Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 7 of 425
Found at i:1878714 original size:73 final size:73
Alignment explanation
Indices: 1878594--1878830 Score: 260
Period size: 73 Copynumber: 3.1 Consensus size: 73
1878584 TAATTTCTGT
* * *
1878594 TTTTCAA-TTATGCTTTTCAAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTCAATTTATG--TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACA
*
1878658 TGCCGAGGTA
64 CGCCGAGGTA
* * *
1878668 TTTTCAATTTATGTTTCAAGAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
*
1878733 CTGAGGTA
66 CCGAGGTA
* * * * *
1878741 TTTTCAATTCCTGTTTTTTTTAAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGG
1 TTTTCAA----T-TTATGTTT-CAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
1878806 TCACACGCCGAGGTT
59 TCACACGCCGAGGTA
1878821 TTTTCAATTT
1 TTTTCAATTT
1878831 CTATTTTTCA
Statistics
Matches: 137, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
73 59 0.43
74 7 0.05
75 7 0.05
76 1 0.01
77 1 0.01
78 6 0.04
79 4 0.03
80 52 0.38
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (73 bp):
TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
CCGAGGTA
Found at i:1878716 original size:248 final size:243
Alignment explanation
Indices: 1878358--1878921 Score: 675
Period size: 248 Copynumber: 2.3 Consensus size: 243
1878348 AATTTCTGTC
* *
1878358 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAT-ACGCTGAGGTAATTT
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACGCTGAGGTATTTT
* * * **
1878422 CAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TAG-GGCACGCT
65 CAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACGCT
1878485 GAGGTATTTTCAATTTCTGCTTTCCAATTTCTGCTTTTCAAAAAAA-TCAACTCATATTGCGAGA
130 GAGGTATTTTCAA-TTC--C--T---ATTT-T--TTTT-AAAAAAAGTCAACTCATATTGCGAGA
* * * *
1878549 GGTGAGTTGAGCCTCAGG-AAACGCTGAGGTATTTTT-AATTTCTGTTTTTCAA-TTATGCT
183 GGCGAGTTGAGCCTCAGGCAAACGCCGAGGT-TTTTTCAATTTCTATTTTTCAATTTATACT
* * *
1878608 TTTC-AAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGTCACATGCCGAGGTATTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCAC--GCTGAGGTATTT
*
1878671 TCAATTTATG-TT-TCAAGAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACGC
64 TCAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACGC
* *
1878734 TGAGGTATTTTCAATTCCTGTTTTTTTTAAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAG
129 TGAGGTATTTTCAATTCCTATTTTTTTTAAAAAAAGTCAACTCATATTGCGAGAGGCGAGTTGAG
* *
1878799 CCTCAGGTCACACGCCGAGGTTTTTTCAATTTCTATTTTTCAATTTCTACT
194 CCTCAGG-CAAACGCCGAGGTTTTTTCAATTTCTATTTTTCAATTTATACT
* *
1878850 TTTCAAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATT
1 TTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACGCTGAGGTATT
1878914 TTCAATTT
63 TTCAATTT
1878922 CTGCTTTTCA
Statistics
Matches: 275, Mismatches: 24, Indels: 36
0.82 0.07 0.11
Matches are distributed among these distances:
238 7 0.03
239 38 0.14
240 5 0.02
241 26 0.09
242 12 0.04
244 18 0.07
245 1 0.00
246 38 0.14
247 6 0.02
248 75 0.27
249 7 0.03
250 42 0.15
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (243 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACGCTGAGGTATTTTC
AATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACGCTG
AGGTATTTTCAATTCCTATTTTTTTTAAAAAAAGTCAACTCATATTGCGAGAGGCGAGTTGAGCC
TCAGGCAAACGCCGAGGTTTTTTCAATTTCTATTTTTCAATTTATACT
Found at i:1878825 original size:80 final size:80
Alignment explanation
Indices: 1878690--1878838 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
1878680 GTTTCAAGAA
* * *
1878690 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGTCACACGCTGAGGTATTTTCAATTCCTGT
1 TCAACTCATATTGCGAGAGACGAGTTGAGCCTCAAGTCACACGCCGAGGTATTTTCAATTCCTAT
1878755 TTTTTTTAAAAAAAG
66 TTTTTTTAAAAAAAG
* * * * *
1878770 TCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTTTTTTCAATTTCTAT
1 TCAACTCATATTGCGAGAGACGAGTTGAGCCTCAAGTCACACGCCGAGGTATTTTCAATTCCTAT
1878835 TTTT
66 TTTT
1878839 CAATTTCTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (80 bp):
TCAACTCATATTGCGAGAGACGAGTTGAGCCTCAAGTCACACGCCGAGGTATTTTCAATTCCTAT
TTTTTTTAAAAAAAG
Found at i:1878839 original size:14 final size:14
Alignment explanation
Indices: 1878820--1878855 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1878810 ACGCCGAGGT
1878820 TTTTTCAATTTCTA
1 TTTTTCAATTTCTA
1878834 TTTTTCAATTTCTA
1 TTTTTCAATTTCTA
*
1878848 CTTTTCAA
1 TTTTTCAA
1878856 AAAAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTCAATTTCTA
Found at i:1878931 original size:14 final size:14
Alignment explanation
Indices: 1878912--1878947 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1878902 CGCTGAGGTA
*
1878912 TTTTCAATTTCTGC
1 TTTTCAAATTCTGC
1878926 TTTTCAAATTCTGC
1 TTTTCAAATTCTGC
1878940 TTTTCAAA
1 TTTTCAAA
1878948 AAAAATCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (14 bp):
TTTTCAAATTCTGC
Found at i:1879035 original size:90 final size:88
Alignment explanation
Indices: 1878762--1879072 Score: 342
Period size: 90 Copynumber: 3.5 Consensus size: 88
1878752 TGTTTTTTTT
* * * *
1878762 AAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTTTTTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACA-G-CGAGGTATTTTCA
** * **
1878827 ATTTCTATTTTTCAATTTCTACTTTTC
64 ATTTCTGCTTTTCAA-AT-TAAGTTTC
*
1878854 AAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGG-CAC-GCTGAGGTATTTTC
1 -AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGTCACAGC-GAGGTATTTTC
**
1878917 AATTTCTGCTTTTCAAATTCTGCTTTTC
63 AATTTCTGCTTTTCAAATTAAG--TTTC
* *
1878945 AAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGGTCACATGTCGAGGTATTTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACA-G-CGAGGTATTTTCA
**
1879010 AAATCTGCTTTTCAAATTAAGTTTC
64 ATTTCTGCTTTTCAAATTAAGTTTC
*
1879035 --AAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1879073 TGACTCACGT
Statistics
Matches: 190, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
88 36 0.19
89 3 0.02
90 48 0.25
91 29 0.15
92 30 0.16
93 41 0.22
94 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (88 bp):
AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACAGCGAGGTATTTTCAAT
TTCTGCTTTTCAAATTAAGTTTC
Found at i:1879094 original size:88 final size:89
Alignment explanation
Indices: 1878762--1879098 Score: 308
Period size: 88 Copynumber: 3.7 Consensus size: 89
1878752 TGTTTTTTTT
* * * * *
1878762 AAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTC-AGGTCACACGCCGAGGTTTTTTC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA-GTCAC-TGCTGAGGTATTTTC
** ** * *
1878826 AATTTCTATTTTTCAATTTCTA-CTTTTC
63 AAAATCTGCTTTTCAAATT-AAGC-TTTC
* * *
1878854 AAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGGCAC-GCTGAGGTATTTTCA
1 --AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACTGCTGAGGTATTTTCA
** **
1878918 ATTTCTGCTTTTCAAATTCTGCTTTTC
64 AAATCTGCTTTTCAAATTAAGC-TTTC
* *
1878945 AAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGGTCACATG-TCGAGGTATTTTC
1 -AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCAC-TGCT-GAGGTATTTTC
1879009 AAAATCTGCTTTTCAAATTAAG-TTTC
63 AAAATCTGCTTTTCAAATTAAGCTTTC
* * * *
1879035 -AAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACGTGCTGAGTTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCAC-TGCTGAGGTATTTTCAA
1879099 TTTTTGTTTT
Statistics
Matches: 210, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
88 55 0.26
89 1 0.00
90 47 0.22
91 35 0.17
92 30 0.14
93 34 0.16
94 8 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (89 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACTGCTGAGGTATTTTCAAA
ATCTGCTTTTCAAATTAAGCTTTC
Found at i:1879735 original size:25 final size:25
Alignment explanation
Indices: 1879707--1879766 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1879697 CCATTTACAT
*
1879707 CAAAACCTAACAGTAGCCCAAACAC
1 CAAAACCCAACAGTAGCCCAAACAC
*
1879732 CAAAACCCAATAGTAGCCCAAACAC
1 CAAAACCCAACAGTAGCCCAAACAC
*
1879757 TAAAACCCAA
1 CAAAACCCAA
1879767 AATCAAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.50, C:0.35, G:0.07, T:0.08
Consensus pattern (25 bp):
CAAAACCCAACAGTAGCCCAAACAC
Found at i:1880788 original size:21 final size:21
Alignment explanation
Indices: 1880764--1880840 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 21
1880754 TTCTTTATTA
1880764 AATATTATTATTATTTTTTCT
1 AATATTATTATTATTTTTTCT
* *
1880785 AATATTATTA--AGTTTATC-
1 AATATTATTATTATTTTTTCT
1880803 AATATTATTATT-TTTTTT-T
1 AATATTATTATTATTTTTTCT
*
1880822 ATATATTAGTATATATTTT
1 A-ATATTATTAT-TATTTT
1880841 ATTATATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
18 10 0.22
19 11 0.24
20 9 0.20
21 11 0.24
22 4 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
AATATTATTATTATTTTTTCT
Found at i:1880792 original size:18 final size:17
Alignment explanation
Indices: 1880769--1880818 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
1880759 TATTAAATAT
1880769 TATTATTATTTTTTCTAA
1 TATTATTATTTTTTC-AA
* *
1880787 TATTATTAAGTTTATCAA
1 TATTATT-ATTTTTTCAA
1880805 TATTATTATTTTTT
1 TATTATTATTTTTT
1880819 TTTATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTATTATTTTTTCAA
Found at i:1880825 original size:18 final size:18
Alignment explanation
Indices: 1880769--1880829 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1880759 TATTAAATAT
*
1880769 TATTATTATTTTTTCTAA
1 TATTATTATTTTTTTTAA
** * *
1880787 TATTATTAAGTTTATCAA
1 TATTATTATTTTTTTTAA
*
1880805 TATTATTATTTTTTTTTA
1 TATTATTATTTTTTTTAA
1880823 TA-TATTA
1 TATTATTA
1880830 GTATATATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTATTATTTTTTTTAA
Found at i:1880840 original size:22 final size:22
Alignment explanation
Indices: 1880815--1880864 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1880805 TATTATTATT
*
1880815 TTTTTTTATATAT-TAGTATATA
1 TTTTATTATATATGTA-TATATA
1880837 TTTTATTATATATGTATATATA
1 TTTTATTATATATGTATATATA
*
1880859 TATTAT
1 TTTTAT
1880865 AGTGTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTATTATATATGTATATATA
Found at i:1881728 original size:24 final size:24
Alignment explanation
Indices: 1881701--1881748 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1881691 TTATCTTTTT
*
1881701 ATATGTAGTATGTACATA-TTTTCA
1 ATAT-TAGTATGTAAATACTTTTCA
*
1881725 ATATTATTATGTAAATACTTTTCA
1 ATATTAGTATGTAAATACTTTTCA
1881749 TTCATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (24 bp):
ATATTAGTATGTAAATACTTTTCA
Found at i:1887682 original size:27 final size:28
Alignment explanation
Indices: 1887645--1887784 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
1887635 AGCATGGCTG
* *
1887645 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
1887671 CCAGATACAGATA-ATCGTGGCAGGGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
1887699 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
1887726 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* * *
1887753 CTAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
1887780 CCAGA
1 CCAGA
1887785 ACGCTTCCTC
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
26 5 0.05
27 81 0.79
28 16 0.16
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:1889439 original size:26 final size:26
Alignment explanation
Indices: 1889403--1889512 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
1889393 CATGAAATTC
1889403 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1889429 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1889455 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
1889481 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
1889507 TTATCA
1 TTATCA
1889513 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1894593 original size:22 final size:24
Alignment explanation
Indices: 1894562--1894610 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1894552 CATTATTAAA
*
1894562 TAAATTAAAAAT-ATTTAATGATT
1 TAAATTAAAAATCATTTAATAATT
1894585 TAAA-TAAAAATCATTTAATAATT
1 TAAATTAAAAATCATTTAATAATT
1894608 TAA
1 TAA
1894611 TGACTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAATTAAAAATCATTTAATAATT
Found at i:1894632 original size:30 final size:29
Alignment explanation
Indices: 1894598--1894670 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
1894588 ATAAAAATCA
* *
1894598 TTTAATAATTTAATGACT-ATTTTAAAATTT
1 TTTAATAATTTAAT-ACTAAATGTAAAA-TT
*
1894628 TTTAA-AATTAAATACTAAAATGTAAAATT
1 TTTAATAATTTAATACT-AAATGTAAAATT
1894657 TTTAATAATTTAAT
1 TTTAATAATTTAAT
1894671 TTACAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.08
29 14 0.39
30 19 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAATAATTTAATACTAAATGTAAAATT
Found at i:1896780 original size:25 final size:25
Alignment explanation
Indices: 1896746--1896796 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1896736 TTAAGTCACC
1896746 AACTCAATTATGAAGATAAAGGAAT
1 AACTCAATTATGAAGATAAAGGAAT
1896771 AACTCAATTATGAAGATAAAGGAAT
1 AACTCAATTATGAAGATAAAGGAAT
1896796 A
1 A
1896797 TAGGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.24
Consensus pattern (25 bp):
AACTCAATTATGAAGATAAAGGAAT
Found at i:1900245 original size:51 final size:51
Alignment explanation
Indices: 1900169--1900272 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
1900159 ATTGGTTCTT
*
1900169 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCATCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
* *
1900220 TGAAACTGCACAAGTTCATCTATGACCTGAAACAAGCACCACAGGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1900271 TG
1 TG
1900273 GAGCTAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (51 bp):
TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
Found at i:1901202 original size:11 final size:11
Alignment explanation
Indices: 1901174--1901227 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
1901164 TTGACCTTTC
1901174 CAAGGTATGGG
1 CAAGGTATGGG
*
1901185 -TAGGTATGGG
1 CAAGGTATGGG
1901195 CAAGGTATGGG
1 CAAGGTATGGG
1901206 CAAGGTATGGG
1 CAAGGTATGGG
*
1901217 CAAGGAATGGG
1 CAAGGTATGGG
1901228 TATATTCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.28, C:0.07, G:0.46, T:0.19
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:1901533 original size:11 final size:11
Alignment explanation
Indices: 1901517--1901571 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
1901507 TATTAGAATA
*
1901517 TACCCATTCCT
1 TACCCATACCT
1901528 TACCCATACCT
1 TACCCATACCT
* *
1901539 TGCCCATACTT
1 TACCCATACCT
*
1901550 TTCCCATACC-
1 TACCCATACCT
1901560 TACCCATACCT
1 TACCCATACCT
1901571 T
1 T
1901572 GGAAAGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.22, C:0.44, G:0.02, T:0.33
Consensus pattern (11 bp):
TACCCATACCT
Found at i:1901887 original size:18 final size:18
Alignment explanation
Indices: 1901847--1901903 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1901837 CCCAACTACT
* * *
1901847 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTGCC
* * *
1901865 ATATATGTGAATAGTGTC
1 GTATACGTGAATAGTGCC
1901883 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
1901901 GTA
1 GTA
1901904 AATGGTCGTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:1902465 original size:11 final size:11
Alignment explanation
Indices: 1902437--1902490 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
1902427 TTGACCTTTC
1902437 CAAGGTATGGG
1 CAAGGTATGGG
*
1902448 -TAGGTATGGG
1 CAAGGTATGGG
*
1902458 AAAGGTATGGG
1 CAAGGTATGGG
1902469 CAAGGTATGGG
1 CAAGGTATGGG
*
1902480 CAAGGAATGGG
1 CAAGGTATGGG
1902491 TATATTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.30, C:0.06, G:0.46, T:0.19
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:1905136 original size:15 final size:15
Alignment explanation
Indices: 1905111--1905164 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
1905101 TCATATATAT
1905111 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
1905127 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
1905142 AATAATTTCAATCAA
1 TATAAATTCAATCAA
1905157 TATAAATT
1 TATAAATT
1905165 TAATAAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:1907078 original size:2 final size:2
Alignment explanation
Indices: 1907071--1907099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1907061 AATATTCTTT
1907071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1907100 TGGTCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1907867 original size:26 final size:26
Alignment explanation
Indices: 1907831--1907884 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1907821 TCTACACAGT
*
1907831 TCACATATTGAGCTTGTATATCGAGC
1 TCACACATTGAGCTTGTATATCGAGC
* *
1907857 TCACACATTGAGCTTGTGTATCGGGC
1 TCACACATTGAGCTTGTATATCGAGC
1907883 TC
1 TC
1907885 GCATGATACT
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:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
TCACACATTGAGCTTGTATATCGAGC
Found at i:1909703 original size:11 final size:11
Alignment explanation
Indices: 1909680--1909713 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1909670 TATTGATTCG
1909680 ATAAAATAAATA
1 ATAAAA-AAATA
*
1909692 ATTAAAAAATA
1 ATAAAAAAATA
1909703 ATAAAAAAATA
1 ATAAAAAAATA
1909714 GATTCAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:1914053 original size:406 final size:401
Alignment explanation
Indices: 1913281--1914039 Score: 921
Period size: 405 Copynumber: 1.9 Consensus size: 401
1913271 AATTTCAATG
* * * ** *
1913281 TTTCCGATATGAGCAGGTTCGCGAGGGCTTAATTTAAGCGTTCTTGAATATGATCATATCAGTTT
1 TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
* * *
1913346 CATGCTTAGAAAACTAGAGGAATCATGACAAATTGTTGAGTGAATAGAGTTTGAACAAGCTAGAA
66 CATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAGTGAATAGAGTTTGAACAAGCAAGAA
* * *
1913411 CTAGTGAACTGAGACTGATTTCCCATTTGGCCTTGTGTGACCAATCTTTTGAAAATCATATAGAA
131 CTAATGAACCGAGACTGATATCCCATTTGGCCTTGTGTGACCAATCTTTTGAAAATCATATAGAA
* * *
1913476 TCATTGAATGAGGATCAATTTTGATGTTTCCTGTATGATCATATGCACGAGGGCTTAATTTAAGC
196 TCATTGAATGAGGATCAA-TTTGATGCTTCCTGTATGATCATATGCACGAAGGCTTAAATTAAGC
* *** * *
1913541 GATCTTGAATATGATCGTATCAGTTTCATGGTTACTAGAGAAATCATTATAATCAGTCGATTGAA
260 GATCATGAATATGATCGTATCA---T-ATGAACACTAGAGAAATCATTATAATCAGTCAACTGAA
** * *
1913606 TTTAGTTTGAATAAGCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTG
321 TAGAGTTTGAACAACCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTG
1913671 TGACCAGAGGATGAAT
386 TGACCAGAGGATGAAT
* * **
1913687 TTTCCGATACGACCATGTTTGCAAGGGCTTAA-TTAAGCACTCGTGAATATGATTGTATCAGTTT
1 TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
* * *
1913751 CATGCTTAGGAAACTAGAGGAATCCT-AAAAACTAGTTGATTGAATAGAGTTTGAACAAAGCAAG
66 CATGCTTAGAAAACTAGAGGAATCATGAAAAA-TAGTTGAGTGAATAGAGTTTGAAC-AAGCAAG
* ** *
1913815 AACTAATGACCCGAGACTGATATCTGATTCT-GCCTTGTGTGACCAATCTTTTGAAAA-CTGTAT
129 AACTAATGAACCGAGACTGATATCCCATT-TGGCCTTGTGTGACCAATCTTTTGAAAATC-ATAT
* * *
1913878 AGAATCATTGAATGAGGAT-GA-TTGATGCTT-CTGTTATGATCATGTTCTCACGAAGGCTTAAA
192 AGAATCATTGAATGAGGATCAATTTGATGCTTCCTG-TATGATCAT-AT-GCACGAAGGCTTAAA
* * *
1913940 TTAAGCGCTCATGAATATGATCGTAT-A-A-GAACACTAGAGGAATCATTGACT-ATTAGT-AAC
254 TTAAGCGATCATGAATATGATCGTATCATATGAACACTAGAGAAATCATT-A-TAATCAGTCAAC
1914000 TGAATAGAGTTTGAACAACCTAGAACTAGTGGAACTGAGA
317 TGAATAGAGTTTGAACAACCTAGAACTAGT-GAACTGAGA
1914040 GCAATTTCTG
Statistics
Matches: 301, Mismatches: 42, Indels: 27
0.81 0.11 0.07
Matches are distributed among these distances:
398 42 0.14
399 16 0.05
400 1 0.00
402 3 0.01
403 17 0.06
404 6 0.02
405 111 0.37
406 104 0.35
407 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (401 bp):
TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
CATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAGTGAATAGAGTTTGAACAAGCAAGAA
CTAATGAACCGAGACTGATATCCCATTTGGCCTTGTGTGACCAATCTTTTGAAAATCATATAGAA
TCATTGAATGAGGATCAATTTGATGCTTCCTGTATGATCATATGCACGAAGGCTTAAATTAAGCG
ATCATGAATATGATCGTATCATATGAACACTAGAGAAATCATTATAATCAGTCAACTGAATAGAG
TTTGAACAACCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTGTGACC
AGAGGATGAAT
Found at i:1927317 original size:31 final size:32
Alignment explanation
Indices: 1927258--1927318 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1927248 AATAATAAAT
**
1927258 AATATGATATACGAAAATAATACTATATATAA
1 AATATGATATACGAAAATAATAAAATATATAA
1927290 AATATG-TATAC-AAGAATAATAAAATATAT
1 AATATGATATACGAA-AATAATAAAATATAT
1927319 GTACTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 18 0.69
32 6 0.23
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (32 bp):
AATATGATATACGAAAATAATAAAATATATAA
Found at i:1927548 original size:15 final size:14
Alignment explanation
Indices: 1927502--1927549 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1927492 AATATTGAAA
*
1927502 ATATATATACATA-
1 ATATATATATATAC
*
1927515 ATATATATATAAAAC
1 ATATATATAT-ATAC
1927530 ATATATGATATATAC
1 ATATAT-ATATATAC
1927545 ATATA
1 ATATA
1927550 CATTAGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 14 0.48
16 4 0.14
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:1927722 original size:2 final size:2
Alignment explanation
Indices: 1927673--1927703 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1927663 TATATGCATA
*
1927673 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1927704 ATTTAGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1927822 original size:34 final size:33
Alignment explanation
Indices: 1927784--1927858 Score: 78
Period size: 35 Copynumber: 2.2 Consensus size: 33
1927774 CCACAAATAT
* *
1927784 ATATATGCTAAAAATATACATAATAGTATATAAG
1 ATATATACTAAAAATATACATAAT-GTATAAAAG
* * * *
1927818 ATATAATATTTAAAGTATACATAATGTATAAAAT
1 ATAT-ATACTAAAAATATACATAATGTATAAAAG
1927852 ATATATA
1 ATATATA
1927859 TACATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 3 0.09
34 15 0.44
35 16 0.47
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (33 bp):
ATATATACTAAAAATATACATAATGTATAAAAG
Found at i:1927875 original size:12 final size:13
Alignment explanation
Indices: 1927833--1927881 Score: 59
Period size: 12 Copynumber: 4.0 Consensus size: 13
1927823 ATATTTAAAG
*
1927833 TATACATAATGTA
1 TATACATAATATA
*
1927846 TA-AAAT-ATATA
1 TATACATAATATA
1927857 TATACATAATATA
1 TATACATAATATA
1927870 -ATACATAATATA
1 TATACATAATATA
1927882 GACACATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 6 0.19
12 18 0.58
13 7 0.23
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (13 bp):
TATACATAATATA
Found at i:1929851 original size:15 final size:16
Alignment explanation
Indices: 1929818--1929851 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1929808 TTGATTTTTG
*
1929818 AAAAGCATAAATTGAA
1 AAAAACATAAATTGAA
1929834 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
1929850 AA
1 AA
1929852 TACCTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:1929880 original size:91 final size:91
Alignment explanation
Indices: 1929655--1930275 Score: 646
Period size: 91 Copynumber: 6.8 Consensus size: 91
1929645 ACTAGACGTT
* * ** * * *
1929655 AAAAACAAAAATTGAAAATAACTCAACACGTGAG-CCAAGGCTCAACTCACTTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
* * *
1929719 GTTGATTTTTGAAAA-TAGAATTTG-
66 GTTGATTTTTGAAAAGCATAAATTGA
* ** *
1929743 CAAAACAGATGTTGAAAATACCTTGGCATGTGA-CCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
1929807 GTTGATTTTTGAAAAGCATAAATTGAA
66 GTTGATTTTTGAAAAGCATAAATTG-A
* ** *
1929834 AAAAACATAAATTGAAAATACCTCAACATGCGAG-CCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
** *
1929898 GTTGATTTTTTTGGAAGAAATAGAAATTG-
66 GTTGA--TTTTT-GAA-AAGCATAAATTGA
* **
1929927 AAAAA-TGAAATTTTGAAAATACCTCGGCATGTG-GCCCGAGGCTCAACTCACCTCTCGTTATAT
1 AAAAACAGAAA--TTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATAT
*
1929990 GAGTTGATTTTTTTTTAAAAGCATAAATTGA
64 GAGTTGA---TTTTTGAAAAGCATAAATTGA
* * * * *
1930021 AAAAACAGAAATTGAAAATACCTCAGC--GTG-TCCTGAGGCTTAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
1930083 GTTGATTTTTGGAAAGAAATAGAAATTG-
66 GTTGATTTTTGAAAAG-CAT--AAATTGA
*
1930111 AAAAACA-AAATTTTGAAAATACCTCGGCATGTG-GCCCGAGGCTCAACTCACCTCTCGTAATAT
1 AAAAACAGAAA--TTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATAT
1930174 GAGTTGATTTTTTTGAAAAGCATAAATTGA
64 GAGTTGA--TTTTTGAAAAGCATAAATTGA
* * *
1930204 AAAAACAGAAATTGAAAATACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
1930266 GTTGATTTTT
66 GTTGATTTTT
1930276 TTTTTGAAAA
Statistics
Matches: 448, Mismatches: 59, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
88 81 0.18
89 11 0.02
90 44 0.10
91 115 0.26
92 24 0.05
93 77 0.17
94 66 0.15
95 30 0.07
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (91 bp):
AAAAACAGAAATTGAAAATACCTCGGCATGTGAGCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAGCATAAATTGA
Found at i:1930223 original size:183 final size:181
Alignment explanation
Indices: 1929692--1930275 Score: 885
Period size: 183 Copynumber: 3.2 Consensus size: 181
1929682 ACGTGAGCCA
* * * * *
1929692 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-G-A-AAATAGAATTTGCAAAACAGATG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAAATT
* * *
1929754 TTGAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
66 TTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
* *
1929817 GAAAAGCATAAATTGAAAAAAACATAAATTGAAAATACCTCAACATGCGAG-CC-G
131 GAAAAGCATAAATTG-AAAAAACAGAAATTGAAAATACCT---CA-GCGTGTCCTG
*
1929871 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAGAAATAGAAATTGAAAAATGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGGAAGAAATAGAAATTGAAAAA-CAA
*
1929936 ATTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTTATATGAGTTGATTTT
63 ATTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTT
*
1930001 TTTTTAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
127 TTTTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
* *
1930056 AGGCTTAACTCACCTCTTGCAATATGAGTTGATTTTTGGAAAGAAATAGAAATTGAAAAACAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGG-AAGAAATAGAAATTGAAAAAC-AAA
1930121 TTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
64 TTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1930186 TTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
129 TTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
1930239 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1930276 TTTTTGAAAA
Statistics
Matches: 372, Mismatches: 20, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
179 31 0.08
181 5 0.01
182 1 0.00
183 104 0.28
184 101 0.27
185 88 0.24
187 23 0.06
188 19 0.05
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (181 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAAATT
TTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
GAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
Found at i:1930339 original size:78 final size:78
Alignment explanation
Indices: 1930204--1930348 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 78
1930194 CATAAATTGA
* *
1930204 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1930269 GATTTTTTTTTTG
66 GATTTTTTTTTTG
* * * ** *
1930282 AAAAGCAGAAATTGAAAATACCTCAACATGTCTTGTGGCTCAACTCATTTCTTGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1930347 GA
66 GA
1930349 ATCTTGAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (78 bp):
AAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTTTTG
Found at i:1933328 original size:32 final size:32
Alignment explanation
Indices: 1933292--1933356 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1933282 TGTATGCATT
1933292 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1933324 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1933356 T
1 T
1933357 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:1934859 original size:25 final size:26
Alignment explanation
Indices: 1934817--1934868 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1934807 TTTACAGTTT
1934817 TACCCCTAGGAGATAATT-ACCGAAA
1 TACCCCTAGGAGATAATTGACCGAAA
* *
1934842 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGAT-AATTGACCGAAA
1934868 T
1 T
1934869 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGAGATAATTGACCGAAA
Found at i:1945312 original size:2 final size:2
Alignment explanation
Indices: 1945305--1945346 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1945295 GAGTATGTAC
1945305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1945347 GAATAGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1945637 original size:31 final size:32
Alignment explanation
Indices: 1945578--1945638 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1945568 AATAATAAAT
**
1945578 AATATGATATACGAAAATAATACTATATATAA
1 AATATGATATACGAAAATAATAAAATATATAA
1945610 AATATG-TATAC-AAGAATAATAAAATATAT
1 AATATGATATACGAA-AATAATAAAATATAT
1945639 GTACTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 18 0.69
32 6 0.23
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (32 bp):
AATATGATATACGAAAATAATAAAATATATAA
Found at i:1945763 original size:26 final size:24
Alignment explanation
Indices: 1945734--1945856 Score: 74
Period size: 26 Copynumber: 4.9 Consensus size: 24
1945724 ACATATACAT
1945734 ATAATAGTATTTAAGAATATATATAC
1 ATAATA-TATTTAA-AATATATATAC
* * ** *
1945760 ATAAGATGATATGGAA-ATATGTAC
1 ATAATAT-ATTTAAAATATATATAC
*
1945784 ATAGAATAGTATATAAAA-ATATA-AC
1 AT--AATA-TATTTAAAATATATATAC
*
1945809 -TAATAATATTGAAAATATATATAC
1 ATAAT-ATATTTAAAATATATATAC
1945833 ATAATATATATATAAAATATATAT
1 ATAATATAT-T-TAAAATATATAT
1945857 GATATATACA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
22 10 0.13
23 6 0.08
24 16 0.21
25 10 0.13
26 32 0.43
27 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (24 bp):
ATAATATATTTAAAATATATATAC
Found at i:1945838 original size:13 final size:13
Alignment explanation
Indices: 1945820--1945856 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1945810 AATAATATTG
1945820 AAAATATATATAC
1 AAAATATATATAC
* *
1945833 ATAATATATATAT
1 AAAATATATATAC
1945846 AAAATATATAT
1 AAAATATATAT
1945857 GATATATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATATATAC
Found at i:1945839 original size:11 final size:11
Alignment explanation
Indices: 1945825--1945868 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1945815 TATTGAAAAT
1945825 ATATATACATA
1 ATATATACATA
*
1945836 ATATATATATA
1 ATATATACATA
* * *
1945847 AAATATATATG
1 ATATATACATA
1945858 ATATATACATA
1 ATATATACATA
1945869 TACATTAGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATATACATA
Found at i:1945852 original size:24 final size:23
Alignment explanation
Indices: 1945752--1945855 Score: 70
Period size: 24 Copynumber: 4.3 Consensus size: 23
1945742 ATTTAAGAAT
* **
1945752 ATATATACATAAGATGATATGGAA
1 ATATATACATAATAT-ATATTAAA
* *
1945776 ATATGTACATAGAATAGTATATAAAA
1 ATATATACAT--AATA-TATATTAAA
1945802 ATATA-AC-TAATA-ATATTGAAAA
1 ATATATACATAATATATATT--AAA
1945824 TATATATACATAATATATATATAAA
1 -ATATATACATAATATATAT-TAAA
1945849 ATATATA
1 ATATATA
1945856 TGATATATAC
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
20 4 0.06
22 7 0.11
23 5 0.08
24 19 0.30
25 10 0.16
26 17 0.27
27 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATATACATAATATATATTAAA
Found at i:1946150 original size:18 final size:19
Alignment explanation
Indices: 1946127--1946168 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1946117 AGTATATAAG
* *
1946127 ATATAATAT-TTAAAGTAT
1 ATATAATATATAAAAATAT
1946145 ATATAATATATAAAAATAT
1 ATATAATATATAAAAATAT
1946164 ATATA
1 ATATA
1946169 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAATATATAAAAATAT
Found at i:1946170 original size:25 final size:25
Alignment explanation
Indices: 1946089--1946179 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 25
1946079 TGCTCCACAA
1946089 ATATAT-ATATACTAAAAATATACATAAT
1 ATATATAATATA-TAAAAATAT--AT-AT
* * * *
1946117 AGTATATAAGATAT-AATATTTAAAGT
1 A-TATATAATATATAAAAATATATA-T
1946143 ATATATAATATATAAAAATATATAT
1 ATATATAATATATAAAAATATATAT
*
1946168 ATACATAATATA
1 ATATATAATATA
1946180 ATACATAACA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
25 24 0.48
26 10 0.20
28 6 0.12
29 6 0.12
30 4 0.08
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (25 bp):
ATATATAATATATAAAAATATATAT
Found at i:1946183 original size:12 final size:13
Alignment explanation
Indices: 1946091--1946187 Score: 52
Period size: 12 Copynumber: 8.1 Consensus size: 13
1946081 CTCCACAAAT
1946091 ATATATATAC-TA
1 ATATATATACATA
*
1946103 A-AAATATACATA
1 ATATATATACATA
*
1946115 ATAGTATATA-A-G
1 ATA-TATATACATA
**
1946127 ATATA-ATATTTA
1 ATATATATACATA
1946139 A-AGTATAT--ATA
1 ATA-TATATACATA
* *
1946150 ATATATAAAAAT-
1 ATATATATACATA
1946162 ATATATATACATA
1 ATATATATACATA
1946175 ATATA-ATACATA
1 ATATATATACATA
1946187 A
1 A
1946188 CATAGACACA
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
10 3 0.05
11 17 0.26
12 29 0.45
13 11 0.17
14 5 0.08
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (13 bp):
ATATATATACATA
Found at i:1946283 original size:3 final size:3
Alignment explanation
Indices: 1946277--1946338 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1946267 AACAACACAC
1946277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1946325 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
1946339 AGTAGAATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1948160 original size:19 final size:19
Alignment explanation
Indices: 1948124--1948163 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1948114 CAGTAACAAT
* **
1948124 AAAATAGTGAAATGACAGC
1 AAAATAATGAAAAAACAGC
1948143 AAAATAATGAAAAAACAGC
1 AAAATAATGAAAAAACAGC
1948162 AA
1 AA
1948164 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAATAATGAAAAAACAGC
Found at i:1951891 original size:28 final size:28
Alignment explanation
Indices: 1951860--1951914 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1951850 CTATCGATTC
*
1951860 AATAATAATTAAAT-AAATAATTATAAAA
1 AATAATAA-AAAATAAAATAATTATAAAA
*
1951888 AATAATAAAAAATAAAATATTTATAAA
1 AATAATAAAAAATAAAATAATTATAAA
1951915 TTTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAATAAAAAATAAAATAATTATAAAA
Found at i:1955191 original size:31 final size:31
Alignment explanation
Indices: 1955156--1955218 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1955146 TAAAAGTCAA
1955156 TGCAAAATAAAGAGGATTTAGCAACTTCCTT
1 TGCAAAATAAAGAGGATTTAGCAACTTCCTT
1955187 TGCAAAATAAAGAGGATTTAGCAACTTCCTT
1 TGCAAAATAAAGAGGATTTAGCAACTTCCTT
1955218 T
1 T
1955219 TTGTCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (31 bp):
TGCAAAATAAAGAGGATTTAGCAACTTCCTT
Found at i:1955260 original size:3 final size:3
Alignment explanation
Indices: 1955252--1955318 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
1955242 ATTCACAACT
1955252 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1955300 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1955319 CCTCTTCAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1959835 original size:17 final size:20
Alignment explanation
Indices: 1959810--1959847 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1959800 TGATTTTTGG
1959810 AAAATAATTT-AT-TTTTTT
1 AAAATAATTTAATATTTTTT
1959828 AAAA-AATTTAATATTTTTT
1 AAAATAATTTAATATTTTTT
1959847 A
1 A
1959848 GTGATTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATAATTTAATATTTTTT
Found at i:1960441 original size:22 final size:22
Alignment explanation
Indices: 1960415--1960458 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1960405 ATATTAAATA
1960415 ATTTATTAAAATAGTAATTTAT
1 ATTTATTAAAATAGTAATTTAT
* *
1960437 ATTTATTATATTAGTAATTTAT
1 ATTTATTAAAATAGTAATTTAT
1960459 TATATGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTATTAAAATAGTAATTTAT
Found at i:1961176 original size:17 final size:18
Alignment explanation
Indices: 1961143--1961179 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1961133 AAGTCGAGAG
1961143 ATTATAAATATATAAATT
1 ATTATAAATATATAAATT
1961161 ATTA-AAATA-ATAAAATT
1 ATTATAAATATAT-AAATT
1961178 AT
1 AT
1961180 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATATATAAATT
Found at i:1966644 original size:16 final size:16
Alignment explanation
Indices: 1966620--1966652 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1966610 AATGTGTTCT
*
1966620 AAATTACATAATATAA
1 AAATAACATAATATAA
1966636 AAATAACATAATATAA
1 AAATAACATAATATAA
1966652 A
1 A
1966653 GTATTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAACATAATATAA
Found at i:1968215 original size:54 final size:51
Alignment explanation
Indices: 1968136--1968338 Score: 196
Period size: 54 Copynumber: 3.9 Consensus size: 51
1968126 CCATGGCAAC
* *
1968136 AAGTGATAAGTGATATCTGTATAAGACCATAGATAGGCTATGGCATTGGAAAA
1 AAGTGATAAATGAT-TCTGTATAAGACCATAGCT-GGCTATGGCATTGGAAAA
**
1968189 CAAGTGATAAATGATTTCTGTATAAGACCATAGCTGGACTATGGC-TTCGGATTA
1 -AAGTGATAAATGA-TTCTGTATAAGACCATAGCTGG-CTATGGCATT-GGAAAA
* *
1968243 AAGTGATACAAGTGA-TCTGTATAAGACCATAGCTGGCTATGGTA-TGGAGAA
1 AAGTGATA-AA-TGATTCTGTATAAGACCATAGCTGGCTATGGCATTGGAAAA
* * * * * *
1968294 AAGTGATAAGTGCTTCCGTGTAAGACCATATCTGGGATATGGCAT
1 AAGTGATAAATGATTCTGTATAAGACCATAGCT-GGCTATGGCAT
1968339 CGGTATAATA
Statistics
Matches: 126, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
49 2 0.02
50 17 0.13
51 20 0.16
52 7 0.06
53 33 0.26
54 43 0.34
55 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (51 bp):
AAGTGATAAATGATTCTGTATAAGACCATAGCTGGCTATGGCATTGGAAAA
Found at i:1973930 original size:16 final size:16
Alignment explanation
Indices: 1973909--1973945 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1973899 ATGGATCTCA
*
1973909 ATAATTGCAAATAATG
1 ATAATTGCAAAGAATG
1973925 ATAATTGCAAAGAATG
1 ATAATTGCAAAGAATG
1973941 ATAAT
1 ATAAT
1973946 AAACAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (16 bp):
ATAATTGCAAAGAATG
Found at i:1975909 original size:2 final size:2
Alignment explanation
Indices: 1975861--1975892 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1975851 GAATTTACCA
1975861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1975893 TGGTCATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1976330 original size:16 final size:16
Alignment explanation
Indices: 1976309--1976343 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1976299 TATATGTGGA
1976309 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
1976325 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
1976341 AAA
1 AAA
1976344 AAAACTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:1976515 original size:31 final size:31
Alignment explanation
Indices: 1976463--1976525 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1976453 CCTTAAATTT
* * *
1976463 ATTCATTGCATCTGTTAGAAAAATCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
*
1976494 ATTCATTACATCAGTTGGAAAAAGCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
1976525 A
1 A
1976526 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (31 bp):
ATTCATTACATCAGTTAGAAAAAGCAGATTG
Found at i:1977137 original size:2 final size:2
Alignment explanation
Indices: 1977124--1977157 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1977114 GGCCTTTATT
1977124 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1977158 TAAAACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1979139 original size:2 final size:2
Alignment explanation
Indices: 1979132--1979159 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1979122 ATGTAGAACA
1979132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1979160 TAATTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1979473 original size:23 final size:23
Alignment explanation
Indices: 1979427--1979470 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1979417 ATACCAATAA
1979427 TAATATATCATTTTATTATTAAT
1 TAATATATCATTTTATTATTAAT
1979450 TAATA-ATACATTTTA-TATTAA
1 TAATATAT-CATTTTATTATTAA
1979471 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATATCATTTTATTATTAAT
Found at i:1980284 original size:24 final size:21
Alignment explanation
Indices: 1980244--1980287 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
1980234 CTGCCCATAT
1980244 TATTTTTAATTTTTTTTAAAA
1 TATTTTTAATTTTTTTTAAAA
1980265 TATTTGTTATATTTTATTTTAAA
1 TATTT-TTA-ATTTT-TTTTAAA
1980288 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 5 0.25
24 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTTAATTTTTTTTAAAA
Found at i:1984734 original size:190 final size:189
Alignment explanation
Indices: 1984412--1984791 Score: 706
Period size: 190 Copynumber: 2.0 Consensus size: 189
1984402 GAGTAAACAA
*
1984412 CCAAGAAGCAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
1984477 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
66 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
*
1984542 TAAGAATAAGAGAAACTACCTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
131 TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
* *
1984601 CCAAGAAACGAAACAATACCCAGGAAAGAATTCACCTAGATTTCATCTGTCATTATCAATCTAAA
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCA-CTAGATTTCATCTGTCATTATCAATCTAAA
1984666 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
65 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
*
1984731 TTAAGAATAAGAGAAATTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
130 TTAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
1984791 C
1 C
1984792 TATTATCGCA
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
189 31 0.17
190 154 0.83
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (189 bp):
CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
Found at i:1986170 original size:16 final size:16
Alignment explanation
Indices: 1986149--1986185 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1986139 ATGGATCTCA
*
1986149 ATAATTGCAAATAATG
1 ATAATTGCAAAGAATG
1986165 ATAATTGCAAAGAATG
1 ATAATTGCAAAGAATG
1986181 ATAAT
1 ATAAT
1986186 AAACAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (16 bp):
ATAATTGCAAAGAATG
Found at i:1988156 original size:2 final size:2
Alignment explanation
Indices: 1988100--1988139 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1988090 AGAATTTACC
1988100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1988140 TGGTCATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1988578 original size:16 final size:16
Alignment explanation
Indices: 1988557--1988591 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1988547 TATATGTGGA
1988557 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
1988573 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
1988589 AAA
1 AAA
1988592 AAAACTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:1988763 original size:31 final size:31
Alignment explanation
Indices: 1988711--1988773 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1988701 CCTTAAATTT
* * *
1988711 ATTCATTGCATCTGTTAGAAAAATCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
*
1988742 ATTCATTACATCAGTTGGAAAAAGCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
1988773 A
1 A
1988774 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (31 bp):
ATTCATTACATCAGTTAGAAAAAGCAGATTG
Found at i:1989385 original size:2 final size:2
Alignment explanation
Indices: 1989372--1989403 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1989362 GGCCTTTATT
1989372 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
1989404 TAAAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1991385 original size:2 final size:2
Alignment explanation
Indices: 1991378--1991409 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1991368 ATGTAGAACA
1991378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1991410 TAATTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1991723 original size:23 final size:23
Alignment explanation
Indices: 1991677--1991720 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1991667 ATACCAATAA
1991677 TAATATATCATTTTATTATTAAT
1 TAATATATCATTTTATTATTAAT
1991700 TAATA-ATACATTTTA-TATTAA
1 TAATATAT-CATTTTATTATTAA
1991721 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATATCATTTTATTATTAAT
Found at i:1992534 original size:24 final size:21
Alignment explanation
Indices: 1992494--1992537 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
1992484 CTGCCCATAT
1992494 TATTTTTAATTTTTTTTAAAA
1 TATTTTTAATTTTTTTTAAAA
1992515 TATTTGTTATATTTTATTTTAAA
1 TATTT-TTA-ATTTT-TTTTAAA
1992538 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 5 0.25
24 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTTAATTTTTTTTAAAA
Found at i:1996983 original size:190 final size:189
Alignment explanation
Indices: 1996661--1997040 Score: 706
Period size: 190 Copynumber: 2.0 Consensus size: 189
1996651 GAGTAAACAA
*
1996661 CCAAGAAGCAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
1996726 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
66 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
*
1996791 TAAGAATAAGAGAAACTACCTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
131 TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
* *
1996850 CCAAGAAACGAAACAATACCCAGGAAAGAATTCACCTAGATTTCATCTGTCATTATCAATCTAAA
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCA-CTAGATTTCATCTGTCATTATCAATCTAAA
1996915 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
65 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
*
1996980 TTAAGAATAAGAGAAATTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
130 TTAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
1997040 C
1 C
1997041 TATTATCGCA
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
189 31 0.17
190 154 0.83
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (189 bp):
CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
Found at i:1998415 original size:16 final size:16
Alignment explanation
Indices: 1998394--1998430 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1998384 ATGGATCTCA
*
1998394 ATAATTGCAAATAATG
1 ATAATTGCAAAGAATG
1998410 ATAATTGCAAAGAATG
1 ATAATTGCAAAGAATG
1998426 ATAAT
1 ATAAT
1998431 AAACAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (16 bp):
ATAATTGCAAAGAATG
Found at i:1998790 original size:2 final size:2
Alignment explanation
Indices: 1998785--1998810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1998775 GGTTGTTAGA
1998785 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
1998811 GAATTTAAAG
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:2000401 original size:2 final size:2
Alignment explanation
Indices: 2000347--2000384 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2000337 GAATTTACCA
2000347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2000385 TGGTCATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2000823 original size:16 final size:16
Alignment explanation
Indices: 2000802--2000836 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2000792 TATATGTGGA
2000802 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
2000818 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
2000834 AAA
1 AAA
2000837 AAAACTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:2001008 original size:31 final size:31
Alignment explanation
Indices: 2000956--2001018 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2000946 CCTTAAATTT
* * *
2000956 ATTCATTGCATCTGTTAGAAAAATCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
*
2000987 ATTCATTACATCAGTTGGAAAAAGCAGATTG
1 ATTCATTACATCAGTTAGAAAAAGCAGATTG
2001018 A
1 A
2001019 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (31 bp):
ATTCATTACATCAGTTAGAAAAAGCAGATTG
Found at i:2001630 original size:2 final size:2
Alignment explanation
Indices: 2001617--2001648 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2001607 GGCCTTTATT
2001617 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
2001649 TAAAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2003954 original size:23 final size:23
Alignment explanation
Indices: 2003908--2003951 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2003898 ATACCAATAA
2003908 TAATATATCATTTTATTATTAAT
1 TAATATATCATTTTATTATTAAT
2003931 TAATA-ATACATTTTA-TATTAA
1 TAATATAT-CATTTTATTATTAA
2003952 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATATCATTTTATTATTAAT
Found at i:2004764 original size:24 final size:21
Alignment explanation
Indices: 2004724--2004767 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
2004714 CTGCCCATAT
2004724 TATTTTTAATTTTTTTTAAAA
1 TATTTTTAATTTTTTTTAAAA
2004745 TATTTGTTATATTTTATTTTAAA
1 TATTT-TTA-ATTTT-TTTTAAA
2004768 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 5 0.25
24 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTTAATTTTTTTTAAAA
Found at i:2008141 original size:190 final size:189
Alignment explanation
Indices: 2007819--2008198 Score: 706
Period size: 190 Copynumber: 2.0 Consensus size: 189
2007809 GAGTAAACAA
*
2007819 CCAAGAAGCAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
2007884 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
66 TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
*
2007949 TAAGAATAAGAGAAACTACCTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
131 TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
* *
2008008 CCAAGAAACGAAACAATACCCAGGAAAGAATTCACCTAGATTTCATCTGTCATTATCAATCTAAA
1 CCAAGAAACAAAACAATACCCAAGAAAGAATTCA-CTAGATTTCATCTGTCATTATCAATCTAAA
2008073 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
65 TTACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCT
*
2008138 TTAAGAATAAGAGAAATTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
130 TTAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
2008198 C
1 C
2008199 TATTATCGCA
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
189 31 0.17
190 154 0.83
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (189 bp):
CCAAGAAACAAAACAATACCCAAGAAAGAATTCACTAGATTTCATCTGTCATTATCAATCTAAAT
TACGCAATTTCTTCACTTAGTATCTTGATCCGTAGAAATTCCTTAATTATGCTAATATCTCTCTT
TAAGAATAAGAGAAACTAACTCTAGATTGACTAATTGAAATTTCTTTCTAATTAAAACC
Found at i:2011519 original size:2 final size:2
Alignment explanation
Indices: 2011512--2011541 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2011502 AGGATTTACC
2011512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2011542 TGGTCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2022446 original size:31 final size:32
Alignment explanation
Indices: 2022387--2022448 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
2022377 AATAGCCTAA
*
2022387 TGACTTAAATAAAAAAATTTTAAATAGTTCAG
1 TGACTTAAATAAAAAAATTTCAAATAGTTCAG
* *
2022419 TGACTTAAAT-GAAAACTTTCAAATAGTTCA
1 TGACTTAAATAAAAAAATTTCAAATAGTTCA
2022449 ATAATCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (32 bp):
TGACTTAAATAAAAAAATTTCAAATAGTTCAG
Found at i:2022582 original size:28 final size:28
Alignment explanation
Indices: 2022537--2022596 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2022527 TTACCCATTA
2022537 AAAAACACTAAAAATATTTTTATAAA-AT
1 AAAAACACTAAAAATATTTTT-TAAATAT
* * *
2022565 AAAAACATTTAAATTATTTTTTAAATAT
1 AAAAACACTAAAAATATTTTTTAAATAT
2022593 AAAA
1 AAAA
2022597 TTGATATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAACACTAAAAATATTTTTTAAATAT
Found at i:2026961 original size:30 final size:29
Alignment explanation
Indices: 2026927--2026986 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
2026917 TGACCTACTA
2026927 ATCAACTTGTAACTTTTAAATAATTCAATG
1 ATCAACTTGTAACTTTTAAA-AATTCAATG
* * *
2026957 ATCAATTTGTAACTTTTGAAAATTGAATG
1 ATCAACTTGTAACTTTTAAAAATTCAATG
2026986 A
1 A
2026987 CAAAAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (29 bp):
ATCAACTTGTAACTTTTAAAAATTCAATG
Found at i:2031158 original size:21 final size:21
Alignment explanation
Indices: 2031119--2031159 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2031109 TGTAATTATT
*
2031119 ATTAAATCAAAGATTAAATCA
1 ATTAAATCAAAGATCAAATCA
2031140 ATTAAATCAATA-ATCAAATC
1 ATTAAATCAA-AGATCAAATC
2031160 GGTTTGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTAAATCAAAGATCAAATCA
Found at i:2041207 original size:31 final size:31
Alignment explanation
Indices: 2041150--2041208 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2041140 CCTAGTGATG
* *
2041150 ACTTAAATAAAAAGTTTCAAATAGTTTAGTA
1 ACTTAAATAAAAAATTTCAAACAGTTTAGTA
*
2041181 ACTTAAATGAAAAAATTT-GAACAGTTTA
1 ACTTAAAT-AAAAAATTTCAAACAGTTTA
2041209 ATGACCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.67
32 8 0.33
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCAAACAGTTTAGTA
Found at i:2042673 original size:14 final size:14
Alignment explanation
Indices: 2042654--2042692 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
2042644 GAGTAAAACG
2042654 TAAATTAAAAATTT
1 TAAATTAAAAATTT
2042668 TAAATTAAAAATTT
1 TAAATTAAAAATTT
2042682 TAAATTAAAAA
1 TAAATTAAAAA
2042693 AGAAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTAAAAATTT
Found at i:2051025 original size:43 final size:42
Alignment explanation
Indices: 2050959--2051041 Score: 139
Period size: 43 Copynumber: 2.0 Consensus size: 42
2050949 TCCTAATTCA
2050959 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
* *
2051001 GAAAATAGTTTTCCTTATTTTAATAAACTACTAAAACATAA
1 GAAAATAG-TTCCCTTATTCTAATAAACTACTAAAACATAA
2051042 ATAAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 8 0.21
43 30 0.79
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
Found at i:2055774 original size:46 final size:46
Alignment explanation
Indices: 2055707--2055878 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
2055697 AACCCGCCCC
* *
2055707 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
2055753 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
2055801 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
2055846 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
2055879 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 59 0.56
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:2055820 original size:93 final size:93
Alignment explanation
Indices: 2055712--2055882 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
2055702 GCCCCTAAGT
* *
2055712 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2055777 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
2055805 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2055870 CGAGTTCGGATGC
66 CGAGTTCGGATGC
2055883 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2056333 original size:30 final size:30
Alignment explanation
Indices: 2056299--2056358 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2056289 ATTTAATACG
2056299 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
2056329 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
2056359 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:2057408 original size:18 final size:18
Alignment explanation
Indices: 2057385--2057427 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2057375 AATATGAATA
2057385 AAATTTATC-ACCTAAAT
1 AAATTTATCTACCTAAAT
2057402 AAGATTTATCTACCTAAAT
1 AA-ATTTATCTACCTAAAT
2057421 AAATTTA
1 AAATTTA
2057428 AAATATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 10 0.42
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:2063229 original size:53 final size:53
Alignment explanation
Indices: 2063166--2063271 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2063156 AACTCCTCCA
2063166 ACACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
1 ACACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
2063219 ACACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
1 ACACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
2063272 TTTGCCTCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (53 bp):
ACACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
Found at i:2063251 original size:29 final size:29
Alignment explanation
Indices: 2063165--2063254 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 29
2063155 CAACTCCTCC
2063165 AACACCTTCTGTAGCCAAATAAGCTCACA
1 AACACCTTCTGTAGCCAAATAAGCTCACA
* ***
2063194 AACACC-T-TG-AGCC--ATAACCTTGTA
1 AACACCTTCTGTAGCCAAATAAGCTCACA
*
2063218 TACACCTTCTGTAGCCAAATAAGCTCACA
1 AACACCTTCTGTAGCCAAATAAGCTCACA
2063247 AACACCTT
1 AACACCTT
2063255 GAGCCATAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
24 12 0.26
25 1 0.02
26 6 0.13
27 6 0.13
28 1 0.02
29 20 0.43
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.23
Consensus pattern (29 bp):
AACACCTTCTGTAGCCAAATAAGCTCACA
Found at i:2063725 original size:43 final size:44
Alignment explanation
Indices: 2063664--2063761 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 44
2063654 TCCTAATTGG
*
2063664 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAAATA
*
2063707 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAAATA
*
2063751 -AAAATATTTCT
1 GAAAATAGTTCT
2063762 AGAATATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (44 bp):
GAAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:2063774 original size:43 final size:43
Alignment explanation
Indices: 2063664--2063775 Score: 104
Period size: 43 Copynumber: 2.6 Consensus size: 43
2063654 TCCTAATTGG
* * * *
2063664 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
1 GAAAATAGTTCTCTGAATATAATAAACTACTAAAACATAAAAA
* * * *
2063707 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCTCTGAATATAATAAACTACTAAAACATAAAA-A
2063751 -AAAATA-TT-TCTAGAATATGAATAAA
1 GAAAATAGTTCTCT-GAATAT-AATAAA
2063776 ACTTATCTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 3 0.05
42 5 0.08
43 52 0.85
44 1 0.02
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (43 bp):
GAAAATAGTTCTCTGAATATAATAAACTACTAAAACATAAAAA
Found at i:2063800 original size:19 final size:18
Alignment explanation
Indices: 2063778--2063817 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2063768 TGAATAAAAC
2063778 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
2063797 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
2063815 TTA
1 TTA
2063818 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:2067502 original size:43 final size:44
Alignment explanation
Indices: 2067441--2067533 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
2067431 TCCTAATTGG
*
2067441 GAAAATAATTCCCTTATTCTAATAAACTACTAAAATATAAAA-A
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
*
2067484 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
2067528 -AAAATA
1 GAAAATA
2067534 TTTCTAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (44 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
Found at i:2067577 original size:19 final size:18
Alignment explanation
Indices: 2067555--2067594 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2067545 TGAATAAAAC
2067555 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
* *
2067574 TTATTTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
2067592 TTA
1 TTA
2067595 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:2068634 original size:66 final size:67
Alignment explanation
Indices: 2068528--2068660 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 67
2068518 GTGCTCGTGG
**
2068528 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCATCCACTCTTGG-ATAATAT
1 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
2068592 AT
66 AT
2068594 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
1 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
2068659 AT
66 AT
2068661 TCATTTTTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 55 0.86
67 9 0.14
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (67 bp):
GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
AT
Found at i:2073009 original size:29 final size:29
Alignment explanation
Indices: 2072977--2073036 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2072967 ATCCATATCC
2072977 TTGTTTAAAGCAATTTTCTAGTTTTAGTT
1 TTGTTTAAAGCAATTTTCTAGTTTTAGTT
2073006 TTGTTTAAAGCAATTTTCTAGTTTTAGTT
1 TTGTTTAAAGCAATTTTCTAGTTTTAGTT
2073035 TT
1 TT
2073037 CACTTATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (29 bp):
TTGTTTAAAGCAATTTTCTAGTTTTAGTT
Found at i:2073781 original size:48 final size:47
Alignment explanation
Indices: 2073706--2074204 Score: 192
Period size: 48 Copynumber: 10.4 Consensus size: 47
2073696 CCAATTGGAG
* * * * *
2073706 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCA-AACCAGGCA
* * *
2073754 CTCCAATAGGAGCACCAACTCCAAGTGCACCAGCTGC-AACACACGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAAAC-CA-GGCA
* * * * * *
2073802 CACCAGTAGGAGCAGCACCTCC-TGGGGAAGCAGCTGCAAAACAAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAA-CAGCTGC-AAACCAGGCA
* *** * *
2073850 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * *
2073898 TGCCAATAGGAGCACCACCTCC-TG-GCACAGCAGCTGCAACACCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
* *
2073946 CACCAGTAGGAGCACCACCTCC---TGACACACCAACTGCAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTG-CA-A-CAGCTGCAA-ACCAGGCA
* * * *
2073994 TGA-CAATGGGAGCACCACCTCC-TG-GCACACCAGCTGCAACAGCAGGCA
1 -CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
*** * * * ** * * *
2074042 TGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
*** * * * * *
2074090 TGGCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCAGACA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * * * * * * *
2074138 TGCCAATTGGAGCAACTCCTACC-AGTGCAGCAGCTCCAGCAGCAGGCA
1 CACCAATAGGAGCACCACCT-CCAAGTGCAACAGCTGCA-AACCAGGCA
* *
2074186 CACCTATAGAAGCACCACC
1 CACCAATAGGAGCACCACC
2074205 ACCTGGCACT
Statistics
Matches: 353, Mismatches: 79, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
46 5 0.01
47 10 0.03
48 323 0.92
49 10 0.03
50 5 0.01
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (47 bp):
CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAAACCAGGCA
Found at i:2073966 original size:144 final size:142
Alignment explanation
Indices: 2073706--2074111 Score: 363
Period size: 144 Copynumber: 2.8 Consensus size: 142
2073696 CCAATTGGAG
* ** * **
2073706 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCACT-CCAATAGGAGCACC
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCA-TGCCAATAGGAGCACC
* * ** *
2073770 AACTCCAAGTGCAC-CAGCTGCAACACACGGCACACCAGTAGGAGCAGCACCTCCTGGGGA-AGC
64 AACTCC-TG-GCACACAGCTGCAACAC-CGGCACACCAGTAGGAGCACCACCTCCT-GACACACC
*
2073833 AGCTGCAAAACAAGGCA-
125 AACTGCAAAACAAGGCAT
* *
2073850 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCA
1 CACCAATAGGAGCACCATCTCT-GGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
*
2073915 CCTCCTGGCACAGCAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
* *
2073980 TGCAACACCAGGCAT
128 TGCAAAACAAGGCAT
* * * ** * * * * *
2073995 GA-CAATGGGAGCACCACCTCCTGGCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCA
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
* * * *** *
2074059 TCTCCTGGTACATCAGCTGGAACACCAGGCATGGCAATAGGAGCACCACCTCC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCC
2074112 CAGTACATCA
Statistics
Matches: 217, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
142 4 0.02
143 6 0.03
144 204 0.94
145 3 0.01
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (142 bp):
CACCAATAGGAGCACCATCTCTGGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCAA
CTCCTGGCACACAGCTGCAACACCGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGC
AAAACAAGGCAT
Found at i:2074033 original size:96 final size:96
Alignment explanation
Indices: 2073736--2074134 Score: 304
Period size: 96 Copynumber: 4.2 Consensus size: 96
2073726 CCCAGTGCAT
** * * * ** *
2073736 CAGCTGCAGTACCAGGCACTCCAATAGGAGCACCAACTCC-AAGTGCACCAGCTGCAACA-CACG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGA-CACACCAACTGCAACACCA-G
* * * * *
2073799 GCA-CACCAGTAGGAGCAGCACCTCCTGGGGA-AG
64 GCATGA-CAATAGGAGCACCACCTCCT-GGCACAC
* * * *** * * * *
2073832 CAGCTGCAAAACAAGGCACACCAATAGGAGCACCATCT-CTGGGTGCAACAGCTGCAACATCGGG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCT-GACACACCAACTGCAACACCAGG
* *
2073896 CATGCCAATAGGAGCACCACCTCCTGGCACAG
65 CATGACAATAGGAGCACCACCTCCTGGCACAC
* *
2073928 CAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
*
2073993 ATGACAATGGGAGCACCACCTCCTGGCACAC
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
* *** * * * ** * * *
2074024 CAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
* ** * *
2074089 ATGGCAATAGGAGCACCACCTCCCAGTACAT
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
*
2074120 CAGTTGCAACACCAG
1 CAGCTGCAACACCAG
2074135 ACATGCCAAT
Statistics
Matches: 246, Mismatches: 51, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
95 4 0.02
96 239 0.97
97 3 0.01
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.12
Consensus pattern (96 bp):
CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
ATGACAATAGGAGCACCACCTCCTGGCACAC
Found at i:2074172 original size:144 final size:143
Alignment explanation
Indices: 2073874--2074213 Score: 333
Period size: 144 Copynumber: 2.4 Consensus size: 143
2073864 CCATCTCTGG
* *
2073874 GTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
* * * *
2073939 CCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATGACAATGGG
66 CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATGGG
* *
2074004 AGCACCACCTCCT
131 AGCAACACCTCCA
* * * * * * *
2074017 G-GCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAA
1 GTGCA-A-CAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAA
*** * * ** *
2074081 CACCAGGCATGGCAATAGGAGCACCACCTCCCAG-TACATCAGTTGCAACACCAGACATGCCAAT
64 CACCAGGCACACCAATAGGAGCACCACCT-CCAGACACACCAACTGCAACACCAGACATGACAAT
* *
2074145 TGGAGCAACTCCTACCA
128 GGGAGCAACACCT-CCA
* * * ** * * *
2074162 GTGCAGCAGCTCCAGCAGCAGGCACACCTATAGAAGCACCACCACCTGGCAC
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCAC
2074214 TCAAGCTGAA
Statistics
Matches: 154, Mismatches: 38, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
142 3 0.02
143 2 0.01
144 140 0.91
145 6 0.04
146 3 0.02
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (143 bp):
GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATGGG
AGCAACACCTCCA
Found at i:2074359 original size:39 final size:39
Alignment explanation
Indices: 2074287--2074381 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
2074277 AGGCATGGCG
*
2074287 ACAGGAGCACCACCTCCAGCAGCAAAGAAAGGCACAACA
1 ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
* * **
2074326 ACAGGAGCATCACCTCCAGCAG-AAACATCAGGCATGACA
1 ACAGGAGCACCACCTCCAGCAGCAAACA-AAGGCACAACA
* *
2074365 ACAAGAGCACCAACTCC
1 ACAGGAGCACCACCTCC
2074382 TGATGCACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.41, C:0.34, G:0.19, T:0.06
Consensus pattern (39 bp):
ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
Found at i:2074529 original size:48 final size:48
Alignment explanation
Indices: 2074394--2074532 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 48
2074384 ATGCACCAGA
* * * *
2074394 TGCACCAGATGCAACACCTGGCAAGCCAATAGAAGCACCACCTCCTGG
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * **
2074442 TGCACCAGCTTCAAGACCAGGTACGCCAATAGGTTCACCACCTCCTGC
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * *
2074490 TGCGCTAGCTGCAACAACAGGCATGCCAGTAGGAGCACCACCT
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCT
2074533 ACCAGTGCAC
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.28, C:0.35, G:0.22, T:0.15
Consensus pattern (48 bp):
TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
Found at i:2074751 original size:48 final size:48
Alignment explanation
Indices: 2074699--2074791 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
2074689 TCAACTCCTG
* *
2074699 GTGCACCAG-CAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTT
1 GTGCACCAGCCA-CAACACCAAGCACACCAATAGGAACACCACCTCTTT
* * *
2074747 GTGCACCGGCCACAACACCAAGCACGCCAATAGGAGCACCACCTC
1 GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTC
2074792 CCAATGCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.32, C:0.39, G:0.18, T:0.11
Consensus pattern (48 bp):
GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTCTTT
Found at i:2074811 original size:48 final size:48
Alignment explanation
Indices: 2074700--2074840 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
2074690 CAACTCCTGG
** * * ****
2074700 TGCACCAGCAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTTG
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
*
2074748 TGCACCGGCCA-CAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
1 TGCACCAG-CAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
* ** * * * *
2074796 TGCACCAGCTGCAACAGTAGGAAAGCCAATTGGAGCACCACCTCC
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCC
2074841 TGGTGCACCT
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
47 1 0.01
48 71 0.96
49 2 0.03
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.11
Consensus pattern (48 bp):
TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
Found at i:2078026 original size:17 final size:19
Alignment explanation
Indices: 2078006--2078043 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2077996 CAGGGGAAGG
2078006 AAGAAAG-A-AAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
2078023 AAGAAAGAAGAAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
2078042 AA
1 AA
2078044 TTGAAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAGAAAAGAGAA
Found at i:2085651 original size:32 final size:32
Alignment explanation
Indices: 2085599--2085670 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
2085589 TGGCAAACTC
*
2085599 AAATGACCCTAAACCAAAACAACCCGAACATG
1 AAATGACCCTAAACCAAAACAACACGAACATG
* *
2085631 AAATGACCC-AAACCCGAAACAACATGAACATG
1 AAATGACCCTAAA-CCAAAACAACACGAACATG
*
2085663 AATTGACC
1 AAATGACC
2085671 TGAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.49, C:0.29, G:0.11, T:0.11
Consensus pattern (32 bp):
AAATGACCCTAAACCAAAACAACACGAACATG
Found at i:2091899 original size:18 final size:18
Alignment explanation
Indices: 2091844--2091900 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
2091834 ACCGTTTACG
2091844 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
2091862 GCACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
2091880 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
2091898 GTA
1 GTA
2091901 GTTGGGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:2098571 original size:15 final size:16
Alignment explanation
Indices: 2098536--2098569 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2098526 AGTTAGACCT
2098536 AAATTTTAAAATCTAA
1 AAATTTTAAAATCTAA
2098552 AAATTCTTAAAA-CTAA
1 AAATT-TTAAAATCTAA
2098568 AA
1 AA
2098570 TTACATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTTAAAATCTAA
Found at i:2101088 original size:28 final size:28
Alignment explanation
Indices: 2101057--2101132 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
2101047 TTGCACTTCG
* *
2101057 CCACTTCGTGGTGTCATCTCGAAGTTCT
1 CCACTTCGTGGAGACATCTCGAAGTTCT
** *
2101085 CCACTTCGCAGAGACATCTCGTAGTTCT
1 CCACTTCGTGGAGACATCTCGAAGTTCT
*
2101113 CCACTT-GTGGAGACAGCTCG
1 CCACTTCGTGGAGACATCTCG
2101133 CACTTCACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.18, C:0.30, G:0.22, T:0.29
Consensus pattern (28 bp):
CCACTTCGTGGAGACATCTCGAAGTTCT
Found at i:2101794 original size:18 final size:19
Alignment explanation
Indices: 2101758--2101794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2101748 ATATGAGGAA
2101758 ATTGAATTTTAGTATTAAAC
1 ATTGAATTTTAG-ATTAAAC
2101778 ATTGAATTTTA-ATTAAA
1 ATTGAATTTTAGATTAAA
2101795 TTTTACCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTGAATTTTAGATTAAAC
Done.