Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 24 of 32
Found at i:12055286 original size:133 final size:132
Alignment explanation
Indices: 12055045--12055290 Score: 296
Period size: 133 Copynumber: 1.9 Consensus size: 132
12055035 GTATGTAGAG
* * * * * *
12055045 AAGCTTTAGAGTACAGGCTTAGTGTTGTTGTGATCGAGGTAGATAGGCTATATTTATGGGTAAAG
1 AAGCTTTAGAGGACAGGCTTAGTGTGGTTGTGATCGAAGTAGATAGGATATATTTATAGGCAAAG
* *
12055110 TAGAGAGTTAACGTTACAAAATATCAATATAAAATCAGTAAAAAATCAAAAGAAATGAAAAAACT
66 TAGAGAATTAACGTTACAAAATATCAATATAAAATCAG-CAAAAATCAAAAGAAATGAAAAAACT
12055175 GAT
130 GAT
** * * * *
12055178 AAGCTTTAGAGGAGTGGCTTGGTGTGGTTGTGA-CTGAAGTAGGTAGGATGTATTTATAGGCAGA
1 AAGCTTTAGAGGACAGGCTTAGTGTGGTTGTGATC-GAAGTAGATAGGATATATTTATAGGCAAA
* * * * *
12055242 GTAGAGAATTAATGTTATAGAATATCAGTATAAAATTAGCAAAAATCAA
65 GTAGAGAATTAACGTTACAAAATATCAATATAAAATCAGCAAAAATCAA
12055291 GATGCTAAGT
Statistics
Matches: 93, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
132 10 0.11
133 83 0.89
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (132 bp):
AAGCTTTAGAGGACAGGCTTAGTGTGGTTGTGATCGAAGTAGATAGGATATATTTATAGGCAAAG
TAGAGAATTAACGTTACAAAATATCAATATAAAATCAGCAAAAATCAAAAGAAATGAAAAAACTG
AT
Found at i:12055468 original size:81 final size:81
Alignment explanation
Indices: 12055328--12055487 Score: 241
Period size: 81 Copynumber: 2.0 Consensus size: 81
12055318 TTAACATTAT
* * *
12055328 AGAATATCAGCATAAAATCAAAGAAAATCAAGATGTTGAGAAGCTTTCAAGGAGTGGCTTAGTGT
1 AGAAAATCAGCAAAAAATCAAAGAAAATCAAGATGCTGAGAAGCTTTCAAGGAGTGGCTTAGTGT
12055393 GGTTATGACTGAGGAC
66 GGTTATGACTGAGGAC
* *
12055409 AGAAAATCAGCAAAAAATCAAAGAAAATCACGATGCTGAGAAGCTTT-AGAGGAGTGGCTTGGTG
1 AGAAAATCAGCAAAAAATCAAAGAAAATCAAGATGCTGAGAAGCTTTCA-AGGAGTGGCTTAGTG
* *
12055473 TGGTTGTGATTGAGG
65 TGGTTATGACTGAGG
12055488 TAGGTAGGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 70 0.99
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.24
Consensus pattern (81 bp):
AGAAAATCAGCAAAAAATCAAAGAAAATCAAGATGCTGAGAAGCTTTCAAGGAGTGGCTTAGTGT
GGTTATGACTGAGGAC
Found at i:12057003 original size:21 final size:20
Alignment explanation
Indices: 12056957--12057009 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
12056947 TTTTAATTTT
*
12056957 TAACATAAACTATTATTCCA
1 TAACATAAACTATTAATCCA
12056977 TAAACATAAA-TATATAATCACA
1 T-AACATAAACTAT-TAATC-CA
*
12056999 TAACAGAAACT
1 TAACATAAACT
12057010 TCAAAACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (20 bp):
TAACATAAACTATTAATCCA
Found at i:12061478 original size:14 final size:15
Alignment explanation
Indices: 12061445--12061483 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12061435 ATATTATTCT
*
12061445 ATTATATGTATACAA
1 ATTATATATATACAA
*
12061460 ATTATATATAT-CTA
1 ATTATATATATACAA
12061474 ATTATATATA
1 ATTATATATA
12061484 AACTTGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTATATATATACAA
Found at i:12073641 original size:18 final size:18
Alignment explanation
Indices: 12073607--12073640 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12073597 CAGGTATTAT
*
12073607 TTTTTTCTTTCTATTTTG
1 TTTTTTATTTCTATTTTG
12073625 TTTTTTATTT-TATTTT
1 TTTTTTATTTCTATTTT
12073641 TATCATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTATTTCTATTTTG
Found at i:12074832 original size:10 final size:10
Alignment explanation
Indices: 12074817--12074841 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12074807 GAGCCAAGAC
12074817 AAAAAAGAAA
1 AAAAAAGAAA
12074827 AAAAAAGAAA
1 AAAAAAGAAA
12074837 AAAAA
1 AAAAA
12074842 TTTCAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:12083522 original size:73 final size:73
Alignment explanation
Indices: 12083384--12083522 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
12083374 CAAGAGACAA
* * * * * * *
12083384 TGTTAGTCAACTAAGAGCTTATTGTCAAAAATTGGGTTCAGAGATAGAAACGACTTAATCGACTA
1 TGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCAACTA
12083449 AGAAGTTT
66 AGAAGTTT
* * * *
12083457 TGTTAGTCGACTAAGAGCCTATTGCCAGAAACTGAGTTCAGAAACA-AAGATGACTTAATTAACT
1 TGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGAGTTCAGAAACAGAA-ACGACTTAATCAACT
12083521 AA
65 AA
12083523 ATAGCAATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
72 2 0.04
73 52 0.96
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (73 bp):
TGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCAACTA
AGAAGTTT
Found at i:12089419 original size:14 final size:14
Alignment explanation
Indices: 12089400--12089426 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12089390 ATATTTTCTG
12089400 AATTAAAATTTATC
1 AATTAAAATTTATC
12089414 AATTAAAATTTAT
1 AATTAAAATTTAT
12089427 GTATTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAAAATTTATC
Found at i:12090135 original size:14 final size:14
Alignment explanation
Indices: 12090109--12090162 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
12090099 GTATATGAAC
12090109 AAATAGAAT-AAAAT
1 AAATA-AATAAAAAT
12090123 AAATAAATAAAAAT
1 AAATAAATAAAAAT
**
12090137 -AATAATATAAATTT
1 AAATAA-ATAAAAAT
12090151 AAA-AAATAAAAA
1 AAATAAATAAAAA
12090163 AACTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 13 0.39
14 18 0.55
15 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:12090158 original size:18 final size:17
Alignment explanation
Indices: 12090118--12090172 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
12090108 CAAATAGAAT
*
12090118 AAAATAAATAAA-TAAA
1 AAAATAAATAAATTTAA
12090134 AATAATAATATAAATTTAA
1 AA-AATAA-ATAAATTTAA
*
12090153 AAAATAAAAAAACTTTAA
1 AAAATAAATAAA-TTTAA
12090171 AA
1 AA
12090173 TTGAATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 9 0.27
18 17 0.52
19 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAATAAATTTAA
Found at i:12091465 original size:37 final size:37
Alignment explanation
Indices: 12091396--12091467 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
12091386 GGTTAGCAAT
* ** *
12091396 AAAACCATAATTAACCCTAGTGGTATATGTCAAAATC
1 AAAACCACAATTAACCCTAGTGACATAGGTCAAAATC
**
12091433 AAAACCACAATTAATTCTAGTGACATAGGTCAAAA
1 AAAACCACAATTAACCCTAGTGACATAGGTCAAAA
12091468 GTATATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (37 bp):
AAAACCACAATTAACCCTAGTGACATAGGTCAAAATC
Found at i:12091844 original size:26 final size:25
Alignment explanation
Indices: 12091786--12091844 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
12091776 TTGCATAAAA
12091786 ATCATATTCCAAAACCAAAATCGAG
1 ATCATATTCCAAAACCAAAATCGAG
** *
12091811 ATTGTATTCCAAAGGCCAAAA-CAGAG
1 ATCATATTCCAAA-ACCAAAATC-GAG
12091837 ATCATATT
1 ATCATATT
12091845 TATTTATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (25 bp):
ATCATATTCCAAAACCAAAATCGAG
Found at i:12094289 original size:108 final size:108
Alignment explanation
Indices: 12094176--12094385 Score: 339
Period size: 108 Copynumber: 1.9 Consensus size: 108
12094166 TATAAGAAAT
12094176 TTTGAGTAAATTTAAATAAAAGATAAATTAGGTAAGAGTTGAATAATTTCAAAAGAATGTGTACT
1 TTTGAGTAAATTTAAATAAAAGATAAATTAGGTAAGAGTTGAATAATTTCAAAAGAATGTGTACT
*
12094241 TGTAAATTGTGAAAGTTTTAACTAAATCAACATATTTTGTTAA
66 TGTAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGTTAA
* * * * *
12094284 TTTGAGTAAATTTAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTTAAAAGAATTTGTATT
1 TTTGAGTAAATTTAAATAAAAGATAAATTAGGTAAGAGTTGAATAATTTCAAAAGAATGTGTACT
* * *
12094349 TGTAAATTGTGAAAGTTGTAATTAAATTAATATATTT
66 TGTAAATTGTGAAAGTTGTAACTAAATCAACATATTT
12094386 AGTCATTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 93 1.00
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAGATAAATTAGGTAAGAGTTGAATAATTTCAAAAGAATGTGTACT
TGTAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGTTAA
Found at i:12110101 original size:27 final size:27
Alignment explanation
Indices: 12110054--12110275 Score: 169
Period size: 27 Copynumber: 8.1 Consensus size: 27
12110044 TCATAATGTA
* * *
12110054 TAACAATTAAAATTTTCAATACGATGTG
1 TAACAACT-AAATTTTCAATATGACGTG
* *
12110082 TAACAACTAAATTTTCAATATGACATA
1 TAACAACTAAATTTTCAATATGACGTG
* * *
12110109 TAACAACTATATTTTTTAACAT-AGCGTG
1 TAACAACTA-AATTTTCAATATGA-CGTG
* * *
12110137 TAACAATTAAATCTTCAATATGACATG
1 TAACAACTAAATTTTCAATATGACGTG
* * * *
12110164 TAATAACTAAATCTTCAACATGACGTA
1 TAACAACTAAATTTTCAATATGACGTG
* * * *
12110191 TAACAATTGCATTTTTCAATGTGACGTG
1 TAACAACT-AAATTTTCAATATGACGTG
*
12110219 TAACAACTAAATTTTCAACT-TGACGTA
1 TAACAACTAAATTTTCAA-TATGACGTG
* * * *
12110246 TAATAACTACATTTTCAACATGATGTG
1 TAACAACTAAATTTTCAATATGACGTG
12110273 TAA
1 TAA
12110276 TAATTATATT
Statistics
Matches: 150, Mismatches: 38, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
27 102 0.68
28 48 0.32
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (27 bp):
TAACAACTAAATTTTCAATATGACGTG
Found at i:12110172 original size:82 final size:82
Alignment explanation
Indices: 12110054--12110268 Score: 236
Period size: 82 Copynumber: 2.6 Consensus size: 82
12110044 TCATAATGTA
* * * * *
12110054 TAACAATTAAAATTTTCAATACGATGTGTAACAACTAAATTTTCAATATGACATATAACAACTAT
1 TAACAATT-AAATTTTCAATATGACGTGTAATAACTAAATTTTCAACATGACATATAACAACTAC
*
12110119 ATTTTTTAACAT-AGCGTG
65 ATTTTTCAACATGA-CGTG
* * * * * *
12110137 TAACAATTAAATCTTCAATATGACATGTAATAACTAAATCTTCAACATGACGTATAACAATTGCA
1 TAACAATTAAATTTTCAATATGACGTGTAATAACTAAATTTTCAACATGACATATAACAACTACA
**
12110202 TTTTTCAATGTGACGTG
66 TTTTTCAACATGACGTG
* * *
12110219 TAACAACTAAATTTTCAACT-TGACGTATAATAACTACATTTTCAACATGA
1 TAACAATTAAATTTTCAA-TATGACGTGTAATAACTAAATTTTCAACATGA
12110269 TGTGTAATAA
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
82 100 0.91
83 10 0.09
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (82 bp):
TAACAATTAAATTTTCAATATGACGTGTAATAACTAAATTTTCAACATGACATATAACAACTACA
TTTTTCAACATGACGTG
Found at i:12110209 original size:55 final size:54
Alignment explanation
Indices: 12110092--12110303 Score: 178
Period size: 55 Copynumber: 3.9 Consensus size: 54
12110082 TAACAACTAA
* * * * *
12110092 ATTTTCAATATGACATATAACAACTATATTTTTTAACAT-AGCGTGTAACAATTAA
1 ATTTTCAATATGACATGTAACAACTATAATTTTCAACATGA-CGTATAACAATT-C
* * *
12110147 ATCTTCAATATGACATGTAATAACTA-AATCTTCAACATGACGTATAACAATTGC
1 ATTTTCAATATGACATGTAACAACTATAATTTTCAACATGACGTATAACAATT-C
* * * * *
12110201 ATTTTTCAATGTGACGTGTAACAACTA-AATTTTCAACTTGACGTATAATAACTAC
1 A-TTTTCAATATGACATGTAACAACTATAATTTTCAACATGACGTATAACAA-TTC
* ** * * * *
12110256 ATTTTCAACATGATGTGTAATAATTATATTTTTGAACATGACGTATAA
1 ATTTTCAATATGACATGTAACAACTATAATTTTCAACATGACGTATAA
12110304 TACTCCATTT
Statistics
Matches: 128, Mismatches: 25, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
54 41 0.32
55 86 0.67
56 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (54 bp):
ATTTTCAATATGACATGTAACAACTATAATTTTCAACATGACGTATAACAATTC
Found at i:12110276 original size:27 final size:27
Alignment explanation
Indices: 12110086--12110314 Score: 129
Period size: 27 Copynumber: 8.4 Consensus size: 27
12110076 GATGTGTAAC
* * * *
12110086 AACTAAATTTTCAATATGACATATAAC
1 AACTACATTTTCAACATGACGTATAAT
* * * *
12110113 AACTATATTTTTTAACAT-AGCGTGTAAC
1 AACTACA-TTTTCAACATGA-CGTATAAT
* * * * * *
12110141 AATTAAATCTTCAATATGACATGTAAT
1 AACTACATTTTCAACATGACGTATAAT
* * *
12110168 AACTAAATCTTCAACATGACGTATAAC
1 AACTACATTTTCAACATGACGTATAAT
* * ** * *
12110195 AATTGCATTTTTCAATGTGACGTGTAAC
1 AACTACA-TTTTCAACATGACGTATAAT
* *
12110223 AACTAAATTTTCAACTTGACGTATAAT
1 AACTACATTTTCAACATGACGTATAAT
* *
12110250 AACTACATTTTCAACATGATGTGTAAT
1 AACTACATTTTCAACATGACGTATAAT
* * *
12110277 AATTATATTTTTGAACATGACGTATAAT
1 AACTACA-TTTTCAACATGACGTATAAT
*
12110305 -ACTCCATTTT
1 AACTACATTTT
12110315 TTTGAAACTG
Statistics
Matches: 154, Mismatches: 43, Indels: 11
0.74 0.21 0.05
Matches are distributed among these distances:
26 4 0.03
27 93 0.60
28 57 0.37
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (27 bp):
AACTACATTTTCAACATGACGTATAAT
Found at i:12110298 original size:82 final size:82
Alignment explanation
Indices: 12110086--12110299 Score: 225
Period size: 82 Copynumber: 2.6 Consensus size: 82
12110076 GATGTGTAAC
* * * * * *
12110086 AACTAAATTTTCAATATGACATATAACAACTATATTTTTTAACAT-AGCGTGTAACAATTAAATC
1 AACTAAATCTTCAACATGACGTATAACAATTATATTTTTCAACATGA-CGTGTAACAACTAAATC
*
12110150 TTCAATATGACATGTAAT
65 TTCAATATGACATATAAT
** ** *
12110168 AACTAAATCTTCAACATGACGTATAACAATTGCATTTTTCAATGTGACGTGTAACAACTAAATTT
1 AACTAAATCTTCAACATGACGTATAACAATTATATTTTTCAACATGACGTGTAACAACTAAATCT
*
12110233 TCAACT-TGACGTATAAT
66 TCAA-TATGACATATAAT
* * * * * *
12110250 AACTACATTTTCAACATGATGTGTAATAATTATATTTTTGAACATGACGT
1 AACTAAATCTTCAACATGACGTATAACAATTATATTTTTCAACATGACGT
12110300 ATAATACTCC
Statistics
Matches: 107, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
82 105 0.98
83 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (82 bp):
AACTAAATCTTCAACATGACGTATAACAATTATATTTTTCAACATGACGTGTAACAACTAAATCT
TCAATATGACATATAAT
Found at i:12110304 original size:55 final size:54
Alignment explanation
Indices: 12110054--12110314 Score: 166
Period size: 55 Copynumber: 4.8 Consensus size: 54
12110044 TCATAATGTA
* * * * * * * * * *
12110054 TAACAATTAAAATTTTCAATACGATGTGTAACAACTAAATTTTCAATATGACATA
1 TAACAACT-AAATTTTCAACATGACGTATAATAACTACATTTTCAACATGACGTG
* * * * * * * * *
12110109 TAACAACTATATTTTTTAACAT-AGCGTGTAACAATTAAATCTTCAATATGACATG
1 TAACAACTA-AATTTTCAACATGA-CGTATAATAACTACATTTTCAACATGACGTG
* * * * * **
12110164 TAATAACTAAATCTTCAACATGACGTATAACAATTGCATTTTTCAATGTGACGTG
1 TAACAACTAAATTTTCAACATGACGTATAATAACTACA-TTTTCAACATGACGTG
* *
12110219 TAACAACTAAATTTTCAACTTGACGTATAATAACTACATTTTCAACATGATGTG
1 TAACAACTAAATTTTCAACATGACGTATAATAACTACATTTTCAACATGACGTG
* * * * *
12110273 TAATAATTATATTTTTGAACATGACGTATAAT-ACTCCATTTT
1 TAACAACTA-AATTTTCAACATGACGTATAATAACTACATTTT
12110315 TTTGAAACTG
Statistics
Matches: 167, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
54 52 0.31
55 115 0.69
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (54 bp):
TAACAACTAAATTTTCAACATGACGTATAATAACTACATTTTCAACATGACGTG
Found at i:12111373 original size:18 final size:18
Alignment explanation
Indices: 12111352--12111409 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
12111342 AATTGCTACT
12111352 TTCCATTTATTGGTATTC
1 TTCCATTTATTGGTATTC
* * *
12111370 TTCC-TGCTAATTGCTACT-
1 TTCCAT--TTATTGGTATTC
12111388 TTCCATTTATTGGTATTC
1 TTCCATTTATTGGTATTC
12111406 TTCC
1 TTCC
12111410 TGCTAATTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
17 9 0.30
18 12 0.40
19 9 0.30
ACGTcount: A:0.16, C:0.22, G:0.10, T:0.52
Consensus pattern (18 bp):
TTCCATTTATTGGTATTC
Found at i:12111388 original size:36 final size:36
Alignment explanation
Indices: 12111341--12111420 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
12111331 TTGCTAATTT
12111341 TAATTGCTACTTTCCATTTATTGGTATTCTTCCTGC
1 TAATTGCTACTTTCCATTTATTGGTATTCTTCCTGC
12111377 TAATTGCTACTTTCCATTTATTGGTATTCTTCCTGC
1 TAATTGCTACTTTCCATTTATTGGTATTCTTCCTGC
12111413 TAATTGCT
1 TAATTGCT
12111421 GCTATGAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.50
Consensus pattern (36 bp):
TAATTGCTACTTTCCATTTATTGGTATTCTTCCTGC
Found at i:12112807 original size:17 final size:17
Alignment explanation
Indices: 12112785--12112817 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12112775 TCTCAATGTA
12112785 TCTCTTAGTTATACCCT
1 TCTCTTAGTTATACCCT
12112802 TCTCTTAGTTATACCC
1 TCTCTTAGTTATACCC
12112818 CAGATCATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.45
Consensus pattern (17 bp):
TCTCTTAGTTATACCCT
Found at i:12139929 original size:32 final size:33
Alignment explanation
Indices: 12139893--12139954 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
12139883 ATAACATGAC
12139893 ATGCCACGTGACACCAACATAATGA-TTAGATA
1 ATGCCACGTGACACCAACATAATGACTTAGATA
* * *
12139925 ATGCCACGTGGCACTAATATAATGACTTAG
1 ATGCCACGTGACACCAACATAATGACTTAG
12139955 CAATACTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (33 bp):
ATGCCACGTGACACCAACATAATGACTTAGATA
Found at i:12141502 original size:19 final size:19
Alignment explanation
Indices: 12141457--12141503 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12141447 CTAACACTTT
* *
12141457 AGCATGTTAGTGCCACATC
1 AGCATATTAATGCCACATC
*
12141476 ATCATATTAATGCCACAT-
1 AGCATATTAATGCCACATC
12141494 AGCATTATTA
1 AGCA-TATTA
12141504 TGTCATCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (19 bp):
AGCATATTAATGCCACATC
Found at i:12145503 original size:15 final size:15
Alignment explanation
Indices: 12145483--12145520 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
12145473 TTTACAATGC
12145483 AATGTGATTACAGGT
1 AATGTGATTACAGGT
12145498 AATGTGATTACAGGT
1 AATGTGATTACAGGT
*
12145513 AATATGAT
1 AATGTGAT
12145521 AGCAAGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (15 bp):
AATGTGATTACAGGT
Found at i:12147007 original size:16 final size:16
Alignment explanation
Indices: 12146988--12147037 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
12146978 TTTTTTATTA
12146988 TTATTTATTATAATCT
1 TTATTTATTATAATCT
* * *
12147004 TTATATAATATCATCT
1 TTATTTATTATAATCT
*
12147020 TTTTATTATTATAATCT
1 TTAT-TTATTATAATCT
12147037 T
1 T
12147038 ATATATTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTATTATAATCT
Found at i:12147065 original size:30 final size:29
Alignment explanation
Indices: 12146973--12147066 Score: 73
Period size: 30 Copynumber: 3.0 Consensus size: 29
12146963 TTTAATATAT
*
12146973 TTATAT-TTTTTATTATTATTTATTATAATC
1 TTATATATTTTTATTTTTATTT-TT-TAATC
** * *
12147003 TTTATATAATATCATCTTTTTATTATTATAATC
1 -TTATAT-AT-TTTTATTTTTATT-TTTTAATC
12147036 TTATATATTTTTATTTTTATTTCTTTAATC
1 TTATATATTTTTATTTTTATTT-TTTAATC
12147066 T
1 T
12147067 AATTTTTTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
29 1 0.02
30 17 0.35
31 8 0.16
32 6 0.12
33 6 0.12
34 10 0.20
35 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATATATTTTTATTTTTATTTTTTAATC
Found at i:12147102 original size:30 final size:31
Alignment explanation
Indices: 12147059--12147182 Score: 99
Period size: 30 Copynumber: 4.2 Consensus size: 31
12147049 TTTTTATTTC
* *
12147059 TTTAATCTAATTTT-TTATGTTATATATTTAT
1 TTTAAT-TTATTTTCTTATATTATATATTTAT
*
12147090 TTTAATTTATTTTACTTATATTATATA--AAT
1 TTTAATTTATTTT-CTTATATTATATATTTAT
12147120 TTT-A---ATTTT-TTATATT-T-TATTTAT
1 TTTAATTTATTTTCTTATATTATATATTTAT
12147144 TTTAATTT-TTGATTCTTATATTATATATTTTAT
1 TTTAATTTATT--TTCTTATATTATATA-TTTAT
12147177 TTTAAT
1 TTTAAT
12147183 ATTTTTATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
22 2 0.03
23 1 0.01
24 12 0.16
25 1 0.01
26 5 0.07
27 2 0.03
29 3 0.04
30 18 0.24
31 7 0.09
32 13 0.17
33 11 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTAATTTATTTTCTTATATTATATATTTAT
Found at i:12147132 original size:24 final size:24
Alignment explanation
Indices: 12147105--12147153 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12147095 TTTATTTTAC
12147105 TTATATTATATAAATTTTAATTTT
1 TTATATTATATAAATTTTAATTTT
* **
12147129 TTATATTTTATTTATTTTAATTTT
1 TTATATTATATAAATTTTAATTTT
12147153 T
1 T
12147154 GATTCTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATTATATAAATTTTAATTTT
Found at i:12147162 original size:54 final size:56
Alignment explanation
Indices: 12147066--12147170 Score: 155
Period size: 54 Copynumber: 1.9 Consensus size: 56
12147056 TTCTTTAATC
*
12147066 TAATTTTTTATGTTATATATTTATTTTAATTTATTTTACTTATATTATATAAATTT
1 TAATTTTTTATATTATATATTTATTTTAATTTATTTTACTTATATTATATAAATTT
12147122 TAATTTTTTATATT-T-TATTTATTTTAATTT-TTGATT-CTTATATTATATA
1 TAATTTTTTATATTATATATTTATTTTAATTTATT--TTACTTATATTATATA
12147171 TTTTATTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
53 2 0.04
54 28 0.61
55 3 0.07
56 13 0.28
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (56 bp):
TAATTTTTTATATTATATATTTATTTTAATTTATTTTACTTATATTATATAAATTT
Found at i:12147167 original size:24 final size:24
Alignment explanation
Indices: 12147118--12147167 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12147108 TATTATATAA
* *
12147118 ATTTTAATTTTTTATATTTTATTT
1 ATTTTAATTTTTGATATCTTATTT
12147142 ATTTTAATTTTTGAT-TCTTATATT
1 ATTTTAATTTTTGATATCTTAT-TT
12147166 AT
1 AT
12147168 ATATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTAATTTTTGATATCTTATTT
Found at i:12147188 original size:14 final size:14
Alignment explanation
Indices: 12147040--12147196 Score: 65
Period size: 14 Copynumber: 11.1 Consensus size: 14
12147030 ATAATCTTAT
*
12147040 ATATTTTTATTTTT
1 ATATTTTTATTTTA
* *
12147054 AT-TTCTTTAATCTA
1 ATATT-TTTATTTTA
*
12147068 AT-TTTTTATGTT-
1 ATATTTTTATTTTA
*
12147080 ATATATTTATTTTA
1 ATATTTTTATTTTA
* *
12147094 ATTTATTTTACTTATA
1 ATAT-TTTTA-TTTTA
* * **
12147110 TTATATAAATTTTA
1 ATATTTTTATTTTA
*
12147124 ATTTTTTATATTTTA
1 ATATTTT-TATTTTA
* *
12147139 TTTATTTTAATTTT-
1 -ATATTTTTATTTTA
* *
12147153 -TGATTCTTATATT-
1 AT-ATTTTTATTTTA
12147166 ATATATTTTATTTTA
1 ATAT-TTTTATTTTA
12147181 ATATTTTTATTTTA
1 ATATTTTTATTTTA
12147195 AT
1 AT
12147197 TATAACATTA
Statistics
Matches: 102, Mismatches: 30, Indels: 22
0.66 0.19 0.14
Matches are distributed among these distances:
12 3 0.03
13 25 0.25
14 42 0.41
15 21 0.21
16 11 0.11
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (14 bp):
ATATTTTTATTTTA
Found at i:12151468 original size:15 final size:14
Alignment explanation
Indices: 12151439--12151467 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12151429 AACACCAAAT
12151439 TAATATTATATATA
1 TAATATTATATATA
12151453 TAATATT-TATATA
1 TAATATTATATATA
12151466 TA
1 TA
12151468 TTTAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATTATATATA
Found at i:12155942 original size:31 final size:32
Alignment explanation
Indices: 12155872--12155942 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
12155862 AGGAGCTCCT
* *
12155872 TTTTTAAAAAAATTAATAAAATTATATAATTA
1 TTTTTATAAAAATTAATAAAAGTATATAATTA
** *
12155904 TAATTATAAAAATTAATTAAAGGTA-A-AATTA
1 TTTTTATAAAAATTAA-TAAAAGTATATAATTA
12155935 TTTTTATA
1 TTTTTATA
12155943 CTTTTACCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
31 11 0.35
32 14 0.45
33 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
TTTTTATAAAAATTAATAAAAGTATATAATTA
Found at i:12163256 original size:15 final size:15
Alignment explanation
Indices: 12163238--12163285 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
12163228 TGGTCTATGA
12163238 AATTGATTATAAATT
1 AATTGATTATAAATT
*
12163253 AATTGA-T-T-GA--
1 AATTGATTATAAATT
12163263 AATTGATTATAAATT
1 AATTGATTATAAATT
12163278 AATTGATT
1 AATTGATT
12163286 GAAATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 2 0.08
13 2 0.08
14 1 0.04
15 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (15 bp):
AATTGATTATAAATT
Found at i:12163263 original size:25 final size:25
Alignment explanation
Indices: 12163235--12163291 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
12163225 TTTTGGTCTA
12163235 TGAAATTGATTATAAATTAATTGAT
1 TGAAATTGATTATAAATTAATTGAT
12163260 TGAAATTGATTATAAATTAATTGAT
1 TGAAATTGATTATAAATTAATTGAT
12163285 TGAAATT
1 TGAAATT
12163292 TATATTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (25 bp):
TGAAATTGATTATAAATTAATTGAT
Found at i:12170454 original size:31 final size:31
Alignment explanation
Indices: 12170419--12170482 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
12170409 TTATCCTCGC
12170419 AGTTGGTTGGGTTTATTGTTGACAATTCCTA
1 AGTTGGTTGGGTTTATTGTTGACAATTCCTA
12170450 AGTTGGTTGGGTTTATTGTTGACAATTCCTA
1 AGTTGGTTGGGTTTATTGTTGACAATTCCTA
12170481 AG
1 AG
12170483 CTATCTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.27, T:0.44
Consensus pattern (31 bp):
AGTTGGTTGGGTTTATTGTTGACAATTCCTA
Found at i:12173858 original size:15 final size:15
Alignment explanation
Indices: 12173840--12173919 Score: 52
Period size: 15 Copynumber: 5.3 Consensus size: 15
12173830 CCTTTGTTGT
12173840 TGTAGTTGCTGGTGG
1 TGTAGTTGCTGGTGG
** * * *
12173855 TGTAGCCGTTGTTGT
1 TGTAGTTGCTGGTGG
*
12173870 TGTAATTGCTGGTGG
1 TGTAGTTGCTGGTGG
** * * *
12173885 TGTAGCCGTTGTTGT
1 TGTAGTTGCTGGTGG
*
12173900 TGTAATTGCTGGTGG
1 TGTAGTTGCTGGTGG
12173915 TGTAG
1 TGTAG
12173920 CCGTTGTTGT
Statistics
Matches: 41, Mismatches: 24, Indels: 0
0.63 0.37 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.10, C:0.09, G:0.39, T:0.42
Consensus pattern (15 bp):
TGTAGTTGCTGGTGG
Found at i:12173860 original size:30 final size:30
Alignment explanation
Indices: 12173826--12173996 Score: 243
Period size: 30 Copynumber: 5.6 Consensus size: 30
12173816 AGCTGCTTGA
* *
12173826 GTAGCCTTTGTTGTTGTAGTTGCTGGTGGT
1 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
12173856 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
1 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
12173886 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
1 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
* * * *
12173916 GTAGCCGTTGTTGTGGTTGTATTTTCCGGTAGT
1 GTAGCCGTTG-T-T-GTTGTAATTGCTGGTGGT
* *
12173949 GTAGCCATTGTTGTTGTAATTGCTAGTGGT
1 GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
12173979 GTAGCCGTTGTTGTTGTA
1 GTAGCCGTTGTTGTTGTA
12173997 GCTGTTTTTC
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
30 98 0.78
31 2 0.02
32 2 0.02
33 23 0.18
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.44
Consensus pattern (30 bp):
GTAGCCGTTGTTGTTGTAATTGCTGGTGGT
Found at i:12173935 original size:63 final size:62
Alignment explanation
Indices: 12173826--12173992 Score: 239
Period size: 63 Copynumber: 2.7 Consensus size: 62
12173816 AGCTGCTTGA
* * * *
12173826 GTAGCCTTTGTTGTTGTAGTTGCTGGTGGTGTAGCCGTTG-T-TGTTGTAATTGCTGGTGGT
1 GTAGCCATTGTTGTTGTAATTGCTGGTGGTGTAGCCGTTGTTGTGTTGTAATTGCCGGTAGT
* * *
12173886 GTAGCCGTTGTTGTTGTAATTGCTGGTGGTGTAGCCGTTGTTGTGGTTGTATTTTCCGGTAGT
1 GTAGCCATTGTTGTTGTAATTGCTGGTGGTGTAGCCGTTGTTGT-GTTGTAATTGCCGGTAGT
*
12173949 GTAGCCATTGTTGTTGTAATTGCTAGTGGTGTAGCCGTTGTTGT
1 GTAGCCATTGTTGTTGTAATTGCTGGTGGTGTAGCCGTTGTTGT
12173993 TGTAGCTGTT
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
60 38 0.40
61 1 0.01
62 1 0.01
63 56 0.58
ACGTcount: A:0.10, C:0.11, G:0.35, T:0.44
Consensus pattern (62 bp):
GTAGCCATTGTTGTTGTAATTGCTGGTGGTGTAGCCGTTGTTGTGTTGTAATTGCCGGTAGT
Found at i:12174192 original size:6 final size:6
Alignment explanation
Indices: 12174181--12174212 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
12174171 AGAGTTAGCC
12174181 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GG
1 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GG
12174213 CGTCGGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTGCT
Found at i:12174220 original size:18 final size:17
Alignment explanation
Indices: 12174180--12174220 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
12174170 CAGAGTTAGC
*
12174180 CGGTGCTGGTGCTGGTG
1 CGGTGCTGGTGCTGGCG
12174197 CTGGTGCTGGTGCTGGCG
1 C-GGTGCTGGTGCTGGCG
12174215 TCGGTG
1 -CGGTG
12174221 TAGGCACCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.00, C:0.20, G:0.51, T:0.29
Consensus pattern (17 bp):
CGGTGCTGGTGCTGGCG
Found at i:12178760 original size:22 final size:23
Alignment explanation
Indices: 12178734--12178799 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
12178724 TGTGAGTTGT
*
12178734 GCATTGTGTGACTTGTTTGTAGA
1 GCATTGAGTGACTTGTTTGTAGA
*
12178757 -CATTAAGTGACTTGTTTGTA-A
1 GCATTGAGTGACTTGTTTGTAGA
*
12178778 GCATTGCA-TGACTTATTTGTAG
1 GCATTG-AGTGACTTGTTTGTAG
12178800 TAATTGCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (23 bp):
GCATTGAGTGACTTGTTTGTAGA
Found at i:12180175 original size:200 final size:203
Alignment explanation
Indices: 12179712--12180498 Score: 867
Period size: 202 Copynumber: 3.9 Consensus size: 203
12179702 GTTTGTATAT
* * * * * * * * * *
12179712 CGTGACTTGTTATCATGTATTGCGTGACGTTGGGCTC-GTACGTGATTGGATACGTTAGCATAAA
1 CGTGACCTGTTGTTATGTATTGCGTGACATTGGGC-CAATACGTGACTGGTTATGTTGGCATAAT
* * * * *
12179776 GTGAGTGGATATTAGGCATCT-AGTGACTTATTATTAGGTATTGTGAGATTGGCAATGTGTGACT
65 GTGAGTGGATATTAGGCAT-TAAGTGACTTATTATTAGATATTGCGAGACTGACAGTGTGTGACT
* * * * * * *
12179840 TGTGCAATTCATCTCTTATTTTGAGGCATTTATTCACTAGTTTTTAGGTATTGTGTGATTGGTTT
129 TGTGCAATTCATCTCTTGTTTTGAGACTTTTGTTCACTAGTTTTTAGGCATTGCGTGATTAGTTT
*
12179905 TTATATATTG
194 TTATGTATTG
* * *
12179915 CATGACCTGTTGTTATGTATTGCGTGACATTGGGCCATTGCGTGACTGGTTATGTTGGCATAATG
1 CGTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATG
* * * *
12179980 TGAGTAGATATTAGGCATTAAGTGACTTATTATTAGATATTACGAGACTGACATTGCGTGACTTG
66 TGAGTGGATATTAGGCATTAAGTGACTTATTATTAGATATTGCGAGACTGACAGTGTGTGACTTG
* * *
12180045 CGCAATTCATCTCTTG-TTTAAGAC-TTTGTTCATTAG-TTTTAGGCATTGCGTGATTAGTTTTT
131 TGCAATTCATCTCTTGTTTTGAGACTTTTGTTCACTAGTTTTTAGGCATTGCGTGATTAGTTTTT
12180107 ATGTATTG
196 ATGTATTG
* * * * * * * *
12180115 CGTAACCTATTGTCATGTATTACATGACATTGGGCCAATACATGATTGGTTATGTTGGCATAATA
1 CGTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATG
* * * *
12180180 TGAGTGGATATTAGGTATTAAGTGACTTATTATTAGGTATTGCAAGACTGACGGTGTGTGACTTG
66 TGAGTGGATATTAGGCATTAAGTGACTTATTATTAGATATTGCGAGACTGACAGTGTGTGACTTG
** * * *
12180245 TATAATTCATCTCTTGTTTTGAGACTTTTGTTCACTAGTTTTT-GGACA-TGTGTG-GTCGATTT
131 TGCAATTCATCTCTTGTTTTGAGACTTTTGTTCACTAGTTTTTAGG-CATTGCGTGATTAG-TTT
12180307 TTATG-AGTTG
194 TTATGTA-TTG
****
12180317 CGTGACCTGTTGTTATGTATTGCGTGACATTGGGCTTGCACGTGACTGGTTATGTTGGCATAATG
1 CGTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATG
* ** * * * *
12180382 TGAGTGAATACGAGGCATTGAA-TGACTTATTATTGGATATTGTGAGACTGGCGGTGTGTGACTT
66 TGAGTGGATATTAGGCATT-AAGTGACTTATTATTAGATATTGCGAGACTGACAGTGTGTGACTT
* *
12180446 GTGCAATTCATCGT-TTGTTTTGAGGCTTTTGTTTACTAGTTTTTAGGCATTGC
130 GTGCAATTCATC-TCTTGTTTTGAGACTTTTGTTCACTAGTTTTTAGGCATTGC
12180499 ATGAATGTGT
Statistics
Matches: 489, Mismatches: 83, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
200 154 0.31
201 20 0.04
202 182 0.37
203 133 0.27
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (203 bp):
CGTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATG
TGAGTGGATATTAGGCATTAAGTGACTTATTATTAGATATTGCGAGACTGACAGTGTGTGACTTG
TGCAATTCATCTCTTGTTTTGAGACTTTTGTTCACTAGTTTTTAGGCATTGCGTGATTAGTTTTT
ATGTATTG
Found at i:12183396 original size:23 final size:23
Alignment explanation
Indices: 12183353--12183396 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12183343 GTTATCATGC
* *
12183353 AATGACCTATCAATCAGTCACGT
1 AATGACCTATCAACCAATCACGT
*
12183376 AATGACTTATCAACCAATCAC
1 AATGACCTATCAACCAATCAC
12183397 ACAATGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (23 bp):
AATGACCTATCAACCAATCACGT
Found at i:12183402 original size:23 final size:23
Alignment explanation
Indices: 12183352--12183402 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12183342 TGTTATCATG
* * *
12183352 CAATGACCTATCAATCAGTCACG
1 CAATGACCTATCAACCAATCACA
* *
12183375 TAATGACTTATCAACCAATCACA
1 CAATGACCTATCAACCAATCACA
12183398 CAATG
1 CAATG
12183403 TTAAACCCTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (23 bp):
CAATGACCTATCAACCAATCACA
Found at i:12183484 original size:117 final size:115
Alignment explanation
Indices: 12183253--12183873 Score: 510
Period size: 113 Copynumber: 5.5 Consensus size: 115
12183243 TGAACAATAT
* * * *
12183253 TCACGTAATGACCTATTAACAAGTCACACAATGTTAAACCCTAATGCAATCACGCACAACATAAG
1 TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCAC-ACCT-A-
* ** * * *
12183318 TGACGTTATGCCTAAATCTAGTCATGTTATCATGCAATGACCTAT--CAATCA
63 TAACCCTATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATGCCAATCA
* * * * * *
12183369 GTCACGTAATGACTTATCAACCAATCACACAATGTTAAACCCTAATGCAATCATGTAGACCT-TA
1 -TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTATA
* * *
12183433 ACCCCATGCCTAAATCCAGTCATGTTGTCATGCAATGACTTATGAACCAATCA
65 ACCCTATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATG--CCAATCA
* * * * * * * *
12183486 T---GAAAAGACCTATCAACCAGTCATGCATTGTTAAATCCTAATGCAATCACGCATAGCATAAG
1 TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACA-CCT-AT
* * * * *
12183548 AGACGCTATACCTAAATCCAGTCATGCTGTCACGCAATGA-CT-TGTCAATTA
64 A-ACCCTATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATGCCAATCA
* * * * *
12183599 GTTACGCAATAACCGATCAACCAGTCACGTAATGTTAAACCCTAATGCAATCACGCACACCT-TA
1 -TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTATA
* *
12183663 A-CCTCATGCCTAAATCCAGTCATGCTGTCATACAATGGCCTATGAACCAATCA
65 ACCCT-ATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATG--CCAATCA
* * *
12183716 TC-CG-AA-GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCATGCACA-CTCTAA
1 TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTATAA
* * * *
12183777 CCCTAAGCCAAAATCCAATCATGCTGTCATGCAATGACTTAT--CAATCA
66 CCCTATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATGCCAATCA
* * * * *
12183825 GTTACG-CA--A--TATCAATCAGTCATGCAATGTTAAACCTTAATGCAATCAC
1 -TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCAC
12183874 ATACATCTTA
Statistics
Matches: 412, Mismatches: 71, Indels: 51
0.77 0.13 0.10
Matches are distributed among these distances:
108 37 0.09
109 6 0.01
110 2 0.00
111 3 0.01
112 4 0.01
113 195 0.47
114 11 0.03
115 6 0.01
116 9 0.02
117 139 0.34
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (115 bp):
TCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTATAA
CCCTATGCCTAAATCCAGTCATGCTGTCATGCAATGACCTATGCCAATCA
Found at i:12183487 original size:23 final size:23
Alignment explanation
Indices: 12183460--12183512 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
12183450 AGTCATGTTG
* * *
12183460 TCATGCAATGACTTATGAACCAA
1 TCATGCAAAGACCTATCAACCAA
* *
12183483 TCATGAAAAGACCTATCAACCAG
1 TCATGCAAAGACCTATCAACCAA
12183506 TCATGCA
1 TCATGCA
12183513 TTGTTAAATC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.23
Consensus pattern (23 bp):
TCATGCAAAGACCTATCAACCAA
Found at i:12183665 original size:230 final size:226
Alignment explanation
Indices: 12183262--12183873 Score: 723
Period size: 230 Copynumber: 2.7 Consensus size: 226
12183252 TTCACGTAAT
* * ** * *
12183262 GACCTATTAACAAGTCACACAATGTTAAACCCTAATGCAATCACGCACAACATAAGTGACGTTAT
1 GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCACGCAC-ACATAAGAGACGCTAT
* * * * * * *
12183327 GCCTAAATCTAGTCATGTTATCATGCAATGACCTATCAATCAGTCACGTAATGACTTATCAACCA
65 ACCTAAATCCAGTCATGCTGTCATGCAATGACTTATCAATCAGTTACGCAAT-AC--ATCAACCA
* * * * *
12183392 ATCACACAATGTTAAACCCTAATGCAATCATGTAGACCTTAACCCCATGCCTAAATCCAGTCATG
127 GTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTTAACCCCATGCCTAAATCCAGTCATG
* * * *
12183457 TTGTCATGCAATGACTTATGAACCAATCATGAAAA
192 CTGTCATACAATGACCTATGAACCAATCATCAAAA
* * *
12183492 GACCTATCAACCAGTCATGCATTGTTAAATCCTAATGCAATCACGCATAGCATAAGAGACGCTAT
1 GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCACGCACA-CATAAGAGACGCTAT
* * *
12183557 ACCTAAATCCAGTCATGCTGTCACGCAATGACTTGTCAATTAGTTACGCAATAACCGATCAACCA
65 ACCTAAATCCAGTCATGCTGTCATGCAATGACTTATCAATCAGTTACGCAAT-A-C-ATCAACCA
* *
12183622 GTCACGTAATGTTAAACCCTAATGCAATCACGCACACCTTAACCTCATGCCTAAATCCAGTCATG
127 GTCACGCAATGTTAAACCCTAATGCAATCACGCACACCTTAACCCCATGCCTAAATCCAGTCATG
* **
12183687 CTGTCATACAATGGCCTATGAACCAATCATCCGAA
192 CTGTCATACAATGACCTATGAACCAATCATCAAAA
* ** *
12183722 GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCATGCACAC-T-CTA-ACCCTA-A
1 GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCACGCACACATAAGAGACGCTATA
* * *
12183783 GCCAAAATCCAATCATGCTGTCATGCAATGACTTATCAATCAGTTACGCAAT--ATCAATCAGTC
66 -CCTAAATCCAGTCATGCTGTCATGCAATGACTTATCAATCAGTTACGCAATACATCAACCAGTC
* *
12183846 ATGCAATGTTAAACCTTAATGCAATCAC
130 ACGCAATGTTAAACCCTAATGCAATCAC
12183874 ATACATCTTA
Statistics
Matches: 328, Mismatches: 51, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
221 35 0.11
225 1 0.00
226 51 0.16
227 1 0.00
228 1 0.00
229 2 0.01
230 236 0.72
231 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (226 bp):
GACCTATCAACCAGTCATGCAATGTTAAACCCTAATGCAATCACGCACACATAAGAGACGCTATA
CCTAAATCCAGTCATGCTGTCATGCAATGACTTATCAATCAGTTACGCAATACATCAACCAGTCA
CGCAATGTTAAACCCTAATGCAATCACGCACACCTTAACCCCATGCCTAAATCCAGTCATGCTGT
CATACAATGACCTATGAACCAATCATCAAAA
Found at i:12183851 original size:18 final size:18
Alignment explanation
Indices: 12183816--12183852 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12183806 TGCAATGACT
*
12183816 TATCAATCAGTTACGCAA
1 TATCAATCAGTCACGCAA
*
12183834 TATCAATCAGTCATGCAA
1 TATCAATCAGTCACGCAA
12183852 T
1 T
12183853 GTTAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (18 bp):
TATCAATCAGTCACGCAA
Found at i:12189376 original size:2 final size:2
Alignment explanation
Indices: 12189371--12189396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12189361 AGTGCGTACG
12189371 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12189397 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12189446 original size:2 final size:2
Alignment explanation
Indices: 12189396--12189428 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12189386 TCTCTCTCTC
*
12189396 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12189429 CCTCTATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:12195042 original size:2 final size:2
Alignment explanation
Indices: 12195037--12195061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12195027 TTTAAACTGA
12195037 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12195062 AAACAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12196514 original size:21 final size:21
Alignment explanation
Indices: 12196490--12196531 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12196480 AACAAAAAAT
*
12196490 AATACATCAATTA-ATAAATTA
1 AATAC-TCAAATATATAAATTA
12196511 AATACTCAAATATATAAATTA
1 AATACTCAAATATATAAATTA
12196532 TTAGAGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
AATACTCAAATATATAAATTA
Found at i:12201963 original size:20 final size:19
Alignment explanation
Indices: 12201899--12201972 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
12201889 CCACAGAACC
*
12201899 TTAATTAATTTAAATATTT
1 TTAATTAATTTAAATAATT
** * **
12201918 TTAATTACCTTAATACAACC
1 TTAATTAATTTAA-ATAATT
12201938 TTAATTAATTTAAATAATT
1 TTAATTAATTTAAATAATT
12201957 TTAAATTAATTTAAAT
1 TT-AATTAATTTAAAT
12201973 TTACTAATAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATTAATTTAAATAATT
Found at i:12201973 original size:10 final size:10
Alignment explanation
Indices: 12201940--12201973 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
12201930 ATACAACCTT
12201940 AATTAATTTA
1 AATTAATTTA
12201950 AA-TAATTTTA
1 AATTAA-TTTA
12201960 AATTAATTTA
1 AATTAATTTA
12201970 AATT
1 AATT
12201974 TACTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.14
10 16 0.73
11 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTAATTTA
Found at i:12202164 original size:123 final size:122
Alignment explanation
Indices: 12201940--12202188 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 122
12201930 ATACAACCTT
* * *
12201940 AATTAATTTAAATAATTTTAAATTAATTTAAATTTACTAATATAATTATTTGCTTAATTACTTAG
1 AATTAATTTAAATAATTTTAAATTAATATAAATTCACTAATATAATTAATTGCTTAATTACTTAG
*
12202005 TTATAGCACATAACATTACTTACTTAACTATATTATTTAATTAACTCATTAACACTTG
66 -TATAGCACATAACATTACTTACTGAACTATATTATTTAATTAACTCATTAACACTTG
* * * * *
12202063 AATTAATTTAAATAATTTTTAATTAATATAAATTCACTACTTTAATTAATTGCTTCATTGCTTA-
1 AATTAATTTAAATAATTTTAAATTAATATAAATTCACTAATATAATTAATTGCTTAATTACTTAG
** * * * * *
12202127 TA-A-CACATTCCATTGCTTGA-TGAACTAAATTATTTATTTAACTCATTTACACCTTA
66 TATAGCACATAACATTACTT-ACTGAACTATATTATTTAATTAACTCATTAACA-CTTG
12202183 AATTAA
1 AATTAA
12202189 ATAATATTAC
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
119 39 0.36
120 11 0.10
121 2 0.02
123 56 0.52
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (122 bp):
AATTAATTTAAATAATTTTAAATTAATATAAATTCACTAATATAATTAATTGCTTAATTACTTAG
TATAGCACATAACATTACTTACTGAACTATATTATTTAATTAACTCATTAACACTTG
Found at i:12214201 original size:12 final size:12
Alignment explanation
Indices: 12214184--12214208 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12214174 TATGAAAAAT
12214184 TTTTATATAATA
1 TTTTATATAATA
12214196 TTTTATATAATA
1 TTTTATATAATA
12214208 T
1 T
12214209 AAAACATTGG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTATATAATA
Found at i:12214575 original size:48 final size:45
Alignment explanation
Indices: 12214523--12214630 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 45
12214513 TATTTTGAAC
* *
12214523 ATAAAAATAATTTTTTTATTTTTAGAAATTCTGA-AAAAATTTAAGAAA
1 ATAAAAATAATTTTTTAATTTTTAAAAATTCT-ACAAAAA--TAA-AAA
*
12214571 ATAAAAAGTAA-TTTTTAATTTTTAAAAATTCTACAACAATAAAAA
1 ATAAAAA-TAATTTTTTAATTTTTAAAAATTCTACAAAAATAAAAA
*
12214616 ATAGAAATAATTTTT
1 ATAAAAATAATTTTT
12214631 ATTTTGAAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
44 3 0.06
45 13 0.25
46 3 0.06
47 1 0.02
48 30 0.57
49 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40
Consensus pattern (45 bp):
ATAAAAATAATTTTTTAATTTTTAAAAATTCTACAAAAATAAAAA
Found at i:12215928 original size:14 final size:15
Alignment explanation
Indices: 12215909--12215941 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12215899 ACCACTCTAT
12215909 TTTTATATT-TATAA
1 TTTTATATTATATAA
*
12215923 TTTTATATTATATCA
1 TTTTATATTATATAA
12215938 TTTT
1 TTTT
12215942 GTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATATTATATAA
Found at i:12218014 original size:62 final size:62
Alignment explanation
Indices: 12217838--12218692 Score: 729
Period size: 62 Copynumber: 13.9 Consensus size: 62
12217828 CTAATTAAAT
* * * * * * * * * *
12217838 TTGGGTTTAAAATTATTTCGTGTCAATATAACTGGATTTAAACATCTTGGATGCTAGTTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
** * * *
12217900 TTGAACTTAAACTC-TTTTGTGGCAA-AGTAACTAGATTTATACATCTTAGATGCCAGTTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACA-TAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * *
12217961 TTGGGCTTAAACTCCTTTGGTGCCAACCTAACTAGACTTATATATCTTTGATGCCAATTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * ** ** * *
12218023 TTAGGCTTAAAATCATTTTGTGGTAATGTAACTAGACTTAAACATCTTTGATGCCA-TTAT-A
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTT-TGA
* * * * * * * * **
12218084 TTGGGCTTGAACTCTTTTTGTACCCACGTAACTGGACTTATACATCTTGAATGCCAGGTAAA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * ** * * * * * **
12218146 TTAGACTTAAACTC-TTTTCATGCCAATGTAATTGGACTTAAACATCTTGGATGCTAGGTAAA
1 TTGGGCTTAAACTCATTTT-GTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * * * * **
12218208 TTGGGCTTAAACTCTTTTTGTACTAACATAATTGGACTTATATATCTTGGATGCTAGGTAAA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * *
12218270 TTGGGCTTAAA-T-TTTTTCATACCAAAATAACTTGACTTATACATCTTGGATGCCAGTTTGA
1 TTGGGCTTAAACTCATTTT-GTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * **
12218331 TTGGGCTTAAAATCATTTTGTGTCAACATAACTGGACTTATACATCTTGGATGCCAACTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * *
12218393 TTGAGTTTAAACTC-TTTTGTGCCAACATAACTAGACTTATACGTTTTGCATGTCAGTTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * ** *
12218454 TTGGGCTTAAAATCATTTTGTGCTAATGTAACTCGACTTATACATCTTGGATGCCAGTTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * **
12218516 TTGGGCTTAAAATCATTTTGTGTCAACATAACTGGACTTATACATCTTGGATGCCAACTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * *
12218578 TTGAGTTTAAACTC-TTTTGTGCCAACATAACTAGACTTATACGTTTTGCATGTCAGTTTGA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * ** *
12218639 TTGGGCTTAAAATCATTTTGTGCTAATGTAACTCGACTTATACATCTTGGATGC
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGC
12218693 TATAAAAATT
Statistics
Matches: 646, Mismatches: 134, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
60 6 0.01
61 246 0.38
62 386 0.60
63 8 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (62 bp):
TTGGGCTTAAACTCATTTTGTGCCAACATAACTAGACTTATACATCTTGGATGCCAGTTTGA
Found at i:12218087 original size:123 final size:123
Alignment explanation
Indices: 12217838--12218756 Score: 770
Period size: 123 Copynumber: 7.5 Consensus size: 123
12217828 CTAATTAAAT
* * * * * * * * *
12217838 TTGGGTTTAAAATTATTTCGTGTCAATATAACTGGATTTAAACATCTTGGATGCTAGTTTGATTG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
** * * * * *
12217903 AACTTAAACTCTTTTGTGGCAAAGTAACTAGATTTATACATCTTAGATGCCAGTTTGA
66 GGCTTAAAATCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * * * *
12217961 TTGGGCTTAAACTCCTTTGGTGCCAACCTAACTAGACTTATATATCTTTGATGCCAATTTGATTA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
** * *
12218026 GGCTTAAAATCATTTTGTGGTAATGTAACTAGACTTAAACATCTTTGATGCCA-TTAT-A
66 GGCTTAAAATC-TTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTT-TGA
* * * * * * * ** *
12218084 TTGGGCTTGAACTCTTTTTGTACCCACGTAACTGGACTTATACATCTTGAATGCCAGGTAAATTA
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
* * * * * * * * **
12218149 GACTTAAACTCTTTTCATGCCAATGTAATTGGACTTAAACATCTTGGATGCTAGGTAAA
66 GGCTTAAAATCTTTT-GTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * * * **
12218208 TTGGGCTTAAACTCTTTTTGTACTAACATAATTGGACTTATATATCTTGGATGCTAGGTAAATTG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
* * * ** *
12218273 GGCTT-AAATTTTTTCATACCAAAATAACTTGACTTATACATCTTGGATGCCAGTTTGA
66 GGCTTAAAATCTTTT-GTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * **
12218331 TTGGGCTTAAAATCATTTTGTGTCAACATAACTGGACTTATACATCTTGGATGCCAACTTGATTG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
* * * ** * * * *
12218396 AGTTTAAACTCTTTTGTGCCAACATAACTAGACTTATACGTTTTGCATGTCAGTTTGA
66 GGCTTAAAATCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * ** *
12218454 TTGGGCTTAAAATCATTTTGTGCTAATGTAACTCGACTTATACATCTTGGATGCCAGTTTGATTG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
* ** * **
12218519 GGCTTAAAATCATTTTGTGTCAACATAACTGGACTTATACATCTTGGATGCCAACTTGA
66 GGCTTAAAATC-TTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
* * * * * * *
12218578 TTGAGTTTAAACTC-TTTTGTGCCAACATAACTAGACTTATACGTTTTGCATGTCAGTTTGATTG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
* * * ***
12218642 GGCTTAAAATCATTTTGTGCTAATGTAACTCGACTTATACATCTTGGATGCTA-TAAAAA
66 GGCTTAAAATC-TTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGT-TTGA
* ** * * * *
12218701 TTTGGCTTAAGTTC-TCTAGTCCCAACATAACTGGACTTAGACATCTTGGATGCCAG
1 TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAG
12218757 CTAAATGGGC
Statistics
Matches: 640, Mismatches: 148, Indels: 16
0.80 0.18 0.02
Matches are distributed among these distances:
122 4 0.01
123 480 0.75
124 156 0.24
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (123 bp):
TTGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTGATTG
GGCTTAAAATCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCCAGTTTGA
Found at i:12218127 original size:185 final size:185
Alignment explanation
Indices: 12217865--12218755 Score: 812
Period size: 185 Copynumber: 4.8 Consensus size: 185
12217855 TCGTGTCAAT
* * * * * * ** * ** *
12217865 ATAACTGGATTTAAACATCTTGGATGCTAGTTTGATTGAACTTAAACTC-TTTTGTGGCAAAGTA
1 ATAACTAGACTTATACATTTTGCATGCCAGTTTGATTGGGCTTAAAATCATTTTGTACCAATGTA
* * * * * * *
12217929 ACTAGATTTATACATCTTAGATGCCAGTTTGATTGGGCTTAAACTCCTTTGGTGCCAACCTAACT
66 ACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGCCAACATAACT
* * * * * ** *
12217994 AGACTTATATATCTTTGATGCCAATTTGATT-AGGCTTAAAATCATTTTGTGGTAAT
131 GGACTTATACATCTTGGATGCCAACTTGATTGA-GCTTAAACTC-TTTTGTGCCAAC
* * * * * * *
12218050 GTAACTAGACTTAAACATCTTTG-ATGCCA-TTAT-ATTGGGCTTGAACTCTTTTTGTACCCACG
1 ATAACTAGACTTATACAT-TTTGCATGCCAGTT-TGATTGGGCTTAAAATCATTTTGTACCAATG
* * * ** * * * * **
12218112 TAACTGGACTTATACATCTTGAATGCCAGGTAAATTAGACTTAAACTC-TTTTCATGCCAATGTA
64 TAACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTT-GTGCCAACATA
* * * ** ** * * *
12218176 ATTGGACTTAAACATCTTGGATGCTAGGTAAATTGGGCTTAAACTCTTTTTGTACTAAC
128 ACTGGACTTATACATCTTGGATGCCAACTTGATTGAGCTTAAACTC-TTTTGTGCCAAC
* * * * * * * ** * * **
12218235 ATAATTGGACTTATATATCTTGGATGCTAGGTAAATTGGGCTT-AAAT-TTTTTCATACCAAAAT
1 ATAACTAGACTTATACATTTTGCATGCCAGTTTGATTGGGCTTAAAATCATTTT-GTACCAATGT
* *
12218298 AACTTGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGTCAACATAAC
65 AACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGCCAACATAAC
*
12218363 TGGACTTATACATCTTGGATGCCAACTTGATTGAGTTTAAACTCTTTTGTGCCAAC
130 TGGACTTATACATCTTGGATGCCAACTTGATTGAGCTTAAACTCTTTTGTGCCAAC
* * * *
12218419 ATAACTAGACTTATACGTTTTGCATGTCAGTTTGATTGGGCTTAAAATCATTTTGTGCTAATGTA
1 ATAACTAGACTTATACATTTTGCATGCCAGTTTGATTGGGCTTAAAATCATTTTGTACCAATGTA
*
12218484 ACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGTCAACATAACT
66 ACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGCCAACATAACT
*
12218549 GGACTTATACATCTTGGATGCCAACTTGATTGAGTTTAAACTCTTTTGTGCCAAC
131 GGACTTATACATCTTGGATGCCAACTTGATTGAGCTTAAACTCTTTTGTGCCAAC
* * * *
12218604 ATAACTAGACTTATACGTTTTGCATGTCAGTTTGATTGGGCTTAAAATCATTTTGTGCTAATGTA
1 ATAACTAGACTTATACATTTTGCATGCCAGTTTGATTGGGCTTAAAATCATTTTGTACCAATGTA
* *** * ** * * *
12218669 ACTCGACTTATACATCTTGGATGCTA-TAAAAATTTGGCTTAAGTTC-TCTAGTCCCAACATAAC
66 ACTCGACTTATACATCTTGGATGCCAGT-TTGATTGGGCTTAAAATCATTTTGTGCCAACATAAC
*
12218732 TGGACTTAGACATCTTGGATGCCA
130 TGGACTTATACATCTTGGATGCCA
12218756 GCTAAATGGG
Statistics
Matches: 585, Mismatches: 108, Indels: 27
0.81 0.15 0.04
Matches are distributed among these distances:
184 104 0.18
185 460 0.79
186 21 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (185 bp):
ATAACTAGACTTATACATTTTGCATGCCAGTTTGATTGGGCTTAAAATCATTTTGTACCAATGTA
ACTCGACTTATACATCTTGGATGCCAGTTTGATTGGGCTTAAAATCATTTTGTGCCAACATAACT
GGACTTATACATCTTGGATGCCAACTTGATTGAGCTTAAACTCTTTTGTGCCAAC
Found at i:12218169 original size:31 final size:31
Alignment explanation
Indices: 12218134--12218225 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
12218124 TACATCTTGA
*
12218134 ATGCCAGGTAAATTAGACTTAAACTCTTTTC
1 ATGCCAGGTAAATTGGACTTAAACTCTTTTC
* **
12218165 ATGCCAATGT-AATTGGACTTAAACATC-TTGG
1 ATGCC-AGGTAAATTGGACTTAAAC-TCTTTTC
* *
12218196 ATGCTAGGTAAATTGGGCTTAAACTCTTTT
1 ATGCCAGGTAAATTGGACTTAAACTCTTTT
12218226 TGTACTAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
30 5 0.10
31 39 0.80
32 5 0.10
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (31 bp):
ATGCCAGGTAAATTGGACTTAAACTCTTTTC
Found at i:12218272 original size:31 final size:31
Alignment explanation
Indices: 12218175--12218281 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
12218165 ATGCCAATGT
*
12218175 AATTGGACTTAAACATCTTGGATGCTAGGTA
1 AATTGGACTTAAATATCTTGGATGCTAGGTA
* * * * * **
12218206 AATTGGGCTTAAACTCTTTTTG-TACTA-ACA
1 AATTGGACTTAAA-TATCTTGGATGCTAGGTA
*
12218236 TAATTGGACTTATATATCTTGGATGCTAGGTA
1 -AATTGGACTTAAATATCTTGGATGCTAGGTA
*
12218268 AATTGGGCTTAAAT
1 AATTGGACTTAAAT
12218282 TTTTTCATAC
Statistics
Matches: 54, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
30 6 0.11
31 43 0.80
32 5 0.09
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (31 bp):
AATTGGACTTAAATATCTTGGATGCTAGGTA
Found at i:12222752 original size:69 final size:69
Alignment explanation
Indices: 12222620--12222752 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
12222610 TTCTCTTTTC
* *
12222620 ACAAGATCATTTGATCGAGAATCTATGATCTTTTCTATTTTTATTCCATCTTTAATCATTCCCAA
1 ACAAGATCATTTGATCGAGAATCTATGACCTTTTCTATTTTTATTCCATCTTTAATCACTCCCAA
12222685 TTTG
66 TTTG
*
12222689 ACAAGATCATTTGATCGAGAATCTATGACCTTTTCTATTTTTA-TCCAATCTTTAATCCCTCCCA
1 ACAAGATCATTTGATCGAGAATCTATGACCTTTTCTATTTTTATTCC-ATCTTTAATCACTCCCA
12222753 TGAAGAACAC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 3 0.05
69 57 0.95
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (69 bp):
ACAAGATCATTTGATCGAGAATCTATGACCTTTTCTATTTTTATTCCATCTTTAATCACTCCCAA
TTTG
Found at i:12223177 original size:19 final size:17
Alignment explanation
Indices: 12223153--12223200 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
12223143 AGTTTATCAG
12223153 TTGATTTCTTTTTTTTTAT
1 TTGATTT-TTTTTTTTT-T
*
12223172 TTGATTTTTTTGTTTTT
1 TTGATTTTTTTTTTTTT
12223189 TT-ATTTTTTTTT
1 TTGATTTTTTTTT
12223201 CAAAATACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 8 0.30
19 7 0.26
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.83
Consensus pattern (17 bp):
TTGATTTTTTTTTTTTT
Found at i:12225056 original size:18 final size:18
Alignment explanation
Indices: 12225033--12225086 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
12225023 CATCCTAACT
12225033 TAATTCAATTTCATAGAC
1 TAATTCAATTTCATAGAC
*
12225051 TAATTC-A--TCCTA-AC
1 TAATTCAATTTCATAGAC
12225065 TTAATTCAATTTCATAGAC
1 -TAATTCAATTTCATAGAC
12225084 TAA
1 TAA
12225087 CATTGGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 1 0.03
17 1 0.03
18 13 0.45
19 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (18 bp):
TAATTCAATTTCATAGAC
Found at i:12225058 original size:33 final size:33
Alignment explanation
Indices: 12225020--12225086 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12225010 AAGAAATCAT
12225020 ATTCATCCTAACTTAATTCAATTTCATAGACTA
1 ATTCATCCTAACTTAATTCAATTTCATAGACTA
12225053 ATTCATCCTAACTTAATTCAATTTCATAGACTA
1 ATTCATCCTAACTTAATTCAATTTCATAGACTA
12225086 A
1 A
12225087 CATTGGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (33 bp):
ATTCATCCTAACTTAATTCAATTTCATAGACTA
Found at i:12225071 original size:15 final size:15
Alignment explanation
Indices: 12225020--12225072 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
12225010 AAGAAATCAT
12225020 ATTCATCCTAACTTA
1 ATTCATCCTAACTTA
*
12225035 ATTCAATTTCATAGAC-TA
1 ATTC-A--TCCTA-ACTTA
12225053 ATTCATCCTAACTTA
1 ATTCATCCTAACTTA
12225068 ATTCA
1 ATTCA
12225073 ATTTCATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 15 0.48
16 1 0.03
17 1 0.03
18 10 0.32
19 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTCATCCTAACTTA
Found at i:12226171 original size:25 final size:26
Alignment explanation
Indices: 12226121--12226175 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
12226111 CTCGACTTTT
12226121 TCCTTTCTCTCTTGTCCTCTCCTCAC
1 TCCTTTCTCTCTTGTCCTCTCCTCAC
* *
12226147 TCCTTTC-CTCTT-TGCCTTTCTTCAC
1 TCCTTTCTCTCTTGT-CCTCTCCTCAC
12226172 TCCT
1 TCCT
12226176 CTCTGCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 1 0.04
25 18 0.69
26 7 0.27
ACGTcount: A:0.04, C:0.44, G:0.04, T:0.49
Consensus pattern (26 bp):
TCCTTTCTCTCTTGTCCTCTCCTCAC
Found at i:12226214 original size:20 final size:20
Alignment explanation
Indices: 12226152--12226208 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
12226142 CTCACTCCTT
12226152 TCCTCTTTGCCTTTCTTCAC
1 TCCTCTTTGCCTTTCTTCAC
* *
12226172 TCCTCTCTGCCTTTCTCCAC
1 TCCTCTTTGCCTTTCTTCAC
*
12226192 TCCTCTTTGCCTCTCTT
1 TCCTCTTTGCCTTTCTT
12226209 GTCTCCCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.04, C:0.44, G:0.05, T:0.47
Consensus pattern (20 bp):
TCCTCTTTGCCTTTCTTCAC
Found at i:12227168 original size:16 final size:16
Alignment explanation
Indices: 12227133--12227168 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12227123 ATTAAATGAG
* *
12227133 TAATTAATCAAGAAAT
1 TAATTAATCAACAAAA
12227149 TAATTAATCAACAAAA
1 TAATTAATCAACAAAA
12227165 TAAT
1 TAAT
12227169 CATGTATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATTAATCAACAAAA
Found at i:12227237 original size:256 final size:257
Alignment explanation
Indices: 12226782--12227292 Score: 758
Period size: 256 Copynumber: 2.0 Consensus size: 257
12226772 TCAGTAATTT
* * **
12226782 TAGTTAAATTAATTAAGGTTGCATTATATGGTATAATTAAGGTTTAGGAATGGAATGTGTTATAC
1 TAGTTAAATTAATTAAGGTTGCATTATAGGGTATAATGAAGGTTTAGGAATGGAATGCATTATAC
* * *
12226847 TATAAGTAAACAAGAAATTAATTAAATGAGTAATTAATCAATAAATCAATAAGAAATTAAACTAA
66 TATAAGTAAACAAGAAATTAATTAAATGAGTAATTAATCAAGAAATCAATAAGAAATCAAAATAA
* * *
12226912 TCATGGATTAGTAATTAATCAATAAATTAACTTAGTAAATTTAGAAAAATTTAAAACTTACATTA
131 TCATGGATTAGTAACTAATCAATAAATTAAATTAGTAAATTTAGAAAAATTTAAAACTTAAATTA
* * *
12226977 ACTTAATTAAGGTTTA-GTGTAAGCAATAAACTAAATGGGTAAATTTAATAAAATTTAAAAA
196 ACTTAATGAAAGTTTAGGGGTAAGCAATAAACTAAATGGGTAAATTTAATAAAATTTAAAAA
* * *
12227038 TAGTTAAATTAATTGAGGTTGTATTATAGGGTATAATGAGGGTTTAGGAATGGAATGCATTATGA
1 TAGTTAAATTAATTAAGGTTGCATTATAGGGTATAATGAAGGTTTAGGAATGGAATGCATTAT-A
* * **
12227103 -TATAAGTAAATAAGAAATTAATTAAATGAGTAATTAATCAAGAAATTAATTAATCAA-CAAAAT
65 CTATAAGTAAACAAGAAATTAATTAAATGAGTAATTAATCAAGAAATCAA-TAAGAAATCAAAAT
* ** *
12227166 AATCATGTATTAGTAACTAATCAATAGCTTAAATTAGTAAATTTAGAATAATTTAAAACTTAAAT
129 AATCATGGATTAGTAACTAATCAATAAATTAAATTAGTAAATTTAGAAAAATTTAAAACTTAAAT
*
12227231 TAACTTAATGAAAGTTTAGGGGTAAGCAATAAATTAAATGGGTAAATTTAATAAAATTTAAA
194 TAACTTAATGAAAGTTTAGGGGTAAGCAATAAACTAAATGGGTAAATTTAATAAAATTTAAA
12227293 TTAATTAAGG
Statistics
Matches: 227, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
256 180 0.79
257 47 0.21
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (257 bp):
TAGTTAAATTAATTAAGGTTGCATTATAGGGTATAATGAAGGTTTAGGAATGGAATGCATTATAC
TATAAGTAAACAAGAAATTAATTAAATGAGTAATTAATCAAGAAATCAATAAGAAATCAAAATAA
TCATGGATTAGTAACTAATCAATAAATTAAATTAGTAAATTTAGAAAAATTTAAAACTTAAATTA
ACTTAATGAAAGTTTAGGGGTAAGCAATAAACTAAATGGGTAAATTTAATAAAATTTAAAAA
Found at i:12230638 original size:51 final size:51
Alignment explanation
Indices: 12230581--12230682 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
12230571 TTGTTCCTGG
*
12230581 CAGGCTAAAACCTTGAGCCTTTAGTCCGAACTCATTGTACTAAGCCTTCCA
1 CAGGCTAAAACCTTGAGCCTTTAGTCCAAACTCATTGTACTAAGCCTTCCA
*
12230632 CAGGCTATAACCTTGAGCCTTTAGTCCAAACTCATTGTACTAAGCCTTCCA
1 CAGGCTAAAACCTTGAGCCTTTAGTCCAAACTCATTGTACTAAGCCTTCCA
12230683 AACCCATCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28
Consensus pattern (51 bp):
CAGGCTAAAACCTTGAGCCTTTAGTCCAAACTCATTGTACTAAGCCTTCCA
Found at i:12231777 original size:18 final size:19
Alignment explanation
Indices: 12231754--12231800 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12231744 ACTCTTTTTT
12231754 AAAAAATTTTA-TTCTTTA
1 AAAAAATTTTACTTCTTTA
** *
12231772 AAAAAAAGTTACTTTTTTA
1 AAAAAATTTTACTTCTTTA
*
12231791 AAAAAGTTTT
1 AAAAAATTTT
12231801 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (19 bp):
AAAAAATTTTACTTCTTTA
Found at i:12231790 original size:19 final size:19
Alignment explanation
Indices: 12231747--12231795 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
12231737 TCTTGAAACT
**
12231747 CTTTTTT-AAAAAATTTTA
1 CTTTTTTAAAAAAAAGTTA
*
12231765 -TTCTTTAAAAAAAAGTTA
1 CTTTTTTAAAAAAAAGTTA
12231783 CTTTTTTAAAAAA
1 CTTTTTTAAAAAA
12231796 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (19 bp):
CTTTTTTAAAAAAAAGTTA
Found at i:12236877 original size:15 final size:16
Alignment explanation
Indices: 12236853--12236891 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
12236843 CTTCATAATC
*
12236853 AGAAAAAAAGAACCA-
1 AGAAAGAAAGAACCAT
12236868 AGAAAGAAAGAACCAT
1 AGAAAGAAAGAACCAT
12236884 AG-AAGAAA
1 AGAAAGAAA
12236892 TAGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.69, C:0.10, G:0.18, T:0.03
Consensus pattern (16 bp):
AGAAAGAAAGAACCAT
Found at i:12254694 original size:2 final size:2
Alignment explanation
Indices: 12254687--12254714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12254677 GAGTGAATGA
12254687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12254715 GAAAGGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12257499 original size:141 final size:142
Alignment explanation
Indices: 12257248--12257519 Score: 341
Period size: 141 Copynumber: 1.9 Consensus size: 142
12257238 TTTTGTTGGT
* * *
12257248 TGTCATTTGCTCAGATTTTCTACGTTATAGTGTTTAAAAGATATGTATAGTTTTATATAACTAGA
1 TGTCATTTGCTCAAATTTTCTACGTTATAGTGTTTAAAAGATATGTATAGTTTTATAAAACTACA
* *
12257313 ACTGCATTTCCTATCTTTTGATGTTAAGGCATGACCCTCAAATGTGAACATTA-TATGCATTTGA
66 ACTGCATTTCCTATCTTTTGATGTCAAGACATGACCCTCAAATGTGAACATTATTATGCATTTGA
12257377 TGCTTTGTTTAA
131 TGCTTTGTTTAA
* * * * * *
12257389 TGTCGTTTGCTTAAATTTTCTAC-TTCATGGTGTTTAAAAGATGTGTATGGTTTTATAAAATTAC
1 TGTCATTTGCTCAAATTTTCTACGTT-ATAGTGTTTAAAAGATATGTATAGTTTTATAAAACTAC
* * * * * ** * *
12257453 AATTGCTTTTTCTGTCTTTTGATGTCAAGACATGACCTTCGGATGTGGACATTATTATGCTTTTG
65 AACTGCATTTCCTATCTTTTGATGTCAAGACATGACCCTCAAATGTGAACATTATTATGCATTTG
12257518 AT
130 AT
12257520 ATACAAAGTT
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
140 2 0.02
141 96 0.88
142 11 0.10
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (142 bp):
TGTCATTTGCTCAAATTTTCTACGTTATAGTGTTTAAAAGATATGTATAGTTTTATAAAACTACA
ACTGCATTTCCTATCTTTTGATGTCAAGACATGACCCTCAAATGTGAACATTATTATGCATTTGA
TGCTTTGTTTAA
Found at i:12258510 original size:101 final size:101
Alignment explanation
Indices: 12258328--12258529 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 101
12258318 ATGCCCTAGG
* ** * * ** *
12258328 ATGAGATGTGAACACATCATTGGTTGTAAACGTTGCTTATGTCAACATTATTATACTTCTTATAT
1 ATGAGATGTGAACACATCATTAGTCATAAACCTTGCTTATGTCAACATTATCATACTTCCAATAC
* * *
12258393 ACTAATCTTTTATTTTAAATTTACTGTTTTATGGTA
66 ACAAATCTTTTATTTTAAATTCACTGCTTTATGGTA
*
12258429 ATGAGATGTTAATC-CATCATTAGTCATAAACCTTGCTTATGTCAACATTATCATACTTCCAATA
1 ATGAGATGTGAA-CACATCATTAGTCATAAACCTTGCTTATGTCAACATTATCATACTTCCAATA
* *
12258493 CACAAATTTTTTGTTTTAAATTCACTGCTTTATGGTA
65 CACAAATCTTTTATTTTAAATTCACTGCTTTATGGTA
12258530 TTTAAAAGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 85 0.99
102 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (101 bp):
ATGAGATGTGAACACATCATTAGTCATAAACCTTGCTTATGTCAACATTATCATACTTCCAATAC
ACAAATCTTTTATTTTAAATTCACTGCTTTATGGTA
Found at i:12274881 original size:7 final size:7
Alignment explanation
Indices: 12274869--12274896 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12274859 AAATATAACA
12274869 TTTTTAT
1 TTTTTAT
12274876 TTTTTAT
1 TTTTTAT
12274883 TTTTTAT
1 TTTTTAT
12274890 TTTTTAT
1 TTTTTAT
12274897 ATGTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:12276377 original size:9 final size:9
Alignment explanation
Indices: 12276363--12276387 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12276353 GCTCCTCTTT
12276363 TTCTTCTCC
1 TTCTTCTCC
12276372 TTCTTCTCC
1 TTCTTCTCC
12276381 TTCTTCT
1 TTCTTCT
12276388 TCTTGTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:12276717 original size:13 final size:14
Alignment explanation
Indices: 12276692--12276720 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12276682 TTTTATAAAA
12276692 TAATTTAAATTAAT
1 TAATTTAAATTAAT
12276706 TAATTT-AATTAAT
1 TAATTTAAATTAAT
12276719 TA
1 TA
12276721 TTATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTTAAATTAAT
Found at i:12277020 original size:25 final size:25
Alignment explanation
Indices: 12276974--12277021 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12276964 AAAGAGAAAA
* *
12276974 TAAATATTTAGTAATTTTATATATT
1 TAAATATTTAATAATTTAATATATT
12276999 TAAATATTTAAATAA-TTAATATA
1 TAAATATTT-AATAATTTAATATA
12277022 AAAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAAATATTTAATAATTTAATATATT
Found at i:12277052 original size:21 final size:21
Alignment explanation
Indices: 12277026--12277065 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12277016 AATATAAAAA
12277026 TATTATGTTATT-TTTTAATGT
1 TATTAT-TTATTATTTTAATGT
12277047 TATTATTTATTATTTTAAT
1 TATTATTTATTATTTTAAT
12277066 TACTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TATTATTTATTATTTTAATGT
Found at i:12292248 original size:2 final size:2
Alignment explanation
Indices: 12292241--12292276 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12292231 TAAAGAAACC
12292241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12292277 CAGAATCTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12306246 original size:26 final size:27
Alignment explanation
Indices: 12306211--12306270 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
12306201 ATATAATAAT
*
12306211 AATATTTTTTTAA-CATAGCCTGTAAC
1 AATATTTTTTTAACCATAACCTGTAAC
*
12306237 AATA-TTTTTTAACCATAACGTGTAAC
1 AATATTTTTTTAACCATAACCTGTAAC
12306263 -ATATTTTT
1 AATATTTTT
12306271 GTATATGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (27 bp):
AATATTTTTTTAACCATAACCTGTAAC
Found at i:12306266 original size:25 final size:25
Alignment explanation
Indices: 12306211--12306270 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
12306201 ATATAATAAT
*
12306211 AATATTTTTTTAACATAGCCTGTAAC
1 AATA-TTTTTTAACATAACCTGTAAC
*
12306237 AATATTTTTTAACCATAACGTGTAAC
1 AATATTTTTTAA-CATAACCTGTAAC
12306263 -ATATTTTT
1 AATATTTTT
12306271 GTATATGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (25 bp):
AATATTTTTTAACATAACCTGTAAC
Found at i:12306346 original size:76 final size:76
Alignment explanation
Indices: 12306246--12306440 Score: 237
Period size: 76 Copynumber: 2.6 Consensus size: 76
12306236 CAATATTTTT
* * *
12306246 TAACCATAACGTGTAACATATTTTTGTATATGACGTGTAACAATAGTAATTTTTTTCAACATAAC
1 TAACCATGACATGTAACATGTTTTTGTATATGACGTGTAACAATAGTAATTTTTTTCAACATAAC
12306311 ATGTAACAACC
66 ATGTAACAACC
* * * * * * **
12306322 TAACCATGATATGTAACATGTTTTTGTACATGATGTATAATAATAGTATTTTTTTTCAACATGGC
1 TAACCATGACATGTAACATGTTTTTGTATATGACGTGTAACAATAGTAATTTTTTTCAACATAAC
* *
12306387 ATGTAGCAACT
66 ATGTAACAACC
** * *
12306398 TAATTATGGCGTGTAACATGTTTTTGTATATGACGTGTAACAA
1 TAACCATGACATGTAACATGTTTTTGTATATGACGTGTAACAA
12306441 CTTAACTATG
Statistics
Matches: 97, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
76 97 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (76 bp):
TAACCATGACATGTAACATGTTTTTGTATATGACGTGTAACAATAGTAATTTTTTTCAACATAAC
ATGTAACAACC
Found at i:12314353 original size:13 final size:13
Alignment explanation
Indices: 12314335--12314359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12314325 TTTAACACCA
12314335 AAAATAAAAAAAT
1 AAAATAAAAAAAT
12314348 AAAATAAAAAAA
1 AAAATAAAAAAA
12314360 AAACCCCTGA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:12316537 original size:3 final size:3
Alignment explanation
Indices: 12316529--12316553 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12316519 CCATACTTAA
12316529 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
12316554 CAAATGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12316938 original size:7 final size:7
Alignment explanation
Indices: 12316927--12316962 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
12316917 AGAATAGGGT
*
12316927 AGGGACT
1 AGGGACC
12316934 AGGGACC
1 AGGGACC
12316941 AGGGACC
1 AGGGACC
12316948 AGGGACC
1 AGGGACC
12316955 AGGGACC
1 AGGGACC
12316962 A
1 A
12316963 TCCATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.42, T:0.03
Consensus pattern (7 bp):
AGGGACC
Found at i:12317501 original size:4 final size:4
Alignment explanation
Indices: 12317492--12317519 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12317482 TGTCTTCATC
12317492 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
12317520 TGCAAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:12324860 original size:2 final size:2
Alignment explanation
Indices: 12324853--12324893 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12324843 TGAGCAAGCA
12324853 TC TC TC TC TC TC TC TC TC TC -C TC TC T- TC TC TC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12324892 TC
1 TC
12324894 ACACACACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:12324870 original size:12 final size:12
Alignment explanation
Indices: 12324853--12324893 Score: 61
Period size: 11 Copynumber: 3.7 Consensus size: 12
12324843 TGAGCAAGCA
12324853 TCTCTCTCTCTC
1 TCTCTCTCTCTC
12324865 TCTCTCTC-CTC
1 TCTCTCTCTCTC
12324876 TCT-TCTCTC-C
1 TCTCTCTCTCTC
12324886 TCTCTCTC
1 TCTCTCTC
12324894 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.30
11 11 0.41
12 8 0.30
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTCTCTCTCTC
Found at i:12324898 original size:2 final size:2
Alignment explanation
Indices: 12324893--12324919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12324883 TCCTCTCTCT
12324893 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
12324920 GTGCATGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12329337 original size:3 final size:3
Alignment explanation
Indices: 12329329--12329358 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12329319 AATTATTTCT
12329329 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12329359 AAGAATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12331715 original size:7 final size:7
Alignment explanation
Indices: 12331703--12331727 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12331693 GTGATTGTTT
12331703 TGTGTAA
1 TGTGTAA
12331710 TGTGTAA
1 TGTGTAA
12331717 TGTGTAA
1 TGTGTAA
12331724 TGTG
1 TGTG
12331728 AATTGTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (7 bp):
TGTGTAA
Found at i:12332113 original size:19 final size:19
Alignment explanation
Indices: 12332055--12332123 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
12332045 ACATGAAATT
12332055 TTTTTTTATAGAAAG-AAAA
1 TTTTTTTAT-GAAAGTAAAA
*
12332074 TTTTTTTATGTGTAAGATAAAA
1 TTTTTTTA--TGAAAG-TAAAA
* *
12332096 TTTTCTTATGAAAGTAAAT
1 TTTTTTTATGAAAGTAAAA
12332115 TTTGTTTTA
1 TTT-TTTTA
12332124 GTGCTCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 15 0.38
20 13 0.32
21 1 0.03
22 11 0.28
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (19 bp):
TTTTTTTATGAAAGTAAAA
Found at i:12334365 original size:30 final size:30
Alignment explanation
Indices: 12334329--12334392 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
12334319 CAAGAAGTTA
*
12334329 ATGAAGAGATTTAAAATGATCATAGAAATC
1 ATGAAGAGATTCAAAATGATCATAGAAATC
12334359 ATGAAGAGATTCAAAATGATCATAGAAATC
1 ATGAAGAGATTCAAAATGATCATAGAAATC
12334389 ATGA
1 ATGA
12334393 TAAAGAGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (30 bp):
ATGAAGAGATTCAAAATGATCATAGAAATC
Found at i:12335872 original size:17 final size:18
Alignment explanation
Indices: 12335838--12335872 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12335828 TACTATTTGT
*
12335838 GTGAAGTAGTTGTTTCAC
1 GTGAAGTAGTTATTTCAC
12335856 GTGAAGTA-TTATTTCAC
1 GTGAAGTAGTTATTTCAC
12335873 TTGTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (18 bp):
GTGAAGTAGTTATTTCAC
Found at i:12345970 original size:12 final size:12
Alignment explanation
Indices: 12345953--12345988 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12345943 GGCAGTGTTT
*
12345953 GATCTGGATCTG
1 GATCTGGAGCTG
12345965 GATCTGGAGCTG
1 GATCTGGAGCTG
*
12345977 GAGCTGGAGCTG
1 GATCTGGAGCTG
12345989 ACCGGGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.42, T:0.25
Consensus pattern (12 bp):
GATCTGGAGCTG
Found at i:12355942 original size:2 final size:2
Alignment explanation
Indices: 12355935--12355965 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12355925 TCACATTCAC
12355935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12355966 TAAAGAGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12365709 original size:27 final size:27
Alignment explanation
Indices: 12365679--12365760 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
12365669 CTGGTCAAGT
12365679 TGAGAGTGTTTTCATATGAATTGTGGC
1 TGAGAGTGTTTTCATATGAATTGTGGC
*
12365706 TGAGAGTGTTTCCATATGAATTGTGGC
1 TGAGAGTGTTTTCATATGAATTGTGGC
* *
12365733 TGAGAGTGTTTTTATATGAATCGTGGC
1 TGAGAGTGTTTTCATATGAATTGTGGC
12365760 T
1 T
12365761 AGGACTACGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.40
Consensus pattern (27 bp):
TGAGAGTGTTTTCATATGAATTGTGGC
Found at i:12372398 original size:25 final size:25
Alignment explanation
Indices: 12372364--12372412 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12372354 AAAATGATAA
*
12372364 AGAGAGTAGAA-AGGAGAGAGAAAAG
1 AGAGACTAGAATA-GAGAGAGAAAAG
12372389 AGAGACTAGAATAGAGAGAGAAAA
1 AGAGACTAGAATAGAGAGAGAAAA
12372413 TGAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.35, T:0.06
Consensus pattern (25 bp):
AGAGACTAGAATAGAGAGAGAAAAG
Found at i:12376067 original size:21 final size:21
Alignment explanation
Indices: 12376043--12376084 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12376033 TTAATACTTT
12376043 TATTGAAGAGGAAGAAAATGA
1 TATTGAAGAGGAAGAAAATGA
* * *
12376064 TATTGATGATGAAGAAGATGA
1 TATTGAAGAGGAAGAAAATGA
12376085 AGGAGTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (21 bp):
TATTGAAGAGGAAGAAAATGA
Found at i:12376347 original size:25 final size:24
Alignment explanation
Indices: 12376302--12376349 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12376292 AAGCATAAAC
**
12376302 TATTTGTATTATTTATTTATAATA
1 TATTTGTATTATTTAAATATAATA
*
12376326 TATTTGTATATTTTTAAATATAAT
1 TATTTGTAT-TATTTAAATATAAT
12376350 TCTATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTTGTATTATTTAAATATAATA
Found at i:12376355 original size:20 final size:21
Alignment explanation
Indices: 12376317--12376355 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
12376307 GTATTATTTA
* *
12376317 TTTATAATATATTTGTATATT
1 TTTATAATATAATTCTATATT
12376338 TTTA-AATATAATTCTATA
1 TTTATAATATAATTCTATA
12376356 ATTTGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTATAATATAATTCTATATT
Found at i:12378908 original size:29 final size:28
Alignment explanation
Indices: 12378853--12378908 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12378843 TGGAATTAGT
*
12378853 TTTCTTTTCTTTTTTTTTTCCTTCTTTC
1 TTTCTTTTCTTTTTTTTTTCCTCCTTTC
12378881 TTTCTTTT-TCTTTTTTTTTCTCTCCTTT
1 TTTCTTTTCT-TTTTTTTTTC-CTCCTTT
12378909 ATAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 18 0.72
29 6 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTCTTTTCTTTTTTTTTTCCTCCTTTC
Found at i:12378953 original size:117 final size:116
Alignment explanation
Indices: 12378754--12379012 Score: 323
Period size: 117 Copynumber: 2.2 Consensus size: 116
12378744 TGGAATTTTT
*
12378754 TTCTTT-TTTTGTTTTTTTTTCCTTTTTCTCTCATTTACAAATATACTAAAACTTTTTTTTTCTT
1 TTCTTTCTTTT-TTTTCTTTT--TTTTTCTCTCATTTACAAATATACTAAAAC-TTTTTTTTCTT
*
12378818 TTCAACTTTTTCTTCTTTGAAAGCTTGGAATTAGTTTTCTTTTCTTTT-TTTTTTCC
62 TTCAACTTTTTCTCCTTTGAAAGCTTGGAATT-GTTTTCTTTT-TTTTCTTTTTTCC
* * *
12378874 TTCTTTCTTTCTTTTTCTTTTTTTTTCTCTCCTTTATAAATATATTAAAAC-TTTTTTTCTTTTC
1 TTCTTTCTTT-TTTTTCTTTTTTTTTCTCTCATTTACAAATATACTAAAACTTTTTTTTCTTTTC
* *
12378938 AACTTTTGT-TCCTTTGAAAGCTTGGAATTTTTTTCTTTTTTTTCCTTTTTTCG
65 AACTTTT-TCTCCTTTGAAAGCTTGGAATTGTTTTCTTTTTTTT-CTTTTTTCC
*
12378991 TT-TTTC-TTTTTTTCTTTCTTTT
1 TTCTTTCTTTTTTTTCTTTTTTTT
12379013 ATGAATATAC
Statistics
Matches: 126, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
114 13 0.10
115 6 0.05
116 13 0.10
117 48 0.38
118 1 0.01
119 27 0.21
120 6 0.05
121 11 0.09
122 1 0.01
ACGTcount: A:0.14, C:0.16, G:0.05, T:0.66
Consensus pattern (116 bp):
TTCTTTCTTTTTTTTCTTTTTTTTTCTCTCATTTACAAATATACTAAAACTTTTTTTTCTTTTCA
ACTTTTTCTCCTTTGAAAGCTTGGAATTGTTTTCTTTTTTTTCTTTTTTCC
Found at i:12378978 original size:8 final size:8
Alignment explanation
Indices: 12378965--12379012 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
12378955 AAGCTTGGAA
12378965 TTTTTTTC
1 TTTTTTTC
12378973 TTTTTTTTC
1 -TTTTTTTC
*
12378982 CTTTTTTC
1 TTTTTTTC
*
12378990 -GTTTTTC
1 TTTTTTTC
12378997 TTTTTTTC
1 TTTTTTTC
12379005 TTTCTTTT
1 TTT-TTTT
12379013 ATGAATATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.18
8 16 0.47
9 12 0.35
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:12379070 original size:28 final size:29
Alignment explanation
Indices: 12379025--12379081 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
12379015 GAATATACTA
* *
12379025 AACCTTTTTTTTCTTTTCAACTTTTTTTC
1 AACCTTTTTCTTCTTTTCAAATTTTTTTC
12379054 AACC-TTTTCTTCTTTTCAAATTTTTTTC
1 AACCTTTTTCTTCTTTTCAAATTTTTTTC
12379082 CTTTGAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (29 bp):
AACCTTTTTCTTCTTTTCAAATTTTTTTC
Found at i:12387528 original size:23 final size:23
Alignment explanation
Indices: 12387477--12387528 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
12387467 ATAAAATTTA
*
12387477 AAGTGATAGCTAATAAACTTATT
1 AAGTGTTAGCTAATAAACTTATT
12387500 AAGTGTTAGCTAATAAACTTATT
1 AAGTGTTAGCTAATAAACTTATT
12387523 AAGTGT
1 AAGTGT
12387529 AACCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
AAGTGTTAGCTAATAAACTTATT
Found at i:12387748 original size:209 final size:217
Alignment explanation
Indices: 12387509--12388055 Score: 720
Period size: 223 Copynumber: 2.5 Consensus size: 217
12387499 TAAGTGTTAG
* * *
12387509 CTAATAAACTTATTAAGTGTAACCATATAAATAAAGTTTATTATAAGTTATAGTAATACTTATGT
1 CTAATAAACTTATTAAATGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGCTTATGT
12387574 ATAAATTAAATATATGTATATATAATATATTACTTTATTATATATATA-AT-TA-ATG-AT-ACA
66 ATAAATTAAATATATGTATATATAATATATTACTTTATTATATATATATATATATATGAATGACA
* *
12387634 -AA-TTATATGCTCA-AATGTTTTATATC-AAGTTTTTATAAATAATAACTAATTATAAACAATA
131 TAACTTATATG-TCATAATATTTTATATCAAAGTTTATATAAATAATAACTAATTATAAACAATA
* *
12387695 TGTTATAAAATCTAAGATGATAA
195 TATTATAAAATCTAAGATAATAA
* **
12387718 CTAATAAAGTTATTAAATGTAATCATATAAATAAAGTCCATTATAAGTTATAGTAATGCTTATGT
1 CTAATAAACTTATTAAATGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGCTTATGT
*
12387783 ATAAATT-AATATATGTATATATAAGATATTACTTTATTATATATATATATATATATATGAAATT
66 ATAAATTAAATATATGTATATATAATATATTACTTTA-T-TATATATATATATATATATG-----
* * *
12387847 AATGACATAACTTATATGTTATAATATTTTATATCAAAGTTTATATAGATAATAATTAATTATAA
124 AATGACATAACTTATATGTCATAATATTTTATATCAAAGTTTATATAAATAATAACTAATTATAA
12387912 ACAATATATTATAAAATCTAAGATAATAA
189 ACAATATATTATAAAATCTAAGATAATAA
* * * * * *
12387941 CTAATAAATTTATTTAATGTAATCATATAAATAAAATTTATTATAAATTATAATAATGTTTATGT
1 CTAATAAACTTATTAAATGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGCTTATGT
* * *
12388006 ATAAATTAAATATATGTATGTATATTATATTTA-TATAATTATATATATAT
66 ATAAATTAAATATATGTATATATAATATA-TTACT-TTATTATATATATAT
12388056 TCATAACATT
Statistics
Matches: 293, Mismatches: 26, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
208 28 0.10
209 67 0.23
210 10 0.03
211 2 0.01
212 2 0.01
213 3 0.01
219 2 0.01
220 3 0.01
221 4 0.01
222 19 0.06
223 128 0.44
224 20 0.07
225 5 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (217 bp):
CTAATAAACTTATTAAATGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGCTTATGT
ATAAATTAAATATATGTATATATAATATATTACTTTATTATATATATATATATATATGAATGACA
TAACTTATATGTCATAATATTTTATATCAAAGTTTATATAAATAATAACTAATTATAAACAATAT
ATTATAAAATCTAAGATAATAA
Found at i:12387996 original size:22 final size:22
Alignment explanation
Indices: 12387968--12388017 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12387958 TGTAATCATA
12387968 TAAATAAAATTTAT-TATAAAT
1 TAAATAAAATTTATGTATAAAT
**
12387989 TATAATAATGTTTATGTATAAAT
1 TA-AATAAAATTTATGTATAAAT
12388012 TAAATA
1 TAAATA
12388018 TATGTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 14 0.56
23 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TAAATAAAATTTATGTATAAAT
Found at i:12388022 original size:23 final size:23
Alignment explanation
Indices: 12387977--12388029 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
12387967 ATAAATAAAA
12387977 TTTAT-TATAAATTATAATAATG
1 TTTATGTATAAATTATAATAATG
12387999 TTTATGTATAAATTA-AATATATG
1 TTTATGTATAAATTATAATA-ATG
12388022 --TATGTATA
1 TTTATGTATA
12388030 TTATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.28
22 9 0.31
23 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
TTTATGTATAAATTATAATAATG
Found at i:12388027 original size:21 final size:22
Alignment explanation
Indices: 12387971--12388029 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
12387961 AATCATATAA
12387971 ATAA-AAT-TTAT-TATAAATT
1 ATAATAATGTTATGTATAAATT
12387990 ATAATAATGTTTATGTATAAATT
1 ATAATAATG-TTATGTATAAATT
12388013 A-AATATATG-TATGTATA
1 ATAATA-ATGTTATGTATA
12388030 TTATATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.11
20 3 0.09
21 8 0.23
22 8 0.23
23 12 0.34
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
ATAATAATGTTATGTATAAATT
Found at i:12393298 original size:2 final size:2
Alignment explanation
Indices: 12393291--12393321 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12393281 TTGGTCATGT
*
12393291 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12393322 TGTTAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:12422165 original size:7 final size:7
Alignment explanation
Indices: 12422145--12422182 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
12422135 AACTCAGAAG
12422145 AATAAAA
1 AATAAAA
12422152 AATAATAA
1 AATAA-AA
12422160 AA-AATAA
1 AATAA-AA
12422167 AATAAAA
1 AATAAAA
12422174 AATAAAA
1 AATAAAA
12422181 AA
1 AA
12422183 ATAATACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Done.