Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 167 of 211
Found at i:51995332 original size:139 final size:139
Alignment explanation
Indices: 51995082--51995361 Score: 542
Period size: 139 Copynumber: 2.0 Consensus size: 139
51995072 TGACATCATG
*
51995082 ATCATTTTCGCTTTTAATATTTATTTTTTAATTATTTTTGCCATATATTTTTTAATTACTTCCAA
1 ATCATTTTCACTTTTAATATTTATTTTTTAATTATTTTTGCCATATATTTTTTAATTACTTCCAA
*
51995147 ACCAACCATTAAAATTTTATTTGTATTACCGTAATTTTAACAGTTCAGTTAATTTTACTGTCTTG
66 ACCAACCATTAAAATTTTATTTGTATTACCGTAATTTTAACAGTTCAGTTAATTTTACTATCTTG
51995212 AGAAAAGCA
131 AGAAAAGCA
51995221 ATCATTTTCACTTTTAATATTTATTTTTTAATTATTTTTGCCATATATTTTTTAATTACTTCCAA
1 ATCATTTTCACTTTTAATATTTATTTTTTAATTATTTTTGCCATATATTTTTTAATTACTTCCAA
51995286 ACCAACCATTAAAATTTTATTTGTATTACCGTAATTTTAACAGTTCAGTTAATTTTACTATCTTG
66 ACCAACCATTAAAATTTTATTTGTATTACCGTAATTTTAACAGTTCAGTTAATTTTACTATCTTG
51995351 AGAAAAGCA
131 AGAAAAGCA
51995360 AT
1 AT
51995362 TCATCTAAAA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 139 1.00
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (139 bp):
ATCATTTTCACTTTTAATATTTATTTTTTAATTATTTTTGCCATATATTTTTTAATTACTTCCAA
ACCAACCATTAAAATTTTATTTGTATTACCGTAATTTTAACAGTTCAGTTAATTTTACTATCTTG
AGAAAAGCA
Found at i:52002728 original size:3 final size:3
Alignment explanation
Indices: 52002720--52002752 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
52002710 AATGACAATT
52002720 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
52002753 ATAATAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:52004502 original size:3 final size:3
Alignment explanation
Indices: 52004487--52004521 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52004477 TTCATTCTCC
*
52004487 TCT TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
52004522 ATTGTCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:52008051 original size:22 final size:22
Alignment explanation
Indices: 52008021--52008062 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52008011 AACAAATTAA
* *
52008021 TATTATTTTGATATTTTTTTTT
1 TATTATTTTGAAATATTTTTTT
*
52008043 TATTTTTTTGAAATATTTTT
1 TATTATTTTGAAATATTTTT
52008063 GTAAAAGACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
TATTATTTTGAAATATTTTTTT
Found at i:52025075 original size:88 final size:89
Alignment explanation
Indices: 52024921--52025129 Score: 244
Period size: 88 Copynumber: 2.3 Consensus size: 89
52024911 TTTTTTAAAA
* * * *
52024921 AAAAAAGTAATTAACCCTTCCTCTTTTTTTTTTTGCACTCAATGGAGCACTTGAACTTTCAAAAT
1 AAAAAAGCAATTAAGCC--CCTC-TTTTTATTTTGCACTCAATGGAGCACATGAACTTTCAAAAT
* **
52024986 GCATCAAAAAG-CCCTTAAGCTTCTTC
63 GCATAAAAAAGACCCTTAAAATTCTTC
* *
52025012 AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTT-CACTCAATGG-GTACATGAACTTTTAAAATG
1 -AAAAAAGCAATTAAGCCCC-TCTTTTTATTTTGCACTCAATGGAGCACATGAACTTTCAAAATG
* *
52025075 CATAAAAAAGACCTTTAAAATTTTTC
64 CATAAAAAAGACCCTTAAAATTCTTC
*
52025101 AAAAAAGCAATTAAGCCCCTGTTTTTATT
1 AAAAAAGCAATTAAGCCCCTCTTTTTATT
52025130 AGAAAATTAT
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
87 9 0.09
88 45 0.44
89 21 0.20
90 11 0.11
91 2 0.02
92 15 0.15
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (89 bp):
AAAAAAGCAATTAAGCCCCTCTTTTTATTTTGCACTCAATGGAGCACATGAACTTTCAAAATGCA
TAAAAAAGACCCTTAAAATTCTTC
Found at i:52025171 original size:17 final size:18
Alignment explanation
Indices: 52025151--52025187 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52025141 AAATTTTTAA
52025151 AAATATAT-AAAAATTAG
1 AAATATATCAAAAATTAG
*
52025168 AAATTTATCAAAAATTAG
1 AAATATATCAAAAATTAG
52025186 AA
1 AA
52025188 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATATCAAAAATTAG
Found at i:52026065 original size:16 final size:16
Alignment explanation
Indices: 52026044--52026111 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
52026034 TTTGGTTTGC
52026044 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52026060 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
52026076 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
**
52026092 TGTATTGGAACAGAGG
1 TGTATTGGATTAGAGG
52026108 TGTA
1 TGTA
52026112 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.01, G:0.37, T:0.34
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52026152 original size:45 final size:44
Alignment explanation
Indices: 52026092--52026182 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
52026082 GGATTAGAGG
* *
52026092 TGTATTGGAACAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAACAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
52026137 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAACAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
52026181 TG
1 TG
52026183 GAATAGAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAACAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:52026368 original size:18 final size:17
Alignment explanation
Indices: 52026347--52026381 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52026337 TTATTATTAA
*
52026347 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52026365 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52026382 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52026435 original size:157 final size:157
Alignment explanation
Indices: 52026234--52026547 Score: 574
Period size: 157 Copynumber: 2.0 Consensus size: 157
52026224 TAGAATACCC
*
52026234 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
52026299 TTATCAATAATAAATAATTTGATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
52026364 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
52026391 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAATTTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
52026456 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
52026521 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
52026548 CTAATATTCT
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 151 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:52026521 original size:16 final size:16
Alignment explanation
Indices: 52026484--52026525 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52026474 TTAATCATAT
*
52026484 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52026500 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52026515 TTAAAATATAT
1 TTAAAATATAT
52026526 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52026532 original size:14 final size:15
Alignment explanation
Indices: 52026493--52026534 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52026483 TTTAAACATA
*
52026493 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52026508 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52026522 A-TATAATTTAATA
1 ATTATAATTAAATA
52026535 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52026979 original size:13 final size:13
Alignment explanation
Indices: 52026961--52026985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52026951 GCCTTAACAA
52026961 GAGCAGCACTCAT
1 GAGCAGCACTCAT
52026974 GAGCAGCACTCA
1 GAGCAGCACTCA
52026986 AAACAGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:52032934 original size:20 final size:20
Alignment explanation
Indices: 52032901--52032940 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52032891 TTACTCCTCA
*
52032901 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
52032921 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
52032941 TTACTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:52037618 original size:9 final size:9
Alignment explanation
Indices: 52037606--52037638 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
52037596 AAAAATAGAA
*
52037606 AAATTATTG
1 AAATTATCG
52037615 AAATTATCG
1 AAATTATCG
52037624 AAATTATCG
1 AAATTATCG
52037633 AAATTA
1 AAATTA
52037639 AATAAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (9 bp):
AAATTATCG
Found at i:52042202 original size:122 final size:122
Alignment explanation
Indices: 52042051--52042306 Score: 494
Period size: 122 Copynumber: 2.1 Consensus size: 122
52042041 AACGAGTGGA
52042051 GGTATGATCTATTAACTATTTTGTAGAGTTCCTCAATGGATCAATTATTTGGGAAAGGAAGAACT
1 GGTATGATCTATTAACTATTTTGTAGAGTTCCTCAATGGATCAATTATTTGGGAAAGGAAGAACT
52042116 TAAACCCTAGACCTGACAACCCTAAGAAGTCATCAAGGAAGGAATTAACCAAAAATT
66 TAAACCCTAGACCTGACAACCCTAAGAAGTCATCAAGGAAGGAATTAACCAAAAATT
*
52042173 GGTATGATCTATTAACTGTTTTGTAGAGTTCCTCAATGGATCAATTATTTGGGAAAGGAAGAACT
1 GGTATGATCTATTAACTATTTTGTAGAGTTCCTCAATGGATCAATTATTTGGGAAAGGAAGAACT
52042238 TAAACCCTAGACCTGACAACCCTAAGAAGTCATCAAGGAAGGAATTAACCAAAAATT
66 TAAACCCTAGACCTGACAACCCTAAGAAGTCATCAAGGAAGGAATTAACCAAAAATT
*
52042295 GGTATGACCTAT
1 GGTATGATCTAT
52042307 CCGTGAACAC
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 132 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (122 bp):
GGTATGATCTATTAACTATTTTGTAGAGTTCCTCAATGGATCAATTATTTGGGAAAGGAAGAACT
TAAACCCTAGACCTGACAACCCTAAGAAGTCATCAAGGAAGGAATTAACCAAAAATT
Found at i:52043722 original size:4 final size:4
Alignment explanation
Indices: 52043713--52043738 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52043703 AATAGAAAGG
52043713 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
52043739 TAAGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:52045286 original size:25 final size:25
Alignment explanation
Indices: 52045258--52045364 Score: 76
Period size: 25 Copynumber: 4.4 Consensus size: 25
52045248 CTCTCTCGAT
*
52045258 CCATATAACGGGAAGCTTATGTGAG
1 CCATATAACGGGAAGCTCATGTGAG
* * * * *
52045283 CCATGTAACGAGAAGCTTATCTGGG
1 CCATATAACGGGAAGCTCATGTGAG
* **
52045308 CTC-TATAATGGGAAGCTCATAAGAG
1 C-CATATAACGGGAAGCTCATGTGAG
* *
52045333 CCATA-ATCAGGAAGCTCATGTGAG
1 CCATATAACGGGAAGCTCATGTGAG
*
52045357 TCA-ATAAC
1 CCATATAAC
52045365 AGGTAGCCCT
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
23 1 0.02
24 19 0.31
25 40 0.66
26 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (25 bp):
CCATATAACGGGAAGCTCATGTGAG
Found at i:52045432 original size:25 final size:24
Alignment explanation
Indices: 52045404--52045473 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
52045394 AGCTCTGGAT
*
52045404 AGCCATATATCGGGAAGTTCAAGCG
1 AGCCATATATCAGGAAGTTCAAG-G
*
52045429 AGCCA-ATATCTA-GAAGCTCCAAGG
1 AGCCATATATC-AGGAAG-TTCAAGG
*
52045453 AGCCATATATCAGGACGTTCA
1 AGCCATATATCAGGAAGTTCA
52045474 TAAGAGCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (24 bp):
AGCCATATATCAGGAAGTTCAAGG
Found at i:52055090 original size:102 final size:102
Alignment explanation
Indices: 52054972--52055173 Score: 280
Period size: 102 Copynumber: 2.0 Consensus size: 102
52054962 CCAATGAGTC
* * * * * *
52054972 GGGGAATCAGCACTTAGCAACC-CCTTTCACATTTAAGATATGGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAACACTTAGCAACCAAC-TTCACATTTAAGATACGGTAGAATCAGCACTTAGCAACA
* * ** *
52055036 ACCAATGATTCGGGGAATCAGTACTTAGCTACCCCTCG
65 ACCAATGAGTCAGGGAATCAACACTTAGCAACCCCTCG
*
52055074 GGGGAATCAACACTTAGCAACCAACTTCACATTTAAGATACGGTAGAATCAGCATTTAGCAACAA
1 GGGGAATCAACACTTAGCAACCAACTTCACATTTAAGATACGGTAGAATCAGCACTTAGCAACAA
52055139 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCT
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCT
52055174 TTCACATTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 86 0.99
103 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCAACTTCACATTTAAGATACGGTAGAATCAGCACTTAGCAACAA
CCAATGAGTCAGGGAATCAACACTTAGCAACCCCTCG
Found at i:52055167 original size:75 final size:75
Alignment explanation
Indices: 52055074--52055325 Score: 389
Period size: 75 Copynumber: 3.4 Consensus size: 75
52055064 CTACCCCTCG
* * * *
52055074 GGGGAATCAACACTTAGCAACCAAC-TTCACATTTAAGATACGGTAGAATCAGCATTTAGCAACA
1 GGGGAATCAACACTTAGCAACC-CCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACC
*
52055138 ACCAATGAGTC
65 ACCAATGAATC
* * *
52055149 AGGGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
52055214 CCAATGAATC
66 CCAATGAATC
* *
52055224 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGCGGAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
52055289 CCAATGAATC
66 CCAATGAATC
*
52055299 GGGGAATCAGCACTTAGCAACCCCTTT
1 GGGGAATCAACACTTAGCAACCCCTTT
52055326 GGGGAATCAG
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
74 1 0.01
75 162 0.99
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (75 bp):
GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATC
Found at i:52055210 original size:42 final size:41
Alignment explanation
Indices: 52055150--52055287 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 41
52055140 CAATGAGTCA
52055150 GGGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACG
1 GGGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACG
* *
52055191 GTGGAATCAACACTTAGCAACCAC---CA-A--T-GAAT-CG
1 G-GGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACG
* *
52055225 GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACG
1 GGGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACG
*
52055266 GCGGAATCAGCACTTAGCAACC
1 G-GGAATCAACACTTAGCAACC
52055288 ACCAATGAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
33 20 0.25
34 3 0.04
35 3 0.04
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 4 0.05
42 41 0.51
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.21
Consensus pattern (41 bp):
GGGAATCAACACTTAGCAACCCCTTTCACATTTAAAATACG
Found at i:52064514 original size:42 final size:42
Alignment explanation
Indices: 52064445--52064557 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
52064435 ATGCTAAACA
* ** * * *
52064445 GAAACCCATAAGGGTTAAATGGTAGCTC-GTAAGAGCTGAACT
1 GAAACCTATAAGGGTTAAACAGAAGCTCAAT-AGAGCTGAACG
52064487 GAAACCTATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
1 GAAACCTATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
* * *
52064529 GAAA-CTCATATGAGTTAAACAAAAGCTCA
1 GAAACCT-ATAAGGGTTAAACAGAAGCTCA
52064558 TGGGAGCTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.03
42 57 0.95
43 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (42 bp):
GAAACCTATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
Found at i:52071475 original size:20 final size:21
Alignment explanation
Indices: 52071433--52071475 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
52071423 TCGAAGACTG
*
52071433 AATAGAAGCACATAAGTGCTA
1 AATAGAAGCACATAAGGGCTA
* *
52071454 AATAGAA-CCCATAAGGGTTA
1 AATAGAAGCACATAAGGGCTA
52071474 AA
1 AA
52071476 CGGAAGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (21 bp):
AATAGAAGCACATAAGGGCTA
Found at i:52071580 original size:21 final size:20
Alignment explanation
Indices: 52071530--52071585 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
52071520 AAAGGTCAAT
*
52071530 AGAGCTAAACGGACACTCATA
1 AGAGCTAAACAGA-ACTCATA
* * *
52071551 TGAGTTAAACAGAAGCTCGTA
1 AGAGCTAAACAGAA-CTCATA
52071572 AGAGCTAAACAGAA
1 AGAGCTAAACAGAA
52071586 AGTAAAGACG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
AGAGCTAAACAGAACTCATA
Found at i:52074063 original size:44 final size:44
Alignment explanation
Indices: 52074000--52074088 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
52073990 ATCAACTAGA
52074000 TAGCCCAGCTGGATAGTTGTGATTGTAATGTATTTATTAATATT
1 TAGCCCAGCTGGATAGTTGTGATTGTAATGTATTTATTAATATT
52074044 TAGCCCAGCTGGATAGTTGTGATTGTAATGTATTTATTAATATT
1 TAGCCCAGCTGGATAGTTGTGATTGTAATGTATTTATTAATATT
52074088 T
1 T
52074089 CTCTCGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (44 bp):
TAGCCCAGCTGGATAGTTGTGATTGTAATGTATTTATTAATATT
Found at i:52075317 original size:27 final size:27
Alignment explanation
Indices: 52075276--52075345 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
52075266 CATCCTGTTA
52075276 GCCTTTGTGGT-GTACTATGAAAGGAAT
1 GCCTTTGT-GTCGTACTATGAAAGGAAT
*
52075303 GCCTTTGTGTCGTACTGTGAAAGGAAT
1 GCCTTTGTGTCGTACTATGAAAGGAAT
*
52075330 GCCTTTGTGGCGTACT
1 GCCTTTGTGTCGTACT
52075346 CTAAATGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (27 bp):
GCCTTTGTGTCGTACTATGAAAGGAAT
Found at i:52078826 original size:47 final size:49
Alignment explanation
Indices: 52078733--52078827 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 49
52078723 TCTATTGATA
*
52078733 AATGAATGTCCATAACCCCCTCAAATTTATCCTATTGTAACCCCTAAAG
1 AATGAATGTCCATAACCCCCTCAAATTTATCATATTGTAACCCCTAAAG
* * *
52078782 AATGAATGTCCATAA-CCCCT-AAATTTATTATCTTGTAACGCCTAAA
1 AATGAATGTCCATAACCCCCTCAAATTTATCATATTGTAACCCCTAAA
52078828 TCATTTATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 22 0.52
48 5 0.12
49 15 0.36
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (49 bp):
AATGAATGTCCATAACCCCCTCAAATTTATCATATTGTAACCCCTAAAG
Found at i:52082855 original size:23 final size:24
Alignment explanation
Indices: 52082821--52082865 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
52082811 CCTGGCCTGT
52082821 TTTTTAATTAAAATTAAAATTATA
1 TTTTTAATTAAAATTAAAATTATA
52082845 TTTTTAA-TAAAATTAAAATTA
1 TTTTTAATTAAAATTAAAATTA
52082866 ATTGTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTTTAATTAAAATTAAAATTATA
Found at i:52082884 original size:16 final size:16
Alignment explanation
Indices: 52082859--52082895 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
52082849 TAATAAAATT
*
52082859 AAAATTAATTGTTATC
1 AAAATAAATTGTTATC
*
52082875 AAAATAAATTGTTATT
1 AAAATAAATTGTTATC
52082891 AAAAT
1 AAAAT
52082896 TGTATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
AAAATAAATTGTTATC
Found at i:52087383 original size:10 final size:10
Alignment explanation
Indices: 52087368--52087399 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
52087358 GCCTAAAATT
52087368 ATATATAATG
1 ATATATAATG
*
52087378 ATATATAATA
1 ATATATAATG
52087388 ATATATAATG
1 ATATATAATG
52087398 AT
1 AT
52087400 GGGGACGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:52089540 original size:19 final size:19
Alignment explanation
Indices: 52089500--52089540 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52089490 TTTATTTTTT
***
52089500 AAATGAAGATAATTATTTA
1 AAATGAAGATAATTAAACA
52089519 AAATGAAGATAATTAAACA
1 AAATGAAGATAATTAAACA
52089538 AAA
1 AAA
52089541 CCATTTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (19 bp):
AAATGAAGATAATTAAACA
Found at i:52093777 original size:36 final size:36
Alignment explanation
Indices: 52093737--52093808 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
52093727 AATATTGCCG
52093737 TTACTGTTACCGATTC-AGCACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATA
*
52093773 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
52093809 CTGTTACCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (36 bp):
TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
Found at i:52093890 original size:126 final size:127
Alignment explanation
Indices: 52093701--52093950 Score: 328
Period size: 126 Copynumber: 1.9 Consensus size: 127
52093691 ACTGTTACTG
52093701 TTACCGATTTGGCACTTTATGTGTCAAATATTGCCGTTACTGTTACCGATTCAGCACTTTGTGTG
1 TTACCGATTTGGCACTTTATGTGTCAAATATTGCCGTTACTGTTACCGATTCAGCACTTTGTGTG
*
52093766 TCGAATA-T-TACTGTTA-T-CGATTCGACACTTTGTGTGTCGAATACTGTTACCATTATTA
66 TCGAATACTCTACTGTTATTACGATTCGACACTTTATGTGTCGAATACTGTTACCATTATTA
* * ** * *
52093824 TTACTGATTTGGCACTTTGTGTGTTGAATATTGTTACCGTTACTGTTACTGATTCCGCACTTTGT
1 TTACCGATTTGGCACTTTATGTGTCAAATATTG---CCGTTACTGTTACCGATTCAGCACTTTGT
*
52093889 GTGTCGAATACTGCTACTGTTATTGTTACCGATTCGACACTTTATGTGTTGAATACTGTTAC
63 GTGTCGAATACT-CTACTGTTA---TTA-CGATTCGACACTTTATGTGTCGAATACTGTTAC
52093951 TGTTACTGCT
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
123 29 0.27
126 37 0.35
127 1 0.01
129 8 0.07
133 1 0.01
135 31 0.29
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (127 bp):
TTACCGATTTGGCACTTTATGTGTCAAATATTGCCGTTACTGTTACCGATTCAGCACTTTGTGTG
TCGAATACTCTACTGTTATTACGATTCGACACTTTATGTGTCGAATACTGTTACCATTATTA
Found at i:52093912 original size:90 final size:90
Alignment explanation
Indices: 52093773--52093958 Score: 250
Period size: 90 Copynumber: 2.1 Consensus size: 90
52093763 GTGTCGAATA
* * * *
52093773 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATACTGTTACCATTATTATTACTGATTTGGCA
1 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATACTGCTACCATTATTATTACCGATTCGACA
* *
52093838 CTTTGTGTGTTGAATATTGTTACCG
66 CTTTATGTGTTGAATACTGTTACCG
** *
52093863 TTACTGTTA-CTGATTCCG-CACTTTGTGTGTCGAATACTGCTACTGTTATTGTTACCGATTCGA
1 TTACTGTTATC-GATT-CGACACTTTGTGTGTCGAATACTGCTACCATTATTATTACCGATTCGA
*
52093926 CACTTTATGTGTTGAATACTGTTACTG
64 CACTTTATGTGTTGAATACTGTTACCG
52093953 TTACTG
1 TTACTG
52093959 CTACCGTTAC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 1 0.01
90 81 0.96
91 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (90 bp):
TTACTGTTATCGATTCGACACTTTGTGTGTCGAATACTGCTACCATTATTATTACCGATTCGACA
CTTTATGTGTTGAATACTGTTACCG
Found at i:52093964 original size:45 final size:45
Alignment explanation
Indices: 52093773--52093964 Score: 215
Period size: 45 Copynumber: 4.3 Consensus size: 45
52093763 GTGTCGAATA
* *
52093773 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATACTGTTACCA
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * * * * * *
52093818 TTATTATTACTGATTTGGCACTTTGTGTGTTGAATATTGTTACCG
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * *
52093863 TTACTGTTACTGATTCCG-CACTTTGTGTGTCGAATACTGCTACTG
1 TTACTGTTACCGATT-CGACACTTTGTGTGTCGAATACTGTTACCG
* * * *
52093908 TTATTGTTACCGATTCGACACTTTATGTGTTGAATACTGTTACTG
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACCG
*
52093953 TTACTGCTACCG
1 TTACTGTTACCG
52093965 TTACTGATTA
Statistics
Matches: 122, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.02
45 119 0.98
46 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (45 bp):
TTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACCG
Found at i:52097782 original size:53 final size:50
Alignment explanation
Indices: 52097646--52097807 Score: 154
Period size: 47 Copynumber: 3.2 Consensus size: 50
52097636 TTGCACATCG
* * * *
52097646 TCACATATCACACACCGAAGCCATAACCCACCTATGGTCTTACACGGAAA
1 TCACATATCACACACCGATGCCATAGCCCAGCTATGGTCTTACACGAAAA
* * *
52097696 -CACATAT--CACACCGATACCATATG-CCAGATATGGTCTTACATGAAAA
1 TCACATATCACACACCGATGCCATA-GCCCAGCTATGGTCTTACACGAAAA
* * *
52097743 TCACATATCACATCACATCGATGCCATAGCCCAGCTATGGTATTATACG-GAA
1 TCACATATCACA-CAC--CGATGCCATAGCCCAGCTATGGTCTTACACGAAAA
52097795 TCACATAATCACA
1 TCACAT-ATCACA
52097808 TTTTCACATG
Statistics
Matches: 90, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
47 32 0.36
48 7 0.08
49 7 0.08
50 2 0.02
51 3 0.03
52 9 0.10
53 30 0.33
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.22
Consensus pattern (50 bp):
TCACATATCACACACCGATGCCATAGCCCAGCTATGGTCTTACACGAAAA
Found at i:52098864 original size:15 final size:15
Alignment explanation
Indices: 52098827--52098866 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
52098817 TGCAAATATC
*
52098827 ATGATAACAAATACA
1 ATGATAATAAATACA
52098842 AT-AGTAATAAATACA
1 ATGA-TAATAAATACA
52098857 ATGATAATAA
1 ATGATAATAA
52098867 TTTTAACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (15 bp):
ATGATAATAAATACA
Found at i:52100782 original size:45 final size:44
Alignment explanation
Indices: 52100722--52100921 Score: 146
Period size: 44 Copynumber: 4.6 Consensus size: 44
52100712 CGGCTTTAAC
**
52100722 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGGCAT-CTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATACTT-AGT
* * *
52100767 CTGCCCCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAGT
* * * * *
52100811 TTGCTCCACTGCAACTTCAGAGAGATAAGACTAG-ATGC-GA-T
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
* * * * * *
52100852 ATGCT-CTCTGCAACTTCAGAGAGATAAGATCTATG-GT-TTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATACTTAGT
*
52100895 CCGCTCCACTGCAACTTCAGGGAGATA
1 CTGCTCCACTGCAACTTCAGGGAGATA
52100922 GGATCATTGG
Statistics
Matches: 124, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
40 23 0.19
41 7 0.06
42 4 0.03
43 6 0.05
44 54 0.44
45 30 0.24
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
Found at i:52100831 original size:44 final size:45
Alignment explanation
Indices: 52100722--52100842 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 45
52100712 CGGCTTTAAC
* **
52100722 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGGCATCTTCAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGGCATCTTCAGT
* *
52100767 CTGCCCCACTGCAACTTCAGA-AGGATAAGACTT-GCTTACTT-AGT
1 CTGCTCCACTGCAACTTCAGAGA-GATAAGACTTGGCAT-CTTCAGT
*
52100811 TTGCTCCACTGCAACTTCAGAGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACT
52100843 AGATGCGATA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 35 0.53
45 31 0.47
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGGCATCTTCAGT
Found at i:52112815 original size:15 final size:15
Alignment explanation
Indices: 52112779--52112817 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
52112769 GCAAATATCG
*
52112779 TGATAACAAATACAA
1 TGATAATAAATACAA
52112794 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
52112809 TGATAATAA
1 TGATAATAA
52112818 TTTTAACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:52113053 original size:24 final size:24
Alignment explanation
Indices: 52113012--52113095 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
52113002 TGAAGCTTAA
* *
52113012 AAAATATACAT-ATGATTTACATAT
1 AAAATATATATAAT-ATTTATATAT
52113036 AAAATATATATAATATTTATATTAT
1 AAAATATATATAATATTTATA-TAT
* *
52113061 CAAAATAAATAAAATATGTGTATATAT
1 -AAAATATATATAATAT-T-TATATAT
52113088 ATAAATAT
1 A-AAATAT
52113096 GAGAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 16 0.33
25 5 0.10
26 15 0.31
27 9 0.18
28 4 0.08
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATATATATAATATTTATATAT
Found at i:52113148 original size:16 final size:17
Alignment explanation
Indices: 52113117--52113149 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52113107 TAGTTGGAAA
52113117 AAAAATATAAATATGTAC
1 AAAAATAT-AATATGTAC
52113135 AAAAATAT-ATATGTA
1 AAAAATATAATATGTA
52113150 TATAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAATATGTAC
Found at i:52113440 original size:22 final size:22
Alignment explanation
Indices: 52113400--52113468 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 22
52113390 GCTAAATTGA
52113400 AATT-AAAAATAAATTAAAAGGCG
1 AATTAAAAAATAAA--AAAAGGCG
** *
52113423 AATTAAAAAATAAAAAAAACCT
1 AATTAAAAAATAAAAAAAGGCG
*
52113445 AATTATAAAACATTAAAAAAGGCG
1 AATTA-AAAA-ATAAAAAAAGGCG
52113469 GAGGGACTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 10 0.28
23 8 0.22
24 18 0.50
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (22 bp):
AATTAAAAAATAAAAAAAGGCG
Found at i:52119194 original size:6 final size:6
Alignment explanation
Indices: 52119177--52119225 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
52119167 GCCAATGAAC
* * *
52119177 CATTTCT CATTTT CATTTT CATTTT CATTTC CATTTC CATTTC CATTTT
1 CATTT-T CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
52119226 TGAGAAACTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (6 bp):
CATTTT
Found at i:52119200 original size:12 final size:12
Alignment explanation
Indices: 52119177--52119225 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
52119167 GCCAATGAAC
52119177 CATTTCTCATTTT
1 CATTTC-CATTTT
*
52119190 CATTTTCATTTT
1 CATTTCCATTTT
*
52119202 CATTTCCATTTC
1 CATTTCCATTTT
52119214 CATTTCCATTTT
1 CATTTCCATTTT
52119226 TGAGAAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 27 0.84
13 5 0.16
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
CATTTCCATTTT
Found at i:52119828 original size:130 final size:129
Alignment explanation
Indices: 52119620--52119869 Score: 344
Period size: 130 Copynumber: 1.9 Consensus size: 129
52119610 AATAGTAATC
* * * * *
52119620 AAGTCATTCATCACAAAGACGAACGACCCGTTACCACATTTACTTTTCCTTAACCATGCAATGGC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* *
52119685 AATAAGGGGATATCATTTA-CCTGTATTTTAGGCTATGAATTCTACTATTGTGAATGTCAATACA
66 AAT-AGGGGATATCATTTAGCC-GTATTTTAGGCTATGAATACCACTATTGTGAATGTCAATACA
52119749 A
129 A
*
52119750 AAGTCATTCATCATAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAAT-GC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* *
52119814 TAAT-GGGAGAATATCATTTAGCCGTGTTTTAGGTTATGAATACCACTATTGTGAAT
66 -AATAGGG-G-ATATCATTTAGCCGTATTTTAGGCTATGAATACCACTATTGTGAAT
52119870 TACGCTACAT
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
128 3 0.03
129 3 0.03
130 98 0.92
131 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (129 bp):
AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
AATAGGGGATATCATTTAGCCGTATTTTAGGCTATGAATACCACTATTGTGAATGTCAATACAA
Found at i:52121209 original size:25 final size:25
Alignment explanation
Indices: 52121181--52121228 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
52121171 CCCTCTCTTG
*
52121181 AGCCATATGATGAGAAGCTCATGTA
1 AGCCATATAATGAGAAGCTCATGTA
*
52121206 AGCCATATAATGGGAAGCTCATG
1 AGCCATATAATGAGAAGCTCATG
52121229 CGAGCTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (25 bp):
AGCCATATAATGAGAAGCTCATGTA
Found at i:52121273 original size:25 final size:26
Alignment explanation
Indices: 52121245--52121353 Score: 88
Period size: 25 Copynumber: 4.4 Consensus size: 26
52121235 AATAACGGGT
52121245 AGCTCCGAAGAGCCATTA-ATCGAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
* * *
52121270 AGCTCCGGATAGCCA-TATATCGAAA
1 AGCTCCGAAGAGCCATTATATCGAGA
* *
52121295 AG-TTC-AAGTG--AGTTATATCGAGA
1 AGCTCCGAAGAGCCA-TTATATCGAGA
* *
52121318 AGCTCCGGAGAGCCATTA-ATCAAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
52121343 AGCTCACGAAG
1 AGCTC-CGAAG
52121354 GGTCATATAT
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
21 1 0.02
23 13 0.21
24 6 0.10
25 35 0.56
26 7 0.11
27 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
AGCTCCGAAGAGCCATTATATCGAGA
Found at i:52129031 original size:25 final size:25
Alignment explanation
Indices: 52129001--52129062 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
52128991 GCCCCCTCTC
*
52129001 GAGCCATATAACGGGAAGATCATGT
1 GAGCCATGTAACGGGAAGATCATGT
* *
52129026 GAGCCATGTAATGGGAAGCTCATGT
1 GAGCCATGTAACGGGAAGATCATGT
52129051 GAGCCATGTAAC
1 GAGCCATGTAAC
52129063 TAGAAGCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (25 bp):
GAGCCATGTAACGGGAAGATCATGT
Found at i:52129068 original size:25 final size:25
Alignment explanation
Indices: 52129001--52129070 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
52128991 GCCCCCTCTC
* * *
52129001 GAGCCATATAACGGGAAGATCATGT
1 GAGCCATGTAACTGGAAGCTCATGT
52129026 GAGCCATGTAA-TGGGAAGCTCATGT
1 GAGCCATGTAACT-GGAAGCTCATGT
*
52129051 GAGCCATGTAACTAGAAGCT
1 GAGCCATGTAACTGGAAGCT
52129071 TATCCATACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 38 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (25 bp):
GAGCCATGTAACTGGAAGCTCATGT
Found at i:52129225 original size:23 final size:23
Alignment explanation
Indices: 52129181--52129228 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
52129171 GGATAGCTAT
* *
52129181 ATATTGGGAAGTTCAAGCGAGCC
1 ATATTGGGAAGCTCAAGAGAGCC
**
52129204 ATATTGGGAAGCTCGGGAGAGCC
1 ATATTGGGAAGCTCAAGAGAGCC
52129227 AT
1 AT
52129229 TAATCAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (23 bp):
ATATTGGGAAGCTCAAGAGAGCC
Found at i:52130047 original size:17 final size:18
Alignment explanation
Indices: 52130019--52130052 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52130009 ATCTTACCAA
*
52130019 ACATTCATACACTATTAT
1 ACATTCATACACCATTAT
52130037 ACATT-ATACACCATTA
1 ACATTCATACACCATTA
52130053 CTAAGTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (18 bp):
ACATTCATACACCATTAT
Found at i:52130369 original size:44 final size:44
Alignment explanation
Indices: 52130306--52130461 Score: 222
Period size: 44 Copynumber: 3.4 Consensus size: 44
52130296 TTATCAATTG
* *
52130306 TCACTTGTCATTGAACAGATAAGCGTAGCTAAAGCTACCACTTA
1 TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
52130350 TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
52130394 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCA----T---TGATCAGATAAGTGTAGCTAAAGCTACCACTTA
*
52130445 TCACTTGTCACTGATCA
1 TCACTTGTCATTGATCA
52130462 AAAGTACTCA
Statistics
Matches: 102, Mismatches: 3, Indels: 14
0.86 0.03 0.12
Matches are distributed among these distances:
44 58 0.57
48 1 0.01
51 43 0.42
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
Found at i:52130399 original size:51 final size:51
Alignment explanation
Indices: 52130344--52130456 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
52130334 CTAAAGCTAC
* *
52130344 CACTTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
52130395 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
52130446 CACTTGTCACT
1 CACTTGTCACT
52130457 GATCAAAAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:52132032 original size:21 final size:21
Alignment explanation
Indices: 52132008--52132049 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52131998 CTTTTTGTTC
52132008 AATTAATT-ATCGAAACTTTAA
1 AATTAATTAAT-GAAACTTTAA
**
52132029 AATTTCTTAATGAAACTTTAA
1 AATTAATTAATGAAACTTTAA
52132050 TACTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AATTAATTAATGAAACTTTAA
Found at i:52132687 original size:5 final size:5
Alignment explanation
Indices: 52132663--52132696 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
52132653 TAATTTAATA
52132663 CAATT CATATT CATATT CAATT CAATT CAATT CA
1 CAATT CA-ATT CA-ATT CAATT CAATT CAATT CA
52132697 CATCTTAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CAATT
Found at i:52143892 original size:43 final size:43
Alignment explanation
Indices: 52143794--52143951 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 43
52143784 ATGTTCCAAT
** * ** * *
52143794 ATCGATTTGAGATCCCGTATAAGACCATATATGGGATA-TGAC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
52143836 ATCAATTTGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
52143879 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGC
** *
52143923 ATCGATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
52143952 GTTTGTGACC
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 30 0.30
43 33 0.33
44 24 0.24
45 12 0.12
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:52143935 original size:44 final size:43
Alignment explanation
Indices: 52143844--52143951 Score: 162
Period size: 44 Copynumber: 2.5 Consensus size: 43
52143834 ACATCAATTT
* **
52143844 GAGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATTT
1 GAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAC
52143887 GAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGCATCGATAC
1 GAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGCATCGATAC
*
52143931 GAGATTTCCATGTAAGACCAT
1 GAGATTT-CGTGTAAGACCAT
52143952 GTTTGTGACC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 23 0.39
44 24 0.41
45 12 0.20
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
GAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAC
Found at i:52146695 original size:32 final size:32
Alignment explanation
Indices: 52146658--52146725 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
52146648 GGCTTAAAGT
*
52146658 GCATTCATTACTAGGAGGTTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
*
52146690 GCATTCATTCCTAGGAGGCTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
52146722 -CATT
1 GCATT
52146726 ATTTTGGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (32 bp):
GCATTCATTACTAGGAGGCTGATTACGAATAA
Found at i:52150060 original size:17 final size:17
Alignment explanation
Indices: 52150026--52150063 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52150016 TGTAAATTAT
*
52150026 AAATATATATAATTTAA
1 AAATATATATAATATAA
52150043 AAATA-ATATAAATATAA
1 AAATATATAT-AATATAA
52150060 AAAT
1 AAAT
52150064 TTATTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATATATAATATAA
Found at i:52157224 original size:1 final size:1
Alignment explanation
Indices: 52157218--52157249 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
52157208 TGGTGAGTTC
*
52157218 TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
52157250 ATAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:52170773 original size:101 final size:101
Alignment explanation
Indices: 52170637--52170859 Score: 311
Period size: 101 Copynumber: 2.2 Consensus size: 101
52170627 CATGCATTAC
* * ** *
52170637 CATGGCCCAGCCATGGTCTTACATTCTTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATG
1 CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATG
* * *
52170702 CCATAACTTAGCTATGGTCTTACTTATAAATACTGT
66 ACATAACTTAGCTATAGTCTTACTTATAAATACTAT
* * * *
52170738 CATGGTCCAACCATGGTCTTACGTTCAAAGTGCCATAACCTAGTTATGGTCTTTTCATTAAAATG
1 CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATG
** *
52170803 ACATAGTTTAGCTATAGTCTTACTTATAGATACTAT
66 ACATAACTTAGCTATAGTCTTACTTATAAATACTAT
52170839 CATGGTCCAACCATGGTCTTA
1 CATGGTCCAACCATGGTCTTA
52170860 TCCGTCAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 107 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (101 bp):
CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATG
ACATAACTTAGCTATAGTCTTACTTATAAATACTAT
Found at i:52173881 original size:34 final size:34
Alignment explanation
Indices: 52173838--52173909 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
52173828 ACATTCCTTC
*
52173838 ATCAGATGCCATATAATGAGTGCAGCCATTGTCA
1 ATCAGATGCCATATAATAAGTGCAGCCATTGTCA
52173872 ATCAGATGCCATATAATAAGTGCAGCCATTGTCA
1 ATCAGATGCCATATAATAAGTGCAGCCATTGTCA
52173906 ATCA
1 ATCA
52173910 ACCAATCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (34 bp):
ATCAGATGCCATATAATAAGTGCAGCCATTGTCA
Found at i:52176655 original size:20 final size:20
Alignment explanation
Indices: 52176630--52176678 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
52176620 CTAACCTCCG
*
52176630 AAATCTTCATTGAATCGTTA
1 AAATCTTCATTGAATCCTTA
52176650 AAATCTTCATTGAATCCTTA
1 AAATCTTCATTGAATCCTTA
*
52176670 AAATATTCA
1 AAATCTTCA
52176679 AATCCCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATCTTCATTGAATCCTTA
Found at i:52176688 original size:17 final size:17
Alignment explanation
Indices: 52176662--52176704 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
52176652 ATCTTCATTG
*
52176662 AATCCTTAAAATATTCA
1 AATCCCTAAAATATTCA
*
52176679 AATCCCT-AAATCTTCA
1 AATCCCTAAAATATTCA
52176695 AATCCCTAAA
1 AATCCCTAAA
52176705 TCGTTAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (17 bp):
AATCCCTAAAATATTCA
Found at i:52176694 original size:16 final size:16
Alignment explanation
Indices: 52176670--52176706 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
52176660 TGAATCCTTA
*
52176670 AAATATTCAAATCCCT
1 AAATCTTCAAATCCCT
52176686 AAATCTTCAAATCCCT
1 AAATCTTCAAATCCCT
52176702 AAATC
1 AAATC
52176707 GTTAGCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATCTTCAAATCCCT
Found at i:52177101 original size:117 final size:117
Alignment explanation
Indices: 52176893--52177103 Score: 341
Period size: 117 Copynumber: 1.8 Consensus size: 117
52176883 TTTGATTTGT
* * *
52176893 TGGTTATTTGTGATTCATTATTGCAATTTCAGTGCCACAATGTAGTGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTCATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
* * **
52176958 GATGCTATAGTGGTCCCGATTTTGTTGATAAAATTGTTGTCAAAATTGTAGA
66 GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
* *
52177010 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTTGATTTGT
1 TGGTTAATTGTGATTCATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
52177075 GATGCGACAGTGGTCCCGATGATGTTGAT
66 GATGCGACAGTGGTCCCGATGATGTTGAT
52177104 TTCTGTTATC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 85 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (117 bp):
TGGTTAATTGTGATTCATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
Found at i:52181968 original size:16 final size:16
Alignment explanation
Indices: 52181947--52181983 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
52181937 GAATGCTAAC
*
52181947 GATTTAGGGATTTTAA
1 GATTTAGGGATTTGAA
52181963 GATTTAGGGATTTGAA
1 GATTTAGGGATTTGAA
52181979 GATTT
1 GATTT
52181984 TAAGGGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (16 bp):
GATTTAGGGATTTGAA
Found at i:52185168 original size:13 final size:12
Alignment explanation
Indices: 52185149--52185178 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
52185139 GCTTACTGCA
52185149 TTTTTTCTTTTT
1 TTTTTTCTTTTT
52185161 TCTTTTTCTTTTT
1 T-TTTTTCTTTTT
52185174 TTTTT
1 TTTTT
52185179 AAGTTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:52189696 original size:40 final size:41
Alignment explanation
Indices: 52189648--52189736 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
52189638 ACCAATTTGG
* *
52189648 CACCCAGTACTTCATCGGAT-AATTCGAAGTAGTAAATTGA
1 CACCCAGTACTTCATCGAATAAATCCGAAGTAGTAAATTGA
* * *
52189688 CACTCAGTATTTCATTGAATAAATCCGAAGTAGTAAATTGA
1 CACCCAGTACTTCATCGAATAAATCCGAAGTAGTAAATTGA
52189729 CACCCAGT
1 CACCCAGT
52189737 GTCTCATCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 16 0.38
41 26 0.62
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (41 bp):
CACCCAGTACTTCATCGAATAAATCCGAAGTAGTAAATTGA
Found at i:52190702 original size:21 final size:20
Alignment explanation
Indices: 52190669--52190707 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
52190659 CTTCGTCTCC
52190669 TTCTTTCTCCCTTTTCTTTCT
1 TTCTTTCTCCC-TTTCTTTCT
* *
52190690 TTCTTTTTTCCTTTCTTT
1 TTCTTTCTCCCTTTCTTT
52190708 TTCCTTCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTCTCCCTTTCTTTCT
Found at i:52191052 original size:13 final size:13
Alignment explanation
Indices: 52191034--52191068 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
52191024 ACTAACTTCT
52191034 TAAATATTTTTAA
1 TAAATATTTTTAA
52191047 TAAATATTTTTAA
1 TAAATATTTTTAA
52191060 TAAATATTT
1 TAAATATTT
52191069 ATGAGTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:52198517 original size:23 final size:23
Alignment explanation
Indices: 52198485--52198528 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52198475 ACTACCATTT
52198485 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
52198508 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
52198529 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:52198521 original size:13 final size:11
Alignment explanation
Indices: 52198489--52198531 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
52198479 CCATTTTCTA
*
52198489 AATAAAATAAT
1 AATAAAATATT
52198500 AAT-AAATATCT
1 AATAAAATAT-T
52198511 AAGTAAAATATT
1 AA-TAAAATATT
52198523 AATAAAATA
1 AATAAAATA
52198532 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:52204613 original size:124 final size:124
Alignment explanation
Indices: 52204393--52204672 Score: 483
Period size: 124 Copynumber: 2.3 Consensus size: 124
52204383 TTATTTCGAG
* *
52204393 TTGACGTTTC-TGGTCAAATAGTAAAAAATCGCTTCTATCAGGATGCTATTTGAGAAGAAATTGG
1 TTGACGTTTCTTAG-CAAATAGTATAAAATCGCTTCTATCAGGATGCTATTTGAGAAGAAATTGG
52204457 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
52204517 TTGACGTTTCTTAGCAAATAGTATAAAATCGCTTCTA-CAAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTTAGCAAATAGTATAAAATCGCTTCTATC-AGGATGCTATTTGAGAAGAAATTGG
*
52204581 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATATTTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
52204641 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
1 TTGACGTTTCTTAGCAAATAGTATAAAATCGC
52204673 GCCCTCGTGG
Statistics
Matches: 149, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
123 1 0.01
124 146 0.98
125 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGACGTTTCTTAGCAAATAGTATAAAATCGCTTCTATCAGGATGCTATTTGAGAAGAAATTGGG
AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:52207869 original size:29 final size:29
Alignment explanation
Indices: 52207805--52208441 Score: 957
Period size: 29 Copynumber: 22.0 Consensus size: 29
52207795 TTTTGTTAAT
* *
52207805 GGTTAGGGGTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52207834 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
52207864 GGTTAGGGTTTTTAATTAAATTATGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
52207893 GGTTAGGGTTTTTAATTAAATCAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52207922 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
52207951 GGTTAGGGTTTTTAATTAAGTTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52207980 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
52208009 GGTTAGGGTTTCTAATTAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
52208038 GGTTAGGGTTTTTAATTAAATCAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208067 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52208096 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* **
52208125 GGTTAGGGTTTTCAATT-TCTCATA-GTTAG
1 GGTTAGGGTTTTTAATTAAAT--TAGGTTAG
52208154 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208183 GGTTAAGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52208212 GGTTTAGGGTTTTTAATT-AA--A--TTA-
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
52208236 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208265 AGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208294 GGTTTAGGGTTTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
52208324 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52208353 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208382 TGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 -GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
52208412 TGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 -GGTTAGGGTTTTTAATTAAATTAGGTTAG
52208442 TGTTTACATC
Statistics
Matches: 561, Mismatches: 33, Indels: 27
0.90 0.05 0.04
Matches are distributed among these distances:
23 15 0.03
24 4 0.01
25 3 0.01
26 1 0.00
27 1 0.00
28 6 0.01
29 401 0.71
30 130 0.23
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:52209581 original size:7 final size:7
Alignment explanation
Indices: 52209555--52209593 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
52209545 TTATATACAT
*
52209555 AATACAA
1 AATACTA
52209562 AATACTA
1 AATACTA
52209569 AATACTA
1 AATACTA
52209576 AATACTA
1 AATACTA
*
52209583 AAGACTA
1 AATACTA
52209590 AATA
1 AATA
52209594 TCAATCCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23
Consensus pattern (7 bp):
AATACTA
Found at i:52210579 original size:25 final size:25
Alignment explanation
Indices: 52210529--52210584 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
52210519 CTTTTATAAG
*
52210529 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
52210554 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
52210577 AAATAATA
1 AAATAATA
52210585 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:52210724 original size:30 final size:31
Alignment explanation
Indices: 52210675--52210740 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
52210665 GCCATTGATG
52210675 AAAATATAAAAAGATTTAAAATTATTTTAAA
1 AAAATATAAAAAGATTTAAAATTATTTTAAA
52210706 AAAATATAAAAA-ATTTAAAATTATTTTAAA
1 AAAATATAAAAAGATTTAAAATTATTTTAAA
52210736 AAAAT
1 AAAAT
52210741 GAAATTGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAATATAAAAAGATTTAAAATTATTTTAAA
Found at i:52210799 original size:22 final size:21
Alignment explanation
Indices: 52210774--52210824 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 21
52210764 TAATATGGAT
52210774 TTGAGAGATTTTTGGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
52210796 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
52210818 TTGAGAG
1 TTGAGAG
52210825 TTTGAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:52210831 original size:30 final size:30
Alignment explanation
Indices: 52210796--52210854 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
52210786 TGGAAGGAAA
*
52210796 TTGAGAGGATTTTGGAAGGAAATTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
52210826 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
52210855 GATTTCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:52210833 original size:52 final size:52
Alignment explanation
Indices: 52210773--52210875 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
52210763 TTAATATGGA
* **
52210773 TTTGAGAGATTTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTCAGAAGGAAATTGAGAG
52210825 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTCAGAAGGAAATTGAGA
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTCAGAAGGAAATTGAGA
52210876 TAGGATTTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.01, G:0.33, T:0.29
Consensus pattern (52 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTCAGAAGGAAATTGAGAG
Found at i:52210854 original size:22 final size:22
Alignment explanation
Indices: 52210826--52210875 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
52210816 AATTGAGAGT
**
52210826 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTCAGAAGGAAA
*
52210848 TTGAGAGGATTTCAGAAGGAAA
1 TTGAGAGAATTTCAGAAGGAAA
52210870 TTGAGA
1 TTGAGA
52210876 TAGGATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGAGAGAATTTCAGAAGGAAA
Found at i:52216375 original size:14 final size:15
Alignment explanation
Indices: 52216346--52216384 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
52216336 GGCACGAGCT
*
52216346 AAATTAGAAAATTGA
1 AAATTAGAAAACTGA
52216361 AAATT-GAAAACTGA
1 AAATTAGAAAACTGA
*
52216375 AAATAAGAAA
1 AAATTAGAAA
52216385 TTAGTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.64, C:0.03, G:0.13, T:0.21
Consensus pattern (15 bp):
AAATTAGAAAACTGA
Found at i:52221101 original size:3 final size:3
Alignment explanation
Indices: 52221093--52221136 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
52221083 AAAAACTGAA
*
52221093 TTC TTC TTC TTC TTC TTC TTC TTC TTC TAC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52221137 ATTCGTCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:52229760 original size:27 final size:28
Alignment explanation
Indices: 52229700--52229766 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
52229690 GGTTCAGCAT
* * *
52229700 TGGGTGTCGCCTGTCAGGTACCCTTCAT
1 TGGGTGCCGCCTGTCAGGTAACCTTCAC
*
52229728 TGGGTGCTGCCTGTCAGG-AACCTTCCAC
1 TGGGTGCCGCCTGTCAGGTAACCTT-CAC
52229756 T-GGTGCCGCCT
1 TGGGTGCCGCCT
52229767 CTCAATCATC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 14 0.42
28 19 0.58
ACGTcount: A:0.10, C:0.31, G:0.30, T:0.28
Consensus pattern (28 bp):
TGGGTGCCGCCTGTCAGGTAACCTTCAC
Found at i:52242884 original size:29 final size:29
Alignment explanation
Indices: 52242850--52242909 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
52242840 AAAAATTACC
52242850 ATTTAAGCTATTGAATTGTTAAATTATTA
1 ATTTAAGCTATTGAATTGTTAAATTATTA
52242879 ATTTAAGCTATTGAATTGTTAAATTATTA
1 ATTTAAGCTATTGAATTGTTAAATTATTA
52242908 AT
1 AT
52242910 AGATAAAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (29 bp):
ATTTAAGCTATTGAATTGTTAAATTATTA
Found at i:52247330 original size:43 final size:43
Alignment explanation
Indices: 52247264--52247387 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
52247254 GGCTCGTACA
* *
52247264 ATGCCAATGTCCAAGACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAATGTCCAAGACGTGGTCTTACACGTAAACACA-AGTCG
* *
52247307 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAATGTCCAAGAC-GTGGTCTTACACGTAAACACAAGTCG
** *
52247350 ATGCCAACATCCCAA-ACGTGGTCTTACACGAAAACACA
1 ATGCCAATGT-CCAAGACGTGGTCTTACACGTAAACACA
52247388 TATCGGAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.03
43 62 0.91
44 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAATGTCCAAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:52248905 original size:14 final size:14
Alignment explanation
Indices: 52248886--52248913 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52248876 TTTTGTTTCT
52248886 TTTAATAATCTAAA
1 TTTAATAATCTAAA
52248900 TTTAATAATCTAAA
1 TTTAATAATCTAAA
52248914 AGAGCACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAATAATCTAAA
Found at i:52248994 original size:23 final size:23
Alignment explanation
Indices: 52248942--52248986 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
52248932 TATCAGTAAA
*
52248942 AAATTTATTTTTCACTTAGTATT
1 AAATATATTTTTCACTTAGTATT
*
52248965 AAATATATTTTTCACTTTGTAT
1 AAATATATTTTTCACTTAGTAT
52248987 AATCTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (23 bp):
AAATATATTTTTCACTTAGTATT
Found at i:52252577 original size:101 final size:100
Alignment explanation
Indices: 52252388--52252632 Score: 355
Period size: 101 Copynumber: 2.4 Consensus size: 100
52252378 AATTCATCCT
* * * * * *
52252388 TTACATTCGTAGTGCCATAACCCAGTTATGGCTTTATCATTAGAATGCCATAGCTCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGTC-TTATCATCAGAATGCCATAGCCCAACTATGGT
52252453 CTTACATATAAACACTACCATGGTCCAACCATGGTC
65 CTTACATATAAACACTACCATGGTCCAACCATGGTC
*
52252489 TTACGTTTATAGTGCCATAACCCAGTTATAGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTAT-GTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* *
52252554 CTTACATATAAACACTGCTATGGTCCAACCATGGTC
65 CTTACATATAAACACTACCATGGTCCAACCATGGTC
* *
52252590 TTGCGTTCATAGTGCCATAAACCAGTTATGGTCTTATCCATCA
1 TTACGTTCATAGTGCCATAACCCAGTTAT-GTCTTAT-CATCA
52252633 ATTCATCTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 122 0.95
102 7 0.05
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (100 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGTCTTATCATCAGAATGCCATAGCCCAACTATGGTC
TTACATATAAACACTACCATGGTCCAACCATGGTC
Found at i:52255634 original size:22 final size:22
Alignment explanation
Indices: 52255583--52255641 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
52255573 TTATCGTTCC
* * *
52255583 GCACTTCAATGCCTACTGTTTT
1 GCACTTCGATGCCTAATGATTT
*
52255605 GCACTTCGATGCTTAATGATTT
1 GCACTTCGATGCCTAATGATTT
*
52255627 GCACTTCGGTGCCTA
1 GCACTTCGATGCCTA
52255642 GTGTTATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (22 bp):
GCACTTCGATGCCTAATGATTT
Found at i:52258001 original size:23 final size:22
Alignment explanation
Indices: 52257958--52258015 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
52257948 AAAGGGTATC
* *
52257958 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
52257979 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
52258002 TGCATATCATATCT
1 TACAAATCATATCT
52258016 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:52258390 original size:21 final size:21
Alignment explanation
Indices: 52258364--52258422 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
52258354 AAAATTTACC
52258364 TAAGGTATCGATACCTAAGGG
1 TAAGGTATCGATACCTAAGGG
*
52258385 TAAGGTATCGATACTTAAGGG
1 TAAGGTATCGATACCTAAGGG
*
52258406 TAAGGTACCGATACCTA
1 TAAGGTATCGATACCTA
52258423 GAGCTTGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (21 bp):
TAAGGTATCGATACCTAAGGG
Found at i:52260053 original size:24 final size:23
Alignment explanation
Indices: 52260024--52260081 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
52260014 TAATTCTTTT
52260024 TATTTTTAGGTTTTATAATATTAA
1 TATTTTTAGGTTTTATAA-ATTAA
* ** *
52260048 TTTTTTTATTTTTTTTTAAATTAA
1 TATTTTTA-GGTTTTATAAATTAA
52260072 TATTTTTAGG
1 TATTTTTAGG
52260082 ATTAAAGGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (23 bp):
TATTTTTAGGTTTTATAAATTAA
Found at i:52260235 original size:92 final size:89
Alignment explanation
Indices: 52260109--52260317 Score: 249
Period size: 92 Copynumber: 2.3 Consensus size: 89
52260099 TGCTCAAATT
* * * *
52260109 TTTTCAAAAAAATCAATTAATCCCCT-CCTTTTTTTTGCACTCAATTGAGCACTTAAACTTTCAA
1 TTTTAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTCAA
* * *
52260173 AATTCATTAAAAAGGCCCTCAAAC
66 AATGCATTAAAAAGACCCTCAAAA
* * * * *
52260197 TTCTTAAAAAAAAAGCACTTAAGCCCCTGCTTTGTTTTTTTCACTCAATTGGGTACTTGAACTTT
1 TT-TT-AAAAAAAAGCAATTAAGCCCCTGCTTT-TTTTTTGCACTCAATTGAGCACTTAAACTTT
52260262 CAAAATGCATTAAAAAGACCCTCAAAA
63 CAAAATGCATTAAAAAGACCCTCAAAA
** *
52260289 TTTTTCAAAAAAGCAATTAAGTCCCTGCT
1 TTTTAAAAAAAAGCAATTAAGCCCCTGCT
52260318 CTTATTAAAG
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.02
89 2 0.02
90 39 0.39
91 5 0.05
92 53 0.52
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (89 bp):
TTTTAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTCAA
AATGCATTAAAAAGACCCTCAAAA
Found at i:52260367 original size:19 final size:18
Alignment explanation
Indices: 52260319--52260396 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 18
52260309 GTCCCTGCTC
52260319 TTATTAAAGATTATAAAAAA
1 TTATTAAA-ATT-TAAAAAA
*
52260339 --A-TAAATTTTAGAAAAA
1 TTATTAAAATTTA-AAAAA
52260355 TTATTAAAATTTAATAAAA
1 TTATTAAAATTTAA-AAAA
*
52260374 TT-TTAATATTTATTAAAAA
1 TTATTAAAATTTA--AAAAA
52260393 TTAT
1 TTAT
52260397 ATTTTTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.04
16 7 0.15
17 4 0.09
18 12 0.26
19 20 0.43
20 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATTAAAATTTAAAAAA
Found at i:52260384 original size:18 final size:19
Alignment explanation
Indices: 52260351--52260396 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
52260341 AAATTTTAGA
52260351 AAAATTATTAAAATTTAAT
1 AAAATTATTAAAATTTAAT
* *
52260370 AAAATT-TTAATATTTATT
1 AAAATTATTAAAATTTAAT
52260388 AAAAATTAT
1 -AAAATTAT
52260397 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 12 0.52
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATTATTAAAATTTAAT
Found at i:52260651 original size:19 final size:19
Alignment explanation
Indices: 52260627--52260699 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
52260617 AATCTTTAGG
*
52260627 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
52260646 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
52260665 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52260684 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
52260700 AGATATGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52260725 original size:22 final size:21
Alignment explanation
Indices: 52260640--52260725 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 21
52260630 ATGCAATCCT
*
52260640 AGATATGATATGCAATCTT--
1 AGATATGATATGTAATCTTAG
*
52260659 AGATATGATATATAATCTT--
1 AGATATGATATGTAATCTTAG
*
52260678 AGATATGATATGCAATCTTAG
1 AGATATGATATGTAATCTTAG
*
52260699 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TATGTAATCTTAG
52260722 AGAT
1 AGAT
52260726 TTAATTTGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
19 34 0.60
22 12 0.21
23 11 0.19
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (21 bp):
AGATATGATATGTAATCTTAG
Found at i:52262599 original size:19 final size:20
Alignment explanation
Indices: 52262577--52262626 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
52262567 TTTTAGGAAA
52262577 TTTTACAATTTTTTATATTT
1 TTTTACAATTTTTTATATTT
*
52262597 TTTTACGA-TTTTTATA-TT
1 TTTTACAATTTTTTATATTT
52262615 TTTTA-AATTTTT
1 TTTTACAATTTTT
52262627 AATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 8 0.30
20 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTACAATTTTTTATATTT
Found at i:52280452 original size:16 final size:16
Alignment explanation
Indices: 52280425--52280459 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52280415 GGGGCAGAAG
52280425 AGAAGTTTTTATTAACA
1 AGAAGTTTTTATTAA-A
52280442 AGAAG-TTTTATTAAA
1 AGAAGTTTTTATTAAA
52280457 AGA
1 AGA
52280460 CTTAGATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 9 0.50
17 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (16 bp):
AGAAGTTTTTATTAAA
Found at i:52297295 original size:19 final size:19
Alignment explanation
Indices: 52297251--52297307 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
52297241 ATTACAAAAA
52297251 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
52297270 TATAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
52297289 AAAAATTCAAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
52297307 A
1 A
52297308 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:52297630 original size:26 final size:25
Alignment explanation
Indices: 52297601--52297650 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
52297591 TCGATTTGAT
*
52297601 TCGACTCGACTCGAATATCATTTCAC
1 TCGACTCGACTCGAA-ATAATTTCAC
* *
52297627 TCGACTTGATTCGAAATAATTTCA
1 TCGACTCGACTCGAAATAATTTCA
52297651 AATTGAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (25 bp):
TCGACTCGACTCGAAATAATTTCAC
Found at i:52300665 original size:30 final size:30
Alignment explanation
Indices: 52300629--52300688 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
52300619 AAAGTTAGAC
52300629 TCGAATGAATATATTAGCTCGCCATACTTG
1 TCGAATGAATATATTAGCTCGCCATACTTG
52300659 TCGAATGAATATATTAGCTCGCCATACTTG
1 TCGAATGAATATATTAGCTCGCCATACTTG
52300689 ACGGATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (30 bp):
TCGAATGAATATATTAGCTCGCCATACTTG
Found at i:52302670 original size:39 final size:40
Alignment explanation
Indices: 52302627--52302725 Score: 119
Period size: 46 Copynumber: 2.4 Consensus size: 40
52302617 TCGAGTCTAT
*
52302627 AACATATGCAAGAG-CCTATTCTTGTAATTTCTAGTCCGC
1 AACATATGCAAGAGACCTATTCTTGTAATTTCGAGTCCGC
*
52302666 AACATATGCAAGAGCTTAGAACCTATTCTTGTATTTTCGAGTCCGC
1 AACATATGC-A-AG---AG-ACCTATTCTTGTAATTTCGAGTCCGC
52302712 AACATATGCAAGAG
1 AACATATGCAAGAG
52302726 TTTAGAACCT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
39 9 0.18
40 1 0.02
41 4 0.08
44 4 0.08
45 1 0.02
46 32 0.63
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
AACATATGCAAGAGACCTATTCTTGTAATTTCGAGTCCGC
Found at i:52302709 original size:46 final size:46
Alignment explanation
Indices: 52302641--52302807 Score: 244
Period size: 46 Copynumber: 3.6 Consensus size: 46
52302631 TATGCAAGAG
* *
52302641 CCTATTCTTGTAATTTCTAGTCCGCAACATATGCAAGAGCTTAGAA
1 CCTATTCTTGTATTTTCGAGTCCGCAACATATGCAAGAGCTTAGAA
*
52302687 CCTATTCTTGTATTTTCGAGTCCGCAACATATGCAAGAGTTTAGAA
1 CCTATTCTTGTATTTTCGAGTCCGCAACATATGCAAGAGCTTAGAA
* * * * **
52302733 CCTATTCATGTATTCTGGAGTTCGCAACATATGCAAGAGCTCGGAA
1 CCTATTCTTGTATTTTCGAGTCCGCAACATATGCAAGAGCTTAGAA
*
52302779 CCTATTCTTGTATTTTCGAGTCCACAACA
1 CCTATTCTTGTATTTTCGAGTCCGCAACA
52302808 CATGTAGGAA
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 106 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (46 bp):
CCTATTCTTGTATTTTCGAGTCCGCAACATATGCAAGAGCTTAGAA
Found at i:52309588 original size:21 final size:20
Alignment explanation
Indices: 52309564--52309602 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
52309554 TTTGGTCTAT
*
52309564 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTT-AAGGTTGG
52309585 GGTTTAAGGTTTAAGGTT
1 GGTTTAAGGTTTAAGGTT
52309603 AATATGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTAAGGTTGG
Found at i:52312703 original size:27 final size:27
Alignment explanation
Indices: 52312665--52313516 Score: 886
Period size: 27 Copynumber: 30.6 Consensus size: 27
52312655 ATTTGGTTAA
*
52312665 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
52312692 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52312719 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52312746 TTGCGTAACTTACGTAAATTAAGTTAATTAAATAAC
1 TTACATAACTTAC----A-T-A---AATTAAATAAC
*
52312782 TTACATAAATTA-ACTAAATTAAATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* *
52312809 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52312836 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52312863 TTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
1 TTACATAACTTAC----A-T-A---AATTAAATAAC
*
52312899 TTACATAAATTA-AGTAAATTAAATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* * *
52312926 TTAAATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52312953 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52312980 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52313007 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52313034 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* * *
52313061 TTGCATAACTTACGTAAATTAAGTTAA-
1 TTACATAACTTACATAAATTAA-ATAAC
* *
52313088 TTAAATAACTTACATAAATTAAGTTAA-
1 TTACATAACTTACATAAATTAA-ATAAC
* *
52313115 TTAAATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52313142 TTGCATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
52313169 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52313196 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52313223 TTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
1 TTACATAACTTAC----A-T-A---AATTAAATAAC
*
52313259 TTACATAAATTA-AGTAAATTAAATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* * *
52313286 TTAAATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52313313 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52313340 TTGCATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52313367 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52313394 TTACATAACTTACATAAATTAAGTAAA
1 TTACATAACTTACATAAATTAAATAAC
* * *
52313421 TTAAATAACTTACATAACTTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
* * *
52313448 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* * * * * *
52313475 TTAAATATCTTACATTACTTACATAGC
1 TTACATAACTTACATAAATTAAATAAC
*
52313502 TTACATTACTTACAT
1 TTACATAACTTACAT
52313517 GGGGCATACA
Statistics
Matches: 704, Mismatches: 89, Indels: 64
0.82 0.10 0.07
Matches are distributed among these distances:
26 2 0.00
27 620 0.88
28 5 0.01
30 3 0.00
31 9 0.01
32 3 0.00
33 3 0.00
36 59 0.08
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:52312808 original size:117 final size:114
Alignment explanation
Indices: 52312665--52313499 Score: 871
Period size: 117 Copynumber: 7.4 Consensus size: 114
52312655 ATTTGGTTAA
* * *
52312665 TTACATAACTTACAAAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACTT
1 TTACATAAATTAC-TAAATTAAATAACTTACATAACTTACATAAATTAAATAATTTACATAACTT
* * * *
52312730 ACATAAATTAAATATCTTGCGTAACTTACGTAAATTAAGTTAATTAAATAAC
65 ACATAAATTAAGTATCTTACATAACTTACATAAATTAA--TAATTAAATAAC
*
52312782 TTACATAAATTAACTAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACTT
1 TTACATAAATT-ACTAAATTAAATAACTTACATAACTTACATAAATTAAATAATTTACATAACTT
* * *
52312847 ACATAAATTAAATATCTTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
65 ACATAAATTAAGTATCTTACATAACTTACATAAATTAA--TAATTAAATAAC
* * *
52312899 TTACATAAATTAAGTAAATTAAATAACTTAAATAACTTACATAAATTAAGTAATTTACATAACTT
1 TTACATAAATT-ACTAAATTAAATAACTTACATAACTTACATAAATTAAATAATTTACATAACTT
*
52312964 ACATAAATTAAATATCTTACATAACTTACATAAATT-A-AA-T--AT--C
65 ACATAAATTAAGTATCTTACATAACTTACATAAATTAATAATTAAATAAC
* * * *
52313007 TTACATAACTTACATAAATTAAGTAATTTACATAACTTACATAAATTAAAT-ATCTTGCATAACT
1 TTACATAAATTAC-TAAATTAAATAACTTACATAACTTACATAAATTAAATAAT-TTACATAACT
* * *
52313071 TACGTAAATTAAGT-TAATTAAATAACTTACATAAATTAAGTTAATTAAATAAC
64 TACATAAATTAAGTAT-CTTACATAACTTACATAAATTAA--TAATTAAATAAC
* *
52313124 TTACATAAA-T--TAAA-T--AT--CTTGCATAACTTACATAAATTAAATAACTTACATAACTTA
1 TTACATAAATTACTAAATTAAATAACTTACATAACTTACATAAATTAAATAATTTACATAACTTA
* **
52313181 CATAAATTAAGTAAT-TTACATAACTTACATAAATTAAATATCTTGCATAAC
66 CATAAATTAAGT-ATCTTACATAACTTACATAAATT-AATA-ATTAAATAAC
* * * * * *
52313232 TTACGTAAATTAAGTTAATTAAATAACTTACATAAATTA-AGTAAATTAAATAACTTAAATAACT
1 TTACATAAATT-ACTAAATTAAATAACTTACATAACTTACA-TAAATTAAATAATTTACATAACT
52313296 TACATAAATTAAGTAAT-TTACATAACTTACATAAATT-A-AA-T--AT--C
64 TACATAAATTAAGT-ATCTTACATAACTTACATAAATTAATAATTAAATAAC
* * *
52313340 TTGCATAACTTACATAAATTAAATATCTTACATAACTTACATAAATTAAAT-ATCTTACATAACT
1 TTACATAAATTAC-TAAATTAAATAACTTACATAACTTACATAAATTAAATAAT-TTACATAACT
** * * *
52313404 TACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAACTTACATAAC
64 TACATAAATTAAGTATCTTACATAACTTACATAAATTA-ATAA-TTAAATAAC
* * *
52313457 TTACATAACTTACATAAATTAAATATCTTACATTACTTACATA
1 TTACATAAATTAC-TAAATTAAATAACTTACATAACTTACATA
52313500 GCTTACATTA
Statistics
Matches: 628, Mismatches: 49, Indels: 82
0.83 0.06 0.11
Matches are distributed among these distances:
107 9 0.01
108 245 0.39
109 6 0.01
110 7 0.01
111 2 0.00
112 8 0.01
113 9 0.01
114 1 0.00
115 7 0.01
116 3 0.00
117 329 0.52
118 2 0.00
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (114 bp):
TTACATAAATTACTAAATTAAATAACTTACATAACTTACATAAATTAAATAATTTACATAACTTA
CATAAATTAAGTATCTTACATAACTTACATAAATTAATAATTAAATAAC
Found at i:52313504 original size:18 final size:18
Alignment explanation
Indices: 52312665--52313516 Score: 592
Period size: 18 Copynumber: 47.3 Consensus size: 18
52312655 ATTTGGTTAA
* *
52312665 TTACATAACTTACAAAAA
1 TTACATAACTTACATAAC
*
52312683 TTAAATAACTTACATAAC
1 TTACATAACTTACATAAC
* *
52312701 TTACATAAATTA-AGTAAT
1 TTACATAACTTACA-TAAC
*
52312719 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* * * *
52312737 TTAAATATCTTGCGTAAC
1 TTACATAACTTACATAAC
* *
52312755 TTACGTAAATTA-AGTTAA-
1 TTACATAACTTACA--TAAC
* *
52312773 TTAAATAACTTACATAAA
1 TTACATAACTTACATAAC
* *
52312791 TTA-ACTAAATTAAATAAC
1 TTACA-TAACTTACATAAC
*
52312809 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
*
52312827 TTA-AGTAATTTACATAAC
1 TTACA-TAACTTACATAAC
* * *
52312845 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
* * *
52312863 TTGCATAACTTACGTAAA
1 TTACATAACTTACATAAC
*
52312881 TTA-AGTTAA-TTAAATAAC
1 TTACA--TAACTTACATAAC
* *
52312899 TTACATAAATTA-AGTAAA
1 TTACATAACTTACA-TAAC
* *
52312917 TTAAATAACTTAAATAAC
1 TTACATAACTTACATAAC
* *
52312935 TTACATAAATTA-AGTAAT
1 TTACATAACTTACA-TAAC
*
52312953 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* *
52312971 TTAAATATCTTACATAAC
1 TTACATAACTTACATAAC
* * *
52312989 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
*
52313007 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
*
52313025 TTA-AGTAATTTACATAAC
1 TTACA-TAACTTACATAAC
* * *
52313043 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
* * *
52313061 TTGCATAACTTACGTAAA
1 TTACATAACTTACATAAC
*
52313079 TTA-AGTTAA-TTAAATAAC
1 TTACA--TAACTTACATAAC
*
52313097 TTACATAAATTA-AGTTAA-
1 TTACATAACTTACA--TAAC
* *
52313115 TTAAATAACTTACATAAA
1 TTACATAACTTACATAAC
* * *
52313133 TTAAATATCTTGCATAAC
1 TTACATAACTTACATAAC
* *
52313151 TTACATAAATTAAATAAC
1 TTACATAACTTACATAAC
*
52313169 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
*
52313187 TTA-AGTAATTTACATAAC
1 TTACA-TAACTTACATAAC
* * *
52313205 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
* * *
52313223 TTGCATAACTTACGTAAA
1 TTACATAACTTACATAAC
*
52313241 TTA-AGTTAA-TTAAATAAC
1 TTACA--TAACTTACATAAC
* *
52313259 TTACATAAATTA-AGTAAA
1 TTACATAACTTACA-TAAC
* *
52313277 TTAAATAACTTAAATAAC
1 TTACATAACTTACATAAC
* *
52313295 TTACATAAATTA-AGTAAT
1 TTACATAACTTACA-TAAC
*
52313313 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* * *
52313331 TTAAATATCTTGCATAAC
1 TTACATAACTTACATAAC
* * *
52313349 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
*
52313367 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* *
52313385 TTAAATATCTTACATAAC
1 TTACATAACTTACATAAC
* *
52313403 TTACATAAATTA-AGTAAA
1 TTACATAACTTACA-TAAC
*
52313421 TTAAATAACTTACATAAC
1 TTACATAACTTACATAAC
52313439 TTACATAACTTACATAAC
1 TTACATAACTTACATAAC
*
52313457 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* * *
52313475 TTAAATATCTTACATTAC
1 TTACATAACTTACATAAC
* *
52313493 TTACATAGCTTACATTAC
1 TTACATAACTTACATAAC
52313511 TTACAT
1 TTACAT
52313517 GGGGCATACA
Statistics
Matches: 646, Mismatches: 148, Indels: 80
0.74 0.17 0.09
Matches are distributed among these distances:
17 29 0.04
18 587 0.91
19 30 0.05
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (18 bp):
TTACATAACTTACATAAC
Found at i:52319036 original size:21 final size:21
Alignment explanation
Indices: 52319011--52319079 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
52319001 CAGCAACTTA
*
52319011 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
52319032 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* *
52319053 AAGCAGATGCCGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
52319074 AAGCAG
1 AAGCAG
52319080 CGAGAGAAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:52319081 original size:12 final size:12
Alignment explanation
Indices: 52319064--52319091 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52319054 AGCAGATGCC
52319064 GCAGCGAGAGAA
1 GCAGCGAGAGAA
52319076 GCAGCGAGAGAA
1 GCAGCGAGAGAA
52319088 GCAG
1 GCAG
52319092 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:52319669 original size:41 final size:42
Alignment explanation
Indices: 52319544--52319831 Score: 323
Period size: 43 Copynumber: 6.8 Consensus size: 42
52319534 TTTAGTGGTT
**** * *
52319544 TCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTATAGAACATTA
1 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGA
* * *
52319586 -CTTTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGA
1 TC-TTTAGCGGCGTTTT-TTTCTAAGCGCCGCTAAAGAACATGA
* * * *
52319629 GCTTTAGCGGCGTTTATTT-TAAGTGCCGCTAAAAAACATGA
1 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGA
*
52319670 TCTTTAGCGCCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGA
1 TCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAGAACATGA
*
52319713 TCTTTAGGGGC-TTTTTTT-TAAGCGCCGCTAAAGAACATGA
1 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGA
* *
52319753 TCTTTAGGGGCGTTTTTTTCTAAGCGCCGCTAAAGAATATGA
1 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGA
* * *
52319795 GCTTTAGCGGCGTTTCTTTATGTAAGCGCCGCAAAAG
1 TCTTTAGCGGCGTTT-TTT-TCTAAGCGCCGCTAAAG
52319832 TTAGCGACGT
Statistics
Matches: 212, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
40 33 0.16
41 44 0.21
42 55 0.26
43 64 0.30
44 16 0.08
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGA
Found at i:52324685 original size:23 final size:23
Alignment explanation
Indices: 52324643--52324686 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52324633 AACATGATTA
*
52324643 AAGTTAACTAAATTTGATTAAGT
1 AAGTTAACTAAATTTAATTAAGT
52324666 AAGTTAACTAAGA-TTAATTAA
1 AAGTTAACTAA-ATTTAATTAA
52324687 TAAAACTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (23 bp):
AAGTTAACTAAATTTAATTAAGT
Found at i:52326800 original size:32 final size:32
Alignment explanation
Indices: 52326422--52326798 Score: 421
Period size: 32 Copynumber: 11.8 Consensus size: 32
52326412 ATATACGTAT
* *
52326422 ATATATTGTCGAATTGAATTGTATATGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
* *
52326454 TTATATTGCCAAATTGAATTGTATAGGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** * *
52326486 ACCTATAGCCGAATTGAATTGTATATGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
* * *
52326518 TTGTATTGCCGAATTGAATTGTATAGGTATAT
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** *
52326550 ACCTATTGCCGAATTAAATTGTATAGGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** * *
52326582 AGCTATTGCCGAATTGAATTGTATATGCATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
*
52326614 TTATATTGCCGAATTGAATTGTATAGGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** * * *
52326646 ACCTATTGCTGAATTGAATTATATATGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
* *
52326678 TTATATTGCCGAATTGAATTGCATAGGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** * *
52326710 ACCTATTGTCGAATTGAATTGCATAGGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
** * * *
52326742 ACCTATTGTCGAATTAAATTGTATATGTATAC
1 ATATATTGCCGAATTGAATTGTATAGGTATAC
* *
52326774 TTATATTGCCGAATTGATTTGTATA
1 ATATATTGCCGAATTGAATTGTATA
52326799 TGCATTTATA
Statistics
Matches: 289, Mismatches: 56, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 289 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
ATATATTGCCGAATTGAATTGTATAGGTATAC
Found at i:52326813 original size:96 final size:97
Alignment explanation
Indices: 52326421--52326814 Score: 472
Period size: 96 Copynumber: 4.1 Consensus size: 97
52326411 GATATACGTA
* * *** * *
52326421 TATATATTGTCGAATTGAATTGTATATGTATACTTATATTGCCAAATTGAATTGTATAGGTATAC
1 TATATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTAAATTGTATAGGTATAC
** * *
52326486 ACCTATAGCCGAATTGAATTGTATATGTATAC
66 ATATATTGCCGAATTGAATTGTATATGCATAC
* *
52326518 T-TGTATTGCCGAATTGAATTGTATAGGTATATACCTATTGCCGAATTAAATTGTATAGGTATAC
1 TATATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTAAATTGTATAGGTATAC
**
52326582 AGCTATTGCCGAATTGAATTGTATATGCATAC
66 ATATATTGCCGAATTGAATTGTATATGCATAC
* * * *
52326614 T-TATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCTGAATTGAATTATATATGTATAC
1 TATATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTAAATTGTATAGGTATAC
* * * *
52326678 TTATATTGCCGAATTGAATTGCATAGGTATAC
66 ATATATTGCCGAATTGAATTGTATATGCATAC
** * * * *
52326710 -ACCTATTGTCGAATTGAATTGCATAGGTATACACCTATTGTCGAATTAAATTGTATATGTATAC
1 TATATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTAAATTGTATAGGTATAC
* * *
52326774 TTATATTGCCGAATTGATTTGTATATGCAT-T
66 ATATATTGCCGAATTGAATTGTATATGCATAC
52326805 TATATATTGC
1 TATATATTGC
52326815 TGATTTAATT
Statistics
Matches: 255, Mismatches: 40, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
96 254 1.00
97 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (97 bp):
TATATATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTAAATTGTATAGGTATAC
ATATATTGCCGAATTGAATTGTATATGCATAC
Found at i:52329476 original size:19 final size:19
Alignment explanation
Indices: 52329452--52329495 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
52329442 TAAAAGTAAC
52329452 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
52329471 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
52329490 ACAACA
1 ACAACA
52329496 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:52330134 original size:237 final size:235
Alignment explanation
Indices: 52329721--52330156 Score: 838
Period size: 237 Copynumber: 1.8 Consensus size: 235
52329711 AAAAACCATT
52329721 ATAATATACAGCAGCATAAATTAAACAAAAAAAATGTTAAACTACATTTATAAAAAATGGTTGAA
1 ATAATATACAGCAGCATAAATTAAACAAAAAAAATGTTAAACTACATTTATAAAAAATGGTTGAA
52329786 TTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAATAACTAAATTAGAAAGAACAA
66 TTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAATAACTAAATTAGAAAGAACAA
52329851 CAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAATAAT
131 CAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAATAAT
52329916 TGACATTCTTTTCTCCTCAATCGATTAAATTAAAAATTAA
196 TGACATTCTTTTCTCCTCAATCGATTAAATTAAAAATTAA
52329956 ATAATATACAGCAGCATAAATTAAACAAAAAAAATTATGTTAAACTACATTTATAAAAAATGGTT
1 ATAATATACAGCAGCATAAATTAAAC-AAAAAAA--ATGTTAAACTACATTTATAAAAAATGGTT
52330021 GAATTGTTTTATTTTTATAATTATAAG-TTTTGAATATATAAAATAATAACTAAATTAGAAAGAA
63 GAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAATAACTAAATTAGAAAGAA
52330085 CAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAAT
128 CAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAAT
52330150 AATTGAC
193 AATTGAC
52330157 TGCATATTCC
Statistics
Matches: 198, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
235 26 0.13
236 7 0.04
237 109 0.55
238 56 0.28
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (235 bp):
ATAATATACAGCAGCATAAATTAAACAAAAAAAATGTTAAACTACATTTATAAAAAATGGTTGAA
TTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAATAACTAAATTAGAAAGAACAA
CAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAATAAT
TGACATTCTTTTCTCCTCAATCGATTAAATTAAAAATTAA
Done.