560644 TCCCGAAGGG
Statistics
Matches: 557, Mismatches: 32, Indels: 20
0.91 0.05 0.03
Matches are distributed among these distances:
140 1 0.00
141 54 0.10
142 138 0.25
143 274 0.49
144 1 0.00
145 88 0.16
146 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
CCAATGTGATG
Found at i:39563262 original size:40 final size:40
Alignment explanation
Indices: 39563200--39563399 Score: 260
Period size: 40 Copynumber: 5.0 Consensus size: 40
39563190 AGGTCTCGAC
39563200 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
39563239 GATGTATTCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
39563279 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * * *
39563319 GATATATCCGTGCTAA-ACCCGAAGAGCATTCGTGTTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
39563358 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
39563398 GA
1 GA
39563400 CGTGTATTCG
Statistics
Matches: 141, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 36 0.26
40 105 0.74
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:39563276 original size:23 final size:23
Alignment explanation
Indices: 39563210--39563276 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
39563200 GATGATCCGG
39563210 GCTAAGTCCCGAAGAGCATTCAT
1 GCTAAGTCCCGAAGAGCATTCAT
* * **
39563233 GCT-AGT---G-A-TGTATTCGG
1 GCTAAGTCCCGAAGAGCATTCAT
39563250 GCTAAGTCCCGAAGAGCATTCAT
1 GCTAAGTCCCGAAGAGCATTCAT
39563273 GCTA
1 GCTA
39563277 GTGATGTATC
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 1 0.03
21 1 0.03
22 4 0.13
23 12 0.40
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGCATTCAT
Found at i:39564797 original size:85 final size:85
Alignment explanation
Indices: 39564654--39564832 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
39564644 GGCCGGCCAT
39564654 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39564719 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
39564739 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39564804 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
39564824 GGGCATGGG
1 GAGCATGGG
39564833 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:39566252 original size:140 final size:141
Alignment explanation
Indices: 39566093--39566785 Score: 1097
Period size: 140 Copynumber: 4.9 Consensus size: 141
39566083 TATTTGAATA
* *
39566093 AATGTGAAAGTGTATATATGTGAGAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTATATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* *
39566158 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-G
66 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
*
39566222 CCGATGTGATG
131 CCAATGTGATG
*
39566233 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
** *
39566298 TGTGATAAGGCCTAATGGCCGCTGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
66 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
**
39566363 CCGGTGTGATG
131 CCAATGTGATG
39566374 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
39566439 TATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGA
64 TATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGA
39566504 ATGGCCAATGTGATG
127 ATGGCCAATGTGATG
*
39566519 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* * *
39566584 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGTA-GTGTGATAAGGCCGAATG
66 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATG
39566647 GCCAATGTGATG
130 GCCAATGTGATG
* * *
39566659 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * * * *
39566723 ATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAAGTGTATAAATGTGATAAGTCCGAA
65 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
39566786 GGGCAATTGT
Statistics
Matches: 522, Mismatches: 22, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
139 1 0.00
140 254 0.49
141 41 0.08
143 181 0.35
144 1 0.00
145 44 0.08
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
CCAATGTGATG
Found at i:39566421 original size:22 final size:22
Alignment explanation
Indices: 39566393--39566468 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
39566383 GTGTATATAT
39566393 ATGTGATAAGGCCTAATGGCCA
1 ATGTGATAAGGCCTAATGGCCA
* *** ***
39566415 ATGTGATGAATGTGAAAGTGTATA
1 ATGTGAT-AAGGCCTAA-TGGCCA
39566439 TATGTGATAAGGCCTAATGGCCA
1 -ATGTGATAAGGCCTAATGGCCA
39566462 ATGTGAT
1 ATGTGAT
39566469 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 8 0.22
25 7 0.19
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCA
Found at i:39566785 original size:47 final size:47
Alignment explanation
Indices: 39566093--39566779 Score: 1094
Period size: 47 Copynumber: 14.6 Consensus size: 47
39566083 TATTTGAATA
*
39566093 AATGTGAAAGTGTATATATGTGAGAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
39566140 AATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566187 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566233 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
**
39566280 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGCTGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
**
39566327 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGGTGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
39566374 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
39566423 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566470 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566519 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566566 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
39566613 AATGTGAACA-TGTGTA-GTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
39566659 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
39566706 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
39566753 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39566780 TCCGAAGGGC
Statistics
Matches: 612, Mismatches: 20, Indels: 16
0.94 0.03 0.02
Matches are distributed among these distances:
46 90 0.15
47 430 0.70
48 1 0.00
49 91 0.15
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
Found at i:39573346 original size:40 final size:40
Alignment explanation
Indices: 39573134--39573339 Score: 344
Period size: 40 Copynumber: 5.2 Consensus size: 40
39573124 AACCCAAGTA
* *
39573134 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
39573173 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
39573213 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39573253 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39573293 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAGTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
39573333 CCTTCGG
1 CCTTCGG
39573340 ATCTTAGTCC
Statistics
Matches: 158, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 13 0.08
40 144 0.91
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:39578430 original size:59 final size:59
Alignment explanation
Indices: 39578359--39578592 Score: 213
Period size: 59 Copynumber: 3.9 Consensus size: 59
39578349 TCGGCTATCG
* *
39578359 ATTATAAAAAGGGATGCTGATGACAATCAAATATGAGAAGGGATGGTGACGACCATTGA
1 ATTATGAAAAGGGATGCTGATGACAATCAAATATGAAAAGGGATGGTGACGACCATTGA
* * * * *
39578418 ATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACGACCATCGA
1 ATTATGAAAAGGGATGCTGATGACAATCAAATATGAAAAGGGATGGTGACGACCATTGA
* * * * * * * * *
39578477 ATTATGAAAAAGGATAGCT-TTGGCTATCGAATATTGAAAACGAATTGTGATGACCATTGA
1 ATTATGAAAAGGGAT-GCTGATGACAATCAAATA-TGAAAAGGGATGGTGACGACCATTGA
* * * * * *
39578537 ATTATGAAAAGGAATAGCT--TCGGCTATCGATTATGAAAAGGAATGGTGACGACCAT
1 ATTATGAAAAGGGAT-GCTGAT-GACAATCAAATATGAAAAGGGATGGTGACGACCAT
39578593 CAACTATGAA
Statistics
Matches: 146, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
59 95 0.65
60 51 0.35
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (59 bp):
ATTATGAAAAGGGATGCTGATGACAATCAAATATGAAAAGGGATGGTGACGACCATTGA
Found at i:39578600 original size:29 final size:29
Alignment explanation
Indices: 39578359--39578623 Score: 178
Period size: 29 Copynumber: 9.0 Consensus size: 29
39578349 TCGGCTATCG
* * * * *
39578359 ATTATAAAAAGGGATGCTGATGACAATCA
1 ATTATGAAAAGGAATGGTGACGACCATCA
* * * *
39578388 AATATGAGAAGGGATGGTGACGACCATTGA
1 ATTATGAAAAGGAATGGTGACGACCA-TCA
*
39578418 ATTATGAAAAGGGATGGTGACGACCATCA
1 ATTATGAAAAGGAATGGTGACGACCATCA
* *
39578447 ACTATGAAAAGGGATGGTGACGACCATCGA
1 ATTATGAAAAGGAATGGTGACGACCATC-A
* ** * *
39578477 ATTATGAAAAAGG-ATAGCT-TTGGCTATCGA
1 ATTATG-AAAAGGAAT-GGTGACGACCATC-A
* * * *
39578507 A-TATTGAAAACGAATTGTGATGACCATTGA
1 ATTA-TGAAAAGGAATGGTGACGACCA-TCA
* * * * *
39578537 ATTATGAAAAGGAATAGCT-TCGGCTATCG
1 ATTATGAAAAGGAAT-GGTGACGACCATCA
39578566 ATTATGAAAAGGAATGGTGACGACCATCA
1 ATTATGAAAAGGAATGGTGACGACCATCA
* *
39578595 ACTATGAACAGGAATGGTGACGACCATCA
1 ATTATGAAAAGGAATGGTGACGACCATCA
39578624 TGATTCCACT
Statistics
Matches: 185, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.01
29 106 0.57
30 65 0.35
31 12 0.06
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (29 bp):
ATTATGAAAAGGAATGGTGACGACCATCA
Found at i:39585233 original size:29 final size:29
Alignment explanation
Indices: 39585199--39585272 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
39585189 TCATCAACCA
*
39585199 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
* **
39585228 CGCACACTCAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
39585257 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
39585273 ATCTCACAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 3 0.08
29 35 0.92
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:39590305 original size:53 final size:54
Alignment explanation
Indices: 39590122--39590317 Score: 146
Period size: 53 Copynumber: 3.6 Consensus size: 54
39590112 AGGATTCCAA
* * * * * * * * *
39590122 GTAAGACCATGCCAAGGA-ATGGCATTGGTAAGTTTTACAAGGCAAGGAAATCAT
1 GTAAGACCATGTCAA-GACATGACAATGGTAAGTTCTATAAGGCAAAGATACCAC
* * * * * * *
39590176 GTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAAGATCCCAT
1 GTAAGACCATGTCAAGACATGACAATGGT-AAGTTCTATAAGGCAAAGATACCAC
* * * * *
39590231 GTAAGACCAT-ACAAAGGCATGACAATGGTGAGTTC-ATAAGGTAAGGATACCAC
1 GTAAGACCATGTC-AAGACATGACAATGGTAAGTTCTATAAGGCAAAGATACCAC
*
39590284 GTAAGACCATGTCAAGACATGAAAATGGTAAGTT
1 GTAAGACCATGTCAAGACATGACAATGGTAAGTT
39590318 TAAAAAGGAA
Statistics
Matches: 112, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
53 44 0.39
54 29 0.26
55 39 0.35
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (54 bp):
GTAAGACCATGTCAAGACATGACAATGGTAAGTTCTATAAGGCAAAGATACCAC
Found at i:39601741 original size:39 final size:40
Alignment explanation
Indices: 39601644--39601747 Score: 174
Period size: 40 Copynumber: 2.6 Consensus size: 40
39601634 CGGATGATAA
39601644 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACTATAT
*
39601684 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACTATAT
* *
39601724 CC-GGCTAATTCCCGAAGGTAATTG
1 CCGGGCTAAGTCCCGAAGGCAATTG
39601748 GGTTTGGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 20 0.33
40 41 0.67
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACTATAT
Found at i:39607029 original size:13 final size:13
Alignment explanation
Indices: 39607011--39607040 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39607001 AATTAATCGT
39607011 ACACGGGCGTGGC
1 ACACGGGCGTGGC
39607024 ACACGGGCGTGGC
1 ACACGGGCGTGGC
39607037 ACAC
1 ACAC
39607041 CAGCGTGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.33, G:0.40, T:0.07
Consensus pattern (13 bp):
ACACGGGCGTGGC
Found at i:39611254 original size:55 final size:55
Alignment explanation
Indices: 39611130--39611261 Score: 147
Period size: 55 Copynumber: 2.4 Consensus size: 55
39611120 GTGGGCAAAT
* * *
39611130 CTACCAAAATAACACGGGTGTGCGACACGCCCGTACCGAGCAACCATGGAAGAAC
1 CTACCAAAATAACACGGGCGTACGACACGCCCGTACCGAGAAACCATGGAAGAAC
* * ** **
39611185 CTACCAAAACAACACGGGCGTACGACACGCCCGTGCCTTGAAACCATGGCCGAAC
1 CTACCAAAATAACACGGGCGTACGACACGCCCGTACCGAGAAACCATGGAAGAAC
** * *
39611240 CTGTCAAATTAACACAGGCGTA
1 CTACCAAAATAACACGGGCGTA
39611262 GACCTTCATA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.33, C:0.32, G:0.22, T:0.13
Consensus pattern (55 bp):
CTACCAAAATAACACGGGCGTACGACACGCCCGTACCGAGAAACCATGGAAGAAC
Found at i:39622367 original size:13 final size:14
Alignment explanation
Indices: 39622349--39622381 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39622339 AAGAAGCCTT
39622349 ATTACCAAAA-AAA
1 ATTACCAAAATAAA
39622362 ATTACCCAAAATAAA
1 ATTA-CCAAAATAAA
39622377 ATTAC
1 ATTAC
39622382 TTATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (14 bp):
ATTACCAAAATAAA
Found at i:39622379 original size:15 final size:14
Alignment explanation
Indices: 39622349--39622381 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
39622339 AAGAAGCCTT
39622349 ATTA-CCAAAAAAA
1 ATTACCCAAAAAAA
39622362 ATTACCCAAAATAAA
1 ATTACCCAAAA-AAA
39622377 ATTAC
1 ATTAC
39622382 TTATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 6 0.33
15 8 0.44
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (14 bp):
ATTACCCAAAAAAA
Found at i:39625859 original size:26 final size:27
Alignment explanation
Indices: 39625830--39625882 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
39625820 ATATCGAAAA
*
39625830 CATATTAGGAAA-GAAAGACTTTGTGG
1 CATAATAGGAAAGGAAAGACTTTGTGG
* * *
39625856 CATAATATGAAAGGAATGCCTTTGTGG
1 CATAATAGGAAAGGAAAGACTTTGTGG
39625883 AAAACTCCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (27 bp):
CATAATAGGAAAGGAAAGACTTTGTGG
Found at i:39625897 original size:27 final size:27
Alignment explanation
Indices: 39625867--39625936 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
39625857 ATAATATGAA
*
39625867 AGGAATGCCTTTGTGGAAAACTCCGTT
1 AGGAATGCCTTTGTGGAAAACTCCATT
* *
39625894 AGGAATACCTTTATGGAAAACTCCATT
1 AGGAATGCCTTTGTGGAAAACTCCATT
*
39625921 AGGAATGCCTTCGTGG
1 AGGAATGCCTTTGTGG
39625937 TGTACTCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (27 bp):
AGGAATGCCTTTGTGGAAAACTCCATT
Found at i:39628392 original size:33 final size:33
Alignment explanation
Indices: 39628350--39628415 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
39628340 ACCACGTCTT
* *
39628350 TCATTTACTTATTGAACCATTCGAAATACTATA
1 TCATTTACTTATTGAACCAATCAAAATACTATA
39628383 TCATTTACTTATTGAACCAATCAAAATACTATA
1 TCATTTACTTATTGAACCAATCAAAATACTATA
39628416 GGATACATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (33 bp):
TCATTTACTTATTGAACCAATCAAAATACTATA
Found at i:39629241 original size:21 final size:20
Alignment explanation
Indices: 39629213--39629251 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
39629203 CAAAACTTGT
39629213 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
39629233 ATAATCTATCATCAAACAT
1 ATAA-CTATCATCAAACAT
39629252 CAAAATACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:39636273 original size:31 final size:31
Alignment explanation
Indices: 39636162--39636276 Score: 180
Period size: 31 Copynumber: 3.7 Consensus size: 31
39636152 TTAGTCTTGA
*
39636162 CATAT-ACTAGGCCGAAG-CTTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTT-CATAAAT
*
39636192 CATATCACTGGGCCGAAGCCTTTACATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
39636223 CATATCACTGGGCCCAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
39636254 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
39636277 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.06
31 69 0.88
32 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:39636347 original size:42 final size:42
Alignment explanation
Indices: 39636300--39636433 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
39636290 TGGCCCTTAG
*
39636300 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
39636342 GCCCATTTCAATATCATATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
39636384 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
39636426 GCCCATTT
1 GCCCATTT
39636434 GGGGAGACTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:39637465 original size:27 final size:26
Alignment explanation
Indices: 39637435--39637511 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
39637425 AGGCATATTC
*
39637435 GTCATTTTACCATATAAGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
* * *
39637462 GTCACTTTACCCTACAGGGGT-TTATG
1 GTCATTTTA-CCTATAGGGGTATTACG
*
39637488 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-TAGGGGTATT
39637512 TTAGTCATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
25 4 0.10
26 17 0.43
27 17 0.43
28 2 0.05
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:39637582 original size:27 final size:27
Alignment explanation
Indices: 39637552--39637659 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
39637542 GTAAATCTAC
39637552 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
39637579 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* **
39637605 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
39637635 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
39637660 ACAAATTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 42 0.62
28 7 0.10
29 17 0.25
30 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:39637665 original size:27 final size:27
Alignment explanation
Indices: 39637601--39637771 Score: 132
Period size: 27 Copynumber: 6.3 Consensus size: 27
39637591 TTTCTATAAT
* * *
39637601 TTTTAGAAAGTCAAGGGTATTTTTGTAA
1 TTTTACAAA-TCAGGGGTATTTTGGTAA
**
39637629 TTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
* *
39637656 TTTTACAAAT-TGAGGGTATTTCGGTAA
1 TTTTACAAATCAG-GGGTATTTTGGTAA
* * * * *
39637683 TTTCACTAACCAGTGGTATTTCGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
39637710 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
* ** *
39637737 TTCTATCCTAT-AGGGGTATTTTAGTAA
1 TTTTA-CAAATCAGGGGTATTTTGGTAA
*
39637764 TTTCACAA
1 TTTTACAA
39637772 TCGAGGGTAA
Statistics
Matches: 113, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.03
27 100 0.88
28 10 0.09
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (27 bp):
TTTTACAAATCAGGGGTATTTTGGTAA
Found at i:39637804 original size:27 final size:27
Alignment explanation
Indices: 39637770--39637967 Score: 272
Period size: 27 Copynumber: 7.3 Consensus size: 27
39637760 GTAATTTCAC
*
39637770 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
39637797 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTCTGTA
*
39637824 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
39637851 AATCAAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
39637878 AATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
39637905 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
**
39637932 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTGTA
39637959 AATCGAGGG
1 AATCGAGGG
39637968 CATTTCAGTA
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 150 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:39637887 original size:81 final size:81
Alignment explanation
Indices: 39637770--39637967 Score: 317
Period size: 81 Copynumber: 2.4 Consensus size: 81
39637760 GTAATTTCAC
* * *
39637770 AATCGAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAATC-GAGGGTAAAATAGTAATTTTGTAAATCGAGGGT
*
39637834 AAAACGGTAATTCTGTA
65 AAAACGGTAATTCTATA
* *
39637851 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTA
39637916 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
*
39637932 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
39637968 CATTTCAGTA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
81 107 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:39650010 original size:37 final size:37
Alignment explanation
Indices: 39649960--39650038 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39649950 TTATTACGAA
* * *
39649960 GTCTTACCCGGACATAATCTCCACACGA-AGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATCGG
39649997 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
39650034 GTCTT
1 GTCTT
39650039 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
Found at i:39650267 original size:47 final size:47
Alignment explanation
Indices: 39650156--39650425 Score: 468
Period size: 47 Copynumber: 5.7 Consensus size: 47
39650146 GCCCTTCGGG
39650156 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATAC
*
39650206 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
39650253 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
**
39650300 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
*
39650347 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
*
39650394 ACTTTCACATTCGTCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
39650426 ATACTATCAT
Statistics
Matches: 214, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
47 175 0.82
49 35 0.16
50 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
Found at i:39650363 original size:25 final size:25
Alignment explanation
Indices: 39650287--39650365 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
39650277 ATTAGGCCCT
39650287 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
**** ***
39650312 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
39650334 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
39650359 ATCACAT
1 ATCACAT
39650366 CGGCCATTAG
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:39658569 original size:25 final size:25
Alignment explanation
Indices: 39658541--39658594 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
39658531 TTCAAAAATA
39658541 AAATAAAAGAAGTGTAGTTTTATAT
1 AAATAAAAGAAGTGTAGTTTTATAT
***
39658566 AAATTTTAGAAGTGTAGTTTTATAT
1 AAATAAAAGAAGTGTAGTTTTATAT
39658591 AAAT
1 AAAT
39658595 TTTACTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (25 bp):
AAATAAAAGAAGTGTAGTTTTATAT
Found at i:39658595 original size:25 final size:25
Alignment explanation
Indices: 39658548--39658598 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39658538 ATAAAATAAA
39658548 AGAAGTGTAGTTTTATATAAATTTT
1 AGAAGTGTAGTTTTATATAAATTTT
39658573 AGAAGTGTAGTTTTATATAAATTTT
1 AGAAGTGTAGTTTTATATAAATTTT
39658598 A
1 A
39658599 CTTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
AGAAGTGTAGTTTTATATAAATTTT
Done.