Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 127 of 325
Found at i:38292895 original size:13 final size:13
Alignment explanation
Indices: 38292873--38292905 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
38292863 AAGGGTTTGT
38292873 TTAT-TAAACTAA
1 TTATCTAAACTAA
38292885 TTATCTAAACTAA
1 TTATCTAAACTAA
*
38292898 TTAACTAA
1 TTATCTAA
38292906 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:38294966 original size:20 final size:20
Alignment explanation
Indices: 38294933--38294976 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38294923 AAAAAAAAGT
* *
38294933 AAATGCAATGGAAAGTAATA
1 AAATGCAATGGAAAATAAGA
38294953 AAATGCAAAT-GAAAATAAGA
1 AAATGC-AATGGAAAATAAGA
38294973 AAAT
1 AAAT
38294977 TTGAAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATGCAATGGAAAATAAGA
Found at i:38296358 original size:2 final size:2
Alignment explanation
Indices: 38296346--38296379 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
38296336 ATTATGTATG
38296346 AT AT GAT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38296380 TGATATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38304701 original size:55 final size:53
Alignment explanation
Indices: 38304572--38304969 Score: 333
Period size: 55 Copynumber: 7.5 Consensus size: 53
38304562 AACTTACCAT
* * *
38304572 TGCCATGTCTTGACATGGTCTTACGTGGTATCC-TTGCCTTAT-GAGCTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGG-A-CCTTTGCCTTATAGAACTCATCAA
* *
38304625 TGCCATGCCTTGGCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACAT-GGACCTTTGCCTTATAG-AACTCATCAA
*
38304680 TGCCATGTCTTGACATGGTCTTACAT-GATTTCC-TTGCCTTATAGAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGA---CCTTTGCCTTATAGAACTCATCAA
* * * * * *
38304734 TGCCATGCCTTGGCATGGTCTTACAT-GA--TAT--CTT-T--ATCTTAACAAA
1 TGCCATGTCTTGACATGGTCTTACATGGACCTTTGCCTTATAGAACTCATC-AA
*** * *
38304780 TGCCATGTTCCAAACATGGTTTTACATGGTATCC-TTGTCTTAT-GAACTCA-CTAA
1 TGCCATG-TCTTGACATGGTCTTACATGG-A-CCTTTGCCTTATAGAACTCATC-AA
38304834 TGCCATGTCTTGACATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACAT-GGACCTTTGCCTTATAG-AACTCATCAA
* ** *
38304889 TGCCATGTCTTGACATGGTCTCACAT-GATTTTCTTGCCTTATAGAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGA-CCT-TTGCCTTATAGAACTCATCAA
* *
38304943 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGTCTTGACATGGTCTTACATG
38304970 ATATCCTTAT
Statistics
Matches: 283, Mismatches: 35, Indels: 52
0.76 0.09 0.14
Matches are distributed among these distances:
45 6 0.02
46 9 0.03
47 14 0.05
48 4 0.01
49 1 0.00
50 1 0.00
51 1 0.00
52 4 0.01
53 64 0.23
54 85 0.30
55 91 0.32
56 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (53 bp):
TGCCATGTCTTGACATGGTCTTACATGGACCTTTGCCTTATAGAACTCATCAA
Found at i:38304757 original size:54 final size:54
Alignment explanation
Indices: 38304572--38304977 Score: 376
Period size: 54 Copynumber: 7.6 Consensus size: 54
38304562 AACTTACCAT
* * * * *
38304572 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAGCTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* *
38304625 TGCCATGCCTTGGCATGGTCTTACAT-AGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGA-TATCC-TTGCCTTATAG-AACTCATCAA
* * *
38304680 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * **
38304734 TGCCATGCCTTGGCATGGTCTTACATGATATCTTTATC-T-T--AA--CA--AA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
** * * *
38304780 TGCCATGTTCC-AAACATGGTTTTACATGGTATCCTTGTCTTAT-GAACTCA-CTAA
1 TGCCATG--CCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATC-AA
* *
38304834 TGCCATGTCTTGACATGGTCTTACAT-AGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGA-TATCC-TTGCCTTATAG-AACTCATCAA
* * * * *
38304889 TGCCATGTCTTGACATGGTCTCACATGATTTTCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
*
38304943 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTT
38304978 ATCTTACCAA
Statistics
Matches: 287, Mismatches: 43, Indels: 45
0.77 0.11 0.12
Matches are distributed among these distances:
46 9 0.03
47 21 0.07
48 4 0.01
49 1 0.00
50 4 0.01
52 8 0.03
53 56 0.20
54 91 0.32
55 87 0.30
56 6 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:38304944 original size:209 final size:209
Alignment explanation
Indices: 38304584--38305030 Score: 786
Period size: 209 Copynumber: 2.1 Consensus size: 209
38304574 CCATGTCTTG
* * * * *
38304584 ACATGGTCTTACGTGGTATCCTTGCCTTATGAGCTCACCAATGCCATGCCTTGGCATGGTCTTAC
1 ACATGGTATTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGGTCTTAC
*
38304649 ATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCT
66 ATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTCACATGATTTCCT
*
38304714 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCTTTATCTTAACAA
131 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTAACAA
38304779 ATGCCATGTTCCAA
196 ATGCCATGTTCCAA
* * *
38304793 ACATGGTTTTACATGGTATCCTTGTCTTATGAACTCACTAATGCCATGTCTTGACATGGTCTTAC
1 ACATGGTATTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGGTCTTAC
*
38304858 ATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTCACATGATTTTCT
66 ATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTCACATGATTTCCT
*
38304923 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
131 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTAACAA
38304988 ATGCCATGTTCCAA
196 ATGCCATGTTCCAA
38305002 ACATGGTATTACATGGTATCCTTGTCTTA
1 ACATGGTATTACATGGTATCCTTGTCTTA
38305031 CCAAATGTCA
Statistics
Matches: 226, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 226 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (209 bp):
ACATGGTATTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGGTCTTAC
ATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTCACATGATTTCCT
TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTAACAA
ATGCCATGTTCCAA
Found at i:38305014 original size:47 final size:47
Alignment explanation
Indices: 38304956--38305124 Score: 275
Period size: 47 Copynumber: 3.6 Consensus size: 47
38304946 CATGCCTTGG
* *
38304956 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* *
38305003 CATGGTATTACATGGTATCCTTGTCTTACCAAATGTCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
38305050 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* * *
38305097 CGTAGTTTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
38305125 GTGCCAATGC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 113 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:38305200 original size:47 final size:45
Alignment explanation
Indices: 38305147--38305258 Score: 118
Period size: 45 Copynumber: 2.4 Consensus size: 45
38305137 CATCTTGATG
* * *
38305147 TGGTCTTACAT-GGAGTCCTTAATCAATGCCGATGTCATGTCTTGACA
1 TGGTCTTACATGGGA-TCCTT--GCAATACCAATGTCATGTCTTGACA
* **
38305194 TGGTCTTACACGGGATCCTTGCCTTACCAATGTCATGTCTTGACA
1 TGGTCTTACATGGGATCCTTGCAATACCAATGTCATGTCTTGACA
* *
38305239 TGGTCTTACATTGTATCCTT
1 TGGTCTTACATGGGATCCTT
38305259 AACCATCAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
45 37 0.67
47 15 0.27
48 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (45 bp):
TGGTCTTACATGGGATCCTTGCAATACCAATGTCATGTCTTGACA
Found at i:38305328 original size:44 final size:44
Alignment explanation
Indices: 38305264--38305347 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
38305254 TCCTTAACCA
* *
38305264 TCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCTG
1 TCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCTG
* *
38305308 TCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
38305348 GAGATATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (44 bp):
TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCTG
Found at i:38307119 original size:15 final size:15
Alignment explanation
Indices: 38307099--38307130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38307089 GGTAGAAAAT
*
38307099 GAAAGTTTGTTCATA
1 GAAAGTCTGTTCATA
38307114 GAAAGTCTGTTCATA
1 GAAAGTCTGTTCATA
38307129 GA
1 GA
38307131 TAAACAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (15 bp):
GAAAGTCTGTTCATA
Found at i:38308849 original size:25 final size:25
Alignment explanation
Indices: 38308815--38308863 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38308805 AAGTTGACAC
*
38308815 GGCCTTGGACACT-GGCTTGTTACAT
1 GGCCTTGGACA-TGGGCATGTTACAT
38308840 GGCCTTGGACATGGGCATGTTACA
1 GGCCTTGGACATGGGCATGTTACA
38308864 CGACCGTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (25 bp):
GGCCTTGGACATGGGCATGTTACAT
Found at i:38315987 original size:78 final size:78
Alignment explanation
Indices: 38315857--38316013 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 78
38315847 CATCCCGGTG
* *
38315857 AATGTAGGATGAATAACTAAGCTTGCTTCAAATGTGGTTCCCAAGATCACTTTATCTGAGACTGC
1 AATGTAGGATGAATAACTAAGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCGGAGACTGC
38315922 CCTAAAATGGCTA
66 CCTAAAATGGCTA
* * *
38315935 AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATTACTTTATCGGAGGCTGC
1 AATGTAGGATGAATAACTAAGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCGGAGACTGC
*
38316000 CCTGAAATGGCTA
66 CCTAAAATGGCTA
38316013 A
1 A
38316014 GAAAGATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (78 bp):
AATGTAGGATGAATAACTAAGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCGGAGACTGC
CCTAAAATGGCTA
Found at i:38325154 original size:20 final size:20
Alignment explanation
Indices: 38325126--38325175 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38325116 TGGAGCAGGA
*
38325126 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
38325146 ATATTGATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
38325165 AGTATCGATAC
1 A-TATCGATAC
38325176 TAGATGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:38328419 original size:16 final size:16
Alignment explanation
Indices: 38328400--38328439 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38328390 AATAAAATTT
38328400 TTTTAAAAGTAT-TAAA
1 TTTTAAAA-TATATAAA
38328416 TTTTAAAATATATAAA
1 TTTTAAAATATATAAA
*
38328432 TTATAAAA
1 TTTTAAAA
38328440 AAATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTTAAAATATATAAA
Found at i:38328419 original size:17 final size:17
Alignment explanation
Indices: 38328399--38328448 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
38328389 AAATAAAATT
38328399 TTTTTAAAAGTAT-TAAA
1 TTTTTAAAA-TATATAAA
38328416 -TTTTAAAATATATAAA
1 TTTTTAAAATATATAAA
* * *
38328432 TTATAAAAAAATATAAA
1 TTTTTAAAATATATAAA
38328449 AATCATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.11
16 12 0.43
17 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTTTAAAATATATAAA
Found at i:38328444 original size:19 final size:19
Alignment explanation
Indices: 38328420--38328509 Score: 92
Period size: 19 Copynumber: 4.6 Consensus size: 19
38328410 ATTAAATTTT
*
38328420 AAAATATATAAATTATAAA
1 AAAATATAAAAATTATAAA
*
38328439 AAAATATAAAAATCATAAA
1 AAAATATAAAAATTATAAA
*
38328458 AAAATTATAAAAAATTGTAAA
1 AAAA-TAT-AAAAATTATAAA
**
38328479 AATTTATAAAAATCT-TAAA
1 AAAATATAAAAAT-TATAAA
38328498 AAAATTATAAAA
1 AAAA-TATAAAA
38328510 GGTATTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 33 0.56
20 14 0.24
21 12 0.20
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAATATAAAAATTATAAA
Found at i:38328461 original size:20 final size:19
Alignment explanation
Indices: 38328420--38328509 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
38328410 ATTAAATTTT
* *
38328420 AAAA-TATATAAATTATAA
1 AAAATTATAAAAATCATAA
*
38328438 AAAAATATAAAAATCATAAA
1 AAAATTATAAAAATCAT-AA
**
38328458 AAAATTATAAAAAATTGTAA
1 AAAATTAT-AAAAATCATAA
* *
38328478 AAATTTATAAAAATCTTAAA
1 AAAATTATAAAAATCAT-AA
38328498 AAAATTATAAAA
1 AAAATTATAAAA
38328510 GGTATTTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.07
19 17 0.29
20 31 0.53
21 7 0.12
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:38328479 original size:40 final size:40
Alignment explanation
Indices: 38328429--38328509 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
38328419 TAAAATATAT
38328429 AAATTATAAAAAAATATAAAAATCATAAAAAAATTATAAA
1 AAATTATAAAAAAATATAAAAATCATAAAAAAATTATAAA
* ** *
38328469 AAATTGTAAAAATTTATAAAAATCTTAAAAAAATTATAAA
1 AAATTATAAAAAAATATAAAAATCATAAAAAAATTATAAA
38328509 A
1 A
38328510 GGTATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (40 bp):
AAATTATAAAAAAATATAAAAATCATAAAAAAATTATAAA
Found at i:38328773 original size:9 final size:9
Alignment explanation
Indices: 38328743--38328814 Score: 51
Period size: 10 Copynumber: 7.7 Consensus size: 9
38328733 CTTTATAAAA
38328743 TTTTATAAT
1 TTTTATAAT
38328752 TCTTT-TAGGAT
1 T-TTTATA--AT
38328763 TTTTATAAT
1 TTTTATAAT
*
38328772 TTTTTTAAAT
1 TTTTAT-AAT
*
38328782 TTTTAATAAA
1 TTTT-ATAAT
38328792 TTTTA-AAT
1 TTTTATAAT
38328800 TTTT-TATAT
1 TTTTATA-AT
38328809 TTTTAT
1 TTTTAT
38328815 TAAAATTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 7 0.14
9 17 0.34
10 20 0.40
11 6 0.12
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:38328785 original size:20 final size:20
Alignment explanation
Indices: 38328743--38328818 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
38328733 CTTTATAAAA
* *
38328743 TTTTATAATTCTTTTAGGA-T
1 TTTTATAATTTTTTTA-AATT
38328763 TTTTATAATTTTTTTAAATT
1 TTTTATAATTTTTTTAAATT
* *
38328783 TTTAATAA--ATTTTAAATT
1 TTTTATAATTTTTTTAAATT
38328801 TTTTAT-ATTTTTATTAAA
1 TTTTATAATTTTT-TTAAA
38328819 ATTTAATCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.02
18 14 0.30
19 3 0.07
20 28 0.61
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTTTAAATT
Found at i:38328791 original size:11 final size:10
Alignment explanation
Indices: 38328734--38328807 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
38328724 TTCTTACGAC
*
38328734 TTTATAAAAT
1 TTTATAAATT
38328744 TTTAT-AATT
1 TTTATAAATT
*
38328753 CTTT-TAGGATT
1 -TTTATA-AATT
38328764 TTTAT-AATT
1 TTTATAAATT
*
38328773 TTTTTAAATT
1 TTTATAAATT
38328783 TTTAATAAA-T
1 TTT-ATAAATT
*
38328793 TTTA-AATTT
1 TTTATAAATT
38328802 TTTATA
1 TTTATA
38328808 TTTTTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
8 2 0.04
9 17 0.34
10 23 0.46
11 8 0.16
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTATAAATT
Found at i:38328802 original size:27 final size:28
Alignment explanation
Indices: 38328763--38328824 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
38328753 CTTTTAGGAT
38328763 TTTTATAATTTTTTTAAATTTTTAATAAA
1 TTTTA-AATTTTTTTAAATTTTTAATAAA
* *
38328792 TTTTAAA-TTTTTTATATTTTTATTAAA
1 TTTTAAATTTTTTTAAATTTTTAATAAA
*
38328819 ATTTAA
1 TTTTAA
38328825 TCATTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 23 0.77
28 2 0.07
29 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTAAATTTTTTTAAATTTTTAATAAA
Found at i:38331691 original size:22 final size:22
Alignment explanation
Indices: 38331660--38331710 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
38331650 GTATTTATGT
38331660 ATTTAAATTTCTATT-TTAATTA
1 ATTTAAATTT-TATTGTTAATTA
* *
38331682 TTTTATATTTTATTGTTAATTA
1 ATTTAAATTTTATTGTTAATTA
38331704 ATTTAAA
1 ATTTAAA
38331711 ATAATAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTAAATTTTATTGTTAATTA
Found at i:38333339 original size:3 final size:3
Alignment explanation
Indices: 38333331--38333377 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
38333321 CATAAATCAA
*
38333331 ATT ATT ATT ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
38333378 AAGACAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:38335314 original size:27 final size:27
Alignment explanation
Indices: 38335283--38335336 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
38335273 ATGTTTATAT
* *
38335283 TAAATAAA-AAACTATTTAATTATAAAA
1 TAAATAAATAAA-AATTTAATAATAAAA
38335310 TAAATAAATAAAAATTTAATAATAAAA
1 TAAATAAATAAAAATTTAATAATAAAA
38335337 AGGTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAATAAATAAAAATTTAATAATAAAA
Found at i:38337218 original size:16 final size:17
Alignment explanation
Indices: 38337197--38337233 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
38337187 TAATTTTTTA
*
38337197 AAAAATA-TAATACATT
1 AAAAATACTAAAACATT
38337213 AAAAATACTAAAACATT
1 AAAAATACTAAAACATT
38337230 AAAA
1 AAAA
38337234 CAAATGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATACTAAAACATT
Found at i:38337411 original size:23 final size:23
Alignment explanation
Indices: 38337385--38337437 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
38337375 ATAATAGTGA
*
38337385 AAAAAAAACAACAATAAAACAAT
1 AAAAAAAACAACAAGAAAACAAT
* *
38337408 AAAAAGAACAACAAGAAAGCAAT
1 AAAAAAAACAACAAGAAAACAAT
38337431 AAAAAAA
1 AAAAAAA
38337438 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.77, C:0.11, G:0.06, T:0.06
Consensus pattern (23 bp):
AAAAAAAACAACAAGAAAACAAT
Found at i:38342005 original size:45 final size:44
Alignment explanation
Indices: 38341936--38342072 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 44
38341926 ATTAACTTAA
* * * * * *
38341936 GAAAAGAGAAAGACCCTGGTTGAAAGATA-TCATGGCATTTTACCC
1 GAAATGAGAAAGACCCTAGTTGAAAGATACT-ATGACA-ATAAACC
* *
38341981 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
1 GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
* * *
38342025 GAAATGAGGAAGACCCTAGTTGAAAGATACTATGACACTAAATC
1 GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
38342069 GAAA
1 GAAA
38342073 AATAAACAAG
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 46 0.59
45 31 0.40
46 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (44 bp):
GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
Found at i:38342045 original size:44 final size:44
Alignment explanation
Indices: 38341981--38342149 Score: 157
Period size: 44 Copynumber: 3.8 Consensus size: 44
38341971 CATTTTACCC
38341981 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
* * *
38342025 GAAATGAGGAAGACCCTAGTTGAAAGATACTATGACACTAAA-T
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
* * * * * *
38342068 CGAAAAAT-AAACAAGACCATAGTTGAAACATGCTATGGCATTAAATTT
1 -G--AAATGAGA-AAGACCATAGTTGAAAGATACTATGACAATAAA-CT
*
38342116 G-AATGAATGAAA-ACCATAGTTGAAAGATATTATG
1 GAAATG-A-GAAAGACCATAGTTGAAAGATACTATG
38342150 GCACCACTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 17
0.77 0.11 0.13
Matches are distributed among these distances:
43 1 0.01
44 43 0.42
45 20 0.20
46 35 0.34
47 2 0.02
48 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (44 bp):
GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
Found at i:38345502 original size:48 final size:48
Alignment explanation
Indices: 38345426--38345774 Score: 322
Period size: 48 Copynumber: 7.3 Consensus size: 48
38345416 ATATCCATGC
* * * * *
38345426 CATGGCATCGGTATT-AATATGTGCGCTAGTGTAAGACTATGTTTGGGA
1 CATGGCATCGGCATTGAA-ATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * *
38345474 CATGGCATCGACATTGAAATGAGAGCTAGTTTAAGACCATATCTGGGA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * * * * * * *
38345522 CATGGCATTGGCCTCGACATGTGAGCCAGTGTAAAACCATATTTAGAA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * * *
38345570 TATGGCATCGGCAATGTAATGAGAGCCAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * * *
38345618 CATGGCATTGGCATTGAGACGAGAGCTAGTGTAAGACCATGTTTGGGA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * *
38345666 CACGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * * * * * *
38345714 CATGGCATCGGCCTCGACATGTGAACCACTGGAAGACCATGTTTGGAA
1 CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
38345762 CATGGCATCGGCA
1 CATGGCATCGGCA
38345775 ATTCACCCTC
Statistics
Matches: 243, Mismatches: 57, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
48 241 0.99
49 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
CATGGCATCGGCATTGAAATGAGAGCTAGTGTAAGACCATGTCTGGGA
Found at i:38345591 original size:96 final size:95
Alignment explanation
Indices: 38345444--38345776 Score: 396
Period size: 96 Copynumber: 3.5 Consensus size: 95
38345434 CGGTATTAAT
* * * * * * *
38345444 ATGTGCGCTAGTGTAAGACTATGTTTGGGACATGGCATCGACATTGAAATGAGAGCTAGTTTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATG-AATGAGAGCTAGTGTAAG
*
38345509 ACCATATCTGGGACATGGCATTGGCCTCGAC
65 ACCATGTCTGGGACATGGCATTGGCCTCGAC
* * * * *
38345540 ATGTGAGCCAGTGTAAAACCATATTTAGAATATGGCATCGGCAATGTAATGAGAGCCAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATG-AATGAGAGCTAGTGTAAG
* * *
38345605 ACCATGTCTGGGACATGGCATTGGCATTGAG
65 ACCATGTCTGGGACATGGCATTGGCCTCGAC
* * * * * * *
38345636 ACGAGAGCTAGTGTAAGACCATGTTTGGGACACGGCATCGGCATTGAGACGAGAGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGA-ATGAGAGCTAGTGTAAG
*
38345701 ACCATGTCTGGGACATGGCATCGGCCTCGAC
65 ACCATGTCTGGGACATGGCATTGGCCTCGAC
* * *
38345732 ATGTGAACCACTGGAAGACCATGTTTGGAACATGGCATCGGCAAT
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAAT
38345777 TCACCCTCTT
Statistics
Matches: 194, Mismatches: 42, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
95 1 0.01
96 193 0.99
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (95 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGAATGAGAGCTAGTGTAAGA
CCATGTCTGGGACATGGCATTGGCCTCGAC
Found at i:38353263 original size:48 final size:48
Alignment explanation
Indices: 38353193--38353541 Score: 298
Period size: 48 Copynumber: 7.3 Consensus size: 48
38353183 ATATTCATGC
* * *
38353193 CATGACATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTCGGA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * * **
38353241 CATGGCATCGACCTCGACATGTGAGTTAGTGTAAGACCATTTTTGAAA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * *
38353289 CATGGCATTGGCAATG-TAATGAGAGCCAATGTAAGACCATGTCTGGGA
1 CATGGCATCGACATTGAT-ATGTGAGCTAGTGTAAGACCATGTCTGGGA
*
38353337 CATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* *
38353385 CATGGCATCAGCCACA-T--TATGAGAGCCAGTGTAAGACCATGTCTGGGA
1 CATGGCATC-G--ACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * * *
38353433 TATGGCATC-AGCATTGAGACGAGAACTAGTATAAGACCATGTTTGGGA
1 CATGGCATCGA-CATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * *
38353481 CATGGCATC-AGCCTAT-ACATGTGAGCTAGTGTAAGACCATGTTTGGAA
1 CATGGCATCGA-CAT-TGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
*
38353529 CATGACATCGACA
1 CATGGCATCGACA
38353542 ATTCACCCTC
Statistics
Matches: 238, Mismatches: 52, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
44 1 0.00
45 2 0.01
46 1 0.00
48 226 0.95
49 4 0.02
50 1 0.00
51 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (48 bp):
CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
Found at i:38353468 original size:144 final size:144
Alignment explanation
Indices: 38353193--38353540 Score: 373
Period size: 144 Copynumber: 2.4 Consensus size: 144
38353183 ATATTCATGC
* * *
38353193 CATGACATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTCGGACATGGCATCGACCTCGA
1 CATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACGA
* ** * * ** * * *
38353258 CATGTGAGTTAGTGTAAGACCATTTTTGAAACATGGCATTGGCAATGTAATGAGAGCCAATGTAA
66 CATGAGAGCCAGTGTAAGACCATGTCTGAAACATGGCATCAGCAATGTAACGAGAACCAATATAA
38353323 GACCATGTCTGGGA
131 GACCATGTCTGGGA
38353337 CATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATC-AGCCAC-
1 CATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CCACG
* ** * * * *
38353400 ATTATGAGAGCCAGTGTAAGACCATGTCTGGGATATGGCATCAGCATTG-AGACGAGAACTAGTA
65 A-CATGAGAGCCAGTGTAAGACCATGTCTGAAACATGGCATCAGCAATGTA-ACGAGAACCAATA
*
38353464 TAAGACCATGTTTGGGA
128 TAAGACCATGTCTGGGA
* * * * * *
38353481 CATGGCATC-AGCCTAT-ACATGTGAGCTAGTGTAAGACCATGTTTGGAACATGACATCGAC
1 CATGGCATCGA-CAT-TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC
38353541 AATTCACCCT
Statistics
Matches: 171, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
143 4 0.02
144 165 0.96
145 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (144 bp):
CATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACGA
CATGAGAGCCAGTGTAAGACCATGTCTGAAACATGGCATCAGCAATGTAACGAGAACCAATATAA
GACCATGTCTGGGA
Found at i:38360178 original size:22 final size:23
Alignment explanation
Indices: 38360144--38360186 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
38360134 TATTGAATTC
38360144 AATTCTAAATTTACT-TTTTATA
1 AATTCTAAATTTACTATTTTATA
* *
38360166 AATTTTAATTTTACTATTTTA
1 AATTCTAAATTTACTATTTTA
38360187 ATCAAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTCTAAATTTACTATTTTATA
Found at i:38362090 original size:16 final size:17
Alignment explanation
Indices: 38362071--38362107 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
38362061 TTACATTTTG
38362071 TTTTAATAGTTA-AAAT
1 TTTTAATAGTTATAAAT
*
38362087 TTTT-GTAGTTATAAAT
1 TTTTAATAGTTATAAAT
38362103 TTTTA
1 TTTTA
38362108 TGTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (17 bp):
TTTTAATAGTTATAAAT
Found at i:38362095 original size:15 final size:16
Alignment explanation
Indices: 38362077--38362106 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38362067 TTTGTTTTAA
38362077 TAGTTA-AAATTTTTG
1 TAGTTATAAATTTTTG
38362092 TAGTTATAAATTTTT
1 TAGTTATAAATTTTT
38362107 ATGTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
TAGTTATAAATTTTTG
Found at i:38377433 original size:5 final size:5
Alignment explanation
Indices: 38377423--38377457 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
38377413 AATCTGTGTT
38377423 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT
38377458 CCACAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:38377904 original size:21 final size:21
Alignment explanation
Indices: 38377871--38377913 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38377861 AAATAGTCTT
* *
38377871 ATTTAGCAACCAAGTTCTTAA
1 ATTTAGCAACCAACTTCATAA
* *
38377892 ATTTATCATCCAACTTCATAA
1 ATTTAGCAACCAACTTCATAA
38377913 A
1 A
38377914 CATATCAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTTAGCAACCAACTTCATAA
Found at i:38380582 original size:39 final size:39
Alignment explanation
Indices: 38380535--38380717 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
38380525 AATGTTCGAG
38380535 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
38380574 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
38380613 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
38380652 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
38380692 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
38380718 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:38382464 original size:19 final size:19
Alignment explanation
Indices: 38382440--38382487 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
38382430 AGTTAATAAC
*
38382440 AAATTTGATTACTATGAGT
1 AAATTTGATTACGATGAGT
*
38382459 AAATTTGATTACGGTGAGT
1 AAATTTGATTACGATGAGT
38382478 AAATTTGATT
1 AAATTTGATT
38382488 CTGATGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (19 bp):
AAATTTGATTACGATGAGT
Found at i:38385235 original size:48 final size:48
Alignment explanation
Indices: 38385164--38385309 Score: 238
Period size: 48 Copynumber: 3.0 Consensus size: 48
38385154 CAAGATAAAT
* **
38385164 ATATATATGTGTGGTAAAGCCGAATGGCTAGCGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
38385212 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
38385260 ATATATATATGTGGTAAAGCTGAATAGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
38385308 AT
1 AT
38385310 GTGTGTATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:38385495 original size:37 final size:37
Alignment explanation
Indices: 38385445--38385595 Score: 239
Period size: 37 Copynumber: 4.1 Consensus size: 37
38385435 AACTTGGAAA
*
38385445 TATGTCCGGGTAAGACCCGATGACTACGTGTGAAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
38385482 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
* *
38385519 TATGTTCGGGTAAGACCCGACGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
* * * *
38385556 TTTGTCCGGGTAAGACCCGATAACTACGTGAGGGGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
38385593 TAT
1 TAT
38385596 TCGAGCTAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:38388474 original size:108 final size:108
Alignment explanation
Indices: 38388155--38388506 Score: 325
Period size: 108 Copynumber: 3.2 Consensus size: 108
38388145 TTGTTCTAGC
* * * * *
38388155 CTTCTAATTGCCGGC-CCCAGTATGAAAAAAAAAATTCAAA-ATTTTTGGTGCTGGCCTTGTAAT
1 CTTCTAATGGCCGGCACCAAGTATG--AAAAAAAA-TCAAATTTTTTTAGTACTGGCCTTGTAAT
* * **
38388218 GGCC-GCCACCAGACTACCAGTATTTAAAAAAAATAAATTTTTTTGGTCCTGGT
63 GGCCAG-CACCAGAGTACCAATA-TGGAAAAAAA-AAA-----TTGGTCCTGGT
* * * * *
38388271 CTACTAATGGTCGGCACCAATTATGAAAAAAAATCAAATTTTTTTGGTACTGGCCTTGTAATGGT
1 CTTCTAATGGCCGGCACCAAGTATGAAAAAAAATCAAATTTTTTTAGTACTGGCCTTGTAATGGC
* * ** *
38388336 CGGCACTAGAGTACCAATAT-TTAAAAAAAAATTGGTGCTGGT
66 CAGCACCAGAGTACCAATATGGAAAAAAAAAATTGGTCCTGGT
** **
38388378 CTTCTAATGGCCGGCACCAAGTATGACAAAAATTTCAAATTTTTTTAGTGTTGGCCTTGTAATGG
1 CTTCTAATGGCCGGCACCAAGTATGA-AAAAAAATCAAATTTTTTTAGTACTGGCCTTGTAATGG
* *
38388443 CCAGCACCAGAGTGCCAATATGGAAAAAAAAAAATTGGTCCTAGT
65 CCAGCACCAGAGTACCAATATGG-AAAAAAAAAATTGGTCCTGGT
*
38388488 CTTCGAATGGCCGGCACCA
1 CTTCTAATGGCCGGCACCA
38388507 GGAACTTTTT
Statistics
Matches: 199, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
107 33 0.17
108 50 0.25
110 36 0.18
112 3 0.02
113 6 0.03
114 6 0.03
115 45 0.23
116 13 0.07
117 7 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (108 bp):
CTTCTAATGGCCGGCACCAAGTATGAAAAAAAATCAAATTTTTTTAGTACTGGCCTTGTAATGGC
CAGCACCAGAGTACCAATATGGAAAAAAAAAATTGGTCCTGGT
Found at i:38393323 original size:40 final size:40
Alignment explanation
Indices: 38393265--38393482 Score: 300
Period size: 40 Copynumber: 5.5 Consensus size: 40
38393255 AAATCAAGTA
*
38393265 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCG-ATCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCA-CAAATG
* *
38393304 CCTTTGGGACTCAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
38393344 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
38393384 CCTTCGGGACTTAGCCCGGATATAGTAGCTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38393424 CCTTCAGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38393464 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38393483 TTACCATCTG
Statistics
Matches: 161, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 13 0.08
40 147 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38401398 original size:40 final size:40
Alignment explanation
Indices: 38401328--38401505 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
38401318 AAACCAAGTA
* *
38401328 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
38401367 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
38401407 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
38401447 CCTTCGGGACGTAGCCTGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38401487 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38401506 TTACCATCCG
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 15 0.12
40 112 0.88
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38404866 original size:47 final size:49
Alignment explanation
Indices: 38404641--38404943 Score: 447
Period size: 49 Copynumber: 6.3 Consensus size: 49
38404631 GTATGAGATA
38404641 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
38404690 TATATATGTGGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
38404739 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
38404788 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
38404835 TATATATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * * *
38404882 TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
38404929 TATAAATGTGATAAG
1 TATATATGTGATAAG
38404944 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
47 97 0.41
48 5 0.02
49 136 0.57
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:38410865 original size:75 final size:74
Alignment explanation
Indices: 38410774--38410977 Score: 291
Period size: 75 Copynumber: 2.7 Consensus size: 74
38410764 AAAGATTGAT
* * * * *
38410774 AATTTAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGATACAAAATTTAAATGAAAATTGA
1 AATTTAAATGAAATGAGAAAAAATTTAATTGAAATGAAATGAGAAAAAAATTAAAT-AAAATTGA
38410839 AAGAAAGATA
65 AAGAAAGATA
* *
38410849 AATTTAAATGAAATGAGGAAAAAATTTAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTGA
1 AATTTAAATGAAATGA-GAAAAAATTTAATTGAAATGAAATGAGAAAAAAATTAAATAAAATTGA
38410914 AAGAAAGATA
65 AAGAAAGATA
* * *
38410924 AATTTAAATGAAGTGAGAGAAAAGTTTAATTGAAATGAAATGAGAGAAAAATTA
1 AATTTAAATGAAATGAGA-AAAAATTTAATTGAAATGAAATGAGAAAAAAATTA
38410978 CATGGAAAGA
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
74 2 0.02
75 80 0.69
76 34 0.29
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (74 bp):
AATTTAAATGAAATGAGAAAAAATTTAATTGAAATGAAATGAGAAAAAAATTAAATAAAATTGAA
AGAAAGATA
Found at i:38410897 original size:27 final size:26
Alignment explanation
Indices: 38410773--38410977 Score: 126
Period size: 27 Copynumber: 8.1 Consensus size: 26
38410763 GAAAGATTGA
38410773 TAATTTAAATGAAATGAGAAAAAAAT
1 TAATTTAAATGAAATGAGAAAAAAAT
* * * *
38410799 AAATTGAAATGAAAT--G-ATACAA-
1 TAATTTAAATGAAATGAGAAAAAAAT
*
38410821 -AATTTAAATGAAAATTGA-AAGAAAGAT
1 TAATTTAAATG-AAA-TGAGAA-AAAAAT
* *
38410848 AAATTTAAATGAAATGAGGAAAAAATT
1 TAATTTAAATGAAATGA-GAAAAAAAT
*
38410875 TAATTCAAATGAAATGAGAAAAAAAT
1 TAATTTAAATGAAATGAGAAAAAAAT
* * *
38410901 TAA-ATAAAT---TTGA-AAGAAAGAT
1 TAATTTAAATGAAATGAGAA-AAAAAT
* * **
38410923 AAATTTAAATGAAGTGAGAGAAAAGTT
1 TAATTTAAATGAAATGAGA-AAAAAAT
* *
38410950 TAATTGAAATGAAATGAGAGAAAAAT
1 TAATTTAAATGAAATGAGAAAAAAAT
38410976 TA
1 TA
38410978 CATGGAAAGA
Statistics
Matches: 135, Mismatches: 27, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
21 11 0.08
22 13 0.10
23 10 0.07
24 1 0.01
25 5 0.04
26 38 0.28
27 44 0.33
28 13 0.10
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (26 bp):
TAATTTAAATGAAATGAGAAAAAAAT
Found at i:38410964 original size:102 final size:102
Alignment explanation
Indices: 38410773--38410974 Score: 243
Period size: 102 Copynumber: 2.0 Consensus size: 102
38410763 GAAAGATTGA
* * *
38410773 TAATTTAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGATACAAAATTTAAATGAAAATTG
1 TAATTCAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGAAACAAAATTTAAATG-AAAGTG
*
38410838 AAAGAAAGATAAATTTAAATGAAATGAG-GAAAAAATT
65 AAAGAAAGATAAATTGAAATGAAATGAGAGAAAAAATT
*
38410875 TAATTCAAATGAAATGAGAAAAAAATTAAA-T-AAATTTGAAA-GAAAGATAAATTTAAATG-AA
1 TAATTCAAATGAAATGAGAAAAAAA-TAAATTGAAA--TGAAATGAAACA-AAATTTAAATGAAA
* * *
38410936 GTGAGAGAAAAGTTTAATTGAAATGAAATGAGAGAAAAA
62 GTGAAAG-AAAGATAAATTGAAATGAAATGAGAGAAAAA
38410975 TTACATGGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
101 10 0.12
102 50 0.58
103 26 0.30
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (102 bp):
TAATTCAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGAAACAAAATTTAAATGAAAGTGA
AAGAAAGATAAATTGAAATGAAATGAGAGAAAAAATT
Found at i:38410985 original size:27 final size:27
Alignment explanation
Indices: 38410929--38411008 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
38410919 AGATAAATTT
* * *
38410929 AAATGAAGTGAGAGAAAAGTTTA-ATTG
1 AAATGAAATGAGAGAAAA-ATTACATGG
38410956 AAATGAAATGAGAGAAAAATTACATGG
1 AAATGAAATGAGAGAAAAATTACATGG
* *
38410983 AAA-G--AT-TGATAAAAATTACATGG
1 AAATGAAATGAGAGAAAAATTACATGG
38411006 AAA
1 AAA
38411009 GATTGATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
23 18 0.38
24 2 0.04
26 4 0.09
27 23 0.49
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.23
Consensus pattern (27 bp):
AAATGAAATGAGAGAAAAATTACATGG
Found at i:38411000 original size:23 final size:23
Alignment explanation
Indices: 38410970--38411017 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
38410960 GAAATGAGAG
38410970 AAAAATTACATGGAAAGATTGAT
1 AAAAATTACATGGAAAGATTGAT
38410993 AAAAATTACATGGAAAGATTGAT
1 AAAAATTACATGGAAAGATTGAT
38411016 AA
1 AA
38411018 TTTAAATGAA
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:0.54, C:0.04, G:0.17, T:0.25
Consensus pattern (23 bp):
AAAAATTACATGGAAAGATTGAT
Found at i:38411035 original size:27 final size:23
Alignment explanation
Indices: 38410970--38411035 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
38410960 GAAATGAGAG
* *
38410970 AAAAATTACATGGAAAGATTGAT
1 AAAAATGAAATGGAAAGATTGAT
* *
38410993 AAAAATTACATGGAAAGATTGAT
1 AAAAATGAAATGGAAAGATTGAT
38411016 AATTTAAATGAAATGAGAAA
1 AA---AAATGAAATG-GAAA
38411036 AAAATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 25 0.68
26 8 0.22
27 4 0.11
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.26
Consensus pattern (23 bp):
AAAAATGAAATGGAAAGATTGAT
Found at i:38411076 original size:49 final size:48
Alignment explanation
Indices: 38410738--38411081 Score: 189
Period size: 48 Copynumber: 7.1 Consensus size: 48
38410728 GATAAATTGT
* * **
38410738 ATGAG-AAAAAATTGAAAATTACATGGAAAGATTGAT-AATTTAAATGAA
1 ATGAGAAAAAAATT--AAATTAAATTGAAAGAAAGATAAATTTAAATGAA
* *
38410786 ATGAGAAAAAAA-TAAATTGAAA-TGAAATGATACA-AAATTTAAATGAAA
1 ATGAGAAAAAAATTAAATT-AAATTGAAA-GAAAGATAAATTTAAATG-AA
* * *
38410834 ATTGAAAGAAAGATAAATTTAAATGAAA-TGAGGAA-AAA-ATTTAATTCAAATGAA
1 A-TG--AGAAA-A-AAA-TTAAATTAAATTGA--AAGAAAGA-TAAATTTAAATGAA
38410888 ATGAGAAAAAAATTAAA-TAAATTTGAAAGAAAGATAAATTTAAATGAA
1 ATGAGAAAAAAATTAAATTAAA-TTGAAAGAAAGATAAATTTAAATGAA
* * * * * * *
38410936 GTGAGAGAAAAGTTTAATTGAAA-TGAAATGAGAGA-AAAATTACATGGAA
1 ATGAGAAAAAAATTAAATT-AAATTGAAA-GAAAGATAAATTTAAAT-GAA
*** * * * **
38410985 A-GA-TTGATAA--AAATTACATGGAAAGATTGAT-AATTTAAATGAA
1 ATGAGAAAAAAATTAAATTAAATTGAAAGAAAGATAAATTTAAATGAA
38411028 ATGAGAAAAAAATTAAATTAAATTTGAAAGAAAGATAAATTTAAATGAA
1 ATGAGAAAAAAATTAAATTAAA-TTGAAAGAAAGATAAATTTAAATGAA
38411077 ATGAG
1 ATGAG
38411082 GGAAACTTTT
Statistics
Matches: 225, Mismatches: 39, Indels: 63
0.69 0.12 0.19
Matches are distributed among these distances:
43 4 0.02
44 15 0.07
45 11 0.05
46 9 0.04
47 30 0.13
48 67 0.30
49 41 0.18
50 4 0.02
51 10 0.04
52 1 0.00
53 6 0.03
54 11 0.05
55 14 0.06
56 2 0.01
ACGTcount: A:0.57, C:0.01, G:0.16, T:0.26
Consensus pattern (48 bp):
ATGAGAAAAAAATTAAATTAAATTGAAAGAAAGATAAATTTAAATGAA
Found at i:38411142 original size:17 final size:18
Alignment explanation
Indices: 38411110--38411143 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38411100 TGAAATTAGA
*
38411110 AAAAAATAAATTTAAATT
1 AAAAAATAAATATAAATT
38411128 AAAAAAT-AATATAAAT
1 AAAAAATAAATATAAAT
38411144 GAATTGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATAAATATAAATT
Found at i:38411172 original size:42 final size:43
Alignment explanation
Indices: 38411091--38411172 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
38411081 GGGAAACTTT
* *
38411091 TAATTTAAATGAAATTAGAAAAAAATAAATTTAAATTAAAAAA
1 TAATATAAATGAAATTAGAAAAAAATAAATATAAATTAAAAAA
*
38411134 TAATATAAATG-AATTGAGAAAAAAAT-AATATAATTTAAA
1 TAATATAAATGAAATT-AGAAAAAAATAAATATAAATTAAA
38411173 TGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 15 0.43
43 20 0.57
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (43 bp):
TAATATAAATGAAATTAGAAAAAAATAAATATAAATTAAAAAA
Found at i:38411178 original size:5 final size:5
Alignment explanation
Indices: 38411170--38411269 Score: 58
Period size: 5 Copynumber: 18.6 Consensus size: 5
38411160 AATATAATTT
* * * *
38411170 AAATG AAATG AAATGG AAATAG GAGTGG AAATG AAATT AGAACG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAATG AAATG A-AATG AAATG
* * *
38411219 AAATTG GAATG AAATA AAATT AGAATG AAATG AAAATGG AAA-G AAATG
1 AAA-TG AAATG AAATG AAATG A-AATG AAATG -AAAT-G AAATG AAATG
38411267 AAA
1 AAA
38411270 AAAAAAGTTG
Statistics
Matches: 73, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
4 4 0.05
5 39 0.53
6 29 0.40
7 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.23, T:0.19
Consensus pattern (5 bp):
AAATG
Found at i:38411218 original size:16 final size:16
Alignment explanation
Indices: 38411197--38411269 Score: 92
Period size: 16 Copynumber: 4.6 Consensus size: 16
38411187 AATAGGAGTG
*
38411197 GAAATGAAATTAGAAC
1 GAAATGAAATTAGAAT
*
38411213 GAAATGAAATTGGAAT
1 GAAATGAAATTAGAAT
*
38411229 GAAATAAAATTAGAAT
1 GAAATGAAATTAGAAT
* * *
38411245 GAAATGAAAATGGAAA
1 GAAATGAAATTAGAAT
38411261 GAAATGAAA
1 GAAATGAAA
38411270 AAAAAAGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.19
Consensus pattern (16 bp):
GAAATGAAATTAGAAT
Found at i:38411239 original size:32 final size:32
Alignment explanation
Indices: 38411179--38411270 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
38411169 TAAATGAAAT
* * *
38411179 GAAATGGAAATAGGAGTGGAAATGAAATTAGAAC
1 GAAAT-GAAATTGGAAT-GAAATAAAATTAGAAC
*
38411213 GAAATGAAATTGGAATGAAATAAAATTAGAAT
1 GAAATGAAATTGGAATGAAATAAAATTAGAAC
* *
38411245 GAAATGAAAATGGAAAGAAATGAAAA
1 GAAATGAAATTGGAATGAAAT-AAAA
38411271 AAAAAGTTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 33 0.65
33 13 0.25
34 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.24, T:0.18
Consensus pattern (32 bp):
GAAATGAAATTGGAATGAAATAAAATTAGAAC
Found at i:38411249 original size:11 final size:10
Alignment explanation
Indices: 38411170--38411269 Score: 58
Period size: 11 Copynumber: 9.3 Consensus size: 10
38411160 AATATAATTT
38411170 AAATGAAATG
1 AAATGAAATG
38411180 AAATGGAAATAG
1 AAAT-GAAAT-G
* *
38411192 GAGTGGAAATG
1 AAAT-GAAATG
* *
38411203 AAATTAGAACG
1 AAATGA-AATG
38411214 AAATGAAATTG
1 AAATGAAA-TG
* *
38411225 GAATGAAATA
1 AAATGAAATG
*
38411235 AAATTAGAATG
1 AAATGA-AATG
38411246 AAATGAAAATGG
1 AAATG-AAAT-G
38411258 AAA-GAAATG
1 AAATGAAATG
38411267 AAA
1 AAA
38411270 AAAAAAGTTG
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
9 4 0.06
10 16 0.23
11 35 0.51
12 14 0.20
ACGTcount: A:0.57, C:0.01, G:0.23, T:0.19
Consensus pattern (10 bp):
AAATGAAATG
Found at i:38411270 original size:16 final size:16
Alignment explanation
Indices: 38411176--38411270 Score: 84
Period size: 16 Copynumber: 5.8 Consensus size: 16
38411166 ATTTAAATGA
*
38411176 AATGAAATGGAAATAGG
1 AATGAAATGAAAATA-G
* *
38411193 AGTGGAAATGAAATTAG
1 AAT-GAAATGAAAATAG
* * *
38411210 AACGAAATGAAATTGG
1 AATGAAATGAAAATAG
38411226 AATGAAAT-AAAATTAG
1 AATGAAATGAAAA-TAG
*
38411242 AATGAAATGAAAATGG
1 AATGAAATGAAAATAG
*
38411258 AAAGAAATGAAAA
1 AATGAAATGAAAA
38411271 AAAAAGTTGA
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
15 3 0.05
16 43 0.67
17 8 0.12
18 10 0.16
ACGTcount: A:0.57, C:0.01, G:0.23, T:0.19
Consensus pattern (16 bp):
AATGAAATGAAAATAG
Found at i:38411608 original size:36 final size:36
Alignment explanation
Indices: 38411532--38411606 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
38411522 AAAATTTTAT
* **
38411532 AAATTTAAATGAAAAGAAGTACCAAAATGAAAACAA
1 AAATTTAAATGAAAAGAAATAAAAAAATGAAAACAA
*
38411568 AAATTTAAATGAAAATAAATATAAAAATATGAAAA-AA
1 AAATTTAAATGAAAAGAAATA-AAAAA-ATGAAAACAA
38411605 AA
1 AA
38411607 TTATATTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 19 0.58
37 7 0.21
38 7 0.21
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (36 bp):
AAATTTAAATGAAAAGAAATAAAAAAATGAAAACAA
Found at i:38412092 original size:73 final size:73
Alignment explanation
Indices: 38412005--38412159 Score: 292
Period size: 73 Copynumber: 2.1 Consensus size: 73
38411995 AAGGATTTAA
38412005 CATCAATTTTGACTTTGTAAAAAGCTAAAAATAGAAGATATTATTTTATTTTATTTAGTTTTATT
1 CATCAATTTTGACTTTGTAAAAAGCTAAAAATAGAAGATATTATTTTATTTTATTTAGTTTTATT
38412070 ATTTATTT
66 ATTTATTT
38412078 CATCAATTTTGACTTTGTAAAAAGCTAAAAATAGAAGATATTATTTTATTTTATTTAGTTTTATT
1 CATCAATTTTGACTTTGTAAAAAGCTAAAAATAGAAGATATTATTTTATTTTATTTAGTTTTATT
38412143 ATTTATTT
66 ATTTATTT
* *
38412151 TATTAATTT
1 CATCAATTT
38412160 AGCTTTAGCC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (73 bp):
CATCAATTTTGACTTTGTAAAAAGCTAAAAATAGAAGATATTATTTTATTTTATTTAGTTTTATT
ATTTATTT
Found at i:38412144 original size:13 final size:13
Alignment explanation
Indices: 38412128--38412166 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
38412118 TTATTTTATT
38412128 TTATTTAGTTTTA
1 TTATTTAGTTTTA
38412141 TTATTTA-TTTTA
1 TTATTTAGTTTTA
*
38412153 TTAATTTAGCTTTA
1 TT-ATTTAGTTTTA
38412167 GCCTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:38415928 original size:15 final size:15
Alignment explanation
Indices: 38415908--38415936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38415898 ATACACAAAA
38415908 ATATAAAAAATACAG
1 ATATAAAAAATACAG
38415923 ATATAAAAAATACA
1 ATATAAAAAATACA
38415937 AACATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (15 bp):
ATATAAAAAATACAG
Found at i:38416651 original size:105 final size:107
Alignment explanation
Indices: 38416534--38416826 Score: 376
Period size: 108 Copynumber: 2.7 Consensus size: 107
38416524 ATATATAAGG
* * * *
38416534 TTTGGTGCCGGCCATTAGAAGGCCA-AATCCAAAAAAAATT-AATTTTTTTTCGTATTGGAGTCG
1 TTTGGTGCCGGCCATTACAAGGCCAGCA-CCAAAAAAATTTGAATTTTTTTTCGTATTGGTGTCG
*
38416597 ACCATTAGAAGGCTAAAACAA-TTTTTTTTTAAATATTGGTAC
65 ACCATTAGAAGGCCAAAACAATTTTTTTTTTAAATATTGGTAC
* * * *
38416639 TTTGGTGCCGGCCATTACAAGGTCAGCAGCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCG
1 TTTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCGTA-TTGGTGTCG
** * * *
38416704 ATTATTAGAAGACCAAGACAATTTTTTTTTTAAATATTGGTAG
65 ACCATTAGAAGGCCAAAACAATTTTTTTTTTAAATATTGGTAC
* * * * *
38416747 TCTGGTGTCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCGTACTGGTGTTGG
1 TTTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCGTATTGGTGTCGA
38416812 CCATTAGAAGGCCAA
66 CCATTAGAAGGCCAA
38416827 GAAAAAAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
105 33 0.21
106 14 0.09
107 41 0.26
108 70 0.44
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (107 bp):
TTTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCGTATTGGTGTCGA
CCATTAGAAGGCCAAAACAATTTTTTTTTTAAATATTGGTAC
Found at i:38417962 original size:21 final size:18
Alignment explanation
Indices: 38417930--38417970 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
38417920 AGAAAACTAT
38417930 AACATTTTTTTTATGAATA
1 AACATTTTTTTTAT-AATA
38417949 AACATATTATTTTTATAATA
1 AACAT-TT-TTTTTATAATA
38417969 AA
1 AA
38417971 TAATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (18 bp):
AACATTTTTTTTATAATA
Found at i:38418694 original size:23 final size:24
Alignment explanation
Indices: 38418641--38418701 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
38418631 ATTTTTATTA
38418641 AAAATATAATTTTTTATAAAATCAC
1 AAAATATAA-TTTTTATAAAATCAC
*
38418666 AAAATATAGATTTTTAT-ACAT-AC
1 AAAATATA-ATTTTTATAAAATCAC
38418689 AAAATATATATTT
1 AAAATATA-ATTT
38418702 AGTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.42
24 3 0.09
25 15 0.45
26 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATATAATTTTTATAAAATCAC
Found at i:38418867 original size:4 final size:4
Alignment explanation
Indices: 38418860--38418897 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
38418850 ATGATAAAAC
38418860 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
38418898 TGAAATTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:38419344 original size:30 final size:29
Alignment explanation
Indices: 38419277--38419345 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
38419267 TTATATTTCT
38419277 ATATATTTTATAAATTTTTTCAATTGTTAC
1 ATAT-TTTTATAAATTTTTTCAATTGTTAC
* *
38419307 A-ACTTTTATAAATTTTTTTCTAATTTTTA-
1 ATATTTTTATAAA-TTTTTTC-AATTGTTAC
38419336 ATATTTTTAT
1 ATATTTTTAT
38419346 TATATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 9 0.27
29 9 0.27
30 15 0.45
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (29 bp):
ATATTTTTATAAATTTTTTCAATTGTTAC
Found at i:38422450 original size:32 final size:32
Alignment explanation
Indices: 38422412--38422475 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
38422402 GGAAAAAGAA
38422412 TATCAACTAGTGATAATGAATCACTAACCTGC
1 TATCAACTAGTGATAATGAATCACTAACCTGC
38422444 TATCAACTAGTGATAATGAATCACTAACCTGC
1 TATCAACTAGTGATAATGAATCACTAACCTGC
38422476 ATGAATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (32 bp):
TATCAACTAGTGATAATGAATCACTAACCTGC
Found at i:38422869 original size:7 final size:7
Alignment explanation
Indices: 38422857--38422891 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
38422847 TAAAAAAATA
38422857 AATAAAG
1 AATAAAG
38422864 AATAAAG
1 AATAAAG
38422871 AATAAAG
1 AATAAAG
38422878 AATAAAAG
1 AAT-AAAG
38422886 AATAAA
1 AATAAA
38422892 TTAGTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (7 bp):
AATAAAG
Found at i:38422935 original size:6 final size:6
Alignment explanation
Indices: 38422926--38422963 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
38422916 AATAAAAATA
38422926 AAAACC AAAACC AAAACC AAAACC -AAACC AAAACC AAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAA
38422964 TTGTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:38422941 original size:18 final size:17
Alignment explanation
Indices: 38422920--38422959 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38422910 CAATAAAATA
*
38422920 AAAATAAAAACCAAAACC
1 AAAACAAAAACC-AAACC
*
38422938 AAAACCAAAACCAAACC
1 AAAACAAAAACCAAACC
38422955 AAAAC
1 AAAAC
38422960 CAAATTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.70, C:0.28, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAACAAAAACCAAACC
Found at i:38422955 original size:11 final size:11
Alignment explanation
Indices: 38422927--38422963 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
38422917 ATAAAAATAA
38422927 AAACCAAAACC
1 AAACCAAAACC
38422938 AAAACCAAAACC
1 -AAACCAAAACC
38422950 AAACCAAAACC
1 AAACCAAAACC
38422961 AAA
1 AAA
38422964 TTGTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (11 bp):
AAACCAAAACC
Found at i:38429841 original size:22 final size:21
Alignment explanation
Indices: 38429816--38429864 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38429806 TGTAGGGCTC
*
38429816 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGT-GACCAAGGG
* *
38429838 ACACACCCGTGTGACCATGGG
1 ACACGCCCGTGTGACCAAGGG
38429859 ACACGC
1 ACACGC
38429865 TTGTGCTGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.22, C:0.35, G:0.31, T:0.12
Consensus pattern (21 bp):
ACACGCCCGTGTGACCAAGGG
Found at i:38434099 original size:22 final size:22
Alignment explanation
Indices: 38434058--38434099 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38434048 TTAATCCTTT
*
38434058 TTATTTTATATTATTATTATTA
1 TTATTTTATAATATTATTATTA
38434080 TTATTTTA-AATATTAGTTAT
1 TTATTTTATAATATTA-TTAT
38434100 ATAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTTTATAATATTATTATTA
Found at i:38434173 original size:16 final size:16
Alignment explanation
Indices: 38434148--38434183 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38434138 CATTTTTAAA
* *
38434148 ATTTTTTTATTTATAT
1 ATTTTGTTATATATAT
38434164 ATTTTGTTATATATAT
1 ATTTTGTTATATATAT
38434180 ATTT
1 ATTT
38434184 ATTCTGTTTT
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTTGTTATATATAT
Found at i:38436834 original size:48 final size:48
Alignment explanation
Indices: 38436778--38436870 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
38436768 TCTTGCAACT
*
38436778 GTACTTTCAACTCTTTCAACTCAGTAGGAGCCATTCTGTAAGGTGATA
1 GTACTTTCAACTCTTTCAACTCAGTAGGAACCATTCTGTAAGGTGATA
*
38436826 GTACTTTCAACTCTTTCAATTCAGTAGGAACCATTCTGTAAGGTG
1 GTACTTTCAACTCTTTCAACTCAGTAGGAACCATTCTGTAAGGTG
38436871 CTATGGATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (48 bp):
GTACTTTCAACTCTTTCAACTCAGTAGGAACCATTCTGTAAGGTGATA
Found at i:38443946 original size:20 final size:21
Alignment explanation
Indices: 38443921--38443960 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38443911 CACTTGAGGC
*
38443921 AGGGC-ACATGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
38443941 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
38443961 CCATTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:38445345 original size:46 final size:46
Alignment explanation
Indices: 38445281--38445410 Score: 165
Period size: 46 Copynumber: 2.8 Consensus size: 46
38445271 TCTCAAGGCC
* * *
38445281 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTTTAA-AT-GCG
1 GATGTATGTCCCAGACATGTCTTACACTGGCTCTC--ATAATATGGCG
* *
38445327 GATGTATGTCCCAGACATGTCTTACAATGGCTCTCATAATATGGCT
1 GATGTATGTCCCAGACATGTCTTACACTGGCTCTCATAATATGGCG
* *
38445373 GATGTATGTCCCAAACATGTCTTACACTGGCTCACATA
1 GATGTATGTCCCAGACATGTCTTACACTGGCTCTCATA
38445411 CCACCCAATG
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 3 0.04
45 2 0.03
46 69 0.93
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (46 bp):
GATGTATGTCCCAGACATGTCTTACACTGGCTCTCATAATATGGCG
Found at i:38457977 original size:15 final size:15
Alignment explanation
Indices: 38457957--38457991 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
38457947 TTCTTTATTC
38457957 TTTATTTTTT-GGTG
1 TTTATTTTTTAGGTG
38457971 ATTTATTTTTTAGGTG
1 -TTTATTTTTTAGGTG
38457987 TTTAT
1 TTTAT
38457992 AAGCATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (15 bp):
TTTATTTTTTAGGTG
Found at i:38469900 original size:21 final size:21
Alignment explanation
Indices: 38469870--38469921 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
38469860 GCACCAGCAG
*
38469870 AGTTGAAAGAATTAAAGTCGC
1 AGTTGCAAGAATTAAAGTCGC
38469891 AGTTGCAAGAATTAAAGTCGC
1 AGTTGCAAGAATTAAAGTCGC
38469912 AGTTGCAAGA
1 AGTTGCAAGA
38469922 GTTGACTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
AGTTGCAAGAATTAAAGTCGC
Found at i:38473473 original size:29 final size:30
Alignment explanation
Indices: 38473429--38473486 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
38473419 TTCCCGAGCC
*
38473429 TAGGGGCAAAAGTGTAATTATGCAAAAGTG
1 TAGGGGCAAAAATGTAATTATGCAAAAGTG
* *
38473459 TAGGGG-AAAAATGTAATTTTGCCAAAGT
1 TAGGGGCAAAAATGTAATTATGCAAAAGT
38473487 TCGTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTG
Found at i:38478350 original size:40 final size:39
Alignment explanation
Indices: 38478267--38478418 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 39
38478257 TCGAATGATG
* * * * *
38478267 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGC-GAGTTAATAAA
* * *
38478307 TCCGGACTAGGATCTGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTAATAAA
* * * *
38478347 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
* *
38478386 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGT
38478419 CACTATAACC
Statistics
Matches: 89, Mismatches: 20, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
39 32 0.36
40 50 0.56
41 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
Found at i:38478367 original size:39 final size:38
Alignment explanation
Indices: 38478322--38478458 Score: 148
Period size: 40 Copynumber: 3.5 Consensus size: 38
38478312 ACTAGGATCT
*
38478322 GAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCC
1 GAAGGCATTCGTGCGAGTTACTAAA-CCGGGCTAAGCCC
* * *
38478361 GAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGTTACTAAA-CCGGGCTAAG-CCC
* * *
38478401 GAAGGCATTCGTGCGAGTCACTATAACCGGGCTTCATCCC
1 GAAGGCATTCGTGCGAGTTACTA-AACCGGGC-TAAGCCC
* *
38478441 GAAGGCATTTGAGCGAGT
1 GAAGGCATTCGTGCGAGT
38478459 CGTTATATCC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 31 0.38
40 47 0.57
41 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (38 bp):
GAAGGCATTCGTGCGAGTTACTAAACCGGGCTAAGCCC
Found at i:38478409 original size:79 final size:81
Alignment explanation
Indices: 38478267--38478451 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
38478257 TCGAATGATG
* * * *
38478267 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCTGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
38478331 CGTGCGAGTTAATA-AA
65 CGTGCGAGTCAATATAA
* **
38478347 TCCGGGCTAAGCCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
*
38478410 CGTGCGAGTCACTATAA
65 CGTGCGAGTCAATATAA
* *
38478427 -CCGGGCTTCATCCCGAAGGCATTTG
1 TCCGGGC-TAAGCCCGAAGGCATTTG
38478452 AGCGAGTCGT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 53 0.59
80 36 0.40
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTCAATATAA
Found at i:38487513 original size:20 final size:20
Alignment explanation
Indices: 38487490--38487527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38487480 CCAAAAGTTT
38487490 AAATATTAATTTGAATTTAA
1 AAATATTAATTTGAATTTAA
* *
38487510 AAATTTTAATTTTAATTT
1 AAATATTAATTTGAATTT
38487528 GTTTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATTAATTTGAATTTAA
Found at i:38490635 original size:20 final size:21
Alignment explanation
Indices: 38490607--38490648 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
38490597 AAGACTATGA
38490607 ACCACTCCATTTACTTA-CAT
1 ACCACTCCATTTACTTAGCAT
*
38490627 ACCATTCCATTTACTTAGCAT
1 ACCACTCCATTTACTTAGCAT
38490648 A
1 A
38490649 AGCTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.36
Consensus pattern (21 bp):
ACCACTCCATTTACTTAGCAT
Found at i:38497818 original size:58 final size:58
Alignment explanation
Indices: 38497680--38497820 Score: 162
Period size: 57 Copynumber: 2.4 Consensus size: 58
38497670 ATCGTATTAT
* * * *
38497680 AGGATTACCAGTCCAGGCTAAATCC-ATTATGTAACGTATGCTCAGAAGAGCTCAATT
1 AGGATTACCAGTCCAGGCTAAATCCTAATATGTAACATATGCTCAGAAGAGATCAATC
* * *
38497737 AGAATTACCAGTCCAGGCTAAATCCTAAT-TGTAACATATGCTC-GAGAGGGATTATATC
1 AGGATTACCAGTCCAGGCTAAATCCTAATATGTAACATATGCTCAGA-AGAGATCA-ATC
* *
38497795 AGGATTACCCGTCTAGGCTAAATCCT
1 AGGATTACCAGTCCAGGCTAAATCCT
38497821 TTCTATAATG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
56 2 0.03
57 42 0.59
58 27 0.38
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (58 bp):
AGGATTACCAGTCCAGGCTAAATCCTAATATGTAACATATGCTCAGAAGAGATCAATC
Found at i:38505384 original size:40 final size:40
Alignment explanation
Indices: 38505335--38505502 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
38505325 TCTTCGGAAT
* *
38505335 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* **** *
38505374 TTAACCCGGAT-TTGGTAGCTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCA-CTAGCACAAATGCCTTCGGGTC
* * * * *
38505414 TTAGCTCGGATATAACAACTCGCACGAATGCCTTCAGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * **
38505454 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAG
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
38505494 TTAGCCCGG
1 TTAGCCCGG
38505503 GTATCATTCA
Statistics
Matches: 100, Mismatches: 26, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
39 5 0.05
40 93 0.93
41 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
Found at i:38508023 original size:24 final size:24
Alignment explanation
Indices: 38507993--38508235 Score: 405
Period size: 24 Copynumber: 10.1 Consensus size: 24
38507983 GAATGTGACT
* *
38507993 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
38508017 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
38508041 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
38508065 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
38508089 ATAGTGAATCGCACACCTAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
38508113 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
38508137 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
38508161 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
38508185 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
38508209 ATAGTAAACCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
38508233 ATA
1 ATA
38508236 TGGTCTTTGC
Statistics
Matches: 210, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 210 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:38510899 original size:25 final size:25
Alignment explanation
Indices: 38510871--38510919 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
38510861 ATTGGTACAC
38510871 TCTCAGGAGCTATAAATCGGTATGT
1 TCTCAGGAGCTATAAATCGGTATGT
*
38510896 TCTCATGAGCTATAAATCGGTATG
1 TCTCAGGAGCTATAAATCGGTATG
38510920 CTTTCACGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (25 bp):
TCTCAGGAGCTATAAATCGGTATGT
Found at i:38510930 original size:25 final size:25
Alignment explanation
Indices: 38510871--38510930 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
38510861 ATTGGTACAC
*
38510871 TCTCAGGAGCTATAAATCGGTATGT
1 TCTCACGAGCTATAAATCGGTATGT
*
38510896 TCTCATGAGCTATAAATCGGTATGCT
1 TCTCACGAGCTATAAATCGGTATG-T
38510922 T-TCACGAGC
1 TCTCACGAGC
38510931 CAGAAATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
TCTCACGAGCTATAAATCGGTATGT
Found at i:38510937 original size:25 final size:25
Alignment explanation
Indices: 38510884--38510942 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
38510874 CAGGAGCTAT
* * *
38510884 AAATCGGTATGTTCTCATGAGCTAT
1 AAATCGGTATGTTCTCACGAGCCAG
38510909 AAATCGGTATGCTT-TCACGAGCCAG
1 AAATCGGTATG-TTCTCACGAGCCAG
*
38510934 AAATTGGTA
1 AAATCGGTA
38510943 ACCCTAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (25 bp):
AAATCGGTATGTTCTCACGAGCCAG
Found at i:38513127 original size:48 final size:48
Alignment explanation
Indices: 38513056--38513168 Score: 147
Period size: 48 Copynumber: 2.4 Consensus size: 48
38513046 ACTCGAGAGT
* * * *
38513056 CTCGCACCCTAAATGCTAATATCATGGCCCAAAGCCAAATCAATGA-AG
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAAT-ATAA
* *
38513104 CTCGCACCCGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATATAA
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATATAA
*
38513152 CTTGCACCCGAAGTGCC
1 CTCGCACCCGAAGTGCC
38513169 CCGAAGCCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 56 0.98
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.18
Consensus pattern (48 bp):
CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATATAA
Found at i:38523024 original size:71 final size:71
Alignment explanation
Indices: 38522940--38523103 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
38522930 CGATTTGTCT
*
38522940 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTAAT
38523005 CTTTCA
66 CTTTCA
38523011 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTAAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTAAT
38523076 CTTTCA
66 CTTTCA
38523082 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
38523104 GATACATCTC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTAAT
CTTTCA
Found at i:38523141 original size:71 final size:70
Alignment explanation
Indices: 38522940--38523137 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
38522930 CGATTTGTCT
* * * * *
38522940 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTAAT
38523005 CTTTCA
65 CTTTCA
* * * *
38523011 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTAAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTAAT
38523076 CTTTCA
65 CTTTCA
* *
38523082 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
38523138 TACAGGGTGT
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 95 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTAATC
TTTCA
Found at i:38529591 original size:40 final size:39
Alignment explanation
Indices: 38529543--38529713 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
38529533 ACGACTAGCT
*
38529543 CAAATGCCTTCGGGAC-AAACCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCCGGTT-TAGTAACTCGCA
* *
38529583 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCCGGTTTAGTAACTCGCA
* *
38529623 CAAATGCCTTCGGGCTTAA-CCCGGATTTATTAACTCGGA
1 CAAATGCCTTCGGGCTTAACCCCGG-TTTAGTAACTCGCA
* * *
38529662 CAAATGCCTTCGGGCTTAACCCAGATTTATTAACTCGCA
1 CAAATGCCTTCGGGCTTAACCCCGGTTTAGTAACTCGCA
* *
38529701 CGAACGCCTTCGG
1 CAAATGCCTTCGG
38529714 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
38 4 0.03
39 60 0.52
40 43 0.37
41 9 0.08
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAACCCCGGTTTAGTAACTCGCA
Found at i:38529657 original size:39 final size:40
Alignment explanation
Indices: 38529543--38529766 Score: 226
Period size: 40 Copynumber: 5.7 Consensus size: 40
38529533 ACGACTAGCT
*
38529543 CAAATGCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCA
* *
38529583 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
38529623 CAAATGCCTTCGGG-CTTAACCCGGATTTATTAACTCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
38529662 CAAATGCCTTCGGG-CTTAACCCAGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * ** * * * **
38529701 CGAACGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAACA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
38529742 CAAA-GCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
38529767 CATCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.01
39 68 0.44
40 73 0.47
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:38542060 original size:46 final size:45
Alignment explanation
Indices: 38542009--38542175 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 45
38541999 GACGAGGGCT
38542009 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC
* * *
38542055 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC
* * * * * *
38542101 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC
* *
38542145 AGTGTAAGACATGTATGGGACATGCGTCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
38542176 ACGGTTACAT
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.02
44 32 0.30
46 70 0.66
47 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC
Found at i:38542105 original size:92 final size:90
Alignment explanation
Indices: 38541958--38542169 Score: 246
Period size: 92 Copynumber: 2.3 Consensus size: 90
38541948 AGATTTGTGT
* * * *
38541958 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTATGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT
38542023 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACGAG-AT--GA
* * * * *
38542052 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
1 GCCAGTGTAAGACATGTATGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
* * * *
38542117 GGGACATGCGTCGGCTACGAGATGT
66 GGGACATGCATCAGCCACGAGATGA
*
38542142 GCTAGTGTAAGACATGTATGGGACATGC
1 GCCAGTGTAAGACATGTATGGGACATGC
38542170 GTCAGCACGG
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 27 0.26
92 49 0.48
93 14 0.14
94 12 0.12
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTATGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA
Found at i:38542210 original size:46 final size:43
Alignment explanation
Indices: 38542009--38542212 Score: 162
Period size: 46 Copynumber: 4.5 Consensus size: 43
38541999 GACGAGGGCT
* * * *
38542009 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C
* * *
38542055 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C
* * *
38542101 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
*
38542144 TAGTGTAAGACATGTATGGGACATGCGTCAGC-ACGGTTACATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C
*
38542191 AGTGTAAGACCTGTCTGGGACA
1 AGTGTAAGACATGTCTGGGACA
38542213 CGGCATCGAC
Statistics
Matches: 136, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
43 3 0.02
44 31 0.23
45 3 0.02
46 96 0.71
47 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
Found at i:38553356 original size:25 final size:26
Alignment explanation
Indices: 38553304--38553357 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
38553294 ATAGCGTAGG
*
38553304 CTCGTGTAAGTGCTCTAGCATCAGAT
1 CTCGTGTAAGTGCTCTAGCATCACAT
*
38553330 CTCGT-TACAGTG-TCTTGCATCACAT
1 CTCGTGTA-AGTGCTCTAGCATCACAT
38553355 CTC
1 CTC
38553358 TACCACCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (26 bp):
CTCGTGTAAGTGCTCTAGCATCACAT
Found at i:38554048 original size:82 final size:82
Alignment explanation
Indices: 38553911--38554075 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
38553901 TTCTCGAGCA
*
38553911 TATTTGCTTAAACATACGAATTCTCTTTCATACTCAGTAACGGTCATCCAGCCTTGTTTCAATTC
1 TATTTGCTTAAACATACGAATTCTCTTTCATACTCAGTAACGGTCATCCAACCTTGTTTCAATTC
38553976 TAGAAACTCTTTATTTT
66 TAGAAACTCTTTATTTT
* * *
38553993 TATTTGCTTAAACATATGAATTCTCTTTCATACTCAGTTATGGTCATCCAACCTTGTTTCAATTC
1 TATTTGCTTAAACATACGAATTCTCTTTCATACTCAGTAACGGTCATCCAACCTTGTTTCAATTC
38554058 TAGAAACTCTTTATTTT
66 TAGAAACTCTTTATTTT
38554075 T
1 T
38554076 TTTTATCAAG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.44
Consensus pattern (82 bp):
TATTTGCTTAAACATACGAATTCTCTTTCATACTCAGTAACGGTCATCCAACCTTGTTTCAATTC
TAGAAACTCTTTATTTT
Found at i:38559814 original size:15 final size:15
Alignment explanation
Indices: 38559769--38559841 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 15
38559759 GAGATGACAT
* *
38559769 GAAAACCAAGACAAA
1 GAAATCCAAGATAAA
* * *
38559784 GAAGTCTAAGACAAA
1 GAAATCCAAGATAAA
*
38559799 GAAATCCTAGATAAA
1 GAAATCCAAGATAAA
*
38559814 GAAATCCAAGATACA
1 GAAATCCAAGATAAA
*
38559829 TAAATCCAAGATA
1 GAAATCCAAGATA
38559842 CAATATCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.56, C:0.16, G:0.14, T:0.14
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:38563611 original size:47 final size:45
Alignment explanation
Indices: 38563555--38563805 Score: 177
Period size: 46 Copynumber: 5.4 Consensus size: 45
38563545 TGCCATATCG
*
38563555 CAGACATGGTTTTACACTGGCTCATATCTC-AAGTCGATGCCATGTCC
1 CAGACAT-GTCTTACACTGGCT-ATATCTCGAAGTCGATG-CATGTCC
* ** * *
38563602 CAAACATGGTCTTACACTAACTATCATCTCGTAGCCGATGCATGTCC
1 CAGACAT-GTCTTACACTGGCTAT-ATCTCGAAGTCGATGCATGTCC
* * *
38563649 CAGACATGTCTTACACTGGCTTATGTCTCGAGGTTGATGCATGTCC
1 CAGACATGTCTTACACTGGC-TATATCTCGAAGTCGATGCATGTCC
* * * *
38563695 CAGACATGTCTTACACTAGC-ACTCGTCTC-AATTCCGATGACATGTAC
1 CAGACATGTCTTACACTGGCTA-T-ATCTCGAAGT-CGATG-CATGTCC
* * * * ** *
38563742 TAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCCGATGCATGTCC
1 CAGACAT-GTCTTACACTGGCTAT-AT-CTCGAAGTCGATGCATGTCC
38563789 CAGACATGTCTTACACT
1 CAGACATGTCTTACACT
38563806 AGCCAAAAAT
Statistics
Matches: 164, Mismatches: 29, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
44 1 0.01
45 3 0.02
46 68 0.41
47 63 0.38
48 28 0.17
49 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (45 bp):
CAGACATGTCTTACACTGGCTATATCTCGAAGTCGATGCATGTCC
Found at i:38563678 original size:46 final size:48
Alignment explanation
Indices: 38563540--38563808 Score: 197
Period size: 47 Copynumber: 5.8 Consensus size: 48
38563530 TGGGTAAGGT
* * * * *
38563540 GCCGATGCCATATCGCAGACATGGTTTTACACTGGCTCATATCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTATATCTCGAA
* * * *
38563587 GTCGATGCCATGTCCCAAACATGGTCTTACACTAAC-TATCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTAT-ATCTCGAA
* * *
38563635 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTATGTCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTATATCTCGAA
** *
38563681 GTTGATG-CATGTCCCAGACAT-GTCTTACACTAGC--ACTCGTCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTA-T-ATCTCGAA
* * * * *
38563726 TTCCGATGACATGTACTAGACATGGTCTTACACTAGCTCTCATAATGT-G--
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-T-AT-ATCTCGAA
38563775 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
38563809 CAAAAATAAC
Statistics
Matches: 178, Mismatches: 31, Indels: 27
0.75 0.13 0.11
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 71 0.40
47 74 0.42
48 26 0.15
51 3 0.02
52 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTATATCTCGAA
Found at i:38563702 original size:93 final size:94
Alignment explanation
Indices: 38563540--38563712 Score: 235
Period size: 93 Copynumber: 1.9 Consensus size: 94
38563530 TGGGTAAGGT
* *
38563540 GCCGATGCCATATCGCAGACATGGTTTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAA
1 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAA
38563605 ACATGGTCTTACACTAACTATCATCTCGTA
66 ACAT-GTCTTACACTAACTATCATCTCGTA
* * * * *
38563635 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTATGTCTCGAGGTTGATG-CATGTCCCA
1 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATATCTC-AAGTCGATGCCATGTCCCA
*
38563697 GACATGTCTTACACTA
65 AACATGTCTTACACTA
38563713 GCACTCGTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 11 0.16
93 32 0.46
94 19 0.28
95 7 0.10
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (94 bp):
GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAA
ACATGTCTTACACTAACTATCATCTCGTA
Found at i:38569019 original size:2 final size:2
Alignment explanation
Indices: 38569012--38569036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38569002 AACAAAAAGA
38569012 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
38569037 AAGAAGTGAG
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:38569904 original size:19 final size:18
Alignment explanation
Indices: 38569857--38569906 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
38569847 CTTTAATAAA
*
38569857 ATTTAT-AAATTTTATTTT
1 ATTTATAAAATATT-TTTT
*
38569875 ATTTATTAAATATTTTTT
1 ATTTATAAAATATTTTTT
38569893 ATTTAATAAAATAT
1 ATTT-ATAAAATAT
38569907 GATTAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATAAAATATTTTTT
Found at i:38573869 original size:25 final size:25
Alignment explanation
Indices: 38573809--38573870 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
38573799 CAGCTCTTAT
*
38573809 GAGCTTACCGATATTCAGCATGGAG
1 GAGCTTACCGTTATTCAGCATGGAG
38573834 GAGCTTACCGTTA-TCTAGC-TCGGAG
1 GAGCTTACCGTTATTC-AGCAT-GGAG
38573859 GAGCTTACCGTT
1 GAGCTTACCGTT
38573871 TACAGTTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCATGGAG
Found at i:38575748 original size:42 final size:42
Alignment explanation
Indices: 38575635--38575784 Score: 140
Period size: 42 Copynumber: 3.5 Consensus size: 42
38575625 ATGATTCCAA
* * * *
38575635 TATATGATTTCGTGTAAGACCATGTTTGGGACGTTGGTATCG
1 TATATGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCG
*
38575677 -ATTTCAGATTTACGTGTAAGACCATGTCTAGGACATTGGCATCG
1 TATAT--GATTT-CGTGTAAGACCATGTCTAGGACATTGGCATCG
* * * * *
38575721 TATATGAGTTCGTGTAAGACCCTGTCTAAGACAGTGGCATCAA
1 TATATGATTTCGTGTAAGACCATGTCTAGGACATTGGCATC-G
* * *
38575764 TATTTGATTACATGTAAGACC
1 TATATGATTTCGTGTAAGACC
38575785 TCGTCTGGGA
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 3 0.03
42 28 0.32
43 26 0.30
44 28 0.32
45 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
TATATGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCG
Found at i:38588273 original size:35 final size:35
Alignment explanation
Indices: 38588234--38588306 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
38588224 ACACATTCTT
38588234 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
38588269 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
38588304 TAT
1 TAT
38588307 ATCACATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:38591485 original size:50 final size:50
Alignment explanation
Indices: 38591399--38591646 Score: 289
Period size: 50 Copynumber: 4.9 Consensus size: 50
38591389 ACCGAAGCTC
* * * * * *
38591399 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * *
38591449 TCTGATACACGTAGTAGCTTGCACTTAGTACTACACATGTGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * ** *
38591499 TCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATATGATCGAAACTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTAACAA
* * * * *
38591550 TCGGGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* **
38591600 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGACCTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
38591647 AACTGTCTTA
Statistics
Matches: 165, Mismatches: 32, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
50 125 0.76
51 40 0.24
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:38591607 original size:101 final size:100
Alignment explanation
Indices: 38591399--38591642 Score: 317
Period size: 101 Copynumber: 2.4 Consensus size: 100
38591389 ACCGAAGCTC
* * * ** * * * *
38591399 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGT
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGACGAAACCATCGGATACACATAAT
* * *
38591464 AGCTTGCACTTAGTACTACACATGTGACCTATCAA
66 AGCCTGCACTTAGTACTACACATGAGACCTAACAA
* * * * *
38591499 TCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATATGATCGAAACTATCGGGTACGCATAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGA-CGAAACCATCGGATACACATAA
38591564 TAGCCTGCACTTAGTACTACACATGAGACCTAACAA
65 TAGCCTGCACTTAGTACTACACATGAGACCTAACAA
*
38591600 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGAC
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGAC
38591643 CTAAAACTGT
Statistics
Matches: 123, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
100 38 0.31
101 85 0.69
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (100 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGACGAAACCATCGGATACACATAAT
AGCCTGCACTTAGTACTACACATGAGACCTAACAA
Found at i:38610500 original size:29 final size:29
Alignment explanation
Indices: 38610466--38610543 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
38610456 GTGACGAGAT
* *
38610466 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
* *
38610495 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
**
38610524 CGGCACTGGGTGTGCGAGCT
1 CGGCACTAAGTGTGCGAGCT
38610544 CGGAGGGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCGAGCTGGAAAAATA
Found at i:38618323 original size:29 final size:29
Alignment explanation
Indices: 38618290--38618391 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
38618280 TGACGAGATC
38618290 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
38618319 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
38618348 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
38618377 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
38618392 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:38620378 original size:25 final size:25
Alignment explanation
Indices: 38620344--38620397 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
38620334 ATGGTTAGTC
38620344 ACACGCCCGTGTGTGAGTCTGTGTG
1 ACACGCCCGTGTGTGAGTCTGTGTG
38620369 ACACGCCCGTGTGTGAGTCTGTGTG
1 ACACGCCCGTGTGTGAGTCTGTGTG
38620394 ACAC
1 ACAC
38620398 CCGTTTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (25 bp):
ACACGCCCGTGTGTGAGTCTGTGTG
Found at i:38620811 original size:30 final size:30
Alignment explanation
Indices: 38620777--38620835 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
38620767 GCTAAGGTCG
*
38620777 TGTTCCCCACACAGCTGAGACATATGGCCA
1 TGTTCCCCACACAGCTGAGACACATGGCCA
*
38620807 TGTTCCCCACACGGCTGAGACACATGGCC
1 TGTTCCCCACACAGCTGAGACACATGGCC
38620836 GTGTCTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.19
Consensus pattern (30 bp):
TGTTCCCCACACAGCTGAGACACATGGCCA
Found at i:38622790 original size:48 final size:48
Alignment explanation
Indices: 38622738--38622954 Score: 231
Period size: 48 Copynumber: 4.5 Consensus size: 48
38622728 GGTGCCGAGT
* ** * *
38622738 CCATGTCCCAGACATGGTCTTTCACCAGCACACATATCATCACCGATA
1 CCATGTCCCAGACATGGTCTTACATTAGCACACATATCATCGCCGATG
* *
38622786 CCATGTCCCAGACATGGTCTTACATTGGCACACATATCAAT-GTCGATG
1 CCATGTCCCAGACATGGTCTTACATTAGCACACATATC-ATCGCCGATG
* *
38622834 CCATGTCCCAGACATGGTCTTACATTAGCACACATATCAACGCCAATG
1 CCATGTCCCAGACATGGTCTTACATTAGCACACATATCATCGCCGATG
* * * * * * *
38622882 CCATGTTCCAGATATGGTCTTACACTGGCTCTCATCTCAGAT-GCCGATG
1 CCATGTCCCAGACATGGTCTTACATTAGCACACATATC--ATCGCCGATG
* *
38622931 CCATGTCCCAGACAAGGTTTTACA
1 CCATGTCCCAGACATGGTCTTACA
38622955 CGGGATCTCA
Statistics
Matches: 141, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.01
48 111 0.79
49 28 0.20
50 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACATTAGCACACATATCATCGCCGATG
Done.