Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 49 of 344
Found at i:16256398 original size:15 final size:15
Alignment explanation
Indices: 16256375--16256424 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
16256365 TTTATTGAAT
16256375 TTATATTGATTAAAA
1 TTATATTGATTAAAA
* * *
16256390 TTATTTTGATTGAAT
1 TTATATTGATTAAAA
*
16256405 TTATATTGATT-GAA
1 TTATATTGATTAAAA
16256419 TTATAT
1 TTATAT
16256425 AATATATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (15 bp):
TTATATTGATTAAAA
Found at i:16256827 original size:23 final size:23
Alignment explanation
Indices: 16256797--16256883 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
16256787 GCTTTATCGA
* *
16256797 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
16256820 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
* *
16256841 TCAAGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
16256863 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
16256884 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 33 0.62
22 2 0.04
23 18 0.34
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:16260888 original size:20 final size:20
Alignment explanation
Indices: 16260863--16260901 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16260853 AACATTCAAA
16260863 ATACCATAATCAC-AACCAAG
1 ATACCATAA-CACAAACCAAG
16260883 ATACCATAACACAAACCAA
1 ATACCATAACACAAACCAA
16260902 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAACCAAG
Found at i:16263342 original size:21 final size:21
Alignment explanation
Indices: 16263311--16263363 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
16263301 TTTTAAAACT
*
16263311 ACTTGACCTTAGTGTCTTACC
1 ACTTGAACTTAGTGTCTTACC
*
16263332 ATTTGAACTTAGTGTCTTACC
1 ACTTGAACTTAGTGTCTTACC
16263353 ACTTGAACTTA
1 ACTTGAACTTA
16263364 ATAAATCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (21 bp):
ACTTGAACTTAGTGTCTTACC
Found at i:16264461 original size:3 final size:3
Alignment explanation
Indices: 16264453--16264487 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16264443 TTAGAAGATT
16264453 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
16264488 TTTTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:16267176 original size:49 final size:49
Alignment explanation
Indices: 16267095--16267190 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
16267085 TTATGCTATG
*
16267095 CATTTCTAAACTTAGTCTTCCACTGTCGACACTCTTATCACTATTTACA
1 CATTGCTAAACTTAGTCTTCCACTGTCGACACTCTTATCACTATTTACA
* * *
16267144 CATTGCTAAATTTAGTCTTCCACTGTCTACACTGTTATCACTATTTA
1 CATTGCTAAACTTAGTCTTCCACTGTCGACACTCTTATCACTATTTA
16267191 TCCCTTCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGTCGACACTCTTATCACTATTTACA
Found at i:16267855 original size:23 final size:26
Alignment explanation
Indices: 16267818--16267871 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
16267808 CTTCTAAAGT
16267818 TACC-AAATATGAAACTAAGC-A-CA
1 TACCAAAATATGAAACTAAGCTAGCA
*
16267841 TACCAAAATAT-AAACTAGGCTAGCA
1 TACCAAAATATGAAACTAAGCTAGCA
16267866 TACCAA
1 TACCAA
16267872 CATAGCCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 12 0.44
24 7 0.26
25 8 0.30
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.19
Consensus pattern (26 bp):
TACCAAAATATGAAACTAAGCTAGCA
Found at i:16280018 original size:21 final size:22
Alignment explanation
Indices: 16279985--16280025 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16279975 TTCATTTATG
*
16279985 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
16280006 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
16280026 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:16280475 original size:27 final size:27
Alignment explanation
Indices: 16280435--16280512 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 27
16280425 GAATCATTTG
16280435 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATTTCG-ACACTAAGTGTCATTCTCA
*
16280463 ATATCTCGACACTAAGTGTCATTCTCA
1 ATATTTCGACACTAAGTGTCATTCTCA
* *
16280490 ATATTTCTTACACTGAGTGTCAT
1 ATATTTC-GACACTAAGTGTCAT
16280513 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATTTCGACACTAAGTGTCATTCTCA
Found at i:16283535 original size:11 final size:12
Alignment explanation
Indices: 16283519--16283549 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
16283509 ACAGAGAAGG
16283519 AAGAAAAAGA-A
1 AAGAAAAAGAGA
16283530 AAGAAAAAGAGA
1 AAGAAAAAGAGA
16283542 AAGAAAAA
1 AAGAAAAA
16283550 AAGGGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:16287167 original size:40 final size:40
Alignment explanation
Indices: 16287121--16287304 Score: 129
Period size: 40 Copynumber: 4.5 Consensus size: 40
16287111 GATTCAGATA
* *
16287121 TATATATGGTACTTAGTGTGTAATAC-GAGATAGCTTCAGC
1 TATATATGGCACTTAGTGTGCAATACAGA-ATAGCTTCAGC
* * * *
16287161 TTTATATGGCACTTAGTGTGCGATTCAGAATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCAATACAGAATAGCTTCAGC
* * * * * *
16287201 TATATATGACACTTAGTGTGCGAGACTGAGATAACTTCGGC
1 TATATATGGCACTTAGTGTGCAATACAGA-ATAGCTTCAGC
* * * * * *
16287242 TATGTAAGGCACTTAGTGTACGAGAT-TATAATAGCTTCGGC
1 TATATATGGCACTTAGTGTGC-A-ATACAGAATAGCTTCAGC
* *
16287283 TTTGTATTGGCACTTAGTGTGC
1 TATATA-TGGCACTTAGTGTGC
16287305 GAGATATCGA
Statistics
Matches: 114, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
40 55 0.48
41 44 0.39
42 14 0.12
43 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCAATACAGAATAGCTTCAGC
Found at i:16287255 original size:41 final size:40
Alignment explanation
Indices: 16287150--16287308 Score: 165
Period size: 41 Copynumber: 3.9 Consensus size: 40
16287140 GTAATACGAG
* * * ** *
16287150 ATAGCTTCAGCTTTATATGGCACTTAGTGTGCGATTCAGA
1 ATAGCTTCGGCTATGTATGGCACTTAGTGTGCGAGACTGA
* *
16287190 ATAGCTTCGGCTATATATGACACTTAGTGTGCGAGACTGA
1 ATAGCTTCGGCTATGTATGGCACTTAGTGTGCGAGACTGA
* * * * *
16287230 GATAACTTCGGCTATGTAAGGCACTTAGTGTACGAGATTATA
1 -ATAGCTTCGGCTATGTATGGCACTTAGTGTGCGAGACT-GA
*
16287272 ATAGCTTCGGCTTTGTATTGGCACTTAGTGTGCGAGA
1 ATAGCTTCGGCTATGTA-TGGCACTTAGTGTGCGAGA
16287309 TATCGAGTAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
40 34 0.34
41 47 0.47
42 18 0.18
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
ATAGCTTCGGCTATGTATGGCACTTAGTGTGCGAGACTGA
Found at i:16294687 original size:109 final size:109
Alignment explanation
Indices: 16294472--16294677 Score: 360
Period size: 109 Copynumber: 1.9 Consensus size: 109
16294462 ATGTGTGATT
*
16294472 AGAAGGAGGCTAGACTCATACTGGATATGGAAGAGAGTGCACTCACAGTTACTCAAGGAAAGAAG
1 AGAAGGAGGCTAGACTCATACTGGAGATGGAAGAGAGTGCACTCACAGTTACTCAAGGAAAGAAG
16294537 ACGATCCAAGCCAAGCAAAAGGGAAAGGCTAAAATGCAACCTTC
66 ACGATCCAAGCCAAGCAAAAGGGAAAGGCTAAAATGCAACCTTC
* *
16294581 AGAAGGAGGCTATACTCATACTGGAGATGGGAGAGAGTGCACTCACAGTTACTCAAGGAAAGAAG
1 AGAAGGAGGCTAGACTCATACTGGAGATGGAAGAGAGTGCACTCACAGTTACTCAAGGAAAGAAG
*
16294646 ACGATCCAAG-CAAGGCAAAAGGGGAAGGCTAA
66 ACGATCCAAGCCAA-GCAAAAGGGAAAGGCTAA
16294678 GACTCAACCT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 3 0.03
109 89 0.97
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (109 bp):
AGAAGGAGGCTAGACTCATACTGGAGATGGAAGAGAGTGCACTCACAGTTACTCAAGGAAAGAAG
ACGATCCAAGCCAAGCAAAAGGGAAAGGCTAAAATGCAACCTTC
Found at i:16304479 original size:18 final size:17
Alignment explanation
Indices: 16304458--16304498 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
16304448 ATTTGATTAA
16304458 TTAAAAAATTAAAAAAT
1 TTAAAAAATTAAAAAAT
* *
16304475 GTTAAAATATTAAAATAT
1 -TTAAAAAATTAAAAAAT
16304493 TTAAAA
1 TTAAAA
16304499 CCCGTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAAAAATTAAAAAAT
Found at i:16308389 original size:13 final size:14
Alignment explanation
Indices: 16308362--16308391 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16308352 CTATAATTTT
16308362 AATACAAACTAATA
1 AATACAAACTAATA
16308376 AATACAAA-TAATA
1 AATACAAACTAATA
16308389 AAT
1 AAT
16308392 TTTTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (14 bp):
AATACAAACTAATA
Found at i:16308886 original size:50 final size:51
Alignment explanation
Indices: 16308811--16308911 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 51
16308801 TCCATCTGTT
16308811 CAAAATTTCACATTAACCTCGTGTTAGG-TCAAATAAAAGTTATTTGTACA
1 CAAAATTTCACATTAACCTCGTGTTAGGCTCAAATAAAAGTTATTTGTACA
16308861 CAAAATTTCACATTAACCTCGTGTTAGGCTCAAATAAAAGTTATTTGTACA
1 CAAAATTTCACATTAACCTCGTGTTAGGCTCAAATAAAAGTTATTTGTACA
16308912 TTCTTCTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 28 0.56
51 22 0.44
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (51 bp):
CAAAATTTCACATTAACCTCGTGTTAGGCTCAAATAAAAGTTATTTGTACA
Found at i:16314307 original size:14 final size:14
Alignment explanation
Indices: 16314288--16314317 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16314278 AATAAAAAAT
*
16314288 AATATTATAAATTA
1 AATATTACAAATTA
16314302 AATATTACAAATTA
1 AATATTACAAATTA
16314316 AA
1 AA
16314318 GTACGAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATTACAAATTA
Found at i:16316954 original size:357 final size:356
Alignment explanation
Indices: 16316296--16317014 Score: 1156
Period size: 357 Copynumber: 2.0 Consensus size: 356
16316286 TAACATCATA
* *
16316296 GAACATCAATCCCTAGTAGTAATGCTTAAAAGGAAAAAAAGAAAAGCTTGATTGAGCTTCCGCGA
1 GAACATCAATCCCTAGTAGTAATGCTTAAAAGAAAAAAAAGAAAAGCTTGACTGAGCTTCCGCGA
* *
16316361 CATTGACCCGCTCAAGATTAGGGACCACCTGAAATCCAATCAATAACAAAGTGAGTTGTGAACTC
66 CACTGACCCGCTCAAGATTAGGGACCACCTAAAATCCAATCAATAACAAAGTGAGTTGTGAACTC
* * * * * *
16316426 AATTCATAAAAGTAGTTTAATTAAATAATGTTTGCTCATAAAGAAATTCCAAATTTAGAGATTCG
131 AATGCATAAAAGGAGTTAAATTAAATAATGTTCGCTCATAAAGAAATTCCAAATTCAAAGATTCG
* *
16316491 GTTGATATAAGAGTAATTTCAGTCTAGATTCAGAGTAGATGAGTTACATATATGTATATATATAC
196 GTTGATATAAGAGTAATTTCAGTCCAGATTCAGAGCAGATGAGTTACATATATGTATATATATAC
*
16316556 GATTTCAATTCAAATATTGTTCAGATCAGATTCAAATGCAATATTCCTATTTCCG-TCTGCTACA
261 GATTTCAATTCAAATATGGTTCAGATCAGATTCAAATGCAATATTCCTATTTCCGTTC-GCTACA
* *
16316620 CATCATCTTC-GTCCATCCCAACACACCACTAT
325 CACCATCTTCAGT-CATCCCAACACACCACAAT
16316652 GAACATCAATCCCTAGTAGTAATGCTTAAAATGAAAAAAAAGAAAAGCTTGACTGAGCTTCCGCG
1 GAACATCAATCCCTAGTAGTAATGCTTAAAA-GAAAAAAAAGAAAAGCTTGACTGAGCTTCCGCG
*
16316717 ACACTGACCCGCTCAAGATT-GGGATCACCTAAAATCCAATCAATAACAAAGTGAGTTGTGAACT
65 ACACTGACCCGCTCAAGATTAGGGACCACCTAAAATCCAATCAATAACAAAGTGAGTTGTGAACT
* * * *
16316781 CAATGCGTAAAAGGAGTTAAAATTCAATAATGTTCGCTTATAAAGAAATTCCAAATTCAAAGGTT
130 CAATGCATAAAAGGAGTT-AAATTAAATAATGTTCGCTCATAAAGAAATTCCAAATTCAAAGATT
*
16316846 CGGTTGATATATGAGTAATTTCAGTCCAGATTCAGAGCAGATGAGTTACATATATGTATATATAT
194 CGGTTGATATAAGAGTAATTTCAGTCCAGATTCAGAGCAGATGAGTTACATATATGTATATATAT
* *
16316911 ACGATTTCAATTCAAATATGGTTCAGATCAGATTCAGATGCAATATTCCTATTTTCGTTCGCTAC
259 ACGATTTCAATTCAAATATGGTTCAGATCAGATTCAAATGCAATATTCCTATTTCCGTTCGCTAC
*
16316976 ACACCATCTTCAGTCATCTCAACACACCACAAT
324 ACACCATCTTCAGTCATCCCAACACACCACAAT
*
16317009 GGACAT
1 GAACAT
16317015 TTAATGCCCA
Statistics
Matches: 334, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
356 88 0.26
357 242 0.72
358 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (356 bp):
GAACATCAATCCCTAGTAGTAATGCTTAAAAGAAAAAAAAGAAAAGCTTGACTGAGCTTCCGCGA
CACTGACCCGCTCAAGATTAGGGACCACCTAAAATCCAATCAATAACAAAGTGAGTTGTGAACTC
AATGCATAAAAGGAGTTAAATTAAATAATGTTCGCTCATAAAGAAATTCCAAATTCAAAGATTCG
GTTGATATAAGAGTAATTTCAGTCCAGATTCAGAGCAGATGAGTTACATATATGTATATATATAC
GATTTCAATTCAAATATGGTTCAGATCAGATTCAAATGCAATATTCCTATTTCCGTTCGCTACAC
ACCATCTTCAGTCATCCCAACACACCACAAT
Found at i:16323829 original size:32 final size:32
Alignment explanation
Indices: 16323788--16323852 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
16323778 GAAAAGAAAG
16323788 ATCTCATCTTTTCTTCATCTTCTCTCCACCGA
1 ATCTCATCTTTTCTTCATCTTCTCTCCACCGA
16323820 ATCTCATCTTTTCTTCATCTTCTCTCCACCGA
1 ATCTCATCTTTTCTTCATCTTCTCTCCACCGA
16323852 A
1 A
16323853 AATGGCAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.37, G:0.03, T:0.43
Consensus pattern (32 bp):
ATCTCATCTTTTCTTCATCTTCTCTCCACCGA
Found at i:16331651 original size:46 final size:46
Alignment explanation
Indices: 16331515--16331829 Score: 282
Period size: 46 Copynumber: 6.7 Consensus size: 46
16331505 GTTATTGTTG
* * * * *
16331515 GCTAGTGTAAGACATATTTGGGACATGCATCGGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGA
* * * * * * *
16331561 GCCAATTTAAAACCATGTCTTGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAGA
16331609 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGA
*
16331655 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGA
* * *
16331701 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAGA
* * ** * * *
16331747 G-TCAGTGTAAGACCATGCCTGGGACATGGCAT-TGATTTGAGATGTGA
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAGA
16331794 GCTAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
16331830 ACTTTACCCA
Statistics
Matches: 225, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
45 3 0.01
46 120 0.53
47 73 0.32
48 28 0.12
49 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGA
Found at i:16331717 original size:92 final size:95
Alignment explanation
Indices: 16331515--16331829 Score: 344
Period size: 92 Copynumber: 3.4 Consensus size: 95
16331505 GTTATTGTTG
* * * * * * * *
16331515 GCTAGTGTAAGACATATTTGGGACATGCATCGGCC-AC-ATTATGAGAGCCAATTTAAAACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTACGA-GACGATAGCCAGTGTAAGACCATG
*
16331578 TCTTGGACATGGCATCGGCATTGAGACG-AGA
65 TCTGGGACATGGCATCGGCATTGAGACGTA-A
16331609 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACG-TAAGCCAGTGTAAGA-CATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGAT-AGCCAGTGTAAGACCATG
* *
16331671 TCTGGGACAT-GCATCGGCCTCGAGACGTAA
65 TCTGGGACATGGCATCGGCATTGAGACGTAA
* * * *
16331701 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGATAGTCAGTGTAAGACCATGC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGATAGCCAGTGTAAGACCATGT
* * *
16331765 CTGGGACATGGCAT-TG-ATTTGAGATGTGA
66 CTGGGACATGGCATCGGCA-TTGAGACGTAA
16331794 GCTAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
16331830 ACTTTACCCA
Statistics
Matches: 188, Mismatches: 21, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
91 2 0.01
92 66 0.35
93 49 0.26
94 63 0.34
95 8 0.04
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (95 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGATAGCCAGTGTAAGACCATGT
CTGGGACATGGCATCGGCATTGAGACGTAA
Found at i:16334416 original size:15 final size:16
Alignment explanation
Indices: 16334385--16334425 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
16334375 TCAATTGCAG
16334385 AAAGAAGAAAAAAATA
1 AAAGAAGAAAAAAATA
*
16334401 AAAGAA-AAAAAGATA
1 AAAGAAGAAAAAAATA
16334416 AAAGATAGAA
1 AAAGA-AGAA
16334426 GAAGGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.59
16 7 0.32
17 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (16 bp):
AAAGAAGAAAAAAATA
Found at i:16342540 original size:11 final size:10
Alignment explanation
Indices: 16342525--16342560 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
16342515 CAAAAAGAAG
16342525 AAAAAATAAA
1 AAAAAATAAA
*
16342535 AGAAAAATGAA
1 A-AAAAATAAA
16342546 AAAAAATAAA
1 AAAAAATAAA
16342556 AAAAA
1 AAAAA
16342561 GGAAGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:16342557 original size:22 final size:21
Alignment explanation
Indices: 16342516--16342567 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
16342506 AATAAATTGC
16342516 AAAAAGAAGAAAAAATAAAAG
1 AAAAAGAAGAAAAAATAAAAG
16342537 AAAAATGAA-AAAAAATAAAA-
1 AAAAA-GAAGAAAAAATAAAAG
*
16342557 AAAAGGAAGAA
1 AAAAAGAAGAA
16342568 TAGGAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 6 0.21
21 16 0.57
22 3 0.11
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAAGAAGAAAAAATAAAAG
Found at i:16344824 original size:14 final size:13
Alignment explanation
Indices: 16344803--16344842 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
16344793 ATCAATTTAT
16344803 ATTAAAAATTAAA
1 ATTAAAAATTAAA
*
16344816 GTATAAAAATTAAA
1 AT-TAAAAATTAAA
*
16344830 ATTAAAATTTAAA
1 ATTAAAAATTAAA
16344843 CCTAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
ATTAAAAATTAAA
Found at i:16345363 original size:41 final size:42
Alignment explanation
Indices: 16345297--16345389 Score: 127
Period size: 41 Copynumber: 2.2 Consensus size: 42
16345287 CAAAAAGTAT
* *
16345297 TTATATTAAAAAAATACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAAATACTACAATAAATACAATAAATATTTTA
*
16345339 TTATATTAAAAAAA-ACATA-AATAAATACAATATATATTTTA
1 TTATATTAAAAAAATAC-TACAATAAATACAATAAATATTTTA
*
16345380 TTGTATTAAA
1 TTATATTAAA
16345390 TATATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 30 0.65
42 16 0.35
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (42 bp):
TTATATTAAAAAAATACTACAATAAATACAATAAATATTTTA
Found at i:16345511 original size:4 final size:5
Alignment explanation
Indices: 16345473--16345518 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
16345463 GTTAGTGAGC
*
16345473 TAATA TAAATA TAAATA TAATT TAATA T-ATA TAAT- TAATA TAATA T
1 TAATA T-AATA T-AATA TAATA TAATA TAATA TAATA TAATA TAATA T
16345519 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 8 0.22
5 17 0.47
6 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:16345511 original size:18 final size:18
Alignment explanation
Indices: 16345473--16345537 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 18
16345463 GTTAGTGAGC
16345473 TAATATAA-ATATAAATA
1 TAATATAATATATAAATA
*
16345490 TAATTTAATATATATAAT-
1 TAATATAATATATA-AATA
***
16345508 TAATATAATAT-TTTTTA
1 TAATATAATATATAAATA
16345525 TAATATAATATAT
1 TAATATAATATAT
16345538 TCGAATTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.03
17 19 0.49
18 16 0.41
19 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATATAATATATAAATA
Found at i:16345518 original size:14 final size:15
Alignment explanation
Indices: 16345480--16345518 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
16345470 AGCTAATATA
16345480 AATATAAATATAATTT
1 AATAT-AATATAATTT
16345496 AATAT-ATATAA-TT
1 AATATAATATAATTT
16345509 AATATAATAT
1 AATATAATAT
16345519 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
16 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATAATATAATTT
Found at i:16353450 original size:25 final size:25
Alignment explanation
Indices: 16353385--16353454 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
16353375 GTAGACACAC
* * *
16353385 CATAGCTTGTATGAGCTTACCGATT
1 CATAGCTCGAATGAGCATACCGATT
*
16353410 CATAGCTCGTGA-GAGCATACCGATT
1 CATAGCTCG-AATGAGCATACCGATT
16353435 CATAGCTCGAATGAGCATAC
1 CATAGCTCGAATGAGCATAC
16353455 ATGTATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 37 0.95
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
CATAGCTCGAATGAGCATACCGATT
Found at i:16354805 original size:10 final size:10
Alignment explanation
Indices: 16354790--16354845 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
16354780 TATTTTAAAA
16354790 GATAAATAAG
1 GATAAATAAG
16354800 GATAAATAAG
1 GATAAATAAG
*
16354810 GATAAATAAA
1 GATAAATAAG
16354820 GATAAAT-AG
1 GATAAATAAG
*
16354829 AGATAAATAAA
1 -GATAAATAAG
16354840 GATAAA
1 GATAAA
16354846 AGCTAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
9 1 0.02
10 39 0.95
11 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (10 bp):
GATAAATAAG
Found at i:16354815 original size:20 final size:20
Alignment explanation
Indices: 16354789--16354845 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
16354779 ATATTTTAAA
*
16354789 AGATAAATAAGGATAAATA-
1 AGATAAATAAAGATAAATAG
16354808 AGGATAAATAAAGATAAATAG
1 A-GATAAATAAAGATAAATAG
16354829 AGATAAATAAAGATAAA
1 AGATAAATAAAGATAAA
16354846 AGCTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AGATAAATAAAGATAAATAG
Found at i:16354821 original size:30 final size:30
Alignment explanation
Indices: 16354787--16354845 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16354777 CTATATTTTA
*
16354787 AAAGATAAATA-AGGATAAATAAGGATAAAT
1 AAAGATAAATAGA-GATAAATAAAGATAAAT
16354817 AAAGATAAATAGAGATAAATAAAGATAAA
1 AAAGATAAATAGAGATAAATAAAGATAAA
16354846 AGCTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (30 bp):
AAAGATAAATAGAGATAAATAAAGATAAAT
Found at i:16356827 original size:5 final size:5
Alignment explanation
Indices: 16356817--16356854 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
16356807 ATTAATATCC
*
16356817 AAACA AAACA AAACA AAACA AAACA AAACA AAATA AAA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAA
16356855 TAATAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.03
Consensus pattern (5 bp):
AAACA
Found at i:16356855 original size:5 final size:5
Alignment explanation
Indices: 16356821--16356889 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
16356811 ATATCCAAAC
* * * * * *
16356821 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAT AAAAT AATAA- ATAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
16356871 AAAAT -AAAT AAAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAA
16356890 ATTTGTCTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 6 0.11
5 45 0.79
6 6 0.11
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:16356869 original size:20 final size:20
Alignment explanation
Indices: 16356841--16356889 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
16356831 AAAACAAAAC
*
16356841 AAAACAAAATAAAAT-AATA
1 AAAATAAAATAAAATAAATA
16356860 AATAATAAAATAAAATAAATA
1 AA-AATAAAATAAAATAAATA
16356881 AAAATAAAA
1 AAAATAAAA
16356890 ATTTGTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAAATAAATA
Found at i:16361460 original size:10 final size:10
Alignment explanation
Indices: 16361442--16361490 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
16361432 CTAAATTCTA
16361442 AAAGATAAAG
1 AAAGATAAAG
* *
16361452 AAGGATAAAT
1 AAAGATAAAG
*
16361462 AAAGATAAAT
1 AAAGATAAAG
* *
16361472 AGAGATAAAT
1 AAAGATAAAG
16361482 AAAGATAAA
1 AAAGATAAA
16361491 AGCTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (10 bp):
AAAGATAAAG
Found at i:16361467 original size:20 final size:20
Alignment explanation
Indices: 16361442--16361491 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
16361432 CTAAATTCTA
16361442 AAAGATAAAGAAG-GATAAAT
1 AAAGATAAA-AAGAGATAAAT
*
16361462 AAAGATAAATAGAGATAAAT
1 AAAGATAAAAAGAGATAAAT
16361482 AAAGATAAAA
1 AAAGATAAAA
16361492 GCTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAGATAAAAAGAGATAAAT
Found at i:16368418 original size:19 final size:19
Alignment explanation
Indices: 16368364--16368421 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
16368354 ATTTTGTAGA
16368364 AAAATATTTTATT-ATTTT
1 AAAATATTTTATTAATTTT
*
16368382 AATAAGATTTAATATTAATTTT
1 AA-AATATTT--TATTAATTTT
*
16368404 TAAATATTTTATTAATTT
1 AAAATATTTTATTAATTT
16368422 AATATTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 2 0.06
19 15 0.45
21 10 0.30
22 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AAAATATTTTATTAATTTT
Found at i:16368896 original size:26 final size:26
Alignment explanation
Indices: 16368867--16368921 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
16368857 CAGGCAAATT
* * *
16368867 TTAATATCGGGCGTATACTTTCTTCC
1 TTAACATCGGGCGGATACTTTCATCC
16368893 TTAACATCGGGCGGATACTTTCATCC
1 TTAACATCGGGCGGATACTTTCATCC
16368919 TTA
1 TTA
16368922 CACAAAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (26 bp):
TTAACATCGGGCGGATACTTTCATCC
Found at i:16369212 original size:48 final size:48
Alignment explanation
Indices: 16369157--16369252 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
16369147 TCAACAATTG
* *
16369157 TACATAACATTTAACACCTACAGAGTCATATTAACTTACTATTTTCAA
1 TACATAACATATAACACATACAGAGTCATATTAACTTACTATTTTCAA
* * *
16369205 TACATAACATATATCACATACAGAGTCATATTGACTTACTCTTTTCAA
1 TACATAACATATAACACATACAGAGTCATATTAACTTACTATTTTCAA
16369253 ATATTTCCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (48 bp):
TACATAACATATAACACATACAGAGTCATATTAACTTACTATTTTCAA
Found at i:16371257 original size:21 final size:21
Alignment explanation
Indices: 16371231--16371284 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
16371221 TCCCTTACAC
*
16371231 TTCTACCGATACTCTGTTGGG
1 TTCTACCGATACTCTATTGGG
16371252 TTCTACCGATACTCTATTGGG
1 TTCTACCGATACTCTATTGGG
16371273 TTCTACCGATAC
1 TTCTACCGATAC
16371285 CAGTTGGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (21 bp):
TTCTACCGATACTCTATTGGG
Found at i:16373583 original size:29 final size:29
Alignment explanation
Indices: 16373546--16373640 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
16373536 AAACAAACAT
* * *
16373546 CTTTT-TGGTTTTCTTAGTTAAATGAATG
1 CTTTTGTGGTTATCTTAGTTAAAAGGATG
*
16373574 CTTTTGTGGTGATCTTAGTTAAAAGGATG
1 CTTTTGTGGTTATCTTAGTTAAAAGGATG
* * * *
16373603 CCTTTGTGGCTACCTTTGTTAAAAGGATG
1 CTTTTGTGGTTATCTTAGTTAAAAGGATG
16373632 CTTTTGTGG
1 CTTTTGTGG
16373641 CCATTCTTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 5 0.09
29 51 0.91
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.45
Consensus pattern (29 bp):
CTTTTGTGGTTATCTTAGTTAAAAGGATG
Found at i:16373650 original size:29 final size:29
Alignment explanation
Indices: 16373557--16373654 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
16373547 TTTTTGGTTT
* * **
16373557 TCTTAGTTAAATGAATGCTTTTGTGGTGA
1 TCTTAGTTAAAAGGATGCTTTTGTGGCCA
* *
16373586 TCTTAGTTAAAAGGATGCCTTTGTGGCTA
1 TCTTAGTTAAAAGGATGCTTTTGTGGCCA
* *
16373615 CCTTTGTTAAAAGGATGCTTTTGTGGCCA
1 TCTTAGTTAAAAGGATGCTTTTGTGGCCA
16373644 TTCTT-GTTAAA
1 -TCTTAGTTAAA
16373655 GGAATTCGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 55 0.95
30 3 0.05
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.42
Consensus pattern (29 bp):
TCTTAGTTAAAAGGATGCTTTTGTGGCCA
Found at i:16377917 original size:16 final size:16
Alignment explanation
Indices: 16377892--16377924 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16377882 AACGAGATTA
16377892 TAAATAATTTTTCTAT
1 TAAATAATTTTTCTAT
*
16377908 TAAATTATTTTTCTAT
1 TAAATAATTTTTCTAT
16377924 T
1 T
16377925 TTATGGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATAATTTTTCTAT
Found at i:16379479 original size:29 final size:29
Alignment explanation
Indices: 16379447--16379503 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
16379437 TTTAAATCAG
16379447 AAAACATTGATCTACAAATAAATAATCCA
1 AAAACATTGATCTACAAATAAATAATCCA
16379476 AAAACATTGATCTACAAATAAATAATCC
1 AAAACATTGATCTACAAATAAATAATCC
16379504 GACTTTTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.25
Consensus pattern (29 bp):
AAAACATTGATCTACAAATAAATAATCCA
Found at i:16388204 original size:8 final size:8
Alignment explanation
Indices: 16388191--16388221 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
16388181 CTTTATCTTA
16388191 TTTGTTGT
1 TTTGTTGT
16388199 TTTGTTGT
1 TTTGTTGT
16388207 TTTGTTGT
1 TTTGTTGT
*
16388215 TGTGTTG
1 TTTGTTG
16388222 ATGAACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (8 bp):
TTTGTTGT
Found at i:16394077 original size:55 final size:55
Alignment explanation
Indices: 16394001--16394127 Score: 157
Period size: 55 Copynumber: 2.3 Consensus size: 55
16393991 CGAGCCTGCC
* * *
16394001 AAAACAACACGGGCGTGCGACACGCCCGTGTGGAAGAACCATGGGT-AAACCTGTT
1 AAAACAACACGGACGTGCGACACGCCCGTATGGAACAACCAT-GGTCAAACCTGTT
* * * *
16394056 AAAACAGCACGGACGTTCGACATGCCCGTATGGAACACCCATGGTCAAACCTGTT
1 AAAACAACACGGACGTGCGACACGCCCGTATGGAACAACCATGGTCAAACCTGTT
**
16394111 AAATTAACACGGACGTG
1 AAAACAACACGGACGTG
16394128 AGGTTTACAC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 3 0.05
55 57 0.95
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (55 bp):
AAAACAACACGGACGTGCGACACGCCCGTATGGAACAACCATGGTCAAACCTGTT
Found at i:16399023 original size:24 final size:24
Alignment explanation
Indices: 16398991--16399040 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
16398981 TAGCTTAATC
16398991 TAGCTAGCCCATTGGTCAATTTGT
1 TAGCTAGCCCATTGGTCAATTTGT
*
16399015 TAGCTAGCCTATTGGTCAATTTGT
1 TAGCTAGCCCATTGGTCAATTTGT
16399039 TA
1 TA
16399041 AGTTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (24 bp):
TAGCTAGCCCATTGGTCAATTTGT
Found at i:16403215 original size:16 final size:17
Alignment explanation
Indices: 16403179--16403217 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16403169 TTTTGAAAAG
16403179 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
* *
16403196 AAAACGAATGAGTCTTA
1 AAAACAAATGAATCTTA
16403213 AAAAC
1 AAAAC
16403218 TTAATAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:16408983 original size:167 final size:167
Alignment explanation
Indices: 16408704--16409030 Score: 636
Period size: 167 Copynumber: 2.0 Consensus size: 167
16408694 AGTGAATGGC
*
16408704 ATCATCAGAAACGCCATTAATTTTGAAAGTGTCACAAAACTCCAGAAAATTCGCCAATTGAGTGT
1 ATCATCAGAAACGCCATTAATTTTGAAAGTGTCACAAAACTCCAGAAAATTCGCCAAGTGAGTGT
*
16408769 TGGGATCCTCATCCTGCAAACCATCAAACTGAACAAACTGTTGTATCATCTGAATTGTGTTAGGT
66 TGGGATCCTCATCCTGCAAACCATCAAACTGAACAAACTGCTGTATCATCTGAATTGTGTTAGGT
16408834 TTCAGTTCAAAATTATTCGTAGCAATAGCAATTCAAA
131 TTCAGTTCAAAATTATTCGTAGCAATAGCAATTCAAA
16408871 ATCATCAGAAACGCCATTAATTTTGAAAGTGTCACAAAACTCCAGAAAATTCGCCAAGTGAGTGT
1 ATCATCAGAAACGCCATTAATTTTGAAAGTGTCACAAAACTCCAGAAAATTCGCCAAGTGAGTGT
16408936 TGGGATCCTCATCCTGCAAACCATCAAACTGAACAAACTGCTGTATCATCTGAATTGTGTTAGGT
66 TGGGATCCTCATCCTGCAAACCATCAAACTGAACAAACTGCTGTATCATCTGAATTGTGTTAGGT
16409001 TTCAGTTCAAAATTATTCGTAGCAATAGCA
131 TTCAGTTCAAAATTATTCGTAGCAATAGCA
16409031 GGTCTAACTA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 158 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (167 bp):
ATCATCAGAAACGCCATTAATTTTGAAAGTGTCACAAAACTCCAGAAAATTCGCCAAGTGAGTGT
TGGGATCCTCATCCTGCAAACCATCAAACTGAACAAACTGCTGTATCATCTGAATTGTGTTAGGT
TTCAGTTCAAAATTATTCGTAGCAATAGCAATTCAAA
Found at i:16416500 original size:21 final size:21
Alignment explanation
Indices: 16416474--16416514 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16416464 AGACGAGCAA
* *
16416474 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16416495 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16416515 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16429381 original size:2 final size:2
Alignment explanation
Indices: 16429376--16429407 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16429366 TGTGTGTATG
16429376 TA TA TA TA TA TA TA T- TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16429408 AATGTGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16429396 original size:13 final size:13
Alignment explanation
Indices: 16429378--16429407 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16429368 TGTGTATGTA
16429378 TATATATATATAT
1 TATATATATATAT
16429391 TATATATATATAT
1 TATATATATATAT
16429404 TATA
1 TATA
16429408 AATGTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATATATAT
Found at i:16432591 original size:48 final size:48
Alignment explanation
Indices: 16432391--16432610 Score: 148
Period size: 48 Copynumber: 4.6 Consensus size: 48
16432381 TGAGATCTCG
* * * *
16432391 TATATGACCATATCTGGGATATGGCATTGGCATCGATATATGATCCCA
1 TATAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCA
* * * * *
16432439 TATAAGGCCATGTTTGGGACATGGCATTGGCATCGATATGAG-TACATCG
1 TATAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGAT-C-CCA
* * * * *
16432488 TGTAAGAGCATAG-CTGGG-CTATCG-ACTTTG-AT--ATGTGTGATCCCA
1 TATAAGACCAT-GTCTGGGAC-ATGGCA-TTGGCATCGATATGTGATCCCA
* * *
16432533 TATAATACCATGTCTAGGACATGGCATTGGCATCGATATGTGGTCCCA
1 TATAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCA
* * * * *
16432581 TGTAAGACCATATCGGGGATATGGCGTTGG
1 TATAAGACCATGTCTGGGACATGGCATTGG
16432611 AACCCTACTA
Statistics
Matches: 126, Mismatches: 34, Indels: 24
0.68 0.18 0.13
Matches are distributed among these distances:
44 1 0.01
45 19 0.15
46 10 0.08
47 2 0.02
48 74 0.59
49 19 0.15
50 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (48 bp):
TATAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCA
Found at i:16442179 original size:24 final size:23
Alignment explanation
Indices: 16442152--16442222 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 23
16442142 TGAATTAGGC
16442152 TAAAATTAGCATATAGAATGTATA
1 TAAAATTAGCATAT-GAATGTATA
* * **
16442176 TAAATTTAG---ATGGAT-TAGC
1 TAAAATTAGCATATGAATGTATA
16442195 TAAAATTAGCATATGGAATGTATA
1 TAAAATTAGCATAT-GAATGTATA
16442219 TAAA
1 TAAA
16442223 TAACTTGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 2 0.06
22 2 0.06
23 3 0.09
24 14 0.41
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.34
Consensus pattern (23 bp):
TAAAATTAGCATATGAATGTATA
Found at i:16442204 original size:43 final size:44
Alignment explanation
Indices: 16442137--16442223 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
16442127 TGGTTGGTTG
16442137 TTAGATGAATTAGGCTAAAATTAGCATATAGAATGTATATAAAT
1 TTAGATGAATTAGGCTAAAATTAGCATATAGAATGTATATAAAT
* *
16442181 TTAGATGGATTA-GCTAAAATTAGCATATGGAATGTATATAAAT
1 TTAGATGAATTAGGCTAAAATTAGCATATAGAATGTATATAAAT
16442224 AACTTGTATG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 30 0.73
44 11 0.27
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (44 bp):
TTAGATGAATTAGGCTAAAATTAGCATATAGAATGTATATAAAT
Found at i:16443459 original size:21 final size:21
Alignment explanation
Indices: 16443433--16443474 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16443423 TTTGATAGTG
16443433 TGCTTTGAAGATATAATTTTT
1 TGCTTTGAAGATATAATTTTT
16443454 TGCTTTGAAGATATAATTTTT
1 TGCTTTGAAGATATAATTTTT
16443475 CTCTGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (21 bp):
TGCTTTGAAGATATAATTTTT
Found at i:16449359 original size:45 final size:45
Alignment explanation
Indices: 16449300--16449422 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 45
16449290 TGATGCCGAT
* * * * *
16449300 GTCCCAAACATGGTCTTACACGTAACCACGTATATCGATGCCAAC
1 GTCCCAGACGTGGTCTTACACGAAACCACATATATCGATACCAAC
* *
16449345 GTCCTAGACGTGGTCTTACACGAAATCACATATATCGATACCAAC
1 GTCCCAGACGTGGTCTTACACGAAACCACATATATCGATACCAAC
* * *
16449390 TTCCCAGACGTGGTCTTTCACGAAATCACATAT
1 GTCCCAGACGTGGTCTTACACGAAACCACATAT
16449423 CGAAATCCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (45 bp):
GTCCCAGACGTGGTCTTACACGAAACCACATATATCGATACCAAC
Found at i:16456697 original size:24 final size:24
Alignment explanation
Indices: 16456670--16456766 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
16456660 GAAATGACCT
16456670 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
16456694 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGGATTTGAA
16456718 TGGCACTATGTGTGCGGATTT-ATA
1 TGGCACTATGTGTGCGGATTTGA-A
** *
16456742 CAGTACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
16456766 T
1 T
16456767 CGTCGATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:16464122 original size:24 final size:24
Alignment explanation
Indices: 16464095--16464254 Score: 130
Period size: 24 Copynumber: 6.6 Consensus size: 24
16464085 GAAATGACCT
16464095 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
16464119 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGGATTTGAA
* * *
16464143 TAGCACTATGTATACGGATTT-ATA
1 TGGCACTATGTGTGCGGATTTGA-A
* *
16464167 CGGCACTATGTGTGTGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* ** *
16464191 TCGTCGA-TATGTGTATGGATTATTAA
1 T-GGC-ACTATGTGTGCGGATT-TGAA
* *
16464217 -GGCACTATGTGTGCGG-GTTAACA
1 TGGCACTATGTGTGCGGATTTGA-A
*
16464240 TGGCACTATGGGTGC
1 TGGCACTATGTGTGC
16464255 AAATTTCCTT
Statistics
Matches: 108, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 83 0.77
25 16 0.15
26 4 0.04
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:16467291 original size:45 final size:45
Alignment explanation
Indices: 16467176--16467399 Score: 233
Period size: 45 Copynumber: 5.1 Consensus size: 45
16467166 CATGTTATCT
* * *
16467176 TATATCGTTGCC-ACTGTCCCAGACAGGGTCTTACACG-AATCA-A
1 TATATCGATGCCAAC-GTCCCAGACATGGTCTTACACGAAACCACA
* * * * * *
16467219 -ATA-CAATGTCGATGTCCTAGACATGGTCTTACACGTAACCACA
1 TATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACCACA
* * * *
16467262 TATATCGATGCCAATGTCCCAAACGTGGTCTTACACGAAATCACA
1 TATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACCACA
* *
16467307 TATATCGATGCCAACGACCCAGACATGGTCTTACACAAAACCACA
1 TATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACCACA
* * * *
16467352 TATATCGAAGCCAACATCCCAGACATGGTTTTACACGAAATCACA
1 TATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACCACA
16467397 TAT
1 TAT
16467400 CAAAATCCTA
Statistics
Matches: 149, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
41 24 0.16
42 8 0.05
43 1 0.01
44 3 0.02
45 113 0.76
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (45 bp):
TATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACCACA
Found at i:16473542 original size:25 final size:26
Alignment explanation
Indices: 16473493--16473543 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
16473483 TTTATTATTT
*
16473493 TTATTAAAATATATTTAATAATAATC
1 TTATTAAAATATATATAATAATAATC
*
16473519 TTATTAAAATTTA-ATAATAATAATC
1 TTATTAAAATATATATAATAATAATC
16473544 ATCTACCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATTAAAATATATATAATAATAATC
Found at i:16475177 original size:18 final size:21
Alignment explanation
Indices: 16475141--16475181 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
16475131 TTATTTTTTT
16475141 ATTTTATGTATTTTGTTTAAA
1 ATTTTATGTATTTTGTTTAAA
16475162 ATTTTATG-A-TTT-TTTAAA
1 ATTTTATGTATTTTGTTTAAA
16475180 AT
1 AT
16475182 GATTGAGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 1 0.05
21 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTTATGTATTTTGTTTAAA
Found at i:16484774 original size:46 final size:47
Alignment explanation
Indices: 16484672--16484844 Score: 189
Period size: 46 Copynumber: 3.7 Consensus size: 47
16484662 ATATCTATGT
* *
16484672 CGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACGTCTCG-AGC
*
16484718 TGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACGTCTCGA-GC
* * *
16484764 CGATG-CATGTCTCAGACAT-GTCTTACACTGGCGCT-CGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-TTACGTCTCGA-GC
* *
16484810 TGATGCCATGTCCCAGACATGGTCTTAAACTGGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT
16484845 CTCATAATGT
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
44 12 0.11
45 15 0.14
46 56 0.51
47 14 0.13
48 12 0.11
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACGTCTCGAGC
Found at i:16484864 original size:94 final size:92
Alignment explanation
Indices: 16484716--16484886 Score: 222
Period size: 94 Copynumber: 1.8 Consensus size: 92
16484706 ACATCTCGTA
* * * * *
16484716 GCTGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGATGCATGT-CTCAGA
1 GCTGATGCATGTCCCAGACATGTCTTAAACTGGCTTACATATCGAGGCCAATGCATGTCCT-AAA
16484780 CATGTCTTACACTGGCGCTCGTCTCAAT
65 CATGTCTTACACTGGCGCTCGTCTCAAT
*
16484808 GCTGATGCCATGTCCCAGACATGGTCTTAAACTGGCTCT-CATAAT-GTGGCCAATGCATGTCCT
1 GCTGATG-CATGTCCCAGACAT-GTCTTAAACTGGCT-TACAT-ATCGAGGCCAATGCATGTCCT
16484871 AAACATGTCTTACACT
62 AAACATGTCTTACACT
16484887 AGCTCACACA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
92 7 0.10
93 14 0.21
94 43 0.63
95 4 0.06
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (92 bp):
GCTGATGCATGTCCCAGACATGTCTTAAACTGGCTTACATATCGAGGCCAATGCATGTCCTAAAC
ATGTCTTACACTGGCGCTCGTCTCAAT
Found at i:16491396 original size:27 final size:28
Alignment explanation
Indices: 16491353--16491405 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
16491343 AAATATTAAG
*
16491353 ATAATTCTAATAAAAAATTTAGAGAAAT
1 ATAATTCTAATAAAAAATTGAGAGAAAT
*
16491381 ATAATT-TAATAGAAAATTGAGAGAA
1 ATAATTCTAATAAAAAATTGAGAGAA
16491406 TTTTGAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (28 bp):
ATAATTCTAATAAAAAATTGAGAGAAAT
Found at i:16492304 original size:21 final size:20
Alignment explanation
Indices: 16492280--16492318 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16492270 GCCAAGGCTA
*
16492280 ATAAAATAACTATAACCTTGG
1 ATAAAATAAATA-AACCTTGG
*
16492301 ATAATATAAATAAACCTT
1 ATAAAATAAATAAACCTT
16492319 TTAAATCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAAAATAAATAAACCTTGG
Found at i:16492610 original size:18 final size:20
Alignment explanation
Indices: 16492589--16492629 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
16492579 TAAATCATAG
*
16492589 AAAATTATT-AAAATT-ACA
1 AAAATGATTAAAAATTAACA
16492607 AAAATGATTAAAAATTAACA
1 AAAATGATTAAAAATTAACA
16492627 AAA
1 AAA
16492630 GTTTACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATGATTAAAAATTAACA
Found at i:16495184 original size:16 final size:16
Alignment explanation
Indices: 16495143--16495184 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16495133 TATTTGAAAT
*
16495143 AATTAATAATTAATTA
1 AATTAATATTTAATTA
*
16495159 AATTATTATTTAATTGA
1 AATTAATATTTAATT-A
16495176 AA-TAATATT
1 AATTAATATT
16495185 ATTTTTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTAATATTTAATTA
Found at i:16495184 original size:19 final size:19
Alignment explanation
Indices: 16495136--16495188 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
16495126 TATGAAATAT
* *
16495136 TTGAAATAATTAATAATTAA
1 TTGAAATAA-TATTATTTAA
16495156 TT-AAAT--TATTATTTAA
1 TTGAAATAATATTATTTAA
16495172 TTGAAATAATATTATTT
1 TTGAAATAATATTATTT
16495189 TTCATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.36
17 4 0.14
19 12 0.43
20 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
TTGAAATAATATTATTTAA
Found at i:16503397 original size:16 final size:18
Alignment explanation
Indices: 16503373--16503415 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
16503363 AAATCCACCC
*
16503373 AAGTGAAATAA-A-CTTT
1 AAGTTAAATAATATCTTT
*
16503389 AAGTTAAATAATATTTTT
1 AAGTTAAATAATATCTTT
16503407 AAGTTAAAT
1 AAGTTAAAT
16503416 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 1 0.04
18 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTTAAATAATATCTTT
Found at i:16503630 original size:17 final size:19
Alignment explanation
Indices: 16503610--16503655 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
16503600 GGAAAAAAAC
16503610 ATTTTTTTATAA-TTTA-A
1 ATTTTTTTATAATTTTAGA
*
16503627 ATTTTTATATAATTTTTAGA
1 ATTTTTTTATAA-TTTTAGA
16503647 ATTTTTTTA
1 ATTTTTTTA
16503656 AATCTATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
19 4 0.17
20 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTTTTATAATTTTAGA
Found at i:16518792 original size:48 final size:48
Alignment explanation
Indices: 16518590--16518864 Score: 167
Period size: 48 Copynumber: 5.8 Consensus size: 48
16518580 CATAGTAGGG
* * * * * * *
16518590 TGCCAATGCCATATCCCGGATATGGTCTTACATGGG-CCACATATCTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
*
16518637 TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGATCAC---AC-A
1 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
** * * * *
16518681 TATCAA-ACCGATAG-CCCA-ACTATGGTCTTACACAAT-GTA-CTCATATA-GA
1 TGCCAATGCC-AT-GTCCCAGAC-ATGGTCTT--A-TATGGGATCACATA-ACGA
* * *
16518730 TGCCACTGCCATGTCCCGGACATGGTTTTATATGGGATCACATAACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
* * * * * * *
16518778 TGTCAATGCCATGTCGCAAACATGGTCTTACATGGGGTCATATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
* * *
16518826 TGCCAATGCCATATCCCAGATATGGTCTTATACGGGATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATC
16518865 TCATCAACCG
Statistics
Matches: 169, Mismatches: 41, Indels: 35
0.69 0.17 0.14
Matches are distributed among these distances:
43 4 0.02
44 19 0.11
45 4 0.02
46 5 0.03
47 36 0.21
48 80 0.47
49 17 0.10
50 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
Found at i:16520318 original size:29 final size:29
Alignment explanation
Indices: 16520286--16520373 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
16520276 TCGGCTATCA
** *
16520286 ATTATGAAAAGGGATGGTGACAACCATTG
1 ATTATGAAAAGGGATGGTTTCAACCATCG
*
16520315 ATTAATGAAAAGGGATGGTTTCGACCATCG
1 ATT-ATGAAAAGGGATGGTTTCAACCATCG
*
16520345 AATATGAAAAGGGATGGTTTCAACCATCG
1 ATTATGAAAAGGGATGGTTTCAACCATCG
16520374 TTTAGCACAC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 28 0.54
30 24 0.46
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.25
Consensus pattern (29 bp):
ATTATGAAAAGGGATGGTTTCAACCATCG
Found at i:16520352 original size:59 final size:59
Alignment explanation
Indices: 16520259--16520371 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
16520249 ATCATCGACC
* *
16520259 AATGAAAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGTGACAACCATTGATT
1 AATGAAAAGGGATAGCTTCGACCATCAATTATGAAAAGGGATGGTGACAACCATTGATT
* * **
16520318 AATGAAAAGGGATGGTTTCGACCATCGAA-TATGAAAAGGGATGGTTTCAACCAT
1 AATGAAAAGGGATAGCTTCGACCATC-AATTATGAAAAGGGATGGTGACAACCAT
16520372 CGTTTAGCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.96
60 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (59 bp):
AATGAAAAGGGATAGCTTCGACCATCAATTATGAAAAGGGATGGTGACAACCATTGATT
Found at i:16527019 original size:9 final size:9
Alignment explanation
Indices: 16527005--16527038 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16526995 TTTTAGGGAC
16527005 TAAATTGAA
1 TAAATTGAA
16527014 TAAATTGAA
1 TAAATTGAA
* *
16527023 AAAATTGCA
1 TAAATTGAA
16527032 TAAATTG
1 TAAATTG
16527039 TTAATCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (9 bp):
TAAATTGAA
Found at i:16527536 original size:10 final size:11
Alignment explanation
Indices: 16527516--16527547 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
16527506 TAAATTGGAT
16527516 AAATGGAAATG
1 AAATGGAAATG
16527527 AAAT-GAAATG
1 AAATGGAAATG
16527537 AAATGGAAATG
1 AAATGGAAATG
16527548 TGAAATGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (11 bp):
AAATGGAAATG
Found at i:16538771 original size:25 final size:24
Alignment explanation
Indices: 16538729--16538776 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16538719 AAAAGGAAAT
16538729 AGTATTAAAGGAAAATAAAATAAAA
1 AGTATTAAAGGAAAAT-AAATAAAA
*
16538754 AGTACTTAAA-GAAGATAAATAAA
1 AGTA-TTAAAGGAAAATAAATAAA
16538777 GATAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (24 bp):
AGTATTAAAGGAAAATAAATAAAA
Found at i:16538792 original size:17 final size:18
Alignment explanation
Indices: 16538770--16538803 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16538760 TAAAGAAGAT
*
16538770 AAATAAAGATAA-AAATG
1 AAATAAAAATAATAAATG
16538787 AAATAAAAATAATAAAT
1 AAATAAAAATAATAAAT
16538804 AAAAAGTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATAAAAATAATAAATG
Found at i:16552707 original size:15 final size:15
Alignment explanation
Indices: 16552687--16552716 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16552677 CCAGCCCAGT
16552687 CCAACCAACACACCA
1 CCAACCAACACACCA
*
16552702 CCAACCACCACACCA
1 CCAACCAACACACCA
16552717 TGTGGGGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.57, G:0.00, T:0.00
Consensus pattern (15 bp):
CCAACCAACACACCA
Found at i:16555450 original size:28 final size:28
Alignment explanation
Indices: 16555419--16555484 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
16555409 CCATCACAAA
* *
16555419 AACAGTATCAGGTGGGCCTTAGCCCATT
1 AACAGAATCAGGTGGGCCTAAGCCCATT
* *
16555447 AACAGAATTAGGTGGGCCTAAGCCCAAT
1 AACAGAATCAGGTGGGCCTAAGCCCATT
16555475 -ACAGAATCAG
1 AACAGAATCAG
16555485 TATCAGATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (28 bp):
AACAGAATCAGGTGGGCCTAAGCCCATT
Found at i:16568451 original size:21 final size:22
Alignment explanation
Indices: 16568412--16568452 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16568402 GTTGAAATGT
*
16568412 CACACGGGCGTGTTGCCCCTCC
1 CACACGAGCGTGTTGCCCCTCC
16568434 CACACGAGCGTG-TGCCCCT
1 CACACGAGCGTGTTGCCCCT
16568453 GTGTTAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.44, G:0.27, T:0.17
Consensus pattern (22 bp):
CACACGAGCGTGTTGCCCCTCC
Found at i:16576715 original size:33 final size:33
Alignment explanation
Indices: 16576669--16576735 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
16576659 GGCTTTGGCA
* *
16576669 AGGAAAGGCTTGGTTTTTAAGTGGTCAAATTTG
1 AGGAAAGACTTGGTTTTTAAGTGGCCAAATTTG
*
16576702 AGGAAAGATTTGGTTTTTAAGTGGCCAAATTTG
1 AGGAAAGACTTGGTTTTTAAGTGGCCAAATTTG
16576735 A
1 A
16576736 CTCGCCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (33 bp):
AGGAAAGACTTGGTTTTTAAGTGGCCAAATTTG
Found at i:16577723 original size:39 final size:39
Alignment explanation
Indices: 16577668--16577746 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
16577658 TGCCCTCCTG
*
16577668 AAGCTCAGCCCGAAGCGAGAAATCACTAGAGAGATTCTA
1 AAGCTCAGCCCAAAGCGAGAAATCACTAGAGAGATTCTA
*
16577707 AAGCTCAGCCCAAAGCGAGAAATCACTGGAGAGATTCTA
1 AAGCTCAGCCCAAAGCGAGAAATCACTAGAGAGATTCTA
16577746 A
1 A
16577747 CTCGATTGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (39 bp):
AAGCTCAGCCCAAAGCGAGAAATCACTAGAGAGATTCTA
Found at i:16578585 original size:27 final size:28
Alignment explanation
Indices: 16578547--16578603 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
16578537 AAGCAATGGG
*
16578547 AGAAGTTATTTTACATTTT-ATAATTTT
1 AGAAATTATTTTACATTTTGATAATTTT
16578574 AGAAATTATTTTACATTTTGATAATTTT
1 AGAAATTATTTTACATTTTGATAATTTT
16578602 AG
1 AG
16578604 GAAGATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (28 bp):
AGAAATTATTTTACATTTTGATAATTTT
Found at i:16580504 original size:11 final size:11
Alignment explanation
Indices: 16580488--16580517 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16580478 ACACGCCCGT
16580488 GTGGCCTACCC
1 GTGGCCTACCC
16580499 GTGGCCTACCC
1 GTGGCCTACCC
*
16580510 GTGTCCTA
1 GTGGCCTA
16580518 TACTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.40, G:0.27, T:0.23
Consensus pattern (11 bp):
GTGGCCTACCC
Found at i:16589376 original size:17 final size:18
Alignment explanation
Indices: 16589356--16589391 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
16589346 TTTAAAATTT
*
16589356 TAAAATTATTAA-AAAAA
1 TAAAATTATAAATAAAAA
16589373 TAAAATTATAAATAAAAA
1 TAAAATTATAAATAAAAA
16589391 T
1 T
16589392 TATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATTATAAATAAAAA
Found at i:16589411 original size:13 final size:12
Alignment explanation
Indices: 16589369--16589412 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 12
16589359 AATTATTAAA
16589369 AAAATAAAATTAT
1 AAAA-AAAATTAT
16589382 AAATAAAAATTAT
1 AAA-AAAAATTAT
16589395 AAAAAAAAGTTAT
1 AAAAAAAA-TTAT
16589408 AAAAA
1 AAAAA
16589413 TTTTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.17
13 23 0.79
14 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:16589427 original size:13 final size:13
Alignment explanation
Indices: 16589411--16589454 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
16589401 AAGTTATAAA
16589411 AATTTTAAATTAT
1 AATTTTAAATTAT
* * *
16589424 AATTTT-TATAAA
1 AATTTTAAATTAT
16589436 AATTTTAAATTAT
1 AATTTTAAATTAT
16589449 AATTTT
1 AATTTT
16589455 TTGCTAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTTTAAATTAT
Found at i:16589465 original size:27 final size:25
Alignment explanation
Indices: 16589404--16589455 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16589394 TAAAAAAAAG
16589404 TTATAAAAATTTTAAATTATAATTT
1 TTATAAAAATTTTAAATTATAATTT
16589429 TTATAAAAATTTTAAATTATAATTT
1 TTATAAAAATTTTAAATTATAATTT
16589454 TT
1 TT
16589456 TGCTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATAAAAATTTTAAATTATAATTT
Found at i:16590038 original size:12 final size:12
Alignment explanation
Indices: 16590023--16590063 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16590013 CCCGTATTAA
16590023 ATTTTTTATTTT
1 ATTTTTTATTTT
16590035 A--TTTTATTTT
1 ATTTTTTATTTT
* *
16590045 ATTTTTTATATA
1 ATTTTTTATTTT
16590057 ATTTTTT
1 ATTTTTT
16590064 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:16590323 original size:33 final size:33
Alignment explanation
Indices: 16590285--16590349 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16590275 GAAATGACAG
*
16590285 CAAAACAATGGGAAAATAGTAAG-AAAACAACAA
1 CAAAACAATGGAAAAATAGT-AGTAAAACAACAA
16590318 CAAAACAATGGAAAAATAGTAGTAAAACAACA
1 CAAAACAATGGAAAAATAGTAGTAAAACAACA
16590350 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.63, C:0.12, G:0.14, T:0.11
Consensus pattern (33 bp):
CAAAACAATGGAAAAATAGTAGTAAAACAACAA
Found at i:16591197 original size:16 final size:16
Alignment explanation
Indices: 16591176--16591228 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
16591166 TCCTAAATTC
16591176 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
* *
16591192 CTTTTTCGTTTTTCTT
1 CTTTTTCTTTTTTTTT
* * *
16591208 GTTTCTCTTTTATTTT
1 CTTTTTCTTTTTTTTT
16591224 CTTTT
1 CTTTT
16591229 ATCAGTTGTC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:16598562 original size:117 final size:116
Alignment explanation
Indices: 16598356--16598574 Score: 305
Period size: 117 Copynumber: 1.9 Consensus size: 116
16598346 ATCATTAGAG
* * *
16598356 TGCCATAGCCAATATATAGTCTTATATTAAATACTACCATGGTCCAGCCATGGTCTTACGTTCAT
1 TGCCATAGCCAATATATAGTCTTACATTAAATACTACCATGGTCCAACCATGGTATTACGTTCAT
* * *
16598421 AGTGTCATAACCCAGTTATGGTCTTATCCGTCAATTCGTCCTTTACATTAA
66 AGTGCCATAACCCAATTATAGTCTTATCCGTCAATTCGTCCTTTACATTAA
* * * *
16598472 TGCCATAGCCCAA-CTATGGTCTTACATATAAATACTGCCATGGTCCAACCATGGTATTACGTTT
1 TGCCATAG-CCAATATATAGTCTTACAT-TAAATACTACCATGGTCCAACCATGGTATTACGTTC
* *
16598536 ATAGTGCCATAACCTAATTATAGTCTTATTCGTCAATTC
64 ATAGTGCCATAACCCAATTATAGTCTTATCCGTCAATTC
16598575 ATCTTTAGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
116 19 0.21
117 70 0.79
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (116 bp):
TGCCATAGCCAATATATAGTCTTACATTAAATACTACCATGGTCCAACCATGGTATTACGTTCAT
AGTGCCATAACCCAATTATAGTCTTATCCGTCAATTCGTCCTTTACATTAA
Found at i:16600212 original size:15 final size:15
Alignment explanation
Indices: 16600192--16600226 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16600182 TGAGTCAGGT
*
16600192 AAATTTTTGAGGCTG
1 AAATTTTTGAGGCCG
16600207 AAA-TTTTGAGGCCG
1 AAATTTTTGAGGCCG
16600221 AAATTT
1 AAATTT
16600227 CTTTTAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (15 bp):
AAATTTTTGAGGCCG
Found at i:16604417 original size:11 final size:11
Alignment explanation
Indices: 16604401--16604426 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16604391 GAATGAACAT
16604401 TAAAGAGGAGA
1 TAAAGAGGAGA
16604412 TAAAGAGGAGA
1 TAAAGAGGAGA
16604423 TAAA
1 TAAA
16604427 CATCAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (11 bp):
TAAAGAGGAGA
Found at i:16612952 original size:43 final size:42
Alignment explanation
Indices: 16612898--16613040 Score: 180
Period size: 43 Copynumber: 3.3 Consensus size: 42
16612888 TTTATTTAAA
* *
16612898 AAAAACGCCGCTAAAAGTCATGACTTTTAACGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAAGTCATG-CTTTTAACGGCGTTTTTTGG
*
16612941 AAAAGCGCCGCTAAAAGTCATTGCTTTTAACGGCCTTTTTTGG
1 AAAAGCGCCGCTAAAAGTCA-TGCTTTTAACGGCGTTTTTTGG
* * *
16612984 AAAAGCGCCGCTAAAAGTCACGGCTTTTAGCGACGTTTTTATGG
1 AAAAGCGCCGCTAAAAGTCA-TGCTTTTAACGGCGTTTTT-TGG
*
16613028 CAAA-CGCCGCTAA
1 AAAAGCGCCGCTAA
16613041 TTTTGACAGA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 81 0.91
44 8 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAAGTCATGCTTTTAACGGCGTTTTTTGG
Found at i:16613421 original size:21 final size:20
Alignment explanation
Indices: 16613397--16613444 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
16613387 TTTTGCTCTG
16613397 CTCTGCTGCCATCGCTAC-TGC
1 CTCTGCT-CCATCGCT-CGTGC
*
16613418 CTCTGCCTCCCTCGCTCGTGC
1 CTCTG-CTCCATCGCTCGTGC
16613439 CTCTGC
1 CTCTGC
16613445 CTCCCTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.04, C:0.48, G:0.19, T:0.29
Consensus pattern (20 bp):
CTCTGCTCCATCGCTCGTGC
Found at i:16613457 original size:42 final size:42
Alignment explanation
Indices: 16613411--16613504 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
16613401 GCTGCCATCG
16613411 CTACTGCCTCTGCCTCCCTCGCT-CGTGCCT-CTGCCTCCCTCA
1 CTACTGCCTCTGCCTCCCTCGCTGC-TG-CTGCTGCCTCCCTCA
* *
16613453 CTACTGCCGCTGCCTCCCTCGCTGCTGCTGCTGCCTCCCTCT
1 CTACTGCCTCTGCCTCCCTCGCTGCTGCTGCTGCCTCCCTCA
*
16613495 CTGCTGCCTC
1 CTACTGCCTC
16613505 CGCTCTAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.93
43 1 0.02
ACGTcount: A:0.03, C:0.51, G:0.17, T:0.29
Consensus pattern (42 bp):
CTACTGCCTCTGCCTCCCTCGCTGCTGCTGCTGCCTCCCTCA
Found at i:16613482 original size:18 final size:18
Alignment explanation
Indices: 16613441--16613505 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
16613431 GCTCGTGCCT
*
16613441 CTGCCTCCCTCACTACTGCCG
1 CTGCCTCCCTC-C--CTGCTG
*
16613462 CTGCCTCCCTCGCTGCTG
1 CTGCCTCCCTCCCTGCTG
* *
16613480 CTG-CTGCCTCCCTCTCTG
1 CTGCCTCCCTCCCT-GCTG
16613498 CTGCCTCC
1 CTGCCTCC
16613506 GCTCTAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 8 0.22
18 14 0.39
19 3 0.08
21 11 0.31
ACGTcount: A:0.03, C:0.52, G:0.17, T:0.28
Consensus pattern (18 bp):
CTGCCTCCCTCCCTGCTG
Found at i:16613498 original size:21 final size:21
Alignment explanation
Indices: 16613420--16613501 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
16613410 GCTACTGCCT
16613420 CTGCCTCCCTCGCT-CGTGCCT-
1 CTGCCTCCCTCGCTGC-TG-CTG
* * *
16613441 CTGCCTCCCTCACTACTGCCG
1 CTGCCTCCCTCGCTGCTGCTG
16613462 CTGCCTCCCTCGCTGCTGCTG
1 CTGCCTCCCTCGCTGCTGCTG
*
16613483 CTGCCTCCCTCTCTGCTGC
1 CTGCCTCCCTCGCTGCTGC
16613502 CTCCGCTCTA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.02, C:0.51, G:0.18, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCTG
Found at i:16619082 original size:9 final size:9
Alignment explanation
Indices: 16619061--16619181 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
16619051 TATATATTAC
*
16619061 GTAAGTTAA
1 GTAAGTTAT
16619070 GTAAGCTT-T
1 GTAAG-TTAT
16619079 GTAAGTTAT
1 GTAAGTTAT
16619088 GTAAGTTAT
1 GTAAGTTAT
* *
16619097 GTTA-TGAT
1 GTAAGTTAT
* *
16619105 ATACATTTAT
1 GTA-AGTTAT
**
16619115 GTAAGGCAT
1 GTAAGTTAT
16619124 GTAAGTTAT
1 GTAAGTTAT
* *
16619133 GATATGATAT
1 G-TAAGTTAT
* *
16619143 AT-ATTTAT
1 GTAAGTTAT
16619151 GT-A-TTAT
1 GTAAGTTAT
*
16619158 GTAAGTTGT
1 GTAAGTTAT
16619167 GTAAGTTAT
1 GTAAGTTAT
16619176 GATAAG
1 G-TAAG
16619182 ATATATATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 15
0.70 0.18 0.13
Matches are distributed among these distances:
7 6 0.07
8 12 0.14
9 48 0.58
10 17 0.20
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:16619202 original size:56 final size:56
Alignment explanation
Indices: 16619135--16619366 Score: 348
Period size: 56 Copynumber: 4.2 Consensus size: 56
16619125 TAAGTTATGA
16619135 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
16619191 TATGATATATATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
1 TATGATATATATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* * *
16619248 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
16619304 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATG-TAAG-T-TAT-TA
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
16619356 TATGATATATA
1 TATGATATATA
16619367 ATAAACATTA
Statistics
Matches: 163, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
52 12 0.07
53 3 0.02
54 1 0.01
55 4 0.02
56 91 0.56
57 51 0.31
58 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (56 bp):
TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
Found at i:16619264 original size:113 final size:112
Alignment explanation
Indices: 16619135--16619345 Score: 361
Period size: 113 Copynumber: 1.9 Consensus size: 112
16619125 TAAGTTATGA
*
16619135 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
16619200 TATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
66 TATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
* *
16619248 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
*
16619313 TATTTATGTATTATGTAAGTTTTGTAAGTTATG
66 TATTTATGTATTATGTAAGTTGTGTAAGTTATG
16619346 TAAGTTATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
111 1 0.01
112 25 0.27
113 67 0.72
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (112 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
TATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
Found at i:16619309 original size:13 final size:13
Alignment explanation
Indices: 16619291--16619320 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16619281 TAAGTTATGA
16619291 TATGATATATATT
1 TATGATATATATT
16619304 TATGATATATATT
1 TATGATATATATT
16619317 TATG
1 TATG
16619321 TATTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:16619340 original size:9 final size:9
Alignment explanation
Indices: 16619323--16619353 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16619313 TATTTATGTA
16619323 TTATGTAAG
1 TTATGTAAG
*
16619332 TTTTGTAAG
1 TTATGTAAG
16619341 TTATGTAAG
1 TTATGTAAG
16619350 TTAT
1 TTAT
16619354 TATATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (9 bp):
TTATGTAAG
Found at i:16619490 original size:20 final size:20
Alignment explanation
Indices: 16619428--16619492 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
16619418 TCCAAAATAT
16619428 GTAATTTAAAAAATTGTGTC
1 GTAATTTAAAAAATTGTGTC
* *
16619448 GTGATTAAATTGCAAAATATGTGTC
1 GTAATTTAA----AAAAT-TGTGTC
16619473 GTAATTTAAAAAATTGTGTC
1 GTAATTTAAAAAATTGTGTC
16619493 CTGATTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
20 13 0.36
21 5 0.14
24 5 0.14
25 13 0.36
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAATTTAAAAAATTGTGTC
Found at i:16621877 original size:60 final size:60
Alignment explanation
Indices: 16621746--16621875 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
16621736 TTTCAAATTG
* ** * *
16621746 GGGAGAAAGGGG-TAATTATTTTAGGGTTTCAAATTAGGGAAAATGGGGGGAGATAAACTA
1 GGGAG-AAGGGGATAATTATTTTAGGGATTCAAAGAAGGGAAAATGGGGGGAAATAAACCA
* * *
16621806 GGGAGAAGGGGATGATTATTTTAGGGATTCGAAGAAGGGAAAAT-GGGGGAAATAAGCCA
1 GGGAGAAGGGGATAATTATTTTAGGGATTCAAAGAAGGGAAAATGGGGGGAAATAAACCA
16621865 GGGAGAAGGGG
1 GGGAGAAGGGG
16621876 GAAAATGAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 29 0.48
60 32 0.52
ACGTcount: A:0.36, C:0.04, G:0.40, T:0.20
Consensus pattern (60 bp):
GGGAGAAGGGGATAATTATTTTAGGGATTCAAAGAAGGGAAAATGGGGGGAAATAAACCA
Found at i:16622238 original size:117 final size:115
Alignment explanation
Indices: 16621958--16622439 Score: 451
Period size: 114 Copynumber: 4.2 Consensus size: 115
16621948 ATTTGCGACG
* * * *
16621958 TTTTCCCCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACAT-AAACGCCACTAAAAAA
1 TTTTCCCATAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTACCCTAAAACGCCACTAAAAAT
* * *
16622022 CAAACAAAACGATACCGTTTTGATATAAACAGAATAA-ACTTTAGTGGCGT
66 CAAAAAAAACGACACCATTTTGATATAAACAGAATAACA-TTTAGTGGCGT
* *
16622072 TTTTCCCATAGCGCCGCTAAAGGCAAATCAATTGCGGCGTTTCACCCTAAAACGCCACTAAAAAT
1 TTTTCCCATAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTACCCTAAAACGCCACTAAAAAT
* * *
16622137 CCAAAAAAAACGACGA-CATTTTCATATGAACAGAATAACATTTTGTGGCGT
66 -CAAAAAAAACGAC-ACCATTTTGATATAAACAGAATAACATTTAGTGGCGT
* * * * * *
16622188 TTTATCACGA-AGCGCCGCTAAAGGCGAAA-CTATTACGACGTTTTACCCTAAAATGCCACTAAT
1 TTT-TC-CCATAGCGCCGCTAAAGGC-AAACCAATTGCGGCGTTTTACCCTAAAACGCCACTAAA
* * * * *
16622251 AATCGAATAAAACTACATCATTTTGATATAAACAAAATAACCA-TTAGTGGCGT
63 AATCAAAAAAAACGACACCATTTTGATATAAACAGAATAA-CATTTAGTGGCGT
* * * * * * * *
16622304 TTATACCC-TAGCGCCGCTAAA-TCAAACCTATTGTGGCGTTTAAACCAAAAATGCCACTAAAAA
1 TT-TTCCCATAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTACCCTAAAACGCCACTAAAAA
* * * ** * * * *
16622367 TCCATAAAAACTACACTGTTTTGATCTAAACAAAATAACCCTTTAGCGGCGT
65 TCAAAAAAAACGACACCATTTTGATATAAACAGAATAA-CATTTAGTGGCGT
16622419 TTATT-CCATAGCGCCGCTAAA
1 TT-TTCCCATAGCGCCGCTAAA
16622440 TCCAATTTTT
Statistics
Matches: 308, Mismatches: 46, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
113 3 0.01
114 108 0.35
115 55 0.18
116 84 0.27
117 53 0.17
118 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (115 bp):
TTTTCCCATAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTACCCTAAAACGCCACTAAAAAT
CAAAAAAAACGACACCATTTTGATATAAACAGAATAACATTTAGTGGCGT
Found at i:16623406 original size:41 final size:41
Alignment explanation
Indices: 16623342--16623430 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
16623332 GTTAAATAAC
* * **
16623342 TTTTAGCGGCATTTTACCGAAAGCGCTGCTAATGCTCTGGT
1 TTTTAGTGGCATTTTAACGAAAGCGCCACTAATGCTCTGGT
* *
16623383 TTTTAGTGGCATTTTATAC-AAAGCGCCACTAATTCTTTGGT
1 TTTTAGTGGCATTTTA-ACGAAAGCGCCACTAATGCTCTGGT
16623424 TTTTAGT
1 TTTTAGT
16623431 AAGCGCCACT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (41 bp):
TTTTAGTGGCATTTTAACGAAAGCGCCACTAATGCTCTGGT
Found at i:16623435 original size:28 final size:28
Alignment explanation
Indices: 16623403--16623457 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16623393 ATTTTATACA
* * *
16623403 AAGCGCCACTAATTCTTTGGTTTTTAGT
1 AAGCGCCACTAATGCTCTGGCTTTTAGT
16623431 AAGCGCCACTAATGCTCTGGCTTTTAG
1 AAGCGCCACTAATGCTCTGGCTTTTAG
16623458 CGGCGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (28 bp):
AAGCGCCACTAATGCTCTGGCTTTTAGT
Found at i:16623496 original size:40 final size:40
Alignment explanation
Indices: 16623422--16623527 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
16623412 TAATTCTTTG
* * * *
16623422 GTTTTTAGT-AAGCGCCACTAATGCTCTGGCTTTTAGCGGC
1 GTTTTTAGTAAAACGCCACTATTGCTAT-GTTTTTAGCGGC
*
16623462 GTTTTTAGTAAAACGCCATTATTGCTATGTTTTTAGCGGC
1 GTTTTTAGTAAAACGCCACTATTGCTATGTTTTTAGCGGC
* *
16623502 GTTTTTGGTAAAACGCCGCTATTGCT
1 GTTTTTAGTAAAACGCCACTATTGCT
16623528 CTGCATTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 43 0.75
41 14 0.25
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (40 bp):
GTTTTTAGTAAAACGCCACTATTGCTATGTTTTTAGCGGC
Found at i:16626538 original size:16 final size:16
Alignment explanation
Indices: 16626505--16626544 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
16626495 ATAGAATTAC
16626505 AAATAAAAATAAACCT
1 AAATAAAAATAAACCT
16626521 AAATACAAAATAAA-CT
1 AAATA-AAAATAAACCT
*
16626537 AAAGAAAA
1 AAATAAAA
16626545 TTGAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 11 0.50
17 8 0.36
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAAATAAACCT
Found at i:16630221 original size:23 final size:23
Alignment explanation
Indices: 16630191--16630238 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
16630181 TGAAAATATA
16630191 TTTTGGGGATTTATAAAAGCATG
1 TTTTGGGGATTTATAAAAGCATG
16630214 TTTTGGGGATTTATAAAAGCATG
1 TTTTGGGGATTTATAAAAGCATG
16630237 TT
1 TT
16630239 AATAATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42
Consensus pattern (23 bp):
TTTTGGGGATTTATAAAAGCATG
Found at i:16643813 original size:52 final size:52
Alignment explanation
Indices: 16643704--16643873 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 52
16643694 ACTAGTGATT
** * *
16643704 CAAGTGTTATACTATGTGAAGGCCACATTG---AGAAGAGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAAGCCACTTTGTAAAGAA-AGATAGCTTTGGTCA
*
16643753 CAAGTGTGGTACTATGTGAAAGCCACTTTTTAAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAAGCCACTTTGTAAAGAAAGATAGCTTTGGTCA
* * * *
16643805 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGAAT-A
1 CAAGTGTGGTACTATGTGAAAGCCACTTTGTAAAGAAAGATAGCTTTG-GTCA
* *
16643856 CAAGGGTTGTACTATGTG
1 CAAGTGTGGTACTATGTG
16643874 CAGGCCACCG
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 25 0.24
51 35 0.34
52 44 0.42
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAAGCCACTTTGTAAAGAAAGATAGCTTTGGTCA
Found at i:16643869 original size:51 final size:51
Alignment explanation
Indices: 16643704--16643881 Score: 209
Period size: 51 Copynumber: 3.5 Consensus size: 51
16643694 ACTAGTGATT
** * *
16643704 CAAGTGTTATACTATGTGAAGGCCACATTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
* * *
16643753 CAAGTGTGGTACTATGTGAAAGCCACTTTTTAAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGTCA
* *
16643805 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGAAT-A
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTG-GTCA
* * *
16643856 CAAGGGTTGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
16643882 CGGGTATCCG
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 28 0.25
51 42 0.38
52 40 0.36
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
Found at i:16652691 original size:6 final size:6
Alignment explanation
Indices: 16652682--16652706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16652672 TATCTTATTT
16652682 ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A
16652707 ACTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:16658306 original size:17 final size:19
Alignment explanation
Indices: 16658284--16658324 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
16658274 GGTTCATTAT
16658284 TGATTTATAT-TT-TAATA
1 TGATTTATATATTATAATA
*
16658301 TGATTTATATATTATATTA
1 TGATTTATATATTATAATA
16658320 TGATT
1 TGATT
16658325 AATAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TGATTTATATATTATAATA
Found at i:16662314 original size:40 final size:40
Alignment explanation
Indices: 16662268--16662387 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 40
16662258 GCTATGTTTA
16662268 GCACTTAGTGTGTGATTTAAGATAGCTTCAGCTATATACG
1 GCACTTAGTGTGTGATTTAAGATAGCTTCAGCTATATACG
* * *
16662308 GTACTTAGTGTGTG-----AGATA--TT--G--A-GTACC
1 GCACTTAGTGTGTGATTTAAGATAGCTTCAGCTATATACG
*
16662336 GCACTTAGTGTGCGATTTAAGATAGCTTCAGCTATATACG
1 GCACTTAGTGTGTGATTTAAGATAGCTTCAGCTATATACG
16662376 GCACTTAGTGTG
1 GCACTTAGTGTG
16662388 CGAGACATTG
Statistics
Matches: 61, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
28 15 0.25
29 1 0.02
31 1 0.02
33 7 0.11
35 7 0.11
37 1 0.02
39 1 0.02
40 28 0.46
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (40 bp):
GCACTTAGTGTGTGATTTAAGATAGCTTCAGCTATATACG
Done.