Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 66 of 125
Found at i:20261132 original size:14 final size:14
Alignment explanation
Indices: 20261060--20261160 Score: 57
Period size: 14 Copynumber: 7.1 Consensus size: 14
20261050 CTCTCTTCAA
*
20261060 TTAAAAGATTTAAT
1 TTAAAATATTTAAT
*
20261074 TTAAAAGATTTAATTAT
1 TTAAAATATTT-A--AT
*
20261091 TTAATTATATTTAA-
1 TTAA-AATATTTAAT
**
20261105 TT-AAATATGAAAT
1 TTAAAATATTTAAT
20261118 TTAAAATATTTAATT
1 TTAAAATATTTAA-T
* *
20261133 ATTTAATTATTTAA-
1 -TTAAAATATTTAAT
20261147 TT-AAATATTTAAT
1 TTAAAATATTTAAT
20261160 T
1 T
20261161 ATATTTAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
12 15 0.22
13 6 0.09
14 21 0.31
15 3 0.04
16 11 0.16
17 7 0.10
18 5 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TTAAAATATTTAAT
Found at i:20261158 original size:8 final size:8
Alignment explanation
Indices: 20261124--20261149 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20261114 AAATTTAAAA
20261124 TATTTAAT
1 TATTTAAT
20261132 TATTTAAT
1 TATTTAAT
20261140 TATTTAAT
1 TATTTAAT
20261148 TA
1 TA
20261150 AATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTAAT
Found at i:20261168 original size:30 final size:33
Alignment explanation
Indices: 20261081--20261173 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 33
20261071 AATTTAAAAG
*
20261081 ATTTAATTATTTAATTATATTTAATTAAATATGAA
1 ATTTAAATATTTAATTATATTTAATT--ATATGAA
*
20261116 ATTTAAAATATTTAA-T-TATTTAATTAT-T-TA
1 ATTT-AAATATTTAATTATATTTAATTATATGAA
20261146 A-TTAAATATTTAATTATATTTAATTATA
1 ATTTAAATATTTAATTATATTTAATTATA
20261174 AAAAAACAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
28 10 0.19
29 3 0.06
30 13 0.25
31 1 0.02
32 2 0.04
34 9 0.17
35 5 0.10
36 9 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (33 bp):
ATTTAAATATTTAATTATATTTAATTATATGAA
Found at i:20282653 original size:27 final size:28
Alignment explanation
Indices: 20282604--20282660 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
20282594 CTAATTGAGT
* * *
20282604 TTTAAAATTTTTAAGTTTCATTTTTTTG
1 TTTAAAATTATTAAGTTTAATTTTTATG
*
20282632 TTTAAAA-TATTAATTTTAATTTTTATG
1 TTTAAAATTATTAAGTTTAATTTTTATG
20282659 TT
1 TT
20282661 AATAAAGGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTAAAATTATTAAGTTTAATTTTTATG
Found at i:20286221 original size:22 final size:22
Alignment explanation
Indices: 20286196--20286238 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20286186 AAAATATTTC
*
20286196 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
20286218 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
20286239 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:20288924 original size:15 final size:16
Alignment explanation
Indices: 20288894--20288926 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20288884 GCATCACGAT
*
20288894 ATATTATCATTTCATC
1 ATATAATCATTTCATC
20288910 ATATAATCA-TTCATC
1 ATATAATCATTTCATC
20288925 AT
1 AT
20288927 TTGCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAATCATTTCATC
Found at i:20293499 original size:24 final size:23
Alignment explanation
Indices: 20293456--20293500 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
20293446 TTTGCCTGTT
*
20293456 AAGAAAGTTTAAAATAAATAATA
1 AAGAAAGTTTAAAAAAAATAATA
20293479 AAGAAAGTTTAAAAAACAATAA
1 AAGAAAGTTTAAAAAA-AATAA
20293501 ATATAACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (23 bp):
AAGAAAGTTTAAAAAAAATAATA
Found at i:20295188 original size:86 final size:89
Alignment explanation
Indices: 20295034--20295218 Score: 218
Period size: 86 Copynumber: 2.1 Consensus size: 89
20295024 ATTTTCAATT
* * * * * *
20295034 TTTTTTTAAAAAACTAATTAAGTTCTTGTTTTTCTTTTGCGCTCAATTGGATACTTCAACTTTTA
1 TTTTTTCAAAAAACTAATTAAGTCCCTATTTTTCTTTTGCACTCAATTGGATACTTCAACTTTCA
* * *
20295099 AAATGTATTAAAAA-GATCTTCAAA
66 AAATGCATCAAAAAGGCTC-TCAAA
* *
20295123 TTTTTTCAAAAAA-TAATTAAG-CCCTATTTTT-TTTTGTACTCAATT-GAGTACTTGAACTTTC
1 TTTTTTCAAAAAACTAATTAAGTCCCTATTTTTCTTTTGCACTCAATTGGA-TACTTCAACTTTC
20295184 AAAATGCATCAAAAAGGCTCTCAAA
65 AAAATGCATCAAAAAGGCTCTCAAA
20295209 TTTTTTCAAA
1 TTTTTTCAAA
20295219 TAAAGCAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
85 2 0.02
86 51 0.61
87 10 0.12
88 8 0.10
89 12 0.14
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (89 bp):
TTTTTTCAAAAAACTAATTAAGTCCCTATTTTTCTTTTGCACTCAATTGGATACTTCAACTTTCA
AAATGCATCAAAAAGGCTCTCAAA
Found at i:20295243 original size:86 final size:87
Alignment explanation
Indices: 20295075--20295284 Score: 202
Period size: 86 Copynumber: 2.4 Consensus size: 87
20295065 TTCTTTTGCG
* * * * *
20295075 CTCAATTG-GATACTTCAACTTTTAAAATGTATTAAAAAGATCTTCAAATTTTTTCAAAAAATAA
1 CTCAATTGAG-TACTTGAACTTTCAAAATGCATAAAAAAGATCTTCAAATTTTTTCAAAAAACAA
**
20295139 TTAAGCCCTATTTTTTTTTGT-A
65 TTAAGCCCTATTAATTTTTGTCA
* *
20295161 CTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAG-GCTCTCAAATTTTTTCAAATAAAGC
1 CTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGATCT-TCAAATTTTTTCAAA-AAA-C
** *
20295225 AATT-AGGTCT-TTAATTTTTTTCA
63 AATTAAGCCCTATTAATTTTTGTCA
20295248 CTCAATT-AGGTACTTGAA-TTATC-AAATGCATAAAAAA
1 CTCAATTGA-GTACTTGAACTT-TCAAAATGCATAAAAAA
20295285 TGTCCTTTGA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
85 2 0.02
86 72 0.69
87 27 0.26
88 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (87 bp):
CTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGATCTTCAAATTTTTTCAAAAAACAAT
TAAGCCCTATTAATTTTTGTCA
Found at i:20295390 original size:10 final size:10
Alignment explanation
Indices: 20295375--20295429 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
20295365 GTGATATGTG
20295375 ATAAAAAATT
1 ATAAAAAATT
20295385 ATAAAAAAATT
1 AT-AAAAAATT
* **
20295396 GTAAAATTTT
1 ATAAAAAATT
*
20295406 AT-AAAAATC
1 ATAAAAAATT
20295415 AT-AAAAATT
1 ATAAAAAATT
20295424 ATAAAA
1 ATAAAA
20295430 TGTATCAGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 14 0.40
10 12 0.34
11 9 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:20295403 original size:19 final size:20
Alignment explanation
Indices: 20295378--20295429 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
20295368 ATATGTGATA
**
20295378 AAAAATTATAAAAAAATTGT
1 AAAAATTATAAAAAAATCAT
* *
20295398 -AAAATTTTATAAAAATCAT
1 AAAAATTATAAAAAAATCAT
20295417 AAAAATTATAAAA
1 AAAAATTATAAAA
20295430 TGTATCAGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTATAAAAAAATCAT
Found at i:20295636 original size:10 final size:9
Alignment explanation
Indices: 20295622--20295773 Score: 55
Period size: 10 Copynumber: 16.3 Consensus size: 9
20295612 TTTTTATGAA
20295622 TTTTATATT
1 TTTTATATT
*
20295631 TCTTTACATT
1 T-TTTATATT
20295641 TTTTATAATT
1 TTTTAT-ATT
*
20295651 TTCTTACAACTT
1 TT-TTA-TA-TT
* *
20295663 TATTAAATT
1 TTTTATATT
*
20295672 TTATA-ATT
1 TTTTATATT
*
20295680 TTTT-TATA
1 TTTTATATT
20295688 TTTTATAATT
1 TTTTAT-ATT
20295698 TTTTA-ATAT
1 TTTTATAT-T
**
20295707 TTTTATAAAA
1 TTTTAT-ATT
*
20295717 TTTTACCATT
1 TTTTA-TATT
* *
20295727 TTATA-ATC
1 TTTTATATT
20295735 TTTTATGATGT
1 TTTTAT-AT-T
20295746 TTTTA-ATT
1 TTTTATATT
*
20295754 TTTTATAAT
1 TTTTATATT
20295763 TTTTA-ATT
1 TTTTATATT
20295771 TTT
1 TTT
20295774 AATTAAAATT
Statistics
Matches: 107, Mismatches: 20, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
8 31 0.29
9 26 0.24
10 34 0.32
11 13 0.12
12 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATATT
Found at i:20295692 original size:18 final size:17
Alignment explanation
Indices: 20295669--20295773 Score: 95
Period size: 18 Copynumber: 5.8 Consensus size: 17
20295659 ACTTTATTAA
20295669 ATTTTATAATTTTTTTAT
1 ATTTTATAA-TTTTTTAT
20295687 ATTTTATAATTTTTTAAT
1 ATTTTATAATTTTTT-AT
** *
20295705 ATTTTTATAAAATTTTACC
1 A-TTTTATAATTTTTTA-T
*
20295724 ATTTTATAATCTTTTAT
1 ATTTTATAATTTTTTAT
*
20295741 GATGTTTTTAATTTTTTAT
1 -AT-TTTATAATTTTTTAT
20295760 AATTTT-TAATTTTT
1 -ATTTTATAATTTTT
20295774 AATTAAAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
17 14 0.19
18 31 0.42
19 28 0.38
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTTATAATTTTTTAT
Found at i:20295758 original size:37 final size:34
Alignment explanation
Indices: 20295670--20295774 Score: 88
Period size: 37 Copynumber: 2.9 Consensus size: 34
20295660 CTTTATTAAA
*
20295670 TTTTATAATTTTTTTATATTTTATAATTTTTTAATAT
1 TTTTATAA-TTTTTTAAATTTTATAA-TTTTT-ATAT
** *
20295707 TTTTATAAAATTTTACCATTTTATAATCTTTTATGAT
1 TTTTATAATTTTTTA-AATTTTATAAT-TTTTAT-AT
20295744 GTTTT-TAATTTTTTATAATTTT-TAATTTTTA
1 -TTTTATAATTTTTTA-AATTTTATAATTTTTA
20295775 ATTAAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
35 5 0.09
36 12 0.21
37 36 0.63
38 4 0.07
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (34 bp):
TTTTATAATTTTTTAAATTTTATAATTTTTATAT
Found at i:20296803 original size:31 final size:31
Alignment explanation
Indices: 20296767--20296831 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
20296757 ATAAAAAATG
*
20296767 TATAAA-ATTATT-AAATATTAAAATAATATAA
1 TATAAATATTATTAAAAAATT-AAATAA-ATAA
*
20296798 TATAAATATTTTTAAAAAATTAAATAAATAA
1 TATAAATATTATTAAAAAATTAAATAAATAA
20296829 TAT
1 TAT
20296832 GACCGGTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.43
32 11 0.37
33 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TATAAATATTATTAAAAAATTAAATAAATAA
Found at i:20298346 original size:32 final size:32
Alignment explanation
Indices: 20298282--20298346 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
20298272 CAACGGGTCA
* * * *
20298282 GGTCGATCAACTCGGGTCAATGGGTTGGGTCG
1 GGTCGATCAACTCGGATCAACGGGTCGAGTCG
**
20298314 GGTCGATCAACTTTGATCAACGGGTCGAGTCG
1 GGTCGATCAACTCGGATCAACGGGTCGAGTCG
20298346 G
1 G
20298347 TCAATAGACG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.37, T:0.25
Consensus pattern (32 bp):
GGTCGATCAACTCGGATCAACGGGTCGAGTCG
Found at i:20302329 original size:23 final size:23
Alignment explanation
Indices: 20302303--20302354 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
20302293 AAAAGCTATC
20302303 TACAAAATCAAATC-TCTAAGATT
1 TACAAAATCAAATCTTCTAAGA-T
* *
20302326 TACAGAATCAGATCTTCTAAGAT
1 TACAAAATCAAATCTTCTAAGAT
20302349 TACAAA
1 TACAAA
20302355 TCCTCTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (23 bp):
TACAAAATCAAATCTTCTAAGAT
Found at i:20303616 original size:15 final size:14
Alignment explanation
Indices: 20303585--20303650 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
20303575 ATTTTTTTTC
20303585 TTTTTCTTTC--TT
1 TTTTTCTTTCAATT
20303597 TTTTT-TTTCAATT
1 TTTTTCTTTCAATT
20303610 CAATTTTTCTTTCAATT
1 ---TTTTTCTTTCAATT
*
20303627 TTTTTCTTTTCGATT
1 TTTTTC-TTTCAATT
20303642 TTTTTCTTT
1 TTTTTCTTT
20303651 TTTTCGAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
11 4 0.09
12 5 0.11
13 2 0.04
14 9 0.20
15 13 0.28
16 5 0.11
17 8 0.17
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCAATT
Found at i:20303651 original size:15 final size:15
Alignment explanation
Indices: 20303577--20303651 Score: 64
Period size: 15 Copynumber: 4.8 Consensus size: 15
20303567 TCAAACACAT
*
20303577 TTTTTTTCTTTTTC-T
1 TTTTTTTC-TTTTCAA
*
20303592 TTCTTTTTTTTTTCAA
1 TT-TTTTTCTTTTCAA
20303608 TTCAATTTTTC-TTTCAA
1 TT---TTTTTCTTTTCAA
*
20303625 TTTTTTTCTTTTCGA
1 TTTTTTTCTTTTCAA
20303640 TTTTTTTCTTTT
1 TTTTTTTCTTTT
20303652 TTTCGAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.12
15 24 0.48
16 7 0.14
17 8 0.16
18 5 0.10
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTTTCAA
Found at i:20307971 original size:37 final size:38
Alignment explanation
Indices: 20307878--20307971 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
20307868 ATTTTCGGAA
* *
20307878 TGCACCCAAGACTGTTGCTACATAAATATTCTGCAAAT
1 TGCACCCAAGAATGTCGCTACATAAATATTCTGCAAAT
* * * * *
20307916 TGCATCCAA-AACTATCGCTACATAAGTATTCTTC-AGT
1 TGCACCCAAGAA-TGTCGCTACATAAATATTCTGCAAAT
20307953 TGCACCCAAGAATGTCGCT
1 TGCACCCAAGAATGTCGCT
20307972 GCATGAACAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
37 17 0.38
38 28 0.62
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (38 bp):
TGCACCCAAGAATGTCGCTACATAAATATTCTGCAAAT
Found at i:20307996 original size:26 final size:26
Alignment explanation
Indices: 20307961--20308018 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
20307951 GTTGCACCCA
* *
20307961 AGAA-TGTCGCTGCATGAACATGTAC
1 AGAATTGTCGCTACATAAACATGTAC
* *
20307986 AGAATTGTCGCTACATAAACGTGTCC
1 AGAATTGTCGCTACATAAACATGTAC
20308012 AGAATTG
1 AGAATTG
20308019 CGCCCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (26 bp):
AGAATTGTCGCTACATAAACATGTAC
Found at i:20311197 original size:17 final size:17
Alignment explanation
Indices: 20311175--20311240 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
20311165 CTGTAGTATA
*
20311175 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
*
20311192 ATTGTCACTACATTTTT
1 ATTGTCACTGCATTTTT
* * **
20311209 ATTGTCGCTGCATCTAC
1 ATTGTCACTGCATTTTT
*
20311226 ATTGTCATTGCATTT
1 ATTGTCACTGCATTT
20311241 CCATATATAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:20312413 original size:26 final size:26
Alignment explanation
Indices: 20312381--20312434 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
20312371 CACCCAGGAA
20312381 TGTCGCTGCATGAACATGTACAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
* * *
20312407 TGTCGCTGTATGAACTTGTCCAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
20312433 TG
1 TG
20312435 CACCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAGAAT
Found at i:20317647 original size:9 final size:8
Alignment explanation
Indices: 20317633--20317692 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 8
20317623 GCACAAAATC
20317633 TTCTTCATT
1 TTCTTC-TT
20317642 TTCTTCTT
1 TTCTTCTT
*
20317650 TCTTTTCTT
1 T-TCTTCTT
20317659 TTCTTCTCT
1 TTCTTCT-T
*
20317668 TCCTTCTT
1 TTCTTCTT
20317676 CTTC-TCTT
1 -TTCTTCTT
20317684 TTC-TCTT
1 TTCTTCTT
20317691 TT
1 TT
20317693 TCCTCCTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 9 0.20
8 13 0.30
9 22 0.50
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (8 bp):
TTCTTCTT
Found at i:20317662 original size:17 final size:17
Alignment explanation
Indices: 20317640--20317692 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
20317630 ATCTTCTTCA
20317640 TTTTCTTCTTTCTTTTC
1 TTTTCTTCTTTCTTTTC
20317657 TTTTCTTCTCTTCCTTCTTC
1 TTTTCTTCT-TT-CTT-TTC
*
20317677 TTCTCTT-TTCTCTTTT
1 TTTTCTTCTT-TCTTTT
20317693 TCCTCCTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 11 0.35
18 6 0.19
19 5 0.16
20 9 0.29
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTC
Found at i:20317674 original size:22 final size:22
Alignment explanation
Indices: 20317643--20317690 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20317633 TTCTTCATTT
* *
20317643 TCTTCTTTCTT-TTCTTTTCTTC
1 TCTTCCTTCTTCTTCTCTT-TTC
20317665 TCTTCCTTCTTCTTCTCTTTTC
1 TCTTCCTTCTTCTTCTCTTTTC
20317687 TCTT
1 TCTT
20317691 TTTCCTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (22 bp):
TCTTCCTTCTTCTTCTCTTTTC
Found at i:20317690 original size:15 final size:15
Alignment explanation
Indices: 20317643--20317690 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
20317633 TTCTTCATTT
20317643 TCTTCTT-TCTTTTC
1 TCTTCTTCTCTTTTC
* *
20317657 TTTTCTTCTC-TTCC
1 TCTTCTTCTCTTTTC
20317671 TTCTTCTTCTCTTTTC
1 -TCTTCTTCTCTTTTC
20317687 TCTT
1 TCTT
20317691 TTTCCTCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.33
15 15 0.56
16 3 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTCTTCTCTTTTC
Found at i:20317696 original size:25 final size:26
Alignment explanation
Indices: 20317633--20317692 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
20317623 GCACAAAATC
*
20317633 TTCTTCATTTT-CTTCTTTCTTTTCTT
1 TTCTTC-TTTTCCTTCTTTCTTCTCTT
*
20317659 TTCTTCTCTTCCTTC-TTCTTCTCTT
1 TTCTTCTTTTCCTTCTTTCTTCTCTT
20317684 TTC-TCTTTT
1 TTCTTCTTTT
20317693 TCCTCCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 5 0.17
25 15 0.50
26 10 0.33
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (26 bp):
TTCTTCTTTTCCTTCTTTCTTCTCTT
Found at i:20332185 original size:20 final size:20
Alignment explanation
Indices: 20332160--20332199 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20332150 CTACAATAGT
20332160 AAACATCAAACAAATGCCAA
1 AAACATCAAACAAATGCCAA
20332180 AAACATCAAACAAATGCCAA
1 AAACATCAAACAAATGCCAA
20332200 CTCCCCGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.25, G:0.05, T:0.10
Consensus pattern (20 bp):
AAACATCAAACAAATGCCAA
Found at i:20347099 original size:268 final size:268
Alignment explanation
Indices: 20346622--20347161 Score: 929
Period size: 268 Copynumber: 2.0 Consensus size: 268
20346612 TACACAGGTG
* * * *
20346622 AAAATTAACCCTGGAGTTCTTGAATTAGATGTTATTTCTGCATTGTTAGCGCAGGTATCTTCTTT
1 AAAATTAACCCTAGAGTTCTTGAATTAGATGCTATTTCTGCATTGTCAGCGCAAGTATCTTCTTT
* *
20346687 GGCCAACATCGTTAAGAACATGAATGGAACAAGCACCATTTCTCTGATTCAAATGGCCCAACAAA
66 GGCCAACATCATTAAGAACATGAATGGAACAAGCACCATTTCTCCGATTCAAATGGCCCAACAAA
*
20346752 CAGATATGCCGATATTTTCATTCTTGATTTGCGACGACAATCACAGCTATGAAGATTGCTCGCAG
131 CAGATAAGCCGATATTTTCATTCTTGATTTGCGACGACAATCACAGCTATGAAGATTGCTCGCAG
* *
20346817 CATGCAGAAAATGCATATTATGTCAATAACATCCGAGGGGGTTCGTTTGGTAACTCCTATAATAA
196 CATACAGAAAATGCATATTATGTCAATAACATCCGAGGGGGTTCGTTTGGTAACTCCTATAACAA
20346882 TCATTCGC
261 TCATTCGC
20346890 AAAATTAACCCTAGAGTTCTTGAATTAGATGCTATTTCTGCATTGTCAGCGCAAGTATCTTCTTT
1 AAAATTAACCCTAGAGTTCTTGAATTAGATGCTATTTCTGCATTGTCAGCGCAAGTATCTTCTTT
*
20346955 GGCCAACATCATTAAGAACATGAATGGAACAAGCACCATTTCTCCGATTCAAATGGCCCAGCAAA
66 GGCCAACATCATTAAGAACATGAATGGAACAAGCACCATTTCTCCGATTCAAATGGCCCAACAAA
* * *
20347020 CAGATAAGCCGATATTTTCATTCTTGATTTGTGGCGACAATCACAGCTATGAAGATTG-TCCGTA
131 CAGATAAGCCGATATTTTCATTCTTGATTTGCGACGACAATCACAGCTATGAAGATTGCT-CGCA
*
20347084 GCATATAGAAAATGCATATTATGTCAATAACATCCGAGGGGGTTCGTTTGGTAACTCCTATAACA
195 GCATACAGAAAATGCATATTATGTCAATAACATCCGAGGGGGTTCGTTTGGTAACTCCTATAACA
*
20347149 ATCGTTCGC
260 ATCATTCGC
20347158 AAAA
1 AAAA
20347162 ATATTGGGGA
Statistics
Matches: 256, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
267 1 0.00
268 255 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (268 bp):
AAAATTAACCCTAGAGTTCTTGAATTAGATGCTATTTCTGCATTGTCAGCGCAAGTATCTTCTTT
GGCCAACATCATTAAGAACATGAATGGAACAAGCACCATTTCTCCGATTCAAATGGCCCAACAAA
CAGATAAGCCGATATTTTCATTCTTGATTTGCGACGACAATCACAGCTATGAAGATTGCTCGCAG
CATACAGAAAATGCATATTATGTCAATAACATCCGAGGGGGTTCGTTTGGTAACTCCTATAACAA
TCATTCGC
Found at i:20352108 original size:294 final size:294
Alignment explanation
Indices: 20351579--20352166 Score: 1104
Period size: 294 Copynumber: 2.0 Consensus size: 294
20351569 AAAGTCATCA
20351579 ACCTGGTAAAATTTAATTAATGTTGACGCATTTTACTTTAATTTTTTTATTTACTTTTCTATTAT
1 ACCTGGTAAAATTTAATTAATGTTGACGCATTTTACTTTAATTTTTTTATTTACTTTTCTATTAT
20351644 TTCACTTTTCGTCGTGTTGTTTCATATTCTTAGCAAAAATAAAGGTCATATTTTTGTCGATGCAT
66 TTCACTTTTCGTCGTGTTGTTTCATATTCTTAGCAAAAATAAAGGTCATATTTTTGTCGATGCAT
* * *
20351709 TAGAGCATATATTGTTGGTGCATTCAACGATGAGTCAGCATTACCTTTTCTATAAAAATTGCGTC
131 TAGAGCATATATTGTCGGTGCATTCAACGATGAGTCAGCATTACCTTTTCTACAAAAATCGCGTC
20351774 TATTGATTGTTTCTTATCCCAACCGTTGGATCAAAACAAACTTGGTACGATTTGTAGCCTAGCAA
196 TATTGATTGTTTCTTATCCCAACCGTTGGATCAAAACAAACTTGGTACGATTTGTAGCCTAGCAA
20351839 TTAATGGTTGCAGGCGCATCATTTCCCCATATGT
261 TTAATGGTTGCAGGCGCATCATTTCCCCATATGT
*
20351873 ACCTGGTAAAATTTAATTAATGTTGACGCATTTTATTTTAATTTTTTTATTTACTTTTCTATTAT
1 ACCTGGTAAAATTTAATTAATGTTGACGCATTTTACTTTAATTTTTTTATTTACTTTTCTATTAT
*
20351938 TTCACTTTTCGTCGTGTTGTTTCATATTCTTAGCAAAAATAAAGGTCGTATTTTTGTCGATGCAT
66 TTCACTTTTCGTCGTGTTGTTTCATATTCTTAGCAAAAATAAAGGTCATATTTTTGTCGATGCAT
*
20352003 TAGAGCATATATTGTCGGTGCATTCAACGATGAGTCAGCATTACCTTTTCTGCAAAAATCGCGTC
131 TAGAGCATATATTGTCGGTGCATTCAACGATGAGTCAGCATTACCTTTTCTACAAAAATCGCGTC
* *
20352068 TATTGATTGTTTCTTATCCTAACCGTTGGATCAAAACAAACTTGGTACGATTTGTAGCCTGGCAA
196 TATTGATTGTTTCTTATCCCAACCGTTGGATCAAAACAAACTTGGTACGATTTGTAGCCTAGCAA
20352133 TTAATGGTTGCAGGCGCATCATTTCCCCATATGT
261 TTAATGGTTGCAGGCGCATCATTTCCCCATATGT
20352167 TTTCACTCAT
Statistics
Matches: 286, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 286 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (294 bp):
ACCTGGTAAAATTTAATTAATGTTGACGCATTTTACTTTAATTTTTTTATTTACTTTTCTATTAT
TTCACTTTTCGTCGTGTTGTTTCATATTCTTAGCAAAAATAAAGGTCATATTTTTGTCGATGCAT
TAGAGCATATATTGTCGGTGCATTCAACGATGAGTCAGCATTACCTTTTCTACAAAAATCGCGTC
TATTGATTGTTTCTTATCCCAACCGTTGGATCAAAACAAACTTGGTACGATTTGTAGCCTAGCAA
TTAATGGTTGCAGGCGCATCATTTCCCCATATGT
Found at i:20355245 original size:47 final size:47
Alignment explanation
Indices: 20355191--20355290 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 47
20355181 CATTTTATAA
20355191 TTATTTTTTGTATTTTCTAATACATAGCAAGTTAGTTTAAACTCTCG
1 TTATTTTTTGTATTTTCTAATACATAGCAAGTTAGTTTAAACTCTCG
*
20355238 TTATTTTTTGTATTTTCTAATACATAGCAAGTTTGTTTAAACTCTCG
1 TTATTTTTTGTATTTTCTAATACATAGCAAGTTAGTTTAAACTCTCG
20355285 TTATTT
1 TTATTT
20355291 CTATATATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (47 bp):
TTATTTTTTGTATTTTCTAATACATAGCAAGTTAGTTTAAACTCTCG
Found at i:20359214 original size:41 final size:41
Alignment explanation
Indices: 20359169--20359247 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
20359159 ATTTTCAAGG
* *
20359169 CCATGAAATGATACTTGTTGATTTTTCAAAGCTGTCTTGAA
1 CCATGAAATGATACTTGCTGATTTTTAAAAGCTGTCTTGAA
*
20359210 CCATGAAATGATGCTTGCTGATTTTTAAAAGCTGTCTT
1 CCATGAAATGATACTTGCTGATTTTTAAAAGCTGTCTT
20359248 ATTGTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (41 bp):
CCATGAAATGATACTTGCTGATTTTTAAAAGCTGTCTTGAA
Found at i:20363355 original size:15 final size:15
Alignment explanation
Indices: 20363331--20363379 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
20363321 ACAACATATA
*
20363331 TTTCTTTTTTCTTCT
1 TTTCTCTTTTCTTCT
*
20363346 TTTCTCTTTTCCTCT
1 TTTCTCTTTTCTTCT
* *
20363361 TTTTTCTTTCTTTTCT
1 TTTCTCTTT-TCTTCT
20363377 TTT
1 TTT
20363380 TTTGTATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 21 0.75
16 7 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTTTCTTCT
Found at i:20363361 original size:25 final size:26
Alignment explanation
Indices: 20363333--20363381 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
20363323 AACATATATT
20363333 TCTTTTTTC-TTCTTTTCTCTTTTCC
1 TCTTTTTTCTTTCTTTTCTCTTTTCC
*
20363358 TCTTTTTTCTTTCTTTTCTTTTTT
1 TCTTTTTTCTTTCTTTTCTCTTTT
20363382 TGTATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (26 bp):
TCTTTTTTCTTTCTTTTCTCTTTTCC
Found at i:20378703 original size:16 final size:16
Alignment explanation
Indices: 20378661--20378705 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
20378651 TTTTATTGAA
* * *
20378661 TTTATTATTATGTAAT
1 TTTATTTTTATTTTAT
20378677 TTTA-TTTTATTTTAT
1 TTTATTTTTATTTTAT
20378692 TTTATTTTTATTTT
1 TTTATTTTTATTTT
20378706 GGTTCAAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTTTTATTTTAT
Found at i:20378704 original size:6 final size:5
Alignment explanation
Indices: 20378661--20378705 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
20378651 TTTTATTGAA
* *
20378661 TTTAT TATTAT GTAAT TTTAT TTTAT TTTAT TTTATT TTTAT TTT
1 TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT
20378706 GGTTCAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:20380487 original size:21 final size:21
Alignment explanation
Indices: 20380449--20380488 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20380439 ACCTACTATT
*
20380449 GAGGAGGAAGTTGCTGTTGGA
1 GAGGAGGAAGTTACTGTTGGA
20380470 GAGGAGGAAG-TACTTGTTG
1 GAGGAGGAAGTTAC-TGTTG
20380489 AAGATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.05, G:0.45, T:0.25
Consensus pattern (21 bp):
GAGGAGGAAGTTACTGTTGGA
Found at i:20381542 original size:2 final size:2
Alignment explanation
Indices: 20381537--20381562 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20381527 TAAAAAAAAG
20381537 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
20381563 TTTATGATCT
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:20383525 original size:21 final size:20
Alignment explanation
Indices: 20383490--20383551 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
20383480 GAAAAATTAT
20383490 AATAGAAAA-ATTAAATTAAA
1 AATA-AAAATATTAAATTAAA
20383510 AATAAACAATATTAAAATTAAA
1 AATAAA-AATATT-AAATTAAA
* *
20383532 ATTAAAAATTTCTAAATTAA
1 AATAAAAATAT-TAAATTAA
20383552 TAGAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 14 0.39
22 14 0.39
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAATATTAAATTAAA
Found at i:20385847 original size:10 final size:9
Alignment explanation
Indices: 20385814--20385860 Score: 60
Period size: 10 Copynumber: 5.0 Consensus size: 9
20385804 TGGCAATATA
20385814 TTTCTTTTC
1 TTTCTTTTC
20385823 TTT-TTTTC
1 TTTCTTTTC
20385831 TTTTCTTCTTC
1 -TTTCTT-TTC
20385842 TTTCTTTTTC
1 TTTC-TTTTC
20385852 TTTCTTTTC
1 TTTCTTTTC
20385861 GTGAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 5 0.15
9 11 0.32
10 13 0.38
11 5 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:20385849 original size:21 final size:18
Alignment explanation
Indices: 20385814--20385860 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
20385804 TGGCAATATA
20385814 TTTCTTTTCTTTTTTTCT
1 TTTCTTTTCTTTTTTTCT
20385832 TTTCTTCTTCTTTCTTTT-T
1 TTTCTT-TTCTTT-TTTTCT
20385851 CTTTCTTTTC
1 -TTTCTTTTC
20385861 GTGAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 10 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTTCT
Found at i:20385850 original size:16 final size:13
Alignment explanation
Indices: 20385814--20385860 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 13
20385804 TGGCAATATA
20385814 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
20385827 TTTCTTTTCTTCTT
1 TTTCTTTTCTT-TT
20385841 CTTTCTTTTTCTTTCT
1 -TTTC-TTTTCTTT-T
20385857 TTTC
1 TTTC
20385861 GTGAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 11 0.37
14 2 0.07
15 9 0.30
16 8 0.27
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:20395727 original size:23 final size:23
Alignment explanation
Indices: 20395701--20395806 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 23
20395691 ATCACAGTTG
* * *
20395701 TCACATGAATATTTCAACATTAT
1 TCACATGAATATTTAAACATAAA
*
20395724 TCACATTAATATTTAAACATAAA
1 TCACATGAATATTTAAACATAAA
* * *
20395747 TCACATTAA-ATTTTAAGCACAAA
1 TCACATGAATA-TTTAAACATAAA
* *
20395770 TCACATTAATA-TTAAGCATAAA
1 TCACATGAATATTTAAACATAAA
20395792 TCACA-GTAATATTTA
1 TCACATG-AATATTTA
20395807 GCACATTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 20 0.28
23 50 0.70
24 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (23 bp):
TCACATGAATATTTAAACATAAA
Found at i:20395752 original size:46 final size:46
Alignment explanation
Indices: 20395701--20395805 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 46
20395691 ATCACAGTTG
** *
20395701 TCACATGAATATTTCAA-CATTATTCACATTAATATTTAAACATAAA
1 TCACATGAATATTTCAAGCACAAATCACATTAATA-TTAAACATAAA
* * *
20395747 TCACATTAA-ATTTTAAGCACAAATCACATTAATATTAAGCATAAA
1 TCACATGAATATTTCAAGCACAAATCACATTAATATTAAACATAAA
20395792 TCACA-GTAATATTT
1 TCACATG-AATATTT
20395806 AGCACATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
45 23 0.47
46 26 0.53
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (46 bp):
TCACATGAATATTTCAAGCACAAATCACATTAATATTAAACATAAA
Found at i:20395787 original size:22 final size:22
Alignment explanation
Indices: 20395724--20395811 Score: 104
Period size: 22 Copynumber: 3.9 Consensus size: 22
20395714 TCAACATTAT
* *
20395724 TCACATTAATATTTAAACATAAA
1 TCACATTAATA-TTAAGCACAAA
*
20395747 TCACATTAAATTTTAAGCACAAA
1 TCACATT-AATATTAAGCACAAA
*
20395770 TCACATTAATATTAAGCATAAA
1 TCACATTAATATTAAGCACAAA
* *
20395792 TCACAGTAATATTTAGCACA
1 TCACATTAATATTAAGCACA
20395812 TTTAATGATA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
22 30 0.54
23 23 0.41
24 3 0.05
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (22 bp):
TCACATTAATATTAAGCACAAA
Found at i:20395999 original size:66 final size:66
Alignment explanation
Indices: 20395892--20396019 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
20395882 AATCTCCAAT
* * * * *
20395892 CACACCAAAAGACTCATAGAGTCTAACATTTCCCAAGAGTGAAGCAT-ATAGCTAACACTCTCTA
1 CACACCAAAAGACTCACAGAGCCAAACATGTCCCAAAAGTGAAGCATGA-AGCTAACACTCTCTA
20395956 AA
65 AA
20395958 CACACCAAAAGACTCACAGAGCCAAACATGTCCCAAAAGTGAAGCATGAAGCTAACACTCTC
1 CACACCAAAAGACTCACAGAGCCAAACATGTCCCAAAAGTGAAGCATGAAGCTAACACTCTC
20396020 CTTATTTCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.17
Consensus pattern (66 bp):
CACACCAAAAGACTCACAGAGCCAAACATGTCCCAAAAGTGAAGCATGAAGCTAACACTCTCTAA
A
Found at i:20396308 original size:36 final size:36
Alignment explanation
Indices: 20396268--20396566 Score: 402
Period size: 36 Copynumber: 8.2 Consensus size: 36
20396258 TTAGCACAAT
*
20396268 ATATTCACTATCACATGGCATGAATAACATACCCAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* * * *
20396304 ATATTTATTGTCTCATGGCATGAATAACACACCCAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* *
20396340 ATATTTACTATCACATGACATGAATAACATATCCAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* *
20396376 ATATTTACTATCTCATGGCATGAATAACACACCCAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* * *
20396412 ATATTAACTATCACATGACATGAATAACATACCTAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
*
20396448 ATATTTACTATCTCATGGCATGAATAACATACCCAC
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* * *
20396484 ACATTTACTGTCACATGGCATGAATAACATACCCAT
1 ATATTTACTATCACATGGCATGAATAACATACCCAC
* *
20396520 ATATTTACTGT-ATCATGGAATGAATAACACATACCCAC
1 ATATTTACTATCA-CATGGCATGAAT-A-ACATACCCAC
20396558 ATATTTACT
1 ATATTTACT
20396567 TTCATGACAG
Statistics
Matches: 229, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
35 1 0.00
36 209 0.91
37 1 0.00
38 18 0.08
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.29
Consensus pattern (36 bp):
ATATTTACTATCACATGGCATGAATAACATACCCAC
Found at i:20396350 original size:72 final size:72
Alignment explanation
Indices: 20396268--20396566 Score: 445
Period size: 72 Copynumber: 4.1 Consensus size: 72
20396258 TTAGCACAAT
* * * *
20396268 ATATTCACTATCACATGGCATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
1 ATATTTACTATCACATGACATGAATAACATACCCACATATTTACTATCTCATGGCATGAATAACA
20396333 CACCCAC
66 CACCCAC
*
20396340 ATATTTACTATCACATGACATGAATAACATATCCACATATTTACTATCTCATGGCATGAATAACA
1 ATATTTACTATCACATGACATGAATAACATACCCACATATTTACTATCTCATGGCATGAATAACA
20396405 CACCCAC
66 CACCCAC
* *
20396412 ATATTAACTATCACATGACATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
1 ATATTTACTATCACATGACATGAATAACATACCCACATATTTACTATCTCATGGCATGAATAACA
*
20396477 TACCCAC
66 CACCCAC
* * * * * * *
20396484 ACATTTACTGTCACATGGCATGAATAACATACCCATATATTTACTGTATCATGGAATGAATAACA
1 ATATTTACTATCACATGACATGAATAACATACCCACATATTTACTATCTCATGGCATGAATAACA
20396549 CATACCCAC
66 C--ACCCAC
20396558 ATATTTACT
1 ATATTTACT
20396567 TTCATGACAG
Statistics
Matches: 205, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 191 0.93
74 14 0.07
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.29
Consensus pattern (72 bp):
ATATTTACTATCACATGACATGAATAACATACCCACATATTTACTATCTCATGGCATGAATAACA
CACCCAC
Found at i:20419508 original size:18 final size:18
Alignment explanation
Indices: 20419485--20419519 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20419475 TGAAATTCCA
20419485 TCTCAAAA-ATTACCAAAT
1 TCTCAAAACA-TACCAAAT
20419503 TCTCAAAACATACCAAA
1 TCTCAAAACATACCAAA
20419520 ATGTATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
TCTCAAAACATACCAAAT
Found at i:20427916 original size:24 final size:24
Alignment explanation
Indices: 20427888--20427936 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
20427878 ACAACAAAGA
*
20427888 ATAATAACACATAAGGTGTGGAAC
1 ATAATAACACATAAGGTATGGAAC
20427912 ATAATAACACATAAGGTATGGAAC
1 ATAATAACACATAAGGTATGGAAC
20427936 A
1 A
20427937 CCGTCACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (24 bp):
ATAATAACACATAAGGTATGGAAC
Found at i:20443358 original size:26 final size:27
Alignment explanation
Indices: 20443322--20443379 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
20443312 AATGTTAAAG
* * *
20443322 TCAACGGTCAATGGTC-AAGTCAACTA
1 TCAACAGTCAATGGTCAAAATCAACGA
20443348 TCAACAGTCAATGGTCAAAATCAACGA
1 TCAACAGTCAATGGTCAAAATCAACGA
20443375 TCAAC
1 TCAAC
20443380 GGTGAACGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (27 bp):
TCAACAGTCAATGGTCAAAATCAACGA
Found at i:20457978 original size:41 final size:41
Alignment explanation
Indices: 20457921--20457999 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
20457911 CTTAGGGGAC
20457921 TGTATTGAGAAAGCGGAAGTAAACAACTGTGAGTTGCGGAT
1 TGTATTGAGAAAGCGGAAGTAAACAACTGTGAGTTGCGGAT
20457962 TGTATTGAGAAAGCGGAAGTAAACAACTGTGAGTTGCG
1 TGTATTGAGAAAGCGGAAGTAAACAACTGTGAGTTGCG
20458000 AAGATATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Consensus pattern (41 bp):
TGTATTGAGAAAGCGGAAGTAAACAACTGTGAGTTGCGGAT
Found at i:20468727 original size:28 final size:28
Alignment explanation
Indices: 20468685--20468739 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
20468675 AAATGAGCAT
* *
20468685 CATGACCTTTGGGTCAACAGGTAGTAAG
1 CATGACCTTTAGGTCAACAGGGAGTAAG
20468713 CATGACCTTTAGGTCAACAGGGAGTAA
1 CATGACCTTTAGGTCAACAGGGAGTAA
20468740 ATCAGATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (28 bp):
CATGACCTTTAGGTCAACAGGGAGTAAG
Found at i:20476802 original size:17 final size:17
Alignment explanation
Indices: 20476780--20476820 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
20476770 TTAGTTTTCA
20476780 TGCATTT-TTATTGTCAC
1 TGCATTTATT-TTGTCAC
20476797 TGCATTTAATTTTGTCAC
1 TGCATTT-ATTTTGTCAC
20476815 TGCATT
1 TGCATT
20476821 ACTTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (17 bp):
TGCATTTATTTTGTCAC
Found at i:20477425 original size:12 final size:12
Alignment explanation
Indices: 20477399--20477438 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
20477389 AGTTAATTGA
*
20477399 AAAAGGAAAGA-
1 AAAAGAAAAGAG
20477410 AAAAGAAAAGAG
1 AAAAGAAAAGAG
20477422 AAAAGAAAAGAAG
1 AAAAGAAAAG-AG
20477435 AAAA
1 AAAA
20477439 ATGTTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 10 0.38
12 10 0.38
13 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:20477425 original size:13 final size:14
Alignment explanation
Indices: 20477406--20477439 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
20477396 TGAAAAAGGA
20477406 AAGAAAAAGAAAAG
1 AAGAAAAAGAAAAG
20477420 -AG-AAAAGAAAAG
1 AAGAAAAAGAAAAG
20477432 AAGAAAAA
1 AAGAAAAA
20477440 TGTTGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.56
13 4 0.22
14 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:20481003 original size:36 final size:36
Alignment explanation
Indices: 20480961--20481032 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
20480951 GTGGCGACAT
20480961 TTTTGGGCGCAAATTTGGATTCTATTTTGCAGCGAC
1 TTTTGGGCGCAAATTTGGATTCTATTTTGCAGCGAC
20480997 TTTTGGGCGCAAATTTGGATTCTATTTTGCAGCGAC
1 TTTTGGGCGCAAATTTGGATTCTATTTTGCAGCGAC
20481033 AACCCTGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (36 bp):
TTTTGGGCGCAAATTTGGATTCTATTTTGCAGCGAC
Found at i:20489277 original size:34 final size:34
Alignment explanation
Indices: 20489239--20489303 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
20489229 TAGTAACAGG
*
20489239 CATGACCTTCGGGTCAATAGGGAGTAAAATGCAT
1 CATGACCTTCGGGTCAATAGGAAGTAAAATGCAT
* *
20489273 CATGACCTTTGTGTCAATAGGAAGTAAAATG
1 CATGACCTTCGGGTCAATAGGAAGTAAAATG
20489304 GATTATGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (34 bp):
CATGACCTTCGGGTCAATAGGAAGTAAAATGCAT
Found at i:20502239 original size:14 final size:16
Alignment explanation
Indices: 20502216--20502247 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20502206 TTTTACTTTA
20502216 TTTTATTTTTTAT-CT
1 TTTTATTTTTTATGCT
20502231 TTTTA-TTTTTATGCT
1 TTTTATTTTTTATGCT
20502246 TT
1 TT
20502248 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTATGCT
Found at i:20508003 original size:39 final size:39
Alignment explanation
Indices: 20507949--20508025 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
20507939 TAACAACTTA
*
20507949 GACAACTCTCTTCCTTCTTCTATTGTGTCTTTGCTGTAT
1 GACAACTCTCTTCCTTCTTCTATTGTGTCTTTACTGTAT
*
20507988 GACAACTCTCTTCCTTCTTTTATTGTGTCTTTACTGTA
1 GACAACTCTCTTCCTTCTTCTATTGTGTCTTTACTGTA
20508026 GGAATTCGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.14, C:0.25, G:0.12, T:0.49
Consensus pattern (39 bp):
GACAACTCTCTTCCTTCTTCTATTGTGTCTTTACTGTAT
Found at i:20508222 original size:16 final size:16
Alignment explanation
Indices: 20508201--20508233 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20508191 AATGGAAAAG
20508201 GGGTATGTTCGAGAGA
1 GGGTATGTTCGAGAGA
20508217 GGGTATGTTCGAGAGA
1 GGGTATGTTCGAGAGA
20508233 G
1 G
20508234 CTTAAGTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.45, T:0.24
Consensus pattern (16 bp):
GGGTATGTTCGAGAGA
Found at i:20513164 original size:8 final size:8
Alignment explanation
Indices: 20513151--20513189 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
20513141 GTGAGATTTC
20513151 ACACATAA
1 ACACATAA
20513159 ACACATAA
1 ACACATAA
*
20513167 ACACATAC
1 ACACATAA
* *
20513175 ATAGATAA
1 ACACATAA
20513183 ACACATA
1 ACACATA
20513190 TTATCATTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.59, C:0.23, G:0.03, T:0.15
Consensus pattern (8 bp):
ACACATAA
Found at i:20523168 original size:18 final size:17
Alignment explanation
Indices: 20523133--20523180 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
20523123 AACTAAATTA
* **
20523133 ACAAAAGAAATGCAATG
1 ACAAAAAAAATGTGATG
20523150 ACAAAATAAAATGTGATG
1 ACAAAA-AAAATGTGATG
*
20523168 ACAATAAAAATGT
1 ACAAAAAAAATGT
20523181 ATGCAATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (17 bp):
ACAAAAAAAATGTGATG
Found at i:20523179 original size:17 final size:18
Alignment explanation
Indices: 20523147--20523180 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20523137 AAGAAATGCA
20523147 ATGACAAAATAAAATGTG
1 ATGACAAAATAAAATGTG
*
20523165 ATGACAATA-AAAATGT
1 ATGACAAAATAAAATGT
20523181 ATGCAATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (18 bp):
ATGACAAAATAAAATGTG
Found at i:20527671 original size:13 final size:13
Alignment explanation
Indices: 20527653--20527677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20527643 CTATTTACTA
20527653 GGAAGAAATTTCG
1 GGAAGAAATTTCG
20527666 GGAAGAAATTTC
1 GGAAGAAATTTC
20527678 CCTAAGGGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
GGAAGAAATTTCG
Found at i:20531817 original size:16 final size:16
Alignment explanation
Indices: 20531796--20531828 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20531786 AGCAATAAAA
20531796 TTTTTCT-TCTTCTTTT
1 TTTTTCTCT-TTCTTTT
20531812 TTTTTCTCTTTCTTTT
1 TTTTTCTCTTTCTTTT
20531828 T
1 T
20531829 CTCATCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTCTTTCTTTT
Found at i:20538703 original size:28 final size:28
Alignment explanation
Indices: 20538672--20538754 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
20538662 AAGGAGAAAG
* *
20538672 ATGTGGAAATTTTTGGTAAATATGTGAT
1 ATGTGGCAATTTTTGGAAAATATGTGAT
20538700 ATGTGGCAATTTTTGGAAAATATGTGAT
1 ATGTGGCAATTTTTGGAAAATATGTGAT
* * *
20538728 ATATGGCCATTTTATGGCAAATATGTG
1 ATGTGGCAATTTT-TGGAAAATATGTG
20538755 GCAGTTTATC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 37 0.76
29 12 0.24
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (28 bp):
ATGTGGCAATTTTTGGAAAATATGTGAT
Found at i:20551116 original size:28 final size:29
Alignment explanation
Indices: 20551079--20551174 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 29
20551069 AGTTGCCTCG
*
20551079 AAGGC-TCCTTTATCAAAATCAGCCACAA
1 AAGGCTTCCTTTAACAAAATCAGCCACAA
*
20551107 AA-GCTTCCTTTAACAGAATCAGCCACAA
1 AAGGCTTCCTTTAACAAAATCAGCCACAA
* * * * *
20551135 AAGGCTCCCTTTAATAGACTCAGCCA-TA
1 AAGGCTTCCTTTAACAAAATCAGCCACAA
*
20551163 AAGTCTTCCTTT
1 AAGGCTTCCTTT
20551175 CATTGCACCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.03
28 36 0.62
29 20 0.34
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (29 bp):
AAGGCTTCCTTTAACAAAATCAGCCACAA
Found at i:20553339 original size:245 final size:246
Alignment explanation
Indices: 20552860--20553340 Score: 752
Period size: 245 Copynumber: 2.0 Consensus size: 246
20552850 TCCACTATCT
* * *
20552860 TTTCTTTTTATTTAATATCTCATATTAAAATGGAAATATTCTTCGAGAGAAATATATGGAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCTTCGAAAGAAATATATGGAAGGTT
* * *
20552925 TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCCTT
66 CATTAAAACATTATATATTTTCCAAAAGGATATTAACTTCCATATTTTTAATATTCAATTTCCTT
* * *
20552990 TTATATAATATCTCATATTAAAATAAAAATATTTGCTTAGAGAAATATATGGAAGGTTTATTAAA
131 TTATATAATATCTCATATTAAAATAAAAATATTTCCTTAAAGAAATATATGCAAGGTTTATTAAA
* *
20553055 ACATTATATCATTTCCAAAAGGATATTAACTTTCATGTTTTTCATATTCAA
196 ACATTATATCATTTCCAAAAAGATATTAACTTCCATGTTTTTCATATTCAA
* *
20553106 TTTCCTTTTATATAATATCTTATATTAAAATGGAAAT-TTCATT-TAAAGAAATATATGGAAGGT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTC-TTCGAAAGAAATATATGGAAGGT
* *
20553169 TCATTAAAACATTATATATTTTCCAAAAGGATATTAACTTTCATATTTTTAATATTTAATTTCCT
65 TCATTAAAACATTATATATTTTCCAAAAGGATATTAACTTCCATATTTTTAATATTCAATTTCCT
**
20553234 TTTATATAATATCTCATATTAAAATGGAAATA-TTCCTTTAAAGAAATATATGCAAGGTTTATTA
130 TTTATATAATATCTCATATTAAAATAAAAATATTTCC-TTAAAGAAATATATGCAAGGTTTATTA
* *
20553298 AAACATTATATCTTTTCCAAAAAGATGTTAACTTCCATGTTTT
194 AAACATTATATCATTTCCAAAAAGATATTAACTTCCATGTTTT
20553341 AATATTTAAC
Statistics
Matches: 214, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
244 3 0.01
245 175 0.82
246 36 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43
Consensus pattern (246 bp):
TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCTTCGAAAGAAATATATGGAAGGTT
CATTAAAACATTATATATTTTCCAAAAGGATATTAACTTCCATATTTTTAATATTCAATTTCCTT
TTATATAATATCTCATATTAAAATAAAAATATTTCCTTAAAGAAATATATGCAAGGTTTATTAAA
ACATTATATCATTTCCAAAAAGATATTAACTTCCATGTTTTTCATATTCAA
Found at i:20553362 original size:123 final size:123
Alignment explanation
Indices: 20552860--20553346 Score: 739
Period size: 123 Copynumber: 4.0 Consensus size: 123
20552850 TCCACTATCT
* * * *
20552860 TTTCTTTTTATTTAATATCTCATATTAAAATGGAAATATT-CTTCGAGAGAAATATATGGAAGGT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTT-TAAAGAAATATATGGAAGGT
20552924 TTATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
65 TTATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
** * *
20552983 TTTCCTTTTATATAATATCTCATATTAAAATAAAAATATTTGC-TTAGAGAAATATATGGAAGGT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATA-TTCCTTTAAAGAAATATATGGAAGGT
* * *
20553047 TTATTAAAACATTATATCATTTCCAAAAGGATATTAACTTTCATGTTTTTCATATTCAA
65 TTATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
* *
20553106 TTTCCTTTTATATAATATCTTATATTAAAATGGAAAT-TTCATTTAAAGAAATATATGGAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* * * * *
20553170 CATTAAAACATTATATATTTTCCAAAAGGATATTAACTTTCATATTTTTAATATTTAA
66 TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
*
20553228 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGCAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* *
20553293 TATTAAAACATTATATCTTTTCCAAAAAGATGTTAACTTCCATG-TTTTAATATT
66 TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATT
20553347 TAACGAAATC
Statistics
Matches: 331, Mismatches: 29, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
121 2 0.01
122 119 0.36
123 206 0.62
124 3 0.01
125 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43
Consensus pattern (123 bp):
TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
Found at i:20596273 original size:24 final size:24
Alignment explanation
Indices: 20596212--20596274 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
20596202 TAGACTAATA
* * *
20596212 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
20596236 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
20596260 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
20596275 GATTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:20598238 original size:24 final size:24
Alignment explanation
Indices: 20598210--20598260 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20598200 AGTTTGACTC
* *
20598210 AAACAAATAAACATAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
*
20598234 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAACTG
20598258 AAA
1 AAA
20598261 GCTTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:20601813 original size:24 final size:23
Alignment explanation
Indices: 20601756--20601816 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
20601746 TTAAATTACT
* **
20601756 AAATAAAGTTTTTTTTAATTACGA
1 AAAT-AAGTTTTTTTTAATCAAAA
*
20601780 AAATAAGTTTTTTTTTATCAAAA
1 AAATAAGTTTTTTTTAATCAAAA
*
20601803 AAATAAGGTTTTTT
1 AAATAAGTTTTTTT
20601817 AAAAAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (23 bp):
AAATAAGTTTTTTTTAATCAAAA
Found at i:20602154 original size:32 final size:34
Alignment explanation
Indices: 20602111--20602192 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 34
20602101 CAGTTTTATG
* *
20602111 AAATAATAACAAATATCA-AACTTTTATGTTGT-
1 AAATAATAACAAATATCACAACATTAATGTTGTA
* *
20602143 AAATTATAACAAAT-T-ACAACATTAATTTTGTA
1 AAATAATAACAAATATCACAACATTAATGTTGTA
*
20602175 AAATGATAACAAATATCA
1 AAATAATAACAAATATCA
20602193 GCTATCATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 1 0.02
31 12 0.29
32 26 0.63
33 1 0.02
34 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (34 bp):
AAATAATAACAAATATCACAACATTAATGTTGTA
Found at i:20603941 original size:5 final size:5
Alignment explanation
Indices: 20603933--20603976 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
20603923 TGATTTGATC
*
20603933 ATGAA ATGAA ATTGAA ATGAA ATTGAA ATGAGA ATGAT ATGAA A
1 ATGAA ATGAA A-TGAA ATGAA A-TGAA ATGA-A ATGAA ATGAA A
20603977 ATGGAATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 19 0.56
6 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (5 bp):
ATGAA
Found at i:20603948 original size:11 final size:11
Alignment explanation
Indices: 20603934--20603976 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
20603924 GATTTGATCA
20603934 TGAAATGAAAT
1 TGAAATGAAAT
20603945 TGAAATGAAAT
1 TGAAATGAAAT
20603956 TGAAATGAGAA-
1 TGAAATGA-AAT
*
20603967 TGATATGAAA
1 TGAAATGAAA
20603977 ATGGAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 2 0.07
11 26 0.87
12 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:20611446 original size:51 final size:51
Alignment explanation
Indices: 20611367--20611463 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
20611357 CCATACGCCT
20611367 ATGTGTGATAGCTTCAATCTCCAAATGCCCGTGTCTCCAACGCACATGCCC
1 ATGTGTGATAGCTTCAATCTCCAAATGCCCGTGTCTCCAACGCACATGCCC
* * * * *
20611418 ATGTGTGATAGCTTTAGTCTCCAGATGCCCGTGTCTCTAATGCACA
1 ATGTGTGATAGCTTCAATCTCCAAATGCCCGTGTCTCCAACGCACA
20611464 CGCTTGTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (51 bp):
ATGTGTGATAGCTTCAATCTCCAAATGCCCGTGTCTCCAACGCACATGCCC
Found at i:20614786 original size:16 final size:15
Alignment explanation
Indices: 20614765--20614804 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
20614755 GGAGAGTCAT
20614765 AGTCTAGAGTTTTCA
1 AGTCTAGAGTTTTCA
20614780 CAGTCTAGAGTTTTCA
1 -AGTCTAGAGTTTTCA
*
20614796 AATCTAGAG
1 AGTCTAGAG
20614805 AACAATTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (15 bp):
AGTCTAGAGTTTTCA
Found at i:20625419 original size:24 final size:24
Alignment explanation
Indices: 20625392--20625465 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
20625382 GCACAAGTGG
20625392 AAGAAGTGGAAGAAGAGGAAGGAA
1 AAGAAGTGGAAGAAGAGGAAGGAA
* *
20625416 AAGAAGTGAAAGAAGAGGATGGAA
1 AAGAAGTGGAAGAAGAGGAAGGAA
* *
20625440 AAGAGGAAGGAA-AAGAGGAAGGAA
1 AAGAAG-TGGAAGAAGAGGAAGGAA
20625464 AA
1 AA
20625466 TAGGCTGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.93
25 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.04
Consensus pattern (24 bp):
AAGAAGTGGAAGAAGAGGAAGGAA
Found at i:20625443 original size:12 final size:12
Alignment explanation
Indices: 20625399--20625465 Score: 75
Period size: 12 Copynumber: 5.5 Consensus size: 12
20625389 TGGAAGAAGT
20625399 GGAAGAAGAGGAA
1 GGAA-AAGAGGAA
20625412 GGAAAAGAAGTGAA
1 GGAAAAG-AG-GAA
* *
20625426 --AGAAGAGGAT
1 GGAAAAGAGGAA
20625436 GGAAAAGAGGAA
1 GGAAAAGAGGAA
20625448 GGAAAAGAGGAA
1 GGAAAAGAGGAA
20625460 GGAAAA
1 GGAAAA
20625466 TAGGCTGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 33 0.72
13 6 0.13
14 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (12 bp):
GGAAAAGAGGAA
Found at i:20625939 original size:17 final size:18
Alignment explanation
Indices: 20625917--20625995 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 18
20625907 CACATTCCCT
20625917 TTGTCATTGCAATTT-AA
1 TTGTCATTGCAATTTCAA
*
20625934 TTGTCACTGC-ATTTGC-A
1 TTGTCATTGCAATTT-CAA
* *
20625951 TTGTCATTAC-ATTTCCAT
1 TTGTCATTGCAATTT-CAA
*
20625969 TTGTCATTGTAATTT-AA
1 TTGTCATTGCAATTTCAA
*
20625986 -TGTCAGTGCA
1 TTGTCATTGCA
20625996 TTGGGGACAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
16 12 0.25
17 24 0.50
18 8 0.17
19 4 0.08
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (18 bp):
TTGTCATTGCAATTTCAA
Found at i:20628179 original size:50 final size:50
Alignment explanation
Indices: 20628120--20628282 Score: 211
Period size: 50 Copynumber: 3.3 Consensus size: 50
20628110 GCATATACAA
*
20628120 ATATACTGCCACTGATAACACTTTGTGGACAAAG-CACCACTGATTTGTAG
1 ATATACTGCCACTGATAACACTTTGTGGAC-AAGCCACCACTGATTTGAAG
* * * * *
20628170 ATATACTGCCACTAATAACACTTCGTGGATAAGCCACCACTAATTTAAAG
1 ATATACTGCCACTGATAACACTTTGTGGACAAGCCACCACTGATTTGAAG
* * *
20628220 ATATACTGCCACTGATTACACTTTGTGGACAAGTCACCACTGATTTGCAG
1 ATATACTGCCACTGATAACACTTTGTGGACAAGCCACCACTGATTTGAAG
* *
20628270 ATAAACTACCACT
1 ATATACTGCCACT
20628283 TACTTCTACC
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 3 0.03
50 93 0.97
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (50 bp):
ATATACTGCCACTGATAACACTTTGTGGACAAGCCACCACTGATTTGAAG
Found at i:20630476 original size:45 final size:43
Alignment explanation
Indices: 20630367--20630482 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 43
20630357 TGGGTTAATG
20630367 CCATAGTATCTTTCAACTATGGTCTTACTCGTGTCGGATAAATA
1 CCATAGTATC-TTCAACTATGGTCTTACTCGTGTCGGATAAATA
* * ** *
20630411 CCATAGTATCATTCAACTATGGTCTTACAT-GTTTCTGGTTTGATG
1 CCATAGTATC-TTCAACTATGGTCTTAC-TCGTGTC-GGATAAATA
*
20630456 TCATAGTATCTTCCAACTATGGTCTTA
1 CCATAGTATCTT-CAACTATGGTCTTA
20630483 TTCATTCCAG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 33 0.53
45 29 0.47
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (43 bp):
CCATAGTATCTTCAACTATGGTCTTACTCGTGTCGGATAAATA
Found at i:20631625 original size:45 final size:45
Alignment explanation
Indices: 20631481--20631734 Score: 156
Period size: 45 Copynumber: 5.7 Consensus size: 45
20631471 TGAAAAGTAT
* *
20631481 CATAGTATCTTTCAACTATGG-CATTGATA-ATTTTCGA-TATGATGT
1 CATAGTATCTTTCAACTATGGTC-TT-ATACATTTTCGAGT-TAATGC
* * * *
20631526 CATAATATCTTTCGACTATGGTCTTATATGCA---AC-AGATAATGC
1 CATAGTATCTTTCAACTATGGTCTTATA--CATTTTCGAGTTAATGC
** *
20631569 CGCATTATCTTTCAACTATGGTCTTATACATTTTCGAGTTAATGC
1 CATAGTATCTTTCAACTATGGTCTTATACATTTTCGAGTTAATGC
* * * *
20631614 CATAGTATCTTTCAACTATGGTC-T-TAC-TTATGCCAGATAAATGT
1 CATAGTATCTTTCAACTATGGTCTTATACATT-TTCGAG-TTAATGC
* * *
20631658 CATGGTATCTTTCAATTATGGTC-T-TACATGTTTCCG-GTTTGATGC
1 CATAGTATCTTTCAACTATGGTCTTATACAT-TTT-CGAG-TTAATGC
* * *
20631703 CATAATATCTTCCAACTATGGTCTTATTCATT
1 CATAGTATCTTTCAACTATGGTCTTATACATT
20631735 CCGGTAAAGA
Statistics
Matches: 161, Mismatches: 32, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 36 0.22
44 36 0.22
45 75 0.47
46 5 0.03
47 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (45 bp):
CATAGTATCTTTCAACTATGGTCTTATACATTTTCGAGTTAATGC
Found at i:20631705 original size:89 final size:86
Alignment explanation
Indices: 20631486--20631729 Score: 252
Period size: 88 Copynumber: 2.8 Consensus size: 86
20631476 AGTATCATAG
* *
20631486 TATCTTTCAACTATGG-CATTGATA-ATTTTCGA-TATGATGTCATAATATCTTTCGACTATGGT
1 TATCTTTCAACTATGGTC-TT-ATACATTTTCGAGT-TGATGCCATAATATCTTTCAACTATGGT
20631548 CTTATATGCAACAGATAATGCCGCAT
63 CTTATATGC-ACAGATAATG-CGCAT
* *
20631574 TATCTTTCAACTATGGTCTTATACATTTTCGAGTTAATGCCATAGTATCTTTCAACTATGGTCTT
1 TATCTTTCAACTATGGTCTTATACATTTTCGAGTTGATGCCATAATATCTTTCAACTATGGTCTT
*
20631639 ACTTATGC-CAGATAAATG-TCAT
66 A--TATGCACAGAT-AATGCGCAT
* *
20631661 GGTATCTTTCAATTATGGTC-T-TACATGTTTCCG-GTTTGATGCCATAATATCTTCCAACTATG
1 --TATCTTTCAACTATGGTCTTATACAT-TTT-CGAG-TTGATGCCATAATATCTTTCAACTATG
20631723 GTCTTAT
61 GTCTTAT
20631730 TCATTCCGGT
Statistics
Matches: 136, Mismatches: 9, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
87 12 0.09
88 64 0.47
89 55 0.40
90 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (86 bp):
TATCTTTCAACTATGGTCTTATACATTTTCGAGTTGATGCCATAATATCTTTCAACTATGGTCTT
ATATGCACAGATAATGCGCAT
Found at i:20634362 original size:52 final size:52
Alignment explanation
Indices: 20634224--20634566 Score: 399
Period size: 52 Copynumber: 6.6 Consensus size: 52
20634214 TTCATTTTAA
** * * *
20634224 ATACTCACGATGACACAAAGTCATCGGA-C-CATTA-CTTCGTTAAA-GAATCAC
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATC-T-G-TAAAGGATTCAT
* * *
20634275 ATACACACGATAACACCTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* *
20634327 ATACTCACGATGACACGTAGTCATCAGACCACATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * *
20634379 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCGTATAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * *
20634431 ATACTCACGATGACACATAGTCATCGGACCTTATAATGTGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* *
20634483 ATACTCACGATGAAACGTAGTCATCGGGCCTCATAAT-TCGTAAAGGATTTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCT-GTAAAGGA-TTCAT
** * **
20634536 ATACTCATTATGGCATATAGTCATCGGACCT
1 ATACTCACGATGACACGTAGTCATCGGACCT
20634567 TTTCATTCAC
Statistics
Matches: 252, Mismatches: 34, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
51 29 0.12
52 188 0.75
53 34 0.13
54 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
Found at i:20634507 original size:156 final size:157
Alignment explanation
Indices: 20634224--20634566 Score: 444
Period size: 156 Copynumber: 2.2 Consensus size: 157
20634214 TTCATTTTAA
* * * * * * *
20634224 ATACTCACGATGACACAAAGTCATCGGA-C-CATTACTTCGT-TAAAGAATCACATACACACGAT
1 ATACTCACGATGACATATAGTCATCGGACCTCA-TAATCCGTAT-AGGATTCATATACACACGAT
* *
20634286 AACACCTAGTCATCGGACCTCATAATCTGTAAAGGATTCATATACTCACGATGACACGTAGTCAT
64 AACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCATATACTCACGATGAAACGTAGTCAT
20634351 CAGACCACATAA-TCTGTAAAGGA-TTCAT
129 CAGACCACATAATTC-GTAAAGGATTTCAT
* * *
20634379 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCGTATAGGATTCATATACTCACGATGA
1 ATACTCACGATGACATATAGTCATCGGACCTCATAATCCGTATAGGATTCATATACACACGATAA
* * *
20634444 CACATAGTCATCGGACCTTATAATGTGTAAAGGATTCATATACTCACGATGAAACGTAGTCATCG
66 CACATAGTCATCGGACCTCATAATCTGTAAAGGATTCATATACTCACGATGAAACGTAGTCATCA
* *
20634509 GGCCTCATAATTCGTAAAGGATTTCAT
131 GACCACATAATTCGTAAAGGATTTCAT
** *
20634536 ATACTCATTATGGCATATAGTCATCGGACCT
1 ATACTCACGATGACATATAGTCATCGGACCT
20634567 TTTCATTCAC
Statistics
Matches: 162, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
155 25 0.15
156 100 0.62
157 37 0.23
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (157 bp):
ATACTCACGATGACATATAGTCATCGGACCTCATAATCCGTATAGGATTCATATACACACGATAA
CACATAGTCATCGGACCTCATAATCTGTAAAGGATTCATATACTCACGATGAAACGTAGTCATCA
GACCACATAATTCGTAAAGGATTTCAT
Found at i:20640161 original size:16 final size:15
Alignment explanation
Indices: 20640116--20640164 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
20640106 TATCATAAAT
20640116 TTTTTTCTTCTTTTTC
1 TTTTTT-TTCTTTTTC
*
20640132 TTTTTCTTCCCTTTTCTC
1 TTTTT-TT-TCTTTT-TC
20640150 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
20640165 AAGTGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 8 0.29
18 7 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:20659558 original size:12 final size:12
Alignment explanation
Indices: 20659524--20659562 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20659514 ATGGAGCAAG
* *
20659524 AGAAGAAGAGAA
1 AGAAGAAAAGGA
20659536 AGAAGAAAAGGA
1 AGAAGAAAAGGA
*
20659548 AGAAGAGAAGGA
1 AGAAGAAAAGGA
20659560 AGA
1 AGA
20659563 CGAAGAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAGGA
Found at i:20669366 original size:20 final size:20
Alignment explanation
Indices: 20669343--20669382 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20669333 CCGAAGTTTT
20669343 AAAATTG-ATATAATAATAAA
1 AAAATTGAATAT-ATAATAAA
*
20669363 AAAATTTAATATATAATAAA
1 AAAATTGAATATATAATAAA
20669383 TTTAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATTGAATATATAATAAA
Found at i:20669398 original size:15 final size:16
Alignment explanation
Indices: 20669361--20669399 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
20669351 TATAATAATA
20669361 AAAAAATTTAATATAT
1 AAAAAATTTAATATAT
* *
20669377 AATAAATTTAGT-TAT
1 AAAAAATTTAATATAT
20669392 AAAAAATT
1 AAAAAATT
20669400 ACATATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAAATTTAATATAT
Found at i:20674056 original size:18 final size:18
Alignment explanation
Indices: 20674021--20674063 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
20674011 AATAAACATA
20674021 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
20674040 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
20674058 AA-AAAT
1 AATAAAT
20674064 CAAATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:20676360 original size:158 final size:158
Alignment explanation
Indices: 20676066--20676546 Score: 773
Period size: 158 Copynumber: 3.0 Consensus size: 158
20676056 ATCTCTGTAT
* * * * *
20676066 CATGTAGTCCTCACACGAGTTGTGAAATGGGTCTGCTCACATGAGCTGTGGGTCAAGATGTTAGA
1 CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGA
** * * *
20676131 CTACACGATGCTGCTCACACGAGCTACGAAGAATCCGCAACATATGTCGGATCTCAGCCATTGGT
66 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGTCGGATCTCAACCATCGGT
*
20676196 AGGACATCTAAGACCAGTACCCATATAA
131 AGGACATCTAAGACCAGCACCCATATAA
* * *
20676224 CATGTAATGCTCACACGAGCTGTGAAGTGGGTCTGCTCACACGAGCTATGGGTCGAGATGTTACA
1 CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGA
** *
20676289 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCTACAACATATGTCGAATCTCAACCATCGGT
66 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGTCGGATCTCAACCATCGGT
* *
20676354 AAGACATTTAAGACCAGCACCCATATAA
131 AGGACATCTAAGACCAGCACCCATATAA
*
20676382 CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGCGTCGAGATGTTAGA
1 CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGA
*
20676447 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGCCGGATCTCAACCATCGGT
66 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGTCGGATCTCAACCATCGGT
20676512 AGGACATCTAAGACCAGCACCCATATAA
131 AGGACATCTAAGACCAGCACCCATATAA
20676540 CATGTAA
1 CATGTAA
20676547 ATCCCGAAAT
Statistics
Matches: 294, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 294 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (158 bp):
CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGA
CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGTCGGATCTCAACCATCGGT
AGGACATCTAAGACCAGCACCCATATAA
Found at i:20676676 original size:2 final size:2
Alignment explanation
Indices: 20676669--20676693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20676659 ATAAGCAATC
20676669 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
20676694 ATAAATGTAG
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:20682917 original size:21 final size:21
Alignment explanation
Indices: 20682891--20682943 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
20682881 ACCTGCAGTC
20682891 TTCTACCGATAGTAGGGAAAG
1 TTCTACCGATAGTAGGGAAAG
* *
20682912 TTCTACCCATAGTAGGGAGAG
1 TTCTACCGATAGTAGGGAAAG
20682933 TTCTACCGATA
1 TTCTACCGATA
20682944 CAAGTATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (21 bp):
TTCTACCGATAGTAGGGAAAG
Found at i:20683969 original size:158 final size:158
Alignment explanation
Indices: 20683675--20684079 Score: 623
Period size: 158 Copynumber: 2.6 Consensus size: 158
20683665 TATCATGTAG
* * *
20683675 TGCTTACACGAGCTGTGGAGAATCCGTAACATATGTCGGATCTCAGCCATC-AGTAGGACATCTA
1 TGCTCACACGAGCTGTGGAGAATCCGCAACATATGCCGGATCTCAGCCATCGA-TAGGACATCTA
* * *
20683739 AGACCAGCACCTATATAACATGTAATGCTCACACGAGTTGTGAAGTGGGTCTGCTCACACGAGCT
65 AGACCAGCACCTATATAACATGTAATGCTCACACGAGCTGTGAAGTGAGTCTACTCACACGAGCT
* *
20683804 GTGGGTCGAGATGTTAGACTACACGATAT
130 GTAGGTCGAGATGTTAGACTACACGATAC
* *
20683833 TGCTCACACGAGCTGTAGAGAATCCGCAACATATGCCGGATCTCAGCCATCGATAGGACATTTAA
1 TGCTCACACGAGCTGTGGAGAATCCGCAACATATGCCGGATCTCAGCCATCGATAGGACATCTAA
*
20683898 GACCAGCACCCATATAACATGTAATGCTCACACGAGCTGTGAAGTGAGTCTACTCACACGAGCTG
66 GACCAGCACCTATATAACATGTAATGCTCACACGAGCTGTGAAGTGAGTCTACTCACACGAGCTG
*
20683963 TAGGTCGAGATGTTAGACTACACGATGC
131 TAGGTCGAGATGTTAGACTACACGATAC
* * * ** * *
20683991 TGCTCACACGAGCTATGGATAATCTGCAACATATGCCAAATCTCAGCCATCGGTAGGTCATCTAA
1 TGCTCACACGAGCTGTGGAGAATCCGCAACATATGCCGGATCTCAGCCATCGATAGGACATCTAA
20684056 GACCAGCACCTATATAACATGTAA
66 GACCAGCACCTATATAACATGTAA
20684080 ATCCCGAAAT
Statistics
Matches: 224, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
158 223 1.00
159 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (158 bp):
TGCTCACACGAGCTGTGGAGAATCCGCAACATATGCCGGATCTCAGCCATCGATAGGACATCTAA
GACCAGCACCTATATAACATGTAATGCTCACACGAGCTGTGAAGTGAGTCTACTCACACGAGCTG
TAGGTCGAGATGTTAGACTACACGATAC
Found at i:20687903 original size:60 final size:60
Alignment explanation
Indices: 20687810--20687928 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
20687800 TTTCAGGTAG
* *
20687810 TTATAGGAAGGTTTTCTGCCTTTCCATATCTCATATGGTGTCTTGTCCTTTTTCTTGCTA
1 TTATAGGAAGGTTTTCTACCTTTCCATATCTCATATGGTGTCTTGTCCTTTTTATTGCTA
20687870 TTATAGGAAGGTTTTCTACCTTTCCATATCTCATATGGTGTCTTGTCCTTTTTATTGCT
1 TTATAGGAAGGTTTTCTACCTTTCCATATCTCATATGGTGTCTTGTCCTTTTTATTGCT
20687929 GGGTACTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (60 bp):
TTATAGGAAGGTTTTCTACCTTTCCATATCTCATATGGTGTCTTGTCCTTTTTATTGCTA
Found at i:20690356 original size:18 final size:18
Alignment explanation
Indices: 20690321--20690363 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
20690311 AATAAATATA
20690321 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
20690340 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
20690358 AA-AAAT
1 AATAAAT
20690364 CAAATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:20693344 original size:28 final size:27
Alignment explanation
Indices: 20693300--20693352 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20693290 TATTTGATAA
*
20693300 TAATTATATTATTTAAAAGAGTTTTTT
1 TAATTATATTATATAAAAGAGTTTTTT
* *
20693327 TAATATATTTTATATAAAATAGTTTT
1 TAAT-TATATTATATAAAAGAGTTTT
20693353 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (27 bp):
TAATTATATTATATAAAAGAGTTTTTT
Found at i:20694297 original size:83 final size:82
Alignment explanation
Indices: 20694073--20695158 Score: 907
Period size: 83 Copynumber: 13.4 Consensus size: 82
20694063 TTAAAAAAAA
* *
20694073 AATTTCTAATTTAGTTTACTTAATTTATACCATTAGTGATATACCAAAACTTCATTCA-TCATTC
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGGTATACC-AAACTTCATTCACT-ATTC
* * * *
20694137 CAAAAAAACCTTGATACATG
63 CAAACAAATCTTGATATACG
* * * * *
20694157 AACTTCTAATTTAATTTACTTAATTTATACCTTTAGTGGTATACCAAAACTTC-TTCACTATTCT
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGGTATACC-AAACTTCATTCACTATTCC
*
20694221 AAACAAATTTTGATATACG
64 AAACAAATCTTGATATACG
* *
20694240 AATTTCTAATTTAGTTTATTTAATTTATACAATAGTGATATACC-AACATAT-ATTTCACTATTC
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACCAAAC-T-TCA-TTCACTATTC
20694303 CAAACAAATCTTGATATACG
63 CAAACAAATCTTGATATACG
* * *
20694323 AATTGCTAATTTAATTTATTTAATTTATACTATTAGTGGTATATCAAAACTTCATTCACTATTCC
1 AATTTCTAATTTAGTTTATTTAATTTATAC-ATTAGTGGTATA-CCAAACTTCATTCACTATTCC
20694388 AAACAAATCTTGATATACG
64 AAACAAATCTTGATATACG
* * *
20694407 AACTTCTAATTTAGTTTATTTAATTTATATATTAGTGGTATATCAAAGCTTCATTCACTACTT-C
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACCAAA-CTTCATTCACTA-TTCC
*
20694471 AAACAAATCATGATATACG
64 AAACAAATCTTGATATACG
* * *
20694490 AACTTCTAATTTA----ATTT-A--TA-CCATTAGTGATATACCAAAACTTCATTCACTATTCCA
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACC-AAACTTCATTCACTATTCCA
* *
20694547 AACAAATCTTAATATACA
65 AACAAATCTTGATATACG
* * * *
20694565 AATTTTTAATTTAGTTTACTTAATTTATACCATTAGTGGTATACCAAACTTCATTCATTTTTCCA
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGGTATACCAAACTTCATTCACTATTCCA
*
20694630 AA-AAACCTTGATATACG
65 AACAAATCTTGATATACG
** * * * *
20694647 AATTTCTAATTTA---TA--CCA--T-TA-GTGA-T-GTA-CCAAAACTTCATTCACTATTCCAA
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACCAAACTTCATTCACTATTCCAA
*
20694700 ACAAATTTTGATATACG
66 ACAAATCTTGATATACG
* * * *
20694717 AATTTCTAATTTAATTTATTTGATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTT-A
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACC-AAACTTCATTCACTA-TTCC
* *
20694781 AAACAAATTTTGATGTACG
64 AAACAAATCTTGATATACG
* * * * * *
20694800 AACTTCTAATTTAATTTACTTAATTTATACCATTAGTGGTATACTAAAACTTCATTCATTATTTC
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGGTATAC-CAAACTTCATTCACTATTCC
* *
20694865 -AATAAATTTTGATATACG
64 AAACAAATCTTGATATACG
* * * * * * *
20694883 AACTTCTAATTTA----ATTT-A--TA-CCA-TAGTGATATGCCAAAACTTCATTCATTGTTTCA
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACC-AAACTTCATTCACTATTCCA
* **
20694939 AATAAATCTTGATATATA
65 AACAAATCTTGATATACG
* * * *
20694957 AATTTTTAATTTAGTTTACTTAATTTATACTATTAGTGGTATGCCAAAACTTCATTCATTATTTT
1 AATTTCTAATTTAGTTTATTTAATTTATAC-ATTAGTGGTATACC-AAACTTCATTCACTA---T
* * **
20695022 TTCAAATAAATCTTGATGCACG
61 TCCAAACAAATCTTGATATACG
* * * * * * * **
20695044 AATTTTTAATTTATTTTATTTAATTTATATCATAAATGATATGCCAAAACTTCATTCATTATTTT
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGGTATACC-AAACTTCATTCACTATTCC
* *
20695109 AAATAAATCTTAATATATC-
64 AAACAAATCTTGATATA-CG
** *
20695128 AGCTTCTAATTTAATTTATTTAATTTATACA
1 AATTTCTAATTTAGTTTATTTAATTTATACA
20695159 GTTATCGATA
Statistics
Matches: 837, Mismatches: 108, Indels: 115
0.79 0.10 0.11
Matches are distributed among these distances:
69 21 0.03
70 29 0.03
71 1 0.00
72 2 0.00
73 29 0.03
74 32 0.04
75 54 0.06
76 7 0.01
77 2 0.00
78 7 0.01
79 15 0.02
80 5 0.01
81 6 0.01
82 44 0.05
83 272 0.32
84 230 0.27
85 4 0.00
86 3 0.00
87 73 0.09
88 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (82 bp):
AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGGTATACCAAACTTCATTCACTATTCCAA
ACAAATCTTGATATACG
Found at i:20694394 original size:167 final size:166
Alignment explanation
Indices: 20694073--20695157 Score: 1053
Period size: 167 Copynumber: 6.7 Consensus size: 166
20694063 TTAAAAAAAA
*
20694073 AATTTCTAATTTAGTTTACTTAATTTATACCATTAGTGATATACCAAAACTTCATTCA-TCATTC
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGATATACCAAAACTTCATTCACT-ATTC
* * * * * *
20694137 CAAAAAAACCTTGATACATGAACTTCTAATTTAATTTACTTAATTTATACCTTTAGTGGTATACC
64 CAAACAAATCTTGATATACGAA-TTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACC
* *
20694202 AAAACTTC-TTCACTATTCTAAACAAATTTTGATATACG
128 AAAACTTCATTCACTATTCCAAACAAATCTTGATATACG
* *
20694240 AATTTCTAATTTAGTTTATTTAATTTATACAATAGTGATATACCAACA-TAT-ATTTCACTATTC
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGATATACCAAAACT-TCA-TTCACTATTC
* *
20694303 CAAACAAATCTTGATATACGAATTGCTAATTTAATTTATTTAATTTATACTATTAGTGGTATATC
64 CAAACAAATCTTGATATACGAATT-CTAATTTAATTTATTTAATTTATACCATTAGTGGTATACC
20694368 AAAACTTCATTCACTATTCCAAACAAATCTTGATATACG
128 AAAACTTCATTCACTATTCCAAACAAATCTTGATATACG
* * * * *
20694407 AACTTCTAATTTAGTTTATTTAATTTATATATTAGTGGTATATCAAAGCTTCATTCACTACTT-C
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGATATACCAAAACTTCATTCACTA-TTCC
* * *
20694471 AAACAAATCATGATATACGAA--CT--TCT-A---ATTTAATTTATACCATTAGTGATATACCAA
65 AAACAAATCTTGATATACGAATTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACCAA
* *
20694528 AACTTCATTCACTATTCCAAACAAATCTTAATATACA
130 AACTTCATTCACTATTCCAAACAAATCTTGATATACG
* * * * *
20694565 AATTTTTAATTTAGTTTACTTAATTTATACCATTAGTGGTATACC-AAACTTCATTCATTTTTCC
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGATATACCAAAACTTCATTCACTATTCC
* * * *
20694629 AAA-AAACCTTGATATACG-----------AA-TT-TCTAATTTATACCATTAGTGATGTACCAA
65 AAACAAATCTTGATATACGAATTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACCAA
*
20694680 AACTTCATTCACTATTCCAAACAAATTTTGATATACG
130 AACTTCATTCACTATTCCAAACAAATCTTGATATACG
* * * * *
20694717 AATTTCTAATTTAATTTATTTGATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTT-A
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGATATACCAAAACTTCATTCACTA-TTCC
* * * *
20694781 AAACAAATTTTGATGTACGAACTTCTAATTTAATTTACTTAATTTATACCATTAGTGGTATACTA
65 AAACAAATCTTGATATACGAA-TTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACCA
* * * *
20694846 AAACTTCATTCATTATTTC-AATAAATTTTGATATACG
129 AAACTTCATTCACTATTCCAAACAAATCTTGATATACG
* * * * * *
20694883 AACTTCTAATTTA----ATTT-A--TA-CCA-TAGTGATATGCCAAAACTTCATTCATTGTTTCA
1 AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGATATACCAAAACTTCATTCACTATTCCA
* ** * * * * *
20694939 AATAAATCTTGATATATAAATTTTTAATTTAGTTTACTTAATTTATACTATTAGTGGTATGCCAA
66 AACAAATCTTGATATACGAA-TTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACCAA
* * * **
20695004 AACTTCATTCATTATTTTTTCAAATAAATCTTGATGCACG
130 AACTTCATTCACTA---TTCCAAACAAATCTTGATATACG
* * * * * * **
20695044 AATTTTTAATTTATTTTATTTAATTTATATCATAAATGATATGCCAAAACTTCATTCATTATTTT
1 AATTTCTAATTTAGTTTATTTAATTTATA-CATTAGTGATATACCAAAACTTCATTCACTATTCC
* * *
20695109 AAATAAATCTTAATATATC-AGCTTCTAATTTAATTTATTTAATTTATAC
65 AAACAAATCTTGATATA-CGA-ATTCTAATTTAATTTATTTAATTTATAC
20695158 AGTTATCGAT
Statistics
Matches: 775, Mismatches: 96, Indels: 90
0.81 0.10 0.09
Matches are distributed among these distances:
151 16 0.02
152 101 0.13
153 14 0.02
156 2 0.00
157 107 0.14
158 106 0.14
159 15 0.02
160 4 0.01
161 28 0.04
162 6 0.01
164 2 0.00
165 10 0.01
166 120 0.15
167 167 0.22
168 6 0.01
170 2 0.00
171 69 0.09
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (166 bp):
AATTTCTAATTTAGTTTATTTAATTTATACATTAGTGATATACCAAAACTTCATTCACTATTCCA
AACAAATCTTGATATACGAATTCTAATTTAATTTATTTAATTTATACCATTAGTGGTATACCAAA
ACTTCATTCACTATTCCAAACAAATCTTGATATACG
Found at i:20694596 original size:84 final size:82
Alignment explanation
Indices: 20694500--20694659 Score: 239
Period size: 84 Copynumber: 1.9 Consensus size: 82
20694490 AACTTCTAAT
*
20694500 TTAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAATCTTAATATACA
1 TTAATTTATACCATTAGTGATATACC-AAACTTCATTCACTATTCCAAA-AAACCTTAATATACA
*
20694565 AATTTTTAATTTAGTTTAC
64 AATTTCTAATTTAGTTTAC
* * * * *
20694584 TTAATTTATACCATTAGTGGTATACCAAACTTCATTCATTTTTCCAAAAAACCTTGATATACGAA
1 TTAATTTATACCATTAGTGATATACCAAACTTCATTCACTATTCCAAAAAACCTTAATATACAAA
20694649 TTTCTAATTTA
66 TTTCTAATTTA
20694660 TACCATTAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 24 0.35
83 20 0.29
84 25 0.36
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.41
Consensus pattern (82 bp):
TTAATTTATACCATTAGTGATATACCAAACTTCATTCACTATTCCAAAAAACCTTAATATACAAA
TTTCTAATTTAGTTTAC
Found at i:20694669 original size:68 final size:70
Alignment explanation
Indices: 20694585--20694729 Score: 222
Period size: 70 Copynumber: 2.1 Consensus size: 70
20694575 TTAGTTTACT
* * *
20694585 TAATTTATACCATTAGTGGTATACC-AAACTTCATTCATTTTTCCAAA-AAACCTTGATATACGA
1 TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAACCTTGATATACGA
20694648 ATTTC
66 ATTTC
* **
20694653 TAATTTATACCATTAGTGATGTACCAAAACTTCATTCACTATTCCAAACAAATTTTGATATACGA
1 TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAACCTTGATATACGA
20694718 ATTTC
66 ATTTC
20694723 TAATTTA
1 TAATTTA
20694730 ATTTATTTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
68 23 0.33
69 20 0.29
70 26 0.38
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (70 bp):
TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAACCTTGATATACGA
ATTTC
Found at i:20694824 original size:235 final size:235
Alignment explanation
Indices: 20694073--20695125 Score: 921
Period size: 250 Copynumber: 4.3 Consensus size: 235
20694063 TTAAAAAAAA
* * * * *
20694073 AATTTCTAATTTAGTTTACTTAATTTATACCATTAGTGATATACCAAAACTTCATTCATCATTCC
1 AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATACC-AAACTTCATTCATTATTTC
* * * *
20694138 AAAAAAACCTTGATACATGAACTTCTAATTTAATTTACTTAATTTATACCTTTAGTGGTATACCA
65 -AAAAAACCTTGATATACGAAC-TC-----T-A--T-C-TAATTTATACCATTAGTGATATACCA
* *
20694203 AAACTTC-TTCACTATTCTAAACAAATTTTGATATACGAATTTCTAATTTAGTTTATTTAATTTA
118 AAACTTCATTCACTATTC-AAACAAATCTTGATATACGAATTTCTAATTTAATTTATTT-ATTTA
* * * *
20694267 TACAATAGTGATATACCAACA-TAT-ATTTCACTATTCCAAACAAATCTTGATATACG
181 TACATTAGTGGTATACCAAAACT-TCA-TTCACTATT-CAAACAAATCTTGATGTACG
** * * * * *
20694323 AATTGCTAATTTAATTTATTTAATTTATACTATTAGTGGTATATCAAAACTTCATTCACTATTCC
1 AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATA-CCAAACTTCATTCATTATTTC
* * ** * *
20694388 AAACAAATCTTGATATACGAACTTCTAATTTAGTTTATTTAATTTATATATTAGTGGTATATCAA
65 AAA-AAACCTTGATATACGAAC-TCT-ATCTA----ATTT-A--TA-CCATTAGTGATATACCAA
* * * *
20694453 AGCTTCATTCACTACTTCAAACAAATCATGATATACGAACTTCTAATTT-A---ATTTA--TA-C
119 AACTTCATTCACTA-TTCAAACAAATCTTGATATACGAATTTCTAATTTAATTTATTTATTTATA
* * * *
20694511 CATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAATCTTAATATACA
183 CATTAGTGGTATACCAAAACTTCATTCACTATT-CAAACAAATCTTGATGTACG
*
20694565 AATTTTTAATTTAGTTTACTTAATTTATACCATTAGTGGTATACCAAACTTCATTCATT-TTTCC
1 AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATACCAAACTTCATTCATTATTT-C
*
20694629 AAAAAACCTTGATATACGAA-T-T-TCTAATTTATACCATTAGTGATGTACCAAAACTTCATTCA
65 AAAAAACCTTGATATACGAACTCTATCTAATTTATACCATTAGTGATATACCAAAACTTCATTCA
*
20694691 CTATTCCAAACAAATTTTGATATACGAATTTCTAATTTAATTTATTTGATTTATACATTAGTGGT
130 CTATT-CAAACAAATCTTGATATACGAATTTCTAATTTAATTTATTT-ATTTATACATTAGTGGT
* * *
20694756 ATACCAAAACTCCATTCACTACTTAAAACAAATTTTGATGTACG
193 ATACCAAAACTTCATTCACTA-TTCAAACAAATCTTGATGTACG
* * *
20694800 AACTTCTAATTTAATTTACTTAATTTATACCATTAGTGGTATACTAAAACTTCATTCATTATTTC
1 AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATAC-CAAACTTCATTCATTATTTC
* ** * *
20694865 AATAAATTTTGATATACGAACTTCTAATTTAATTTATACCA-TAGTGATATGCCAAAACTTCATT
65 AAAAAACCTTGATATACGAAC-TCT-ATCTAATTTATACCATTAGTGATATACCAAAACTTCATT
* * * ** * * *
20694929 CATTGTTTCAAATAAATCTTGATATATAAATTTTTAATTTAGTTTACTTAATTTATACTATTAGT
128 CACT-ATTCAAACAAATCTTGATATACGAATTTCTAATTTAATTTA-TTTATTTATAC-ATTAGT
* * * *
20694994 GGTATGCCAAAACTTCATTCATTATTTTTTCAAATAAATCTTGATGCACG
190 GGTATACCAAAACTTCATTCACTA----TTCAAACAAATCTTGATGTACG
* * * * * * * *
20695044 AATTTTTAATTTATTTTATTTAATTTATATCATAAATGATATGCCAAAACTTCATTCATTATTTT
1 AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATACC-AAACTTCATTCATTATTTC
* *
20695109 AAATAAATCTTAATATA
65 AAA-AAACCTTGATATA
20695126 TCAGCTTCTA
Statistics
Matches: 669, Mismatches: 94, Indels: 85
0.79 0.11 0.10
Matches are distributed among these distances:
226 2 0.00
227 55 0.08
228 3 0.00
230 1 0.00
231 8 0.01
232 1 0.00
234 2 0.00
235 88 0.13
236 34 0.05
237 4 0.01
238 2 0.00
239 1 0.00
240 82 0.12
241 64 0.10
242 84 0.13
243 5 0.01
244 73 0.11
245 19 0.03
246 5 0.01
248 2 0.00
249 22 0.03
250 108 0.16
251 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (235 bp):
AATTTTTAATTTAATTTACTTAATTTATACCATTAGTGGTATACCAAACTTCATTCATTATTTCA
AAAAACCTTGATATACGAACTCTATCTAATTTATACCATTAGTGATATACCAAAACTTCATTCAC
TATTCAAACAAATCTTGATATACGAATTTCTAATTTAATTTATTTATTTATACATTAGTGGTATA
CCAAAACTTCATTCACTATTCAAACAAATCTTGATGTACG
Found at i:20694929 original size:157 final size:164
Alignment explanation
Indices: 20694653--20695157 Score: 459
Period size: 157 Copynumber: 3.1 Consensus size: 164
20694643 TACGAATTTC
* * * *
20694653 TAATTTATACCATTAGTGATGTACCAAAACTTCATTCACTATTCCAAACAAATTTTGATATACGA
1 TAATTTATACCATTAGTGGTATACCAAAACTTCATTCATTATTTCAAACAAATTTTGATATACGA
* *
20694718 ATTTCTAATTTAATTTATTTGATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTTAAA
66 ACTTCTAATTTAA--TATTTGA-TTATACATTAGTGATATACCAAAACTCCATTCACTACTTAAA
* * *
20694783 ACAAATTTTGATGTACGAACTTCTAATTTAATTTACT
128 ACAAATCTTGATATACAAACTTCTAATTTAATTTACT
* *
20694820 TAATTTATACCATTAGTGGTATACTAAAACTTCATTCATTATTTC-AATAAATTTTGATATACGA
1 TAATTTATACCATTAGTGGTATACCAAAACTTCATTCATTATTTCAAACAAATTTTGATATACGA
* * * * ** * *
20694884 ACTTCTAATTT-A-ATTT-A-TA-CCA-TAGTGATATGCCAAAACTTCATTCATTGTTTCAAATA
66 ACTTCTAATTTAATATTTGATTATACATTAGTGATATACCAAAACTCCATTCACTACTTAAAACA
* * * *
20694943 AATCTTGATATATAAATTTTTAATTTAGTTTACT
131 AATCTTGATATACAAACTTCTAATTTAATTTACT
* * * * **
20694977 TAATTTATACTATTAGTGGTATGCCAAAACTTCATTCATTATTTTTTCAAATAAATCTTGATGCA
1 TAATTTATACCATTAGTGGTATACCAAAACTTCATTCATTA---TTTCAAACAAATTTTGATATA
* * * * * * * * * *
20695042 CGAATTTTTAATTTATTTTATTTAATTTATATCATAAATGATATGCCAAAACTTCATTCATTATT
63 CGAACTTCTAATTTA--ATATTTGA-TTATA-CATTAGTGATATACCAAAACTCCATTCACTACT
* * * * *
20695107 TTAAATAAATCTTAATATATC-AGCTTCTAATTTAATTTATT
124 TAAAACAAATCTTGATATA-CAAACTTCTAATTTAATTTACT
20695148 TAATTTATAC
1 TAATTTATAC
20695158 AGTTATCGAT
Statistics
Matches: 279, Mismatches: 44, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
157 94 0.34
158 2 0.01
159 2 0.01
160 4 0.01
161 26 0.09
162 4 0.01
165 5 0.02
166 29 0.10
167 40 0.14
168 2 0.01
170 2 0.01
171 69 0.25
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (164 bp):
TAATTTATACCATTAGTGGTATACCAAAACTTCATTCATTATTTCAAACAAATTTTGATATACGA
ACTTCTAATTTAATATTTGATTATACATTAGTGATATACCAAAACTCCATTCACTACTTAAAACA
AATCTTGATATACAAACTTCTAATTTAATTTACT
Found at i:20694952 original size:310 final size:305
Alignment explanation
Indices: 20694343--20694969 Score: 764
Period size: 310 Copynumber: 2.0 Consensus size: 305
20694333 TTAATTTATT
* * *
20694343 TAATTTATACTATTAGTGGTATATCAAAACTTCATTCACTATTCCAAACAAATCTTGATATACGA
1 TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAATCTTGATATACGA
* * * * * *
20694408 ACTTCTAATTTAGTTTATTTAATTTATATATTAGTGGTATATCAAAGCTTCATTCACTACTTCAA
66 ACTTCTAATTTAATTTATTTAATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTTAAA
20694473 ACAAATCATGATATACGAACTTCTAATTTAATTTATACCATTAGTGATATACCAAAACTTCATTC
131 ACAAATCATGATATACGAACTTCTAATTTAATTTATACCATTAGTGATATACCAAAACTTCATTC
* *
20694538 ACTATTCCAAACAAATCTTAATATACAAATTTTTAATTTAGTTTACTTAATTTATACCATTAGTG
196 ACTATTCCAAACAAATCTTAATATACAAACTTCTAA--TA--TTA-TTAATTTATACCATTAGTG
* *
20694603 GTATACCAAACTTCATTCATTTTTCCAAAAAACCTTGATATACGAATTTC
256 ATATACCAAACTTCATTCATTTTTCCAAAAAACCTTGATATACAAATTTC
* *
20694653 TAATTTATACCATTAGTGATGTACCAAAACTTCATTCACTATTCCAAACAAATTTTGATATACGA
1 TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAATCTTGATATACGA
* *
20694718 ATTTCTAATTTAATTTATTTGATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTTAAA
66 ACTTCTAATTTAATTTATTTAATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTTAAA
** * * *
20694783 ACAAATTTTGATGTACGAACTTCTAATTTAATTTACTTAATTTATACCATTAGTGGTATACTAAA
131 ACAAATCATGATATACGAACTTC-----TAA--T--TTAATTTATACCATTAGTGATATACCAAA
* * * * * *
20694848 ACTTCATTCATTATTTC-AATAAATTTTGATATACGAACTTCT-A-A-T-TTAATTTATACCA-T
187 ACTTCATTCACTATTCCAAACAAATCTTAATATACAAACTTCTAATATTATTAATTTATACCATT
* * * *
20694907 AGTGATATGCCAAAACTTCATTCATTGTTT-CAAATAAATCTTGATATATAAATTTT
252 AGTGATATACC-AAACTTCATTCATT-TTTCCAAA-AAACCTTGATATACAAATTTC
20694963 TAATTTA
1 TAATTTA
20694970 GTTTACTTAA
Statistics
Matches: 273, Mismatches: 32, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
308 10 0.04
309 31 0.11
310 164 0.60
311 1 0.00
314 1 0.00
315 3 0.01
317 2 0.01
318 19 0.07
319 42 0.15
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.41
Consensus pattern (305 bp):
TAATTTATACCATTAGTGATATACCAAAACTTCATTCACTATTCCAAACAAATCTTGATATACGA
ACTTCTAATTTAATTTATTTAATTTATACATTAGTGGTATACCAAAACTCCATTCACTACTTAAA
ACAAATCATGATATACGAACTTCTAATTTAATTTATACCATTAGTGATATACCAAAACTTCATTC
ACTATTCCAAACAAATCTTAATATACAAACTTCTAATATTATTAATTTATACCATTAGTGATATA
CCAAACTTCATTCATTTTTCCAAAAAACCTTGATATACAAATTTC
Found at i:20695011 original size:84 final size:84
Alignment explanation
Indices: 20694891--20695157 Score: 322
Period size: 87 Copynumber: 3.2 Consensus size: 84
20694881 CGAACTTCTA
* *
20694891 ATTTAATTTATACCA-TAGTGATATGCCAAAACTTCATTCATTGTTTCAAATAAATCTTGATATA
1 ATTTAATTTATACTATTAGTGATATGCCAAAACTTCATTCATTATTTCAAATAAATCTTGATATA
*
20694955 TAAATTTTTAATTTAGTTT
66 TAAATTTTTAATTTAATTT
* *
20694974 ACTTAATTTATACTATTAGTGGTATGCCAAAACTTCATTCATTATTTTTTCAAATAAATCTTGAT
1 ATTTAATTTATACTATTAGTGATATGCCAAAACTTCATTCATTA---TTTCAAATAAATCTTGAT
** ** *
20695039 GCACGAATTTTTAATTTATTTT
63 ATATAAATTTTTAATTTAATTT
* * * *
20695061 ATTTAATTTATA-TCATAAATGATATGCCAAAACTTCATTCATTATTTTAAATAAATCTTAATAT
1 ATTTAATTTATACT-ATTAGTGATATGCCAAAACTTCATTCATTATTTCAAATAAATCTTGATAT
* ** *
20695125 ATCAGCTTCTAATTTAATTT
65 ATAAATTTTTAATTTAATTT
20695145 ATTTAATTTATAC
1 ATTTAATTTATAC
20695158 AGTTATCGAT
Statistics
Matches: 155, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
83 13 0.08
84 68 0.44
86 1 0.01
87 73 0.47
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (84 bp):
ATTTAATTTATACTATTAGTGATATGCCAAAACTTCATTCATTATTTCAAATAAATCTTGATATA
TAAATTTTTAATTTAATTT
Found at i:20695169 original size:84 final size:82
Alignment explanation
Indices: 20694891--20695169 Score: 310
Period size: 84 Copynumber: 3.3 Consensus size: 82
20694881 CGAACTTCTA
* *
20694891 ATTTAATTTATACCA-TAGTGATATGCCAAAACTTCATTCATTGTTTCAAATAAATCTTGATATA
1 ATTTAATTTATA-CATTA-TGATATGCCAAAACTTCATTCATTATTTTAAATAAATCTTGATATA
* *
20694955 TAAATTTTTAATTTAGTTT
64 TCAATTTTTAATTTAATTT
* *
20694974 ACTTAATTTATACTATTAGTGGTATGCCAAAACTTCATTCATTATTTTTTCAAATAAATCTTGAT
1 ATTTAATTTATAC-ATTA-TGATATGCCAAAACTTCATTCATTA--TTTT-AAATAAATCTTGAT
** *
20695039 GCA-CGAATTTTTAATTTATTTT
61 ATATC-AATTTTTAATTTAATTT
* *
20695061 ATTTAATTTATATCATAAATGATATGCCAAAACTTCATTCATTATTTTAAATAAATCTTAATATA
1 ATTTAATTTATA-CAT-TATGATATGCCAAAACTTCATTCATTATTTTAAATAAATCTTGATATA
** *
20695126 TCAGCTTCTAATTTAATTT
64 TCAATTTTTAATTTAATTT
20695145 ATTTAATTTATACAGTTATCGATAT
1 ATTTAATTTATACA-TTAT-GATAT
20695170 TTAATAAATT
Statistics
Matches: 166, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
82 1 0.01
83 16 0.10
84 71 0.43
85 5 0.03
86 3 0.02
87 68 0.41
88 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.46
Consensus pattern (82 bp):
ATTTAATTTATACATTATGATATGCCAAAACTTCATTCATTATTTTAAATAAATCTTGATATATC
AATTTTTAATTTAATTT
Found at i:20695617 original size:17 final size:17
Alignment explanation
Indices: 20695595--20695627 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20695585 AATATTTTTC
20695595 TTTA-TTATTATTTCATA
1 TTTATTTATT-TTTCATA
20695612 TTTATTTATTTTTCAT
1 TTTATTTATTTTTCAT
20695628 TGGCTTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTTTCATA
Found at i:20708448 original size:12 final size:12
Alignment explanation
Indices: 20708431--20708457 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20708421 GCTGTGGTAA
20708431 AGTTTTGAGTTG
1 AGTTTTGAGTTG
20708443 AGTTTTGAGTTG
1 AGTTTTGAGTTG
20708455 AGT
1 AGT
20708458 GGTGATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (12 bp):
AGTTTTGAGTTG
Found at i:20715690 original size:24 final size:24
Alignment explanation
Indices: 20715653--20715702 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
20715643 CTCACCCTCT
* * *
20715653 TCTTTGTGCTTCTTCTTCTTTTTA
1 TCTTTGCGCCTCTTCCTCTTTTTA
20715677 TCTTTGCGCCTCTTCCTCTTTTTA
1 TCTTTGCGCCTCTTCCTCTTTTTA
20715701 TC
1 TC
20715703 CGTCGAACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.28, G:0.08, T:0.60
Consensus pattern (24 bp):
TCTTTGCGCCTCTTCCTCTTTTTA
Found at i:20732219 original size:17 final size:17
Alignment explanation
Indices: 20732190--20732222 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20732180 AAACTTTGCT
20732190 TTTATTTTCTATTTTAG
1 TTTATTTTCTATTTTAG
20732207 TTTATCTTT-TATTTTA
1 TTTAT-TTTCTATTTTA
20732223 TACCTTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATTTTCTATTTTAG
Found at i:20735310 original size:26 final size:26
Alignment explanation
Indices: 20735267--20735320 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
20735257 TTCTGGGCGC
* * *
20735267 AACTCTGGACATGCTCATACAGTGAT
1 AACTCTGAACATACTCATACAGCGAT
* *
20735293 AACTCTGAACATATTCATGCAGCGAT
1 AACTCTGAACATACTCATACAGCGAT
20735319 AA
1 AA
20735321 TTCTAGACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (26 bp):
AACTCTGAACATACTCATACAGCGAT
Found at i:20737946 original size:21 final size:21
Alignment explanation
Indices: 20737922--20737961 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20737912 AAGTGAAAAG
20737922 AACA-AAAAGAAAATGAGTACA
1 AACACAAAAGAAAA-GAGTACA
20737943 AACACAAAAGAAAAGAGTA
1 AACACAAAAGAAAAGAGTA
20737962 AGAAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.68, C:0.10, G:0.15, T:0.07
Consensus pattern (21 bp):
AACACAAAAGAAAAGAGTACA
Found at i:20739736 original size:12 final size:12
Alignment explanation
Indices: 20739715--20739750 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
20739705 CAAACTTTGC
20739715 TTTTATTTTATG
1 TTTTATTTTATG
* *
20739727 TTTTAGTTTATC
1 TTTTATTTTATG
20739739 TTTTATTTTATG
1 TTTTATTTTATG
20739751 CCTTCGAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (12 bp):
TTTTATTTTATG
Found at i:20743144 original size:3 final size:3
Alignment explanation
Indices: 20743136--20743192 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
20743126 ATGGGCTCAA
* * * * *
20743136 ATT ATT ATT ATC ATC ATT ATT CTT ATT CTT ATT ATT CTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20743184 ATT ATT ATT
1 ATT ATT ATT
20743193 TTAAATTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:20744139 original size:153 final size:150
Alignment explanation
Indices: 20743642--20744142 Score: 675
Period size: 153 Copynumber: 3.3 Consensus size: 150
20743632 TTTTAAAACA
* *
20743642 ATTTCGAAATAAAA-TCTTTGATTTTTTTAAGCAAAATAGTGAGTTTCTTTAAAAAAAA-AGAAA
1 ATTTCGAAATAAAAGT-TTGGA--TTTTTAAGCAAAATAGTGATTTTCTTTAAAAAAAAGAGAAA
* * *
20743705 GTTTAGATTTTTTAAAAATAAAAATCTCTTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTA
63 GTTTAGATTTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTA
* *
20743770 ACAAAGTTTTGATTTTTTTCTAAAT
128 ACAAAATTTTGA--TTTTTCTAACT
* * ** *
20743795 ATTTTGAAATAAAAGTTTGGATTTTTAAGAAAAATAACGACTTTCTTTAAAAAAAAGAGAAAGTT
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCTTTAAAAAAAAGAGAAAGTT
*
20743860 TAGATTTTTTAAAAAATAAAAATCTATTTTTTAGTTATTATAAAGAAAAAGTTTAAATTTTTAAC
66 TAGA-TTTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAC
*
20743925 AAACTTTTGATTTTTCTAACT
130 AAAATTTTGATTTTTCTAACT
* *
20743946 ATTTCGAAACAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCTTTAAAAAAAAAAGAGAAAG
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCTTT--AAAAAAAAGAGAAAG
* *
20744011 TTTAGATTTTAAAAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
64 TTTAGATTTT--TAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
* ** *
20744076 AAAAAAAAATTGATTTTT-TAACC
127 AACAAAATTTTGATTTTTCTAACT
* *
20744099 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTT
20744143 TGTTTAATCA
Statistics
Matches: 310, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
151 82 0.26
152 16 0.05
153 147 0.47
154 65 0.21
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (150 bp):
ATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCTTTAAAAAAAAGAGAAAGTT
TAGATTTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACA
AAATTTTGATTTTTCTAACT
Found at i:20745602 original size:243 final size:238
Alignment explanation
Indices: 20745179--20745654 Score: 756
Period size: 243 Copynumber: 2.0 Consensus size: 238
20745169 AAAATCATAA
*
20745179 TAATGATAAAACATTGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAACATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* * *
20745244 TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAATT
66 TTAGGCTTTTTTTAGAATTCTAAAATAGAATAAATTTTAAGAATTGAAAGTATTTTACTAGAATT
* *
20745309 ATTTAGGTATCCTTTATGGTTCTTATTAGGAATAAAAACCTTTAATTTAAGTTTTAAATTAGTTA
131 ATTTAGGTATCATTTATGGTTCTTATTAGGAATAAAAACCTTTAATTTAAGTTTTAAATTAGATA
* *
20745374 AGTTTGGTGAACACGTTTTAGTCAAGTTACAAGTAAATCGAAG
196 AGTTTGGTGAACACGTCTTAATCAAGTTACAAGTAAATCGAAG
* *
20745417 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAAAAA
1 TAATGATAAAACATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGT---AA
* * *
20745482 TTTTTTTAGGGTTTTTTTATAATTCTAAAATAGAATAAATTTTAAGAATTGAAAGTATTTTACTA
63 --CTTTTAGGCTTTTTTTAGAATTCTAAAATAGAATAAATTTTAAGAATTGAAAGTATTTTACTA
* *
20745547 GAATTATTTAGGTATCATTTA-GTGTTCTTATTAGGAGTAAAAATCTTTAATTTAAGTTTTAAAT
126 GAATTATTTAGGTATCATTTATG-GTTCTTATTAGGAATAAAAACCTTTAATTTAAGTTTTAAAT
20745611 TAGATAAGTTTGGTGAACACGTCTTAATCAAGTTACAAGTAAAT
190 TAGATAAGTTTGGTGAACACGTCTTAATCAAGTTACAAGTAAAT
20745655 TGGAGGCATT
Statistics
Matches: 217, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
238 57 0.26
241 2 0.01
242 1 0.00
243 157 0.72
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (238 bp):
TAATGATAAAACATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGCTTTTTTTAGAATTCTAAAATAGAATAAATTTTAAGAATTGAAAGTATTTTACTAGAATT
ATTTAGGTATCATTTATGGTTCTTATTAGGAATAAAAACCTTTAATTTAAGTTTTAAATTAGATA
AGTTTGGTGAACACGTCTTAATCAAGTTACAAGTAAATCGAAG
Found at i:20758207 original size:42 final size:42
Alignment explanation
Indices: 20757626--20758203 Score: 831
Period size: 42 Copynumber: 13.8 Consensus size: 42
20757616 AAGGAAAGCA
*
20757626 TTCATTGGATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
20757668 TTCATCGCATTGAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
20757710 TTCATTGCATTTAGAGGCCCAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
20757752 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
20757794 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
20757836 TTCATTACATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
20757878 TTCATTGCATTCAGAGGCCCAGGTGTAGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
20757920 TTC-TTCGCATTCAGAAGTCCAGGTGTGGAGGCCCATTTACTT
1 TTCATT-GCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
20757962 TTCATTGCATTCATAGGCCCAAGTGTGGAGGTCCATCTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
20758004 TTCTTTGCATTTAGAGGCCTAGGTGTGGAGG-CCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
20758045 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
20758087 TTCATTGCATTTAGAGGCCTAGGTGTGGTGGAT-CATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGG-TCCATTTACTT
* *
20758129 TTCATTACATTTAGAGGCTCAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * *
20758171 TTTATTGCATTTAGAGGCCTAGGGGTAGAGGTC
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC
20758204 TATTCATTTA
Statistics
Matches: 478, Mismatches: 51, Indels: 13
0.88 0.09 0.02
Matches are distributed among these distances:
41 41 0.09
42 433 0.91
43 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Done.