Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 54 of 66
Found at i:19622926 original size:55 final size:55
Alignment explanation
Indices: 19622841--19623036 Score: 221
Period size: 55 Copynumber: 3.6 Consensus size: 55
19622831 TATAATAATT
* * * * * * *
19622841 TTTTCATCATAACATATAATAGCTAAATTTTTTAACATGGTATGTAACAGCTAAA
1 TTTTCAACATAACGTATAATAACTACATTTTTTAACATAGTGTGTAACAACTAAA
* * * * * * * * *
19622896 TTTTCAACGTAATGTGTAACAACTATATTTTTTTATATAGCGTGTAATAACTAAA
1 TTTTCAACATAACGTATAATAACTACATTTTTTAACATAGTGTGTAACAACTAAA
* * *
19622951 TTTTCAACATAACATATAATAACTACAATTTTTAACATAATGTGTAACAACTAAA
1 TTTTCAACATAACGTATAATAACTACATTTTTTAACATAGTGTGTAACAACTAAA
19623006 TTTTCAACATAACGTATAATAACTACATTTT
1 TTTTCAACATAACGTATAATAACTACATTTT
19623037 CAACATAACG
Statistics
Matches: 112, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
55 112 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (55 bp):
TTTTCAACATAACGTATAATAACTACATTTTTTAACATAGTGTGTAACAACTAAA
Found at i:19623048 original size:27 final size:27
Alignment explanation
Indices: 19622940--19623054 Score: 167
Period size: 27 Copynumber: 4.2 Consensus size: 27
19622930 ATATAGCGTG
*
19622940 TAATAACTAAATTTTCAACATAACATA
1 TAATAACTAAATTTTCAACATAACGTA
* * *
19622967 TAATAACTACAATTTTTAACATAATGTG
1 TAATAACTA-AATTTTCAACATAACGTA
*
19622995 TAACAACTAAATTTTCAACATAACGTA
1 TAATAACTAAATTTTCAACATAACGTA
*
19623022 TAATAACTACATTTTCAACATAACGTA
1 TAATAACTAAATTTTCAACATAACGTA
19623049 TAATAA
1 TAATAA
19623055 TTATTTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 55 0.71
28 22 0.29
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (27 bp):
TAATAACTAAATTTTCAACATAACGTA
Found at i:19623051 original size:82 final size:83
Alignment explanation
Indices: 19622841--19623054 Score: 225
Period size: 82 Copynumber: 2.6 Consensus size: 83
19622831 TATAATAATT
* * * * *** * * * *
19622841 TTTTCATCATAACATATAATAGCTAAATTTTTTAACATGGTATGTAACAGCTA-AATTTTCAACG
1 TTTTCAACATAACGTATAATAACTAAA-TTTTCAACATAACATATAATAACTACAATTTTCAACA
*
19622905 TAATGTGTAACAACTATAT
65 TAATGTGTAACAACTATAA
** * * * *
19622924 TTTTTTATATAGCGTGTAATAACTAAATTTTCAACATAACATATAATAACTACAATTTTTAACAT
1 TTTTCAACATAACGTATAATAACTAAATTTTCAACATAACATATAATAACTACAATTTTCAACAT
19622989 AATGTGTAACAACTA-AA
66 AATGTGTAACAACTATAA
* *
19623006 TTTTCAACATAACGTATAATAACTACATTTTCAACATAACGTATAATAA
1 TTTTCAACATAACGTATAATAACTAAATTTTCAACATAACATATAATAA
19623055 TTATTTTCAA
Statistics
Matches: 105, Mismatches: 25, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
82 61 0.58
83 44 0.42
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (83 bp):
TTTTCAACATAACGTATAATAACTAAATTTTCAACATAACATATAATAACTACAATTTTCAACAT
AATGTGTAACAACTATAA
Found at i:19623119 original size:26 final size:27
Alignment explanation
Indices: 19622863--19623120 Score: 90
Period size: 27 Copynumber: 9.6 Consensus size: 27
19622853 CATATAATAG
* * *
19622863 CTAAATTTTTTAACATGGTATGTAACAG
1 CTAAA-TTTTCAACATGGCATGTAACAA
* ****
19622891 CTAAATTTTCAACGTAATGTGTAACAA
1 CTAAATTTTCAACATGGCATGTAACAA
* ** * * * *
19622918 CTATATTTTTTTATATAGCGTGTAATAA
1 CTA-AATTTTCAACATGGCATGTAACAA
** * *
19622946 CTAAATTTTCAACATAACATATAATAA
1 CTAAATTTTCAACATGGCATGTAACAA
* ****
19622973 CTACAATTTTTAACATAATGTGTAACAA
1 CTA-AATTTTCAACATGGCATGTAACAA
** * * *
19623001 CTAAATTTTCAACATAACGTATAATAA
1 CTAAATTTTCAACATGGCATGTAACAA
* ** * * *
19623028 CTACATTTTCAACATAACGTATAATAA
1 CTAAATTTTCAACATGGCATGTAACAA
* * **
19623055 -T-TATTTTCAATATGTTATGTAACAA
1 CTAAATTTTCAACATGGCATGTAACAA
*
19623080 CTAAATTTTAAACATGGCATGTAAC-A
1 CTAAATTTTCAACATGGCATGTAACAA
* *
19623106 TTACATTTTCAACAT
1 CTAAATTTTCAACAT
19623121 TGCGTTAACA
Statistics
Matches: 179, Mismatches: 47, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
25 16 0.09
26 15 0.08
27 102 0.57
28 46 0.26
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (27 bp):
CTAAATTTTCAACATGGCATGTAACAA
Found at i:19634693 original size:12 final size:12
Alignment explanation
Indices: 19634672--19634701 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19634662 AGTATACCCA
*
19634672 AAAAACAAAATG
1 AAAAATAAAATG
19634684 AAAAATAAAATG
1 AAAAATAAAATG
19634696 AAAAAT
1 AAAAAT
19634702 TGATTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAATAAAATG
Found at i:19642934 original size:38 final size:38
Alignment explanation
Indices: 19642892--19642979 Score: 176
Period size: 38 Copynumber: 2.3 Consensus size: 38
19642882 TATTTGTTTT
19642892 CCTGCTAAACTCATTTAGGCAATAGTATATTCATCTTA
1 CCTGCTAAACTCATTTAGGCAATAGTATATTCATCTTA
19642930 CCTGCTAAACTCATTTAGGCAATAGTATATTCATCTTA
1 CCTGCTAAACTCATTTAGGCAATAGTATATTCATCTTA
19642968 CCTGCTAAACTC
1 CCTGCTAAACTC
19642980 TTCAATCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (38 bp):
CCTGCTAAACTCATTTAGGCAATAGTATATTCATCTTA
Found at i:19648443 original size:5 final size:5
Alignment explanation
Indices: 19648433--19648457 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19648423 TATTCTCTCT
19648433 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
19648458 CTTGTCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:19652076 original size:2 final size:2
Alignment explanation
Indices: 19652065--19652112 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
19652055 CTTTTATGCT
19652065 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19652106 TG TA TA T
1 TA TA TA T
19652113 GTATGTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19654952 original size:114 final size:111
Alignment explanation
Indices: 19654784--19654996 Score: 245
Period size: 114 Copynumber: 1.9 Consensus size: 111
19654774 TTAATAATAA
**
19654784 TTAATTAATTATTAATCATAAAAATTATAAATAAATTACTAAAAGTACCTGTATATGTATAAATC
1 TTAATTAACCATTAATCATAAAAATTATAAATAAATTACTAAAAGTA-C-GTATA--TATAAAT-
*
19654849 TTG-TTTAATA-ATTTTCTAAAATTAATTAAATTATCATAAATATATAATG
61 TTGACTTAATACATTTTCTAAAATTAATTAAATTATCATAAATATATAATG
* *
19654898 TTAATTAACCATTAATTATAGAAATTATAAA-AAATGTACTACTAATAGTA-GTATATATAAATT
1 TTAATTAACCATTAATCATAAAAATTATAAATAAAT-TACTA--AA-AGTACGTATATATAAATT
* * *
19654961 TGACTTGATACCTTTTTTAAAATTAATTAAATTATC
62 TGACTTAATACATTTTCTAAAATTAATTAAATTATC
19654997 TTAGAGATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
111 3 0.04
112 12 0.14
113 27 0.32
114 37 0.44
116 2 0.02
117 4 0.05
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (111 bp):
TTAATTAACCATTAATCATAAAAATTATAAATAAATTACTAAAAGTACGTATATATAAATTTGAC
TTAATACATTTTCTAAAATTAATTAAATTATCATAAATATATAATG
Found at i:19666557 original size:47 final size:47
Alignment explanation
Indices: 19666488--19666596 Score: 146
Period size: 47 Copynumber: 2.3 Consensus size: 47
19666478 ACATTTGTAG
* * *
19666488 GTGACTGCAACAAAACTAAATCAGAGTATCATGGGTATACTTCGGCA
1 GTGACTGCAAGAAAACTAAATCAAAGTATCATGGGTATAATTCGGCA
* * * * *
19666535 GTGACTGCAAGAAAAGTAAATCAAAGTATCTTGTGTATAATTTGGCT
1 GTGACTGCAAGAAAACTAAATCAAAGTATCATGGGTATAATTCGGCA
19666582 GTGACTGCAAGAAAA
1 GTGACTGCAAGAAAA
19666597 TTACTTAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (47 bp):
GTGACTGCAAGAAAACTAAATCAAAGTATCATGGGTATAATTCGGCA
Found at i:19667839 original size:38 final size:35
Alignment explanation
Indices: 19667750--19667839 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 35
19667740 AACATTTTAT
* *
19667750 AATAT-TATAATTAAAATAAAAAAAATTAAAATAA
1 AATATATAGAATTAAAATAAAAAAAAATAAAATAA
* *
19667784 AATATATAGTATAAAAATCAAAAAATAAAATAAAATAA
1 AATATATAGAATTAAAAT--AAAAA-AAAATAAAATAA
19667822 AATATA-AGAAATTAAAAT
1 AATATATAG-AATTAAAAT
19667840 TTATATAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 5 0.11
35 9 0.20
37 7 0.16
38 24 0.53
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (35 bp):
AATATATAGAATTAAAATAAAAAAAAATAAAATAA
Found at i:19667914 original size:19 final size:19
Alignment explanation
Indices: 19667864--19667914 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
19667854 TAAACGAAAT
* *
19667864 TAAAATAAAATA-TATAATA
1 TAAAA-AAAATATTAAAAAA
*
19667883 TAAAAAATTATATTAAAAAA
1 TAAAAAA-AATATTAAAAAA
19667903 TAAAAAAAATAT
1 TAAAAAAAATAT
19667915 AAGATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 12 0.46
20 12 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAAAATATTAAAAAA
Found at i:19667943 original size:31 final size:31
Alignment explanation
Indices: 19667865--19667946 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 31
19667855 AAACGAAATT
* *
19667865 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATA-AA-ATATAAAATTATAATAA
*
19667899 AAAAT-AAAA-AAAATATAAGATTATAATAA
1 AAAATAAAAATAAAATATAAAATTATAATAA
*
19667928 GAAATAAAAATAAAATATA
1 AAAATAAAAATAAAATATA
19667947 TGACATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 18 0.43
30 6 0.14
31 9 0.21
32 1 0.02
33 3 0.07
34 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (31 bp):
AAAATAAAAATAAAATATAAAATTATAATAA
Found at i:19687346 original size:23 final size:23
Alignment explanation
Indices: 19687292--19687347 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
19687282 GGTGTTTACG
* *
19687292 TAATTTATGTAAAATTGTTTAAA
1 TAATTTATTTAAAATTATTTAAA
*
19687315 T-ATAATATTTAAAATTATTTAAA
1 TAAT-TTATTTAAAATTATTTAAA
19687338 TAATTTATTT
1 TAATTTATTT
19687348 TTTATTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATTTATTTAAAATTATTTAAA
Found at i:19690583 original size:2 final size:2
Alignment explanation
Indices: 19690578--19690606 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19690568 GAAGACGCTT
19690578 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19690607 ATTGTCTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19690671 original size:2 final size:2
Alignment explanation
Indices: 19690664--19690690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19690654 CAGCTNTAGT
19690664 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
19690691 ATTGTCTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19705435 original size:89 final size:90
Alignment explanation
Indices: 19705262--19705447 Score: 299
Period size: 90 Copynumber: 2.1 Consensus size: 90
19705252 TATTCAAGTC
19705262 CTGTAATCTTTTATTCTTTTCTCATTCTTAGTATTTGGAAACCCAAAAAAAAAAAAAAAAAGGGT
1 CTGTAATCTTTTATTCTTTTCTCATTCTTAGTATTTGGAAA-CCAAAAAAAAAAAAAAAAAGGGT
19705327 GCCGTCTTTTTATAGGCCAATGAAAT
65 GCCGTCTTTTTATAGGCCAATGAAAT
*
19705353 CNTGTAATC-TTTATTCTTTTCTTCTATTCTTAGTATTTGGTAA-C-AAAAAAAAAAAAAAAAGG
1 C-TGTAATCTTTTATTCTTTTC-TC-ATTCTTAGTATTTGGAAACCAAAAAAAAAAAAAAAAAGG
19705415 GTGCCG-CTTTTTATAGGCCAATGAAAT
63 GTGCCGTCTTTTTATAGGCCAATGAAAT
19705442 CTGTAA
1 CTGTAA
19705448 CAAAGTCTTT
Statistics
Matches: 91, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
88 5 0.05
89 22 0.24
90 24 0.26
91 14 0.15
92 9 0.10
93 17 0.19
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (90 bp):
CTGTAATCTTTTATTCTTTTCTCATTCTTAGTATTTGGAAACCAAAAAAAAAAAAAAAAAGGGTG
CCGTCTTTTTATAGGCCAATGAAAT
Found at i:19716216 original size:20 final size:19
Alignment explanation
Indices: 19716188--19716228 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
19716178 CCTCCCTTGC
19716188 TGTTAAATTTTTAGTATTTT
1 TGTTAAATTTTTAG-ATTTT
* *
19716208 TGTTTAATTTTTTGATTTT
1 TGTTAAATTTTTAGATTTT
19716227 TG
1 TG
19716229 CTGAAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (19 bp):
TGTTAAATTTTTAGATTTT
Found at i:19741836 original size:24 final size:21
Alignment explanation
Indices: 19741796--19741851 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 21
19741786 TTTTATTTTT
19741796 TAATTTTATAAAAAATATAATAA
1 TAATTTT-TAAAAAATA-AATAA
19741819 TAATTTTTAAAATTAATAAATAA
1 TAATTTTTAAAA--AATAAATAA
*
19741842 AAATATTTTA
1 TAAT-TTTTA
19741852 GTTTTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 15 0.52
24 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATTTTTAAAAAATAAATAA
Found at i:19746955 original size:12 final size:12
Alignment explanation
Indices: 19746935--19746974 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
19746925 TACTGAAACT
*
19746935 AAAATATTAAAA
1 AAAAAATTAAAA
19746947 AAAAAATT--AA
1 AAAAAATTAAAA
19746957 AAAAAATTAAAA
1 AAAAAATTAAAA
19746969 AAAAAA
1 AAAAAA
19746975 ACTAAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAATTAAAA
Found at i:19746958 original size:10 final size:10
Alignment explanation
Indices: 19746945--19746972 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19746935 AAAATATTAA
19746945 AAAAAAAATT
1 AAAAAAAATT
19746955 AAAAAAAATT
1 AAAAAAAATT
19746965 AAAAAAAA
1 AAAAAAAA
19746973 AAACTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:19779325 original size:2 final size:2
Alignment explanation
Indices: 19779318--19779350 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19779308 AACTAATAGT
*
19779318 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19779351 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19781630 original size:29 final size:29
Alignment explanation
Indices: 19781597--19781656 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
19781587 TGCAGTTCAA
19781597 GGTAAGAAGCAATCTGTGTTGGTGTGGGG
1 GGTAAGAAGCAATCTGTGTTGGTGTGGGG
19781626 GGTAAGAAGCAATCTGTGTTGGTGTGGGG
1 GGTAAGAAGCAATCTGTGTTGGTGTGGGG
19781655 GG
1 GG
19781657 GCCTATCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.07, G:0.47, T:0.27
Consensus pattern (29 bp):
GGTAAGAAGCAATCTGTGTTGGTGTGGGG
Found at i:19783289 original size:39 final size:39
Alignment explanation
Indices: 19783235--19783310 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
19783225 GGAAATTGAT
19783235 TGGAATTGAAATGCAAAGCAGACCCAAGAAACTAAAGTA
1 TGGAATTGAAATGCAAAGCAGACCCAAGAAACTAAAGTA
19783274 TGGAATTGAAATGCAAAGCAGACCCAAGAAACTAAAG
1 TGGAATTGAAATGCAAAGCAGACCCAAGAAACTAAAG
19783311 CAGTTAACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.14
Consensus pattern (39 bp):
TGGAATTGAAATGCAAAGCAGACCCAAGAAACTAAAGTA
Found at i:19784705 original size:2 final size:2
Alignment explanation
Indices: 19784698--19784725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19784688 GCAGTAAGGA
19784698 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19784726 GAAACTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19785217 original size:2 final size:2
Alignment explanation
Indices: 19785210--19785245 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19785200 GGGTTAGAAG
19785210 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19785246 AGGGGAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19802705 original size:12 final size:13
Alignment explanation
Indices: 19802678--19802724 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
19802668 TGGATTAATT
*
19802678 TATATATATAT-A
1 TATATATATGTGA
*
19802690 TATATGTATGTGTA
1 TATATATATGTG-A
19802704 TATATATATGTG-
1 TATATATATGTGA
19802716 TATATATAT
1 TATATATAT
19802725 CGAAACTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 18 0.60
14 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (13 bp):
TATATATATGTGA
Found at i:19802707 original size:14 final size:14
Alignment explanation
Indices: 19802678--19802724 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
19802668 TGGATTAATT
* *
19802678 TATATATATATATA
1 TATATATGTGTATA
*
19802692 TATGTATGTGTATA
1 TATATATGTGTATA
19802706 TATATATGTGTATA
1 TATATATGTGTATA
19802720 TATAT
1 TATAT
19802725 CGAAACTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (14 bp):
TATATATGTGTATA
Found at i:19807144 original size:2 final size:2
Alignment explanation
Indices: 19807139--19807173 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19807129 GCAAAAAATA
19807139 AT AT AT AT AT 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 AT AT AT AT AT A
19807174 GTACTAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19820797 original size:21 final size:20
Alignment explanation
Indices: 19820758--19820798 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19820748 TGTAGACACT
* *
19820758 TAAATAAATAAATATAAATA
1 TAAATAAATAAAAAAAAATA
19820778 TAAATTAAATAAAAAAAAATA
1 TAAA-TAAATAAAAAAAAATA
19820799 AAACCAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAATAAATAAAAAAAAATA
Found at i:19827429 original size:47 final size:47
Alignment explanation
Indices: 19827375--19827515 Score: 237
Period size: 47 Copynumber: 3.0 Consensus size: 47
19827365 AGAGATATGT
19827375 GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATTAAATTCA
1 GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATTAAATTCA
*
19827422 GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATCAAATTCA
1 GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATTAAATTCA
* * * *
19827469 CACATTCCCAAAGTGGGAAAGAATCATTCATCTAAACAGTAAATTCA
1 GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATTAAATTCA
19827516 AAGCTTTTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 88 1.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.27
Consensus pattern (47 bp):
GACATTCCCAAAGTGGGAAAGAATCATTTATCTAAATATTAAATTCA
Found at i:19829767 original size:32 final size:32
Alignment explanation
Indices: 19829725--19829789 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
19829715 TAACGACTTT
*
19829725 TCGGGTACTTATTAACTGACAAAACCGTTGAA
1 TCGGGCACTTATTAACTGACAAAACCGTTGAA
**
19829757 TCGGGCACTTATTAACTGACAGGACCGTTGAA
1 TCGGGCACTTATTAACTGACAAAACCGTTGAA
19829789 T
1 T
19829790 TACATAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (32 bp):
TCGGGCACTTATTAACTGACAAAACCGTTGAA
Found at i:19832726 original size:34 final size:34
Alignment explanation
Indices: 19832683--19832747 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
19832673 CATTGATGGC
19832683 AAGAGAAAGGATAATAAATGCAAGAGAGTTTCGT
1 AAGAGAAAGGATAATAAATGCAAGAGAGTTTCGT
19832717 AAGAGAAAGGATAATAAATGCAAGAGAGTTT
1 AAGAGAAAGGATAATAAATGCAAGAGAGTTT
19832748 TGCGAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.20
Consensus pattern (34 bp):
AAGAGAAAGGATAATAAATGCAAGAGAGTTTCGT
Found at i:19834649 original size:3 final size:3
Alignment explanation
Indices: 19834596--19834629 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19834586 TAAGGATTAC
19834596 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19834630 CGTTGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19835508 original size:251 final size:251
Alignment explanation
Indices: 19835064--19835523 Score: 611
Period size: 251 Copynumber: 1.8 Consensus size: 251
19835054 CACTTAGCAT
* * * * *
19835064 GTAGGTAAAGTTTGAAATTGATTCAACTAGAATGAGAACGAAGAACGAAAAATTTCAAAAGAGTC
1 GTAGGTAAAGTTTGAAACTAATTCAACTAGAATGAGAACAAAGAACGAAAAATTTCAAAAAAATC
* * * * * * * *
19835129 TGAGGTGTGATTTCATTGTCGTTAAAGATAATTTTTGCCTTTTCGAAGTATGAAACTTGATGCAA
66 TGAGATGTGATTTCACTATCGTTAAAGATAATTTTCGCCATTTAGAAGTACGAAACTTGATACAA
* *
19835194 AGGAACTGTAACACTTATCTTCCAAGATTCAACATACCCTTCCTTATTAGTTTGCATCAAATCAG
131 AAGAACTGTAACACTTATCTTCCAAGATTCAACATACCCTTCCTTATTAGTTTGCACCAAATCAG
*
19835259 GGGAGTTATAAATCAGTTAGCATGCAGGTAAAGTTTGAGATTGATTTAATTGGAAC
196 GAGAGTTATAAATCAGTTAGCATGCAGGTAAAGTTTGAGATTGATTTAATTGGAAC
* *
19835315 GTAGGTAAAGTTTGAGACTAATTCAACTAGAATGAGAACAAAGCAC-AGAAAATTTCAAAAAAAT
1 GTAGGTAAAGTTTGAAACTAATTCAACTAGAATGAGAACAAAGAACGA-AAAATTTCAAAAAAAT
*
19835379 TTGAGATGTGATTTCACTATAC-TTAAAGATAATTTTCGCCCATTTAG-AGTACGAAACTTGATA
65 CTGAGATGTGATTTCACTAT-CGTTAAAGATAATTTTCG-CCATTTAGAAGTACGAAACTTGATA
* * **** * * * *
19835442 CAAAATAATTGTAGTGGTTATTTTCTAAGATTCAACATACCTTTTCTTATTAGTTTGCACCAAAT
128 CAAAAGAACTGTAACACTTATCTTCCAAGATTCAACATACCCTTCCTTATTAGTTTGCACCAAAT
19835507 CAGGAGAGTTATAAATC
193 CAGGAGAGTTATAAATC
19835524 GAAGTACAAA
Statistics
Matches: 177, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
250 1 0.01
251 169 0.95
252 7 0.04
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (251 bp):
GTAGGTAAAGTTTGAAACTAATTCAACTAGAATGAGAACAAAGAACGAAAAATTTCAAAAAAATC
TGAGATGTGATTTCACTATCGTTAAAGATAATTTTCGCCATTTAGAAGTACGAAACTTGATACAA
AAGAACTGTAACACTTATCTTCCAAGATTCAACATACCCTTCCTTATTAGTTTGCACCAAATCAG
GAGAGTTATAAATCAGTTAGCATGCAGGTAAAGTTTGAGATTGATTTAATTGGAAC
Found at i:19837962 original size:15 final size:15
Alignment explanation
Indices: 19837942--19837980 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
19837932 AATATATGAG
19837942 TAAATAAAATAAAAA
1 TAAATAAAATAAAAA
*
19837957 TAAATAAAATAATAA
1 TAAATAAAATAAAAA
19837972 TAATATAAA
1 TAA-ATAAA
19837981 TTGAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATAAAATAAAAA
Found at i:19838706 original size:28 final size:27
Alignment explanation
Indices: 19838660--19838768 Score: 94
Period size: 27 Copynumber: 4.0 Consensus size: 27
19838650 TATTAGTGTC
*
19838660 TTACACGACATATTGAAAAATATAATTG
1 TTACACGATATATT-AAAAATATAATTG
* *
19838688 TTACACGATATGTTAAAAATTTAATTG
1 TTACACGATATATTAAAAATATAATTG
* * * * *
19838715 TTATACGTTATATTAAAAAATTTAGTTC
1 TTACACGATATATT-AAAAATATAATTG
* *
19838743 TTACAAGCTATGA-TAAAAATATAATT
1 TTACACGATAT-ATTAAAAATATAATT
19838769 ACATGTCACG
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
27 33 0.50
28 32 0.48
29 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (27 bp):
TTACACGATATATTAAAAATATAATTG
Found at i:19850536 original size:25 final size:25
Alignment explanation
Indices: 19850508--19850573 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
19850498 ATTTAGAAAC
19850508 GAAAATTATATATATCCGATAAAAG
1 GAAAATTATATATATCCGATAAAAG
19850533 GAAAATTATATATATCCGATAAAAG
1 GAAAATTATATATATCCGATAAAAG
19850558 GAAAATTATTATATAT
1 GAAAATTA-TATATAT
19850574 ATATATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.32
Consensus pattern (25 bp):
GAAAATTATATATATCCGATAAAAG
Found at i:19858455 original size:2 final size:2
Alignment explanation
Indices: 19858448--19858473 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19858438 CTTTTATTAT
19858448 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19858474 AAAGCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19863963 original size:22 final size:23
Alignment explanation
Indices: 19863938--19863980 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
19863928 AGACCTTTTA
19863938 ATTAAAA-AT-ATTATATTTAATG
1 ATTAAAATATCATTAT-TTTAATG
19863960 ATTAAAATATCATTATTTTAA
1 ATTAAAATATCATTATTTTAA
19863981 AAACTATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAAAATATCATTATTTTAATG
Found at i:19864376 original size:3 final size:3
Alignment explanation
Indices: 19864361--19864394 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19864351 TAAAGATCTC
*
19864361 CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
19864395 CCACCATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:19864572 original size:24 final size:23
Alignment explanation
Indices: 19864545--19864632 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
19864535 AAAAAGGAAA
*
19864545 GAAGAGAACAAAATGAAAAAAGGG
1 GAAGAAAACAAAAT-AAAAAAGGG
*
19864569 GAAGAAAACAACATAAAAAA--G
1 GAAGAAAACAAAATAAAAAAGGG
* **
19864590 AAAGAAAACAATTTGAAAAAAGGG
1 GAAGAAAACAAAAT-AAAAAAGGG
* *
19864614 CAACAAAACAAAATAAAAA
1 GAAGAAAACAAAATAAAAA
19864633 GAAAAAGGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 12 0.23
22 6 0.12
23 11 0.21
24 23 0.44
ACGTcount: A:0.68, C:0.08, G:0.17, T:0.07
Consensus pattern (23 bp):
GAAGAAAACAAAATAAAAAAGGG
Found at i:19869763 original size:2 final size:2
Alignment explanation
Indices: 19869756--19869794 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19869746 CAACAAAGAA
19869756 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19869795 ATATAAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19885721 original size:11 final size:11
Alignment explanation
Indices: 19885705--19885729 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19885695 ATTCACCCCA
19885705 AAAGAAAAAAG
1 AAAGAAAAAAG
19885716 AAAGAAAAAAG
1 AAAGAAAAAAG
19885727 AAA
1 AAA
19885730 AGAGCAGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:19886262 original size:15 final size:15
Alignment explanation
Indices: 19886220--19886263 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
19886210 CCCACTCCAA
19886220 CAACAACAGCAGCAG
1 CAACAACAGCAGCAG
*
19886235 CAAAGCCACCAGCAGCAG
1 C-AA--CAACAGCAGCAG
19886253 CAACAACAGCA
1 CAACAACAGCA
19886264 ACAGTCTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.33
16 2 0.08
17 2 0.08
18 12 0.50
ACGTcount: A:0.45, C:0.36, G:0.18, T:0.00
Consensus pattern (15 bp):
CAACAACAGCAGCAG
Found at i:19888695 original size:86 final size:83
Alignment explanation
Indices: 19888539--19888781 Score: 303
Period size: 86 Copynumber: 2.9 Consensus size: 83
19888529 GTAAACAAAT
* * *
19888539 AGCCATTCATATTGTTTGATAAACTTTTTTCATAAG-GCACCTTGGCAGAATTAGAATCTTGTTT
1 AGCCATTCTTATTGTTTGATAAAC-TTTTTCAT-AGTGCACCTTGGCAGAATTAGAATCTT-ATC
19888603 AAGATGTTTTTGAGAAAAAAC
63 AAGATGTTTTTGAGAAAAAAC
* *
19888624 GGCCATTCTTATTGTTTGATAAACATTTTTCCATAGTGCACCTCGGCAGAATTAGAATCTTATCA
1 AGCCATTCTTATTGTTTGATAAAC-TTTTT-CATAGTGCACCTTGGCAGAATTAGAATCTTATCA
* *
19888689 ATGATGTTTTTGTGAATAAAC
64 A-GATGTTTTTGAGAAAAAAC
**
19888710 AGCCATT-TATATCATTTGATAAACCTTTTTCATAGTGCACCTTGGCAGAATTAG-ATCTTATCT
1 AGCCATTCT-TATTGTTTGATAAA-CTTTTTCATAGTGCACCTTGGCAGAATTAGAATCTTATC-
19888773 AAGATGTTT
63 AAGATGTTT
19888782 AGACAGATTT
Statistics
Matches: 140, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
84 15 0.11
85 58 0.41
86 66 0.47
87 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (83 bp):
AGCCATTCTTATTGTTTGATAAACTTTTTCATAGTGCACCTTGGCAGAATTAGAATCTTATCAAG
ATGTTTTTGAGAAAAAAC
Found at i:19889488 original size:9 final size:9
Alignment explanation
Indices: 19889467--19889545 Score: 59
Period size: 9 Copynumber: 8.8 Consensus size: 9
19889457 TTCTCAAATG
*
19889467 CAGCAACCA
1 CAGCAACAA
*
19889476 CAGCAACAT
1 CAGCAACAA
* *
19889485 CAGCAGCAG
1 CAGCAACAA
*
19889494 CAACAACAA
1 CAGCAACAA
*
19889503 CAACAACAA
1 CAGCAACAA
*
19889512 CAGCAACAG
1 CAGCAACAA
* *
19889521 CAGCAGCAT
1 CAGCAACAA
*
19889530 CAGCTACAA
1 CAGCAACAA
*
19889539 CAACAAC
1 CAGCAAC
19889546 CTCTGCAACA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.48, C:0.35, G:0.13, T:0.04
Consensus pattern (9 bp):
CAGCAACAA
Found at i:19895148 original size:2 final size:2
Alignment explanation
Indices: 19895141--19895173 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19895131 GTCATCCTCT
19895141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19895174 TTTGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19902287 original size:2 final size:2
Alignment explanation
Indices: 19902280--19902313 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19902270 TTTTATATTT
*
19902280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19902314 CATTTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19906747 original size:52 final size:52
Alignment explanation
Indices: 19906690--19906892 Score: 282
Period size: 52 Copynumber: 3.9 Consensus size: 52
19906680 CTACAACTTT
* * * * *
19906690 TTTGTGAATAGCAAACAATGACCAAGAAATGAGC-ACTGAAGCTTGCGATCAA
1 TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGA-TAAAGCTTGCGACCAA
*
19906742 TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCCATAAAGCTTGCGACCAA
1 TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCGACCAA
* * * *
19906794 TTTATGAATAGCAAACTATGGCTAAGAGGTGAGCGATAAAGCGTGCGACCAA
1 TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCGACCAA
* *
19906846 TATGTGAATAGTAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCG
1 TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCG
19906893 GTCAATAGCG
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 133 0.99
53 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (52 bp):
TTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCGACCAA
Found at i:19908580 original size:2 final size:2
Alignment explanation
Indices: 19908575--19908612 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
19908565 TGCGTGTGTN
*
19908575 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19908613 GTACTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19926972 original size:2 final size:2
Alignment explanation
Indices: 19926965--19926999 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19926955 GTACCAAAGA
19926965 AT AT AT AT AT 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 AT AT AT AT AT A
19927000 AACAGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19928273 original size:17 final size:19
Alignment explanation
Indices: 19928251--19928288 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
19928241 AGATAATTTT
19928251 TATTTTTA-TT-TTAAAAA
1 TATTTTTATTTATTAAAAA
19928268 TATTTTTATTTATTAAAAA
1 TATTTTTATTTATTAAAAA
19928287 TA
1 TA
19928289 ATTACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTTATTTATTAAAAA
Found at i:19931395 original size:18 final size:18
Alignment explanation
Indices: 19931365--19931503 Score: 217
Period size: 18 Copynumber: 7.7 Consensus size: 18
19931355 ATTGCGGCCT
19931365 CCGGCAGCGCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
* *
19931383 CCTGG-ACCGCCTTCTGGC
1 CC-GGCAGCGCCTTCTCGC
*
19931401 CCGGCAGCTCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
19931419 CCGGCAGCGCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
*
19931437 CCGGCAGCTCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
19931455 CCGGCAGCGCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
*
19931473 CCGGGAGCGCCTTCTCGC
1 CCGGCAGCGCCTTCTCGC
19931491 CCGGCAGCGCCTT
1 CCGGCAGCGCCTT
19931504 TTAGTGCACA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
17 2 0.02
18 105 0.96
19 2 0.02
ACGTcount: A:0.06, C:0.48, G:0.27, T:0.19
Consensus pattern (18 bp):
CCGGCAGCGCCTTCTCGC
Found at i:19935097 original size:33 final size:34
Alignment explanation
Indices: 19935060--19935145 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
19935050 TTTTAATGTC
*
19935060 ATATATTTTATTTTCT-TTT-TTTATTATAATTTT
1 ATATATTTTATTTT-TATTTCTTTAATATAATTTT
19935093 ATATATTTTATTTTTATTTCTTTAATATAATTTT
1 ATATATTTTATTTTTATTTCTTTAATATAATTTT
* *
19935127 -TATAGTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
19935146 TAATTTCGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
32 1 0.02
33 25 0.53
34 21 0.45
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (34 bp):
ATATATTTTATTTTTATTTCTTTAATATAATTTT
Found at i:19935142 original size:34 final size:35
Alignment explanation
Indices: 19935068--19935145 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
19935058 TCATATATTT
* * * * *
19935068 TATTTTCTTTTTTTATTATAATTTTATATATTTTA
1 TATTTTATTTCTTTAATATAATTTTATATAGTATA
19935103 T-TTTTATTTCTTTAATATAATTTT-TATAGTATA
1 TATTTTATTTCTTTAATATAATTTTATATAGTATA
19935136 TATTTTATTT
1 TATTTTATTT
19935146 TAATTTCGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 8 0.22
34 28 0.76
35 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (35 bp):
TATTTTATTTCTTTAATATAATTTTATATAGTATA
Found at i:19940861 original size:6 final size:6
Alignment explanation
Indices: 19940850--19940891 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
19940840 ACAAATCGAC
19940850 TAAAAA TAAAAA TAAAAA T--AAA -AAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
19940892 TATAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 3 0.09
5 3 0.09
6 27 0.82
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:19940877 original size:15 final size:15
Alignment explanation
Indices: 19940857--19940913 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
19940847 GACTAAAAAT
19940857 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
19940872 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
* * **
19940887 AATAATATAAATTTA
1 AAAAATAAAAATAAA
*
19940902 AAAAATTAAAAT
1 AAAAATAAAAAT
19940914 TGTGTGAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:19940898 original size:21 final size:21
Alignment explanation
Indices: 19940851--19940891 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19940841 CAAATCGACT
19940851 AAAAATAAAAATAAAAATAAA
1 AAAAATAAAAATAAAAATAAA
19940872 AAAAATAAAAATAAAAATAA
1 AAAAATAAAAATAAAAATAA
19940892 TATAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAATAAAAATAAA
Found at i:19961549 original size:20 final size:19
Alignment explanation
Indices: 19961500--19961550 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
19961490 ATGAGAAAAG
19961500 ATAAAAAATA-GTTAGTTA
1 ATAAAAAATAGGTTAGTTA
*
19961518 AAAAGAAAATAGGTTAGGTTA
1 ATAA-AAAATAGGTTA-GTTA
*
19961539 ATAAAACATAGG
1 ATAAAAAATAGG
19961551 GAAGAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 6 0.22
20 11 0.41
21 7 0.26
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (19 bp):
ATAAAAAATAGGTTAGTTA
Found at i:19966405 original size:19 final size:19
Alignment explanation
Indices: 19966381--19966418 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19966371 ACTTTTTAAC
19966381 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
19966400 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
19966419 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:19972729 original size:20 final size:20
Alignment explanation
Indices: 19972704--19972749 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19972694 CTTCTAAACC
19972704 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
19972724 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
19972744 TCAAAT
1 TCAAAT
19972750 GGAGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:19974367 original size:18 final size:17
Alignment explanation
Indices: 19974344--19974383 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19974334 AAACGAAGAA
19974344 AAAAAAAACAAAGCAACC
1 AAAAAAAAC-AAGCAACC
* *
19974362 AAAAAAATCAAGCAACT
1 AAAAAAAACAAGCAACC
19974379 AAAAA
1 AAAAA
19974384 CCTTAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.72, C:0.17, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAAACAAGCAACC
Found at i:19981660 original size:15 final size:14
Alignment explanation
Indices: 19981635--19981665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
19981625 AAATGGGAAA
19981635 AATAAAAAAATAAT
1 AATAAAAAAATAAT
19981649 AATAATAAAAATAAT
1 AATAA-AAAAATAAT
19981664 AA
1 AA
19981666 GAAATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAAAATAAT
Found at i:19982515 original size:20 final size:20
Alignment explanation
Indices: 19982484--19982532 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
19982474 GAGAAAAGAT
19982484 AAAAAATA-GTTA-GTTAAA
1 AAAAAATAGGTTAGGTTAAA
*
19982502 AAGAAAATAGGTTAGGTTAAT
1 AA-AAAATAGGTTAGGTTAAA
19982523 AAAAAATAGG
1 AAAAAATAGG
19982533 GAAGAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 6 0.22
20 12 0.44
21 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAAAATAGGTTAGGTTAAA
Found at i:19986749 original size:57 final size:60
Alignment explanation
Indices: 19986627--19986751 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 60
19986617 TATTGTTATC
* * ** *
19986627 AGATTTTTAAATTACTATTACTTCATATAATTAATTAGTTAAATTACATTGGTAAGAAATC
1 AGATTTTTAAATTACTATTAC-TAAGATAATTAATTAGTTAAATTACATTGAAAAGAAATA
* * * *
19986688 AGATTTTTAAATTACTATTAC-AAGAT-A-TCATTAGTTAAATTAGATTGAAAATAAGTA
1 AGATTTTTAAATTACTATTACTAAGATAATTAATTAGTTAAATTACATTGAAAAGAAATA
19986745 AGATTTT
1 AGATTTT
19986752 AAAGATGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
57 30 0.55
58 1 0.02
59 3 0.05
61 21 0.38
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (60 bp):
AGATTTTTAAATTACTATTACTAAGATAATTAATTAGTTAAATTACATTGAAAAGAAATA
Found at i:19986848 original size:2 final size:2
Alignment explanation
Indices: 19986841--19986866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19986831 TGTTAAATGG
19986841 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19986867 GATTTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20002687 original size:28 final size:28
Alignment explanation
Indices: 20002643--20002719 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 28
20002633 CGTCATGGCT
*
20002643 TGTAATAACTAAA-TTTTTAA-ATAATA
1 TGTAATAATTAAATTTTTTAATATAATA
*
20002669 TGTAATAATTATATTTTTTAATATAATA
1 TGTAATAATTAAATTTTTTAATATAATA
*
20002697 TGTAATATTTAAA-TTTTTAATAT
1 TGTAATAATTAAATTTTTTAATAT
20002720 GACGTATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
26 11 0.24
27 17 0.38
28 17 0.38
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (28 bp):
TGTAATAATTAAATTTTTTAATATAATA
Found at i:20002779 original size:52 final size:53
Alignment explanation
Indices: 20002671--20002798 Score: 132
Period size: 52 Copynumber: 2.4 Consensus size: 53
20002661 AAATAATATG
* * * * * * * *
20002671 TAATAATTATATTTTTTAATATAATATGTAATATTTAAATTTTTAATATGACGTA
1 TAATAACTATA-TTTTTAACATAACATGTAACAATT-AATTTTCAACATGAAGTA
20002726 TAATAACTATATTTTTAACATAACATGTAACAATT-ATTTTCAACATGAAGTA
1 TAATAACTATATTTTTAACATAACATGTAACAATTAATTTTCAACATGAAGTA
* * *
20002778 TAACAACTAAATTTTCAACAT
1 TAATAACTATATTTTTAACAT
20002799 GACTTCATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
52 32 0.52
54 20 0.32
55 10 0.16
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.43
Consensus pattern (53 bp):
TAATAACTATATTTTTAACATAACATGTAACAATTAATTTTCAACATGAAGTA
Found at i:20004125 original size:33 final size:31
Alignment explanation
Indices: 20004038--20004125 Score: 79
Period size: 33 Copynumber: 2.6 Consensus size: 31
20004028 TCATGCCAAA
*
20004038 TTAATATATCACATTATCATCAATTATAATATG
1 TTAACATATCAC-TTAT-ATCAATTATAATATG
* *
20004071 TTAACATACTTTA-TCATTATCAATTATAATATG
1 TTAACATA--TCACTTA-TATCAATTATAATATG
20004104 TTAACATATCACGTTAGTATCA
1 TTAACATATCAC-TTA-TATCA
20004126 TGCGACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
31 2 0.05
33 39 0.89
34 1 0.02
35 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (31 bp):
TTAACATATCACTTATATCAATTATAATATG
Found at i:20011460 original size:27 final size:27
Alignment explanation
Indices: 20011411--20011466 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
20011401 ATTACATAAT
* *
20011411 ATTGATATAATATGTTGTCATGTTGTA
1 ATTGACATAATATGTTGTCATGTTATA
*
20011438 ATTGACATGATATGTTG-CAATGTTATA
1 ATTGACATAATATGTTGTC-ATGTTATA
20011465 AT
1 AT
20011467 AGATGATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (27 bp):
ATTGACATAATATGTTGTCATGTTATA
Found at i:20018482 original size:56 final size:56
Alignment explanation
Indices: 20018402--20018514 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
20018392 ATGAATTTTG
20018402 TAAAAAGAGACCCAAATGGGATCTCAATAGTAGAAACTAGAAATCAAAGAAATTTC
1 TAAAAAGAGACCCAAATGGGATCTCAATAGTAGAAACTAGAAATCAAAGAAATTTC
*
20018458 TAAAAAGAGACCCAAATGGGATCTCAATGGTAGAAACTAGAAATCAAAGAAATTTC
1 TAAAAAGAGACCCAAATGGGATCTCAATAGTAGAAACTAGAAATCAAAGAAATTTC
20018514 T
1 T
20018515 TTGATTCTAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (56 bp):
TAAAAAGAGACCCAAATGGGATCTCAATAGTAGAAACTAGAAATCAAAGAAATTTC
Found at i:20021681 original size:18 final size:17
Alignment explanation
Indices: 20021651--20021684 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20021641 GCATCAATCA
*
20021651 ATAAATTAAATATTTAG
1 ATAAAATAAATATTTAG
20021668 ATAAAATAATATATTTA
1 ATAAAATAA-ATATTTA
20021685 TTTGATAATT
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:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATAAAATAAATATTTAG
Found at i:20023181 original size:130 final size:134
Alignment explanation
Indices: 20022964--20023228 Score: 439
Period size: 130 Copynumber: 2.0 Consensus size: 134
20022954 CTGTATTTGT
20022964 TCATTCAGGCTGAGGCTCCTCACATTCACAATATATATATCAATACTTGATCCATGTTCAATTAA
1 TCATTCAGGCTGAGGCTCCTCACATTCACAATATATATATCAATACTTGATCCATGTTCAATTAA
20023029 AAGATAATGGGTTGAAAGGCCCATCTAGTC-AGTTCAAGGCCCAAATGCATACTCCATTTATATG
66 AAGATAATGGGTTGAAAGGCCCATCTAGTCGAGTTCAAGGCCCAAATGCATACTCCATTTATATG
20023093 TTTA
131 TTTA
*
20023097 TCATTCAGGCTGAGGCTCCTCACATTC-C-ATATATATATCAATAC-TGATCCATGTTTAATTAA
1 TCATTCAGGCTGAGGCTCCTCACATTCACAATATATATATCAATACTTGATCCATGTTCAATTAA
20023159 AAGATAATGGGTTGAAAGGCCCATCTAGTCTTGGAGGAGTTCAAGGCCCAAATGCATACTCCATT
66 AAGATAATGGGTTGAAAGGCCCATCTAGTC------GAGTTCAAGGCCCAAATGCATACTCCATT
20023224 TATAT
125 TATAT
20023229 ATTTTTAAAA
Statistics
Matches: 124, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
130 47 0.38
131 16 0.13
132 1 0.01
133 27 0.22
137 33 0.27
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (134 bp):
TCATTCAGGCTGAGGCTCCTCACATTCACAATATATATATCAATACTTGATCCATGTTCAATTAA
AAGATAATGGGTTGAAAGGCCCATCTAGTCGAGTTCAAGGCCCAAATGCATACTCCATTTATATG
TTTA
Found at i:20040850 original size:42 final size:42
Alignment explanation
Indices: 20040791--20040878 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
20040781 TGTGGGCATA
20040791 CATGCTCAAAGTCTTATTAGCAAACCAAGAGATGACTCCTCC
1 CATGCTCAAAGTCTTATTAGCAAACCAAGAGATGACTCCTCC
20040833 CATGCTCAAAGTCTTATTAGCAAACCAAGAGATGACTCCTCC
1 CATGCTCAAAGTCTTATTAGCAAACCAAGAGATGACTCCTCC
20040875 CATG
1 CATG
20040879 AGTCCGCTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
CATGCTCAAAGTCTTATTAGCAAACCAAGAGATGACTCCTCC
Found at i:20044230 original size:29 final size:29
Alignment explanation
Indices: 20044176--20044231 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
20044166 ATTATTTTAT
*
20044176 AATAAAATTTAATATTTTTCTGTTGTTCA
1 AATAAAATTTAATATTTTTCTATTGTTCA
* *
20044205 AATAAATTATTAAT-TTTTTTTATTGTT
1 AATAAAAT-TTAATATTTTTCTATTGTT
20044232 TTGGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (29 bp):
AATAAAATTTAATATTTTTCTATTGTTCA
Found at i:20049461 original size:30 final size:30
Alignment explanation
Indices: 20049413--20049484 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
20049403 TACATTTAAT
* * *
20049413 TAAACTCTTATATTTTTATTTTGAGTCAAA
1 TAAATTCTTATGTTTTTATTTTAAGTCAAA
* * *
20049443 TAAGTTTTTATGTTTTTATTTTAATTCAAA
1 TAAATTCTTATGTTTTTATTTTAAGTCAAA
20049473 TAAATTCTTATG
1 TAAATTCTTATG
20049485 ACTAATAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (30 bp):
TAAATTCTTATGTTTTTATTTTAAGTCAAA
Found at i:20049579 original size:33 final size:33
Alignment explanation
Indices: 20049542--20049604 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
20049532 TGAAGTTAAC
*
20049542 ATGATATATTAAAATATTATAATTGATGATGAT
1 ATGATATATTAAAATATTATAACTGATGATGAT
* *
20049575 ATGATATGTTAATATATTATAACTGATGAT
1 ATGATATATTAAAATATTATAACTGATGAT
20049605 AATGTGACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.43
Consensus pattern (33 bp):
ATGATATATTAAAATATTATAACTGATGATGAT
Found at i:20049617 original size:33 final size:33
Alignment explanation
Indices: 20049550--20049620 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
20049540 ACATGATATA
* * * *
20049550 TTAAAATATTATAATTGATGATGATATGATATG
1 TTAATATATTATAACTGATGATAATATGACATG
*
20049583 TTAATATATTATAACTGATGATAATGTGACATG
1 TTAATATATTATAACTGATGATAATATGACATG
20049616 TTAAT
1 TTAAT
20049621 TTGACATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (33 bp):
TTAATATATTATAACTGATGATAATATGACATG
Found at i:20049625 original size:13 final size:13
Alignment explanation
Indices: 20049600--20049633 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20049590 ATTATAACTG
20049600 ATGATAATGTGAC
1 ATGATAATGTGAC
* *
20049613 ATGTTAATTTGAC
1 ATGATAATGTGAC
20049626 ATGATAAT
1 ATGATAAT
20049634 ATCATTGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (13 bp):
ATGATAATGTGAC
Found at i:20063446 original size:75 final size:78
Alignment explanation
Indices: 20063359--20063507 Score: 198
Period size: 75 Copynumber: 1.9 Consensus size: 78
20063349 ATCTTATAGA
* *
20063359 GTAAACTCAAATTTTGAAAATATTTTTCTTA-TT-TTTTTTCA-TATAGAGTAAAAGATGCATTG
1 GTAAACTCAAATTTTGAAAATATTTTTCTTATTTCTTTTTTCATTATAAAGTAAAAGATACATTG
20063421 CTTAACTATAAGT
66 CTTAACTATAAGT
* * *
20063434 GTAAA-TCAAAATTTTGAAATTATTTTTTTTATTTTTCTTTTTTTATTATAAAGTAAAAGATACA
1 GTAAACTC-AAATTTTGAAAATATTTTTCTTA--TTTCTTTTTTCATTATAAAGTAAAAGATACA
20063498 TTGCTTAACT
63 TTGCTTAACT
20063508 TTGTTTAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
74 2 0.03
75 26 0.41
78 2 0.03
79 7 0.11
80 26 0.41
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.48
Consensus pattern (78 bp):
GTAAACTCAAATTTTGAAAATATTTTTCTTATTTCTTTTTTCATTATAAAGTAAAAGATACATTG
CTTAACTATAAGT
Found at i:20065644 original size:32 final size:32
Alignment explanation
Indices: 20065611--20065725 Score: 128
Period size: 32 Copynumber: 3.5 Consensus size: 32
20065601 TTAAAAAATT
20065611 AAAATAAAATATATAACATAGAAAATTATATTA
1 AAAATAAAATATATAACATA-AAAATTATATTA
* *
20065644 AAAATGAAAATA-A-AATATATAAAATTATAATA
1 AAAAT-AAAATATATAACATA-AAAATTATATTA
20065676 AAAATAAAATATATAACATTAAAAA-TATATTTA
1 AAAATAAAATATATAACA-TAAAAATTATA-TTA
*
20065709 AAAATAATATTATATAA
1 AAAATAA-AATATATAA
20065726 AAAATAATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
31 6 0.09
32 26 0.37
33 22 0.31
34 16 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (32 bp):
AAAATAAAATATATAACATAAAAATTATATTA
Found at i:20065654 original size:18 final size:17
Alignment explanation
Indices: 20065611--20065732 Score: 71
Period size: 17 Copynumber: 7.4 Consensus size: 17
20065601 TTAAAAAATT
20065611 AAAATAAAA-TATA-TA
1 AAAATAAAATTATATTA
* *
20065626 ACATAGAAAATTATATTA
1 A-AAATAAAATTATATTA
20065644 AAAATGAAAA-TA-A--A
1 AAAAT-AAAATTATATTA
* *
20065658 ATATATAAAATTATAATA
1 A-AAATAAAATTATATTA
20065676 AAAATAAAA-TATA-TA
1 AAAATAAAATTATATTA
* * *
20065691 ACATTAAAAATATATTTA
1 AAAATAAAATTATA-TTA
* *
20065709 AAAATAATATTATATAA
1 AAAATAAAATTATATTA
20065726 AAAATAA
1 AAAATAA
20065733 TAAAAAATAA
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 6 0.07
15 15 0.18
16 16 0.20
17 24 0.29
18 21 0.26
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATAAAATTATATTA
Found at i:20067118 original size:14 final size:14
Alignment explanation
Indices: 20067099--20067126 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20067089 CAAGCCCTCG
20067099 TGGAAACCTCAAAA
1 TGGAAACCTCAAAA
20067113 TGGAAACCTCAAAA
1 TGGAAACCTCAAAA
20067127 CGTTGTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
TGGAAACCTCAAAA
Found at i:20073209 original size:18 final size:17
Alignment explanation
Indices: 20073177--20073237 Score: 95
Period size: 17 Copynumber: 3.5 Consensus size: 17
20073167 GCTAATGTAT
20073177 TTATTTTTAATAAAAAA
1 TTATTTTTAATAAAAAA
20073194 TTATTTTTAATAAAAAA
1 TTATTTTTAATAAAAAA
*
20073211 TTATTTTTTCATAAAAAAA
1 TTA-TTTTTAAT-AAAAAA
20073230 TTATTTTT
1 TTATTTTT
20073238 TCTATAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 20 0.49
18 12 0.29
19 9 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATTTTTAATAAAAAA
Found at i:20073239 original size:19 final size:19
Alignment explanation
Indices: 20073188--20073244 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
20073178 TATTTTTAAT
*
20073188 AAAAAATTA-TTTTTAAT-
1 AAAAAATTATTTTTTCATA
20073205 AAAAAATTATTTTTTCATA
1 AAAAAATTATTTTTTCATA
20073224 AAAAAATTATTTTTTCTATA
1 AAAAAATTATTTTTTC-ATA
20073244 A
1 A
20073245 TATAACTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
17 9 0.25
18 7 0.19
19 16 0.44
20 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAAATTATTTTTTCATA
Found at i:20073254 original size:20 final size:19
Alignment explanation
Indices: 20073188--20073254 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
20073178 TATTTTTAAT
* *
20073188 AAAAAATTA-TTTTTAAT-
1 AAAAAACTATTTTTTCATA
*
20073205 AAAAAATTATTTTTTCATA
1 AAAAAACTATTTTTTCATA
*
20073224 AAAAAATTATTTTTTCTATA
1 AAAAAACTATTTTTTC-ATA
* *
20073244 ATATAACTATT
1 AAAAAACTATT
20073255 CAATAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
17 9 0.21
18 7 0.16
19 16 0.37
20 11 0.26
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAAAACTATTTTTTCATA
Found at i:20073402 original size:2 final size:2
Alignment explanation
Indices: 20073395--20073423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20073385 CATCTAAAAC
20073395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20073424 TGACAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20076012 original size:2 final size:2
Alignment explanation
Indices: 20076005--20076057 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
20075995 NNTTCAGTTT
20076005 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20076046 TA TA TA TA TA TA
1 TA TA TA TA TA TA
20076058 ATTAAGGGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20097192 original size:76 final size:76
Alignment explanation
Indices: 20097092--20097240 Score: 253
Period size: 76 Copynumber: 2.0 Consensus size: 76
20097082 TCAAAATACT
*
20097092 ATCCTTAATTTTAAGAACTCCTTTTAAAGTAGGAAACAATTTCTTATTTTTATGAATCACCAAAA
1 ATCCTTAATTTTAAGAACTCCTTTTAAAGTAGGAAACAATTTCCTATTTTTATGAATCACCAAAA
20097157 ATTAAAATTCG
66 ATTAAAATTCG
* * * *
20097168 ATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTATGAATCACCCAAA
1 ATCCTTAATTTTAAGAACTCCTTTTAAAGTAGGAAACAATTTCCTATTTTTATGAATCACCAAAA
20097233 ATTAAAAT
66 ATTAAAAT
20097241 ATATGGTATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (76 bp):
ATCCTTAATTTTAAGAACTCCTTTTAAAGTAGGAAACAATTTCCTATTTTTATGAATCACCAAAA
ATTAAAATTCG
Found at i:20102669 original size:2 final size:2
Alignment explanation
Indices: 20102662--20102687 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20102652 AAAGCAAAGA
20102662 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20102688 GATTTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20109364 original size:2 final size:2
Alignment explanation
Indices: 20109357--20109384 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20109347 ATTCTTTTAG
20109357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20109385 TCTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20110393 original size:18 final size:18
Alignment explanation
Indices: 20110370--20110405 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20110360 ACGAAGAGAG
*
20110370 AGGAAAAGAACGAAAAAA
1 AGGAAAAGAAAGAAAAAA
20110388 AGGAAAAGAAAGAAAAAA
1 AGGAAAAGAAAGAAAAAA
20110406 TACAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (18 bp):
AGGAAAAGAAAGAAAAAA
Found at i:20110637 original size:20 final size:20
Alignment explanation
Indices: 20110599--20110646 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
20110589 TAAAATTAAA
* *
20110599 AAATTAAATTATTACAATTTT
1 AAATAAAATAATTACAA-TTT
20110620 AAATAAAATAATTA-AATTT
1 AAATAAAATAATTACAATTT
20110639 AAA-AAAAT
1 AAATAAAAT
20110647 GTACAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 6 0.24
20 2 0.08
21 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAAAATAATTACAATTT
Found at i:20111613 original size:36 final size:36
Alignment explanation
Indices: 20111526--20111601 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 36
20111516 ATTTTTTTAA
** *
20111526 AATATTAATAT-ATTTTATATATAATTAACATTATT
1 AATATTAATATGATTAAATATATAATTAACAATATT
20111561 AATATTAATATGATTAAATATATAATTAA-AATATT
1 AATATTAATATGATTAAATATATAATTAACAATATT
20111596 AATATT
1 AATATT
20111602 TTAAATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 22 0.59
36 15 0.41
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (36 bp):
AATATTAATATGATTAAATATATAATTAACAATATT
Found at i:20111652 original size:16 final size:16
Alignment explanation
Indices: 20111586--20111653 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
20111576 AAATATATAA
*
20111586 TTAAAATATTAATATTT
1 TTAATATATTAA-ATTT
*
20111603 TAAAT-TATT-AATGTT
1 TTAATATATTAAAT-TT
* *
20111618 TT-ATTTATTAAATTA
1 TTAATATATTAAATTT
20111633 TTAATATATTAAATTT
1 TTAATATATTAAATTT
20111649 TTAAT
1 TTAAT
20111654 GAGTACAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 4 0.10
15 11 0.27
16 23 0.56
17 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TTAATATATTAAATTT
Found at i:20111800 original size:27 final size:27
Alignment explanation
Indices: 20111733--20111786 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
20111723 TATTAATAAT
* *
20111733 TAAATTATCAATTAGTAATATTTAAAA
1 TAAATGATAAATTAGTAATATTTAAAA
*
20111760 TAAATGATAAATTATTAATATTTAAAA
1 TAAATGATAAATTAGTAATATTTAAAA
20111787 AATATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (27 bp):
TAAATGATAAATTAGTAATATTTAAAA
Found at i:20111902 original size:15 final size:16
Alignment explanation
Indices: 20111882--20111913 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20111872 AATAAAAAAA
20111882 TTTA-TTTTTTTATTT
1 TTTATTTTTTTTATTT
20111897 TTTATTTTTTTTATTT
1 TTTATTTTTTTTATTT
20111913 T
1 T
20111914 AAAATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTATTTTTTTTATTT
Found at i:20112046 original size:22 final size:21
Alignment explanation
Indices: 20111995--20112062 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
20111985 CCAAATTACA
*
20111995 TAATATTTATTTTA-TTTTAT
1 TAATAATTATTTTATTTTTAT
**
20112015 TTTTAGATTATTTTATTTTTAT
1 TAATA-ATTATTTTATTTTTAT
20112037 ATAATAATTATTTTATTTTTAT
1 -TAATAATTATTTTATTTTTAT
20112059 TAAT
1 TAAT
20112063 TTCGTAAACC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.08
21 12 0.30
22 22 0.55
23 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
TAATAATTATTTTATTTTTAT
Found at i:20126579 original size:2 final size:2
Alignment explanation
Indices: 20126572--20126603 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20126562 TTCTTTCCTC
20126572 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20126604 TAGAGGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20142757 original size:15 final size:15
Alignment explanation
Indices: 20142725--20142767 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
20142715 CAGACAATTG
*
20142725 AAAGAATGAGAAGAA
1 AAAGAATGAAAAGAA
20142740 AAAGAA-GAAAAGAA
1 AAAGAATGAAAAGAA
* *
20142754 AAAAAATAAAAAGA
1 AAAGAATGAAAAGA
20142768 GTGTGTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAGAATGAAAAGAA
Found at i:20144110 original size:15 final size:15
Alignment explanation
Indices: 20144092--20144134 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
20144082 ATGTAATATG
20144092 ATTACAAGTAATGTA
1 ATTACAAGTAATGTA
* * *
20144107 ATTATAAATAATGTG
1 ATTACAAGTAATGTA
*
20144122 ATTGCAAGTAATG
1 ATTACAAGTAATG
20144135 CGATTATAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (15 bp):
ATTACAAGTAATGTA
Found at i:20144141 original size:30 final size:30
Alignment explanation
Indices: 20144085--20144142 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20144075 TTTTATAATG
*
20144085 TAATATGATTACAAGTAATGTAATTATAAA
1 TAATATGATTACAAGTAATGCAATTATAAA
* * *
20144115 TAATGTGATTGCAAGTAATGCGATTATA
1 TAATATGATTACAAGTAATGCAATTATA
20144143 GAGAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (30 bp):
TAATATGATTACAAGTAATGCAATTATAAA
Found at i:20150254 original size:127 final size:127
Alignment explanation
Indices: 20150028--20150279 Score: 477
Period size: 127 Copynumber: 2.0 Consensus size: 127
20150018 ATCCTTGGGC
*
20150028 ATTTGAGCTATAATTAGAAGTGCAAACTACCCAAACTCAACCAAAATTTTAAGAGACAATTAAAG
1 ATTTGAGCTATAATTAGAAGTGCAAACTACCCAAACTCAACCAAAATTTTAACAGACAATTAAAG
* *
20150093 GAGATCAAATACAATCAGTGATTTAAGCTCAGCTAAAATTAAGGCCAACAGAATGAGAAAGT
66 GAGATCAAATACAATCAGTGAGTTAAGCTCAGCTAAAATTAAGGCCAACAGAAAGAGAAAGT
20150155 ATTTGAGCTATAATTAGAAGTGCAAACTACCCAAACTCAACCAAAATTTTAACAGACAATTAAAG
1 ATTTGAGCTATAATTAGAAGTGCAAACTACCCAAACTCAACCAAAATTTTAACAGACAATTAAAG
20150220 GAGATCAAATACAATCAGTGAGTTAAGCTCAGCTAAAATTAAGGCCAACAGAAAGAGAAA
66 GAGATCAAATACAATCAGTGAGTTAAGCTCAGCTAAAATTAAGGCCAACAGAAAGAGAAA
20150280 TATCTTCCAC
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.22
Consensus pattern (127 bp):
ATTTGAGCTATAATTAGAAGTGCAAACTACCCAAACTCAACCAAAATTTTAACAGACAATTAAAG
GAGATCAAATACAATCAGTGAGTTAAGCTCAGCTAAAATTAAGGCCAACAGAAAGAGAAAGT
Found at i:20151253 original size:11 final size:11
Alignment explanation
Indices: 20151237--20151270 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20151227 TTAGTTCACT
20151237 AGAAGGAATAG
1 AGAAGGAATAG
20151248 AGAAGGAATAG
1 AGAAGGAATAG
20151259 A-AAGGTAATAG
1 AGAAGG-AATAG
20151270 A
1 A
20151271 ATAGCCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (11 bp):
AGAAGGAATAG
Found at i:20151762 original size:41 final size:41
Alignment explanation
Indices: 20151714--20151809 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 41
20151704 TTCATTAAAT
*
20151714 TTAAATAATACTAAATAATATTCTTTATTATA-TTATTATA
1 TTAAATAATACTAAATAATATTCTTTATAATATTTATTATA
* *
20151754 TTCAAATAATAATATTAAATAATATTCTTTATAATATTTGTTATA
1 TT---A-AATAATACTAAATAATATTCTTTATAATATTTATTATA
20151799 GTTAAATAATA
1 -TTAAATAATA
20151810 TTAATATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
40 2 0.04
42 7 0.15
43 2 0.04
44 27 0.57
45 7 0.15
46 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (41 bp):
TTAAATAATACTAAATAATATTCTTTATAATATTTATTATA
Found at i:20151882 original size:186 final size:187
Alignment explanation
Indices: 20151663--20152031 Score: 638
Period size: 187 Copynumber: 2.0 Consensus size: 187
20151653 ACCTTTTATG
20151663 ATAATTAAATAATATTTAATATTAAAGGACAAAATATATTCTTCATTAAATTTAAATAATACTAA
1 ATAATTAAATAATATTTAATATTAAAGGACAAAATATATTCTTCATTAAATTTAAATAATACTAA
20151728 ATAATATTCTTTATTATA-TTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATATT
66 ATAATATTCTTTATTATATTTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATATT
* * *
20151792 TGTTATAGTTAAATAATATTAATATATTAAA-CAATATTTAAAT-ATTTTATTTTCCT
131 TATTATAGTTAAATAATATTAATATAATAAATC-ATATTTAAATAAATTTATTTTCCT
*
20151848 NATAATTCAATAATATTTAATATT-AAGAGACAAAATATATTCTTCATTAAATTTAAATAATACT
1 -ATAATTAAATAATATTTAATATTAAAG-GACAAAATATATTCTTCATTAAATTTAAATAATACT
*
20151912 AAATACTATTCTTTATTATATTTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATA
64 AAATAATATTCTTTATTATATTTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATA
20151977 TTTATTATAGTTAAATAATATTAATATAATAAATCATATTTAAATAAATTTATTT
129 TTTATTATAGTTAAATAATATTAATATAATAAATCATATTTAAATAAATTTATTT
20152032 CCTTTTTTGA
Statistics
Matches: 174, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
185 3 0.02
186 77 0.44
187 85 0.49
188 9 0.05
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (187 bp):
ATAATTAAATAATATTTAATATTAAAGGACAAAATATATTCTTCATTAAATTTAAATAATACTAA
ATAATATTCTTTATTATATTTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATATT
TATTATAGTTAAATAATATTAATATAATAAATCATATTTAAATAAATTTATTTTCCT
Found at i:20151949 original size:42 final size:41
Alignment explanation
Indices: 20151900--20152007 Score: 126
Period size: 45 Copynumber: 2.5 Consensus size: 41
20151890 TTCATTAAAT
* *
20151900 TTAAATAATACTAAATACTATTCTTTATTATATTTATTATA
1 TTAAATAATACTAAATAATATTCTTTATAATATTTATTATA
*
20151941 TTCAAATAATAATATTAAATAATATTCTTTATAATATTTATTATA
1 TT---A-AATAATACTAAATAATATTCTTTATAATATTTATTATA
*
20151986 GTTAAATAATATTAATATAATA
1 -TTAAATAATACTAA-ATAATA
20152008 AATCATATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
41 2 0.03
42 11 0.19
43 7 0.12
44 1 0.02
45 35 0.60
46 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (41 bp):
TTAAATAATACTAAATAATATTCTTTATAATATTTATTATA
Found at i:20151952 original size:45 final size:45
Alignment explanation
Indices: 20151903--20151996 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
20151893 ATTAAATTTA
* *
20151903 AATAATACTAAATACTATTCTTTATTATATTTATTATA-TTCAAAT
1 AATAATACTAAATAATATTCTTTATAATATTTATTATAGTT-AAAT
*
20151948 AATAATATTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
1 AATAATACTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
20151993 AATA
1 AATA
20151997 TTAATATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
Found at i:20151998 original size:16 final size:15
Alignment explanation
Indices: 20151934--20151999 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
20151924 TTATTATATT
20151934 TATTATATTCAAATAA
1 TATTATATT-AAATAA
20151950 TA--ATATTAAATAA
1 TATTATATTAAATAA
* *
20151963 TATTCT-TTATAATATT
1 TATTATATTA-AATA-A
20151979 TATTATAGTTAAATAA
1 TATTATA-TTAAATAA
20151995 TATTA
1 TATTA
20152000 ATATAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
13 8 0.20
14 8 0.20
15 5 0.12
16 12 0.30
17 4 0.10
18 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (15 bp):
TATTATATTAAATAA
Found at i:20155798 original size:18 final size:18
Alignment explanation
Indices: 20155764--20155798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20155754 TTTAAAATAA
*
20155764 AAATATAAAAATTTAATT
1 AAATATAAAAATATAATT
*
20155782 AAATATAATAATATAAT
1 AAATATAAAAATATAAT
20155799 AAAAGTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATAAAAATATAATT
Found at i:20155807 original size:29 final size:26
Alignment explanation
Indices: 20155748--20155797 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
20155738 ATATAAGTTT
20155748 ATTTAATTTAAA-ATAAAAATATAAAA
1 ATTTAA-TTAAATATAAAAATATAAAA
*
20155774 ATTTAATTAAATATAATAATATAA
1 ATTTAATTAAATATAAAAATATAA
20155798 TAAAAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTTAATTAAATATAAAAATATAAAA
Found at i:20155812 original size:29 final size:26
Alignment explanation
Indices: 20155748--20155814 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
20155738 ATATAAGTTT
20155748 ATTTAATTTAAA-ATAAAAATATAAAA
1 ATTT-ATTTAAATATAAAAATATAAAA
*
20155774 ATTTAATTAAATATAATAATATAATAAAA
1 ATTTATTTAAATATAA-AA-AT-ATAAAA
*
20155803 GTTTATTTAAAT
1 ATTTATTTAAAT
20155815 TTTTTTATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.18
26 8 0.24
27 2 0.06
28 2 0.06
29 16 0.47
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
ATTTATTTAAATATAAAAATATAAAA
Found at i:20156629 original size:25 final size:27
Alignment explanation
Indices: 20156601--20156668 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
20156591 TATGTAATAA
20156601 ATTTTTGTT-TTTGTTCCTCACTG-TG
1 ATTTTTGTTATTTGTTCCTCACTGATG
*
20156626 ATTTTT-TTATTTGCTCCTCACTGATG
1 ATTTTTGTTATTTGTTCCTCACTGATG
*
20156652 ATTATATGTTATTTGTT
1 ATT-TTTGTTATTTGTT
20156669 TTATTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.06
25 19 0.53
26 5 0.14
27 2 0.06
28 8 0.22
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.59
Consensus pattern (27 bp):
ATTTTTGTTATTTGTTCCTCACTGATG
Found at i:20157477 original size:18 final size:19
Alignment explanation
Indices: 20157443--20157478 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20157433 TTTTTAATTA
20157443 TCTTTTGACTAAAAATATG
1 TCTTTTGACTAAAAATATG
*
20157462 TCTTTT-ACTGAAAATAT
1 TCTTTTGACTAAAAATAT
20157479 TCCTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (19 bp):
TCTTTTGACTAAAAATATG
Found at i:20160647 original size:168 final size:168
Alignment explanation
Indices: 20160339--20160666 Score: 543
Period size: 168 Copynumber: 1.9 Consensus size: 168
20160329 TTATTTGAAA
*
20160339 AAAACAATTGATTTCTTACATTATAACCTTAAATCAATCGTAAAAATCAATTAAAAATGTAAAAA
1 AAAACAATTGATTTC-TACATTATAACCCTAAATCAATCGTAAAAATCAATTAAAAATGTAAAAA
* * *
20160404 TTATCTTGAAATCTCTTGAAGTTGAACAATTTTGCAAATTTAATTTTAATGCTAGAAGAAGAAGA
65 TTATCTTGAAATCTCTTGAAGTTGAACAAATTGGCAAACTTAATTTTAATGCTAGAAGAAGAAGA
20160469 AGGAGAGAAGAAGATAATCAAGTTAGGATAAAAAAGAAG
130 AGGAGAGAAGAAGATAATCAAGTTAGGATAAAAAAGAAG
* * *
20160508 AAAACAATTGATTATC-ACATTATAACCCTAAATCAATTGTAAAAATCACTTAAAAATGTAAATA
1 AAAACAATTGATT-TCTACATTATAACCCTAAATCAATCGTAAAAATCAATTAAAAATGTAAAAA
20160572 TTATCTTGAAATCTCTTGAAGTTGAACAAATTGGCAAACTTAATTTTAATGCTAGAAGAAGGAA-
65 TTATCTTGAAATCTCTTGAAGTTGAACAAATTGGCAAACTTAATTTTAATGCTAGAAGAA-GAAG
*
20160636 AAGGGGAGAAGAAGATAATCAAGTTAGGATA
129 AAGGAGAGAAGAAGATAATCAAGTTAGGATA
20160667 GAACAATTGA
Statistics
Matches: 149, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
168 131 0.88
169 16 0.11
170 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (168 bp):
AAAACAATTGATTTCTACATTATAACCCTAAATCAATCGTAAAAATCAATTAAAAATGTAAAAAT
TATCTTGAAATCTCTTGAAGTTGAACAAATTGGCAAACTTAATTTTAATGCTAGAAGAAGAAGAA
GGAGAGAAGAAGATAATCAAGTTAGGATAAAAAAGAAG
Found at i:20161428 original size:26 final size:26
Alignment explanation
Indices: 20161386--20161474 Score: 97
Period size: 26 Copynumber: 3.2 Consensus size: 26
20161376 CCTAAAACCG
* *
20161386 ATTCAACAAATCTTAAAATCAATTCA
1 ATTCAACAAACCCTAAAATCAATTCA
20161412 ATTCAACAAACCCTAAAATCAATTTAATTCA
1 ATTCAACAAACCCTAAAATC-----AATTCA
* *
20161443 ACTCAACAAACCCTAAAATCAATTCT
1 ATTCAACAAACCCTAAAATCAATTCA
20161469 ATTCAA
1 ATTCAA
20161475 TTTGAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
26 28 0.53
31 25 0.47
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (26 bp):
ATTCAACAAACCCTAAAATCAATTCA
Found at i:20161441 original size:31 final size:32
Alignment explanation
Indices: 20161406--20161476 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 32
20161396 TCTTAAAATC
20161406 AATTCAATTCAACAAACCCTAAAATCAATT-T
1 AATTCAATTCAACAAACCCTAAAATCAATTCT
*
20161437 AATTCAACTCAACAAACCCTAAAATCAATTCT
1 AATTCAATTCAACAAACCCTAAAATCAATTCT
20161469 -ATTCAATT
1 AATTCAATT
20161477 TGAAAAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (32 bp):
AATTCAATTCAACAAACCCTAAAATCAATTCT
Found at i:20161817 original size:17 final size:17
Alignment explanation
Indices: 20161773--20161819 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
20161763 AAGGTTTTTA
20161773 TTTGTAATTTTTTTAAAT
1 TTTGT-ATTTTTTTAAAT
* *
20161791 TTTGTTTTTTTTTAAGT
1 TTTGTATTTTTTTAAAT
20161808 TATT-TATTTTTT
1 T-TTGTATTTTTT
20161820 AAAAAACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTGTATTTTTTTAAAT
Found at i:20175823 original size:19 final size:20
Alignment explanation
Indices: 20175796--20175840 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
20175786 GTTAGGTGGC
* *
20175796 ATTTGTTAAAAT-TAACTAT
1 ATTTATTAAAATACAACTAT
*
20175815 ATTTATTAAAATACAAGTAT
1 ATTTATTAAAATACAACTAT
20175835 ATTTAT
1 ATTTAT
20175841 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTTATTAAAATACAACTAT
Done.