Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 7 of 14
Found at i:1600833 original size:30 final size:30
Alignment explanation
Indices: 1600792--1600893 Score: 118
Period size: 30 Copynumber: 3.3 Consensus size: 30
1600782 ATTATGCCTG
1600792 AAAAA-AAAGAGACAAAAAAAACAACAAAA
1 AAAAACAAAGAGACAAAAAAAACAACAAAA
1600821 AAAAACAAAGAGACAAAAAAAA-AACAAAA
1 AAAAACAAAGAGACAAAAAAAACAACAAAA
* * *
1600850 AAACAACAAAAAAACAAAAAGGAAAACAAAAAACA
1 AAA-AACAAAGAGAC-AAAA--AAAACAACAAA-A
1600885 AAAAACAAA
1 AAAAACAAA
1600894 AAAATAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
29 15 0.24
30 25 0.40
31 4 0.06
33 4 0.06
34 11 0.17
35 4 0.06
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (30 bp):
AAAAACAAAGAGACAAAAAAAACAACAAAA
Found at i:1600838 original size:27 final size:25
Alignment explanation
Indices: 1600808--1600897 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 25
1600798 AAGAGACAAA
*
1600808 AAAAACAACAAAAAAAAACAAAGAGAC
1 AAAAA-AACAAAAAAAAACAAA-AAAC
* *
1600835 -AAAAAA-AAAACAAAA-AAACAAC
1 AAAAAAACAAAAAAAAACAAAAAAC
1600857 AAAAAAACAAAAAGGAAAACAAAAAAC
1 AAAAAAACAAAAA--AAAACAAAAAAC
1600884 -AAAAAACAAAAAAA
1 AAAAAAACAAAAAAA
1600898 TAAAAAGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 2 0.04
23 9 0.17
24 14 0.26
25 2 0.04
26 20 0.38
27 6 0.11
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAACAAAAAAC
Found at i:1600841 original size:19 final size:19
Alignment explanation
Indices: 1600792--1600897 Score: 99
Period size: 19 Copynumber: 5.4 Consensus size: 19
1600782 ATTATGCCTG
1600792 AAAAAAAAGAGACAAAAAAAAC
1 AAAAAAAA-A-AC-AAAAAAAC
* *
1600814 AACAAAAAAAAACAAAGAGAC
1 -A-AAAAAAAAACAAAAAAAC
1600835 AAAAAAAAAACAAAAAAAC
1 AAAAAAAAAACAAAAAAAC
* *
1600854 AACAAAAAAACAAAAAGGA-
1 AAAAAAAAAACAAAAA-AAC
*
1600873 AAACAAAAAAC-AAAAAAC
1 AAAAAAAAAACAAAAAAAC
1600891 AAAAAAA
1 AAAAAAA
1600898 TAAAAAGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
17 1 0.01
18 10 0.14
19 40 0.57
20 2 0.03
21 6 0.09
22 2 0.03
23 2 0.03
24 7 0.10
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAACAAAAAAAC
Found at i:1600849 original size:8 final size:8
Alignment explanation
Indices: 1600819--1600903 Score: 68
Period size: 8 Copynumber: 10.6 Consensus size: 8
1600809 AAAACAACAA
1600819 AAAAAAAC
1 AAAAAAAC
* *
1600827 AAAGAGAC
1 AAAAAAAC
1600835 AAAAAAA-
1 AAAAAAAC
*
1600842 AAACAAA-
1 AAAAAAAC
*
1600849 AAAACAAC
1 AAAAAAAC
1600857 AAAAAAAC
1 AAAAAAAC
*
1600865 AAAAAGGAAA
1 AAAAA--AAC
1600875 ACAAAAAAC
1 A-AAAAAAC
1600884 -AAAAAAC
1 AAAAAAAC
*
1600891 AAAAAAAT
1 AAAAAAAC
1600899 AAAAA
1 AAAAA
1600904 GAAAAATCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
7 18 0.30
8 34 0.56
9 2 0.03
10 3 0.05
11 4 0.07
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1600908 original size:19 final size:18
Alignment explanation
Indices: 1600805--1600908 Score: 72
Period size: 18 Copynumber: 5.7 Consensus size: 18
1600795 AAAAAGAGAC
*
1600805 AAAAAAA-ACAACAAAAA
1 AAAAAAAGAAAACAAAAA
*
1600822 AAAACAAAG-AGACAAAAA
1 AAAA-AAAGAAAACAAAAA
*
1600840 AAAAACAAAAAAACAACAAA
1 AAAAA-AAGAAAACAA-AAA
* **
1600860 AAAACAA-AAAGGAAAACA
1 AAAAAAAGAAAACAAAA-A
1600878 AAAAACAA-AAAACAAAAA
1 AAAAA-AAGAAAACAAAAA
1600896 AATAAAAAGAAAA
1 AA-AAAAAGAAAA
1600909 ATCAAGATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.10
18 31 0.46
19 23 0.34
20 7 0.10
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAAACAAAAA
Found at i:1600909 original size:40 final size:39
Alignment explanation
Indices: 1600807--1600909 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 39
1600797 AAAGAGACAA
* *
1600807 AAAAAACAACAAAAAAAAACAAAGAGACAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAAACAAAAAGACAAAAAAAAAAC
* * *
1600846 AAAAAA-ACAACAAAAAAACAAAAAGGA-AAACAAAAAAC
1 AAAAAACAAAAAAAAAAAACAAAAA-GACAAAAAAAAAAC
*
1600884 AAAAAACAAAAAAATAAAAAGAAAAA
1 AAAAAACAAAAAAA-AAAAACAAAAA
1600910 TCAAGATGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 30 0.57
39 13 0.25
40 10 0.19
ACGTcount: A:0.83, C:0.11, G:0.05, T:0.01
Consensus pattern (39 bp):
AAAAAACAAAAAAAAAAAACAAAAAGACAAAAAAAAAAC
Found at i:1601985 original size:73 final size:73
Alignment explanation
Indices: 1601758--1602161 Score: 571
Period size: 73 Copynumber: 5.4 Consensus size: 73
1601748 TTTCTTTCAA
* *
1601758 GAGGTATTTTTAAATTTCTGCATTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTGAGCC
1 GAGGTATTTTTAAATTTCTG--TTTTTT--TAAAATCAACTCATAATACAGAGGTGAGTTGAGCC
1601823 TCGGGTCACGCT
62 TCGGGTCACGCT
1601835 GAGGTATTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
1 GAGGTATTTTTAAATTTCTGTTTTTTT---AAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
1601900 CGGGTCACGCT
63 CGGGTCACGCT
* *
1601911 GAGGTATTTTTAAATTTCTATTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 GAGGTATTTTTAAATTTCTGTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
1601976 GTCGCGCT
66 GTCACGCT
* *
1601984 GAGGTGTTTTT-AATTTATGTCTTTTTTTTAAAAAAAATCAACTCATAATACAGAGGTGAGTTGA
1 GAGGTATTTTTAAATTTCTG---TTTTTTT----AAAATCAACTCATAATACAGAGGTGAGTTGA
1602048 GCCTCGGGTCACGCT
59 GCCTCGGGTCACGCT
1602063 GAGGTATTTTT-AATTTCTGTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 GAGGTATTTTTAAATTTCTGT-TTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1602127 GGTCACGCT
65 GGTCACGCT
* *
1602136 GAGGTA-TTTTCAACTTCTGTTTTTTT
1 GAGGTATTTTTAAATTTCTGTTTTTTT
1602162 TTAAAAAAAA
Statistics
Matches: 302, Mismatches: 13, Indels: 29
0.88 0.04 0.08
Matches are distributed among these distances:
72 16 0.05
73 114 0.38
75 13 0.04
76 72 0.24
77 26 0.09
79 61 0.20
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (73 bp):
GAGGTATTTTTAAATTTCTGTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
GTCACGCT
Found at i:1602067 original size:152 final size:151
Alignment explanation
Indices: 1601758--1602916 Score: 861
Period size: 152 Copynumber: 7.4 Consensus size: 151
1601748 TTTCTTTCAA
*
1601758 GAGGTATTTTTAAATTTCTGCATTTTTTCAAAAAATCAACTCATAATAC-AAAGGTGAGTTGAGC
1 GAGGTATTTTTAAATTTCTG--TTTTTT--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGC
* * *
1601822 CTCGGGTCACGCTGAGGTATTTTTAAATTTCTG--TTTTTTTCAAAAAATCAACTCATAATACAG
62 CTCGGGTCACGCTGAGGTATTTTT-AATTTATGTCTTTTTTTTAAAAAATCAACTCATATTACAG
1601885 AGGTGAGTTGAGCCTCGGGTCACGCT
126 AGGTGAGTTGAGCCTCGGGTCACGCT
* **
1601911 GAGGTATTTTTAAATTTCTATTTTTTTTAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCG
1 GAGGTATTTTTAAATTTCTGTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
* * *
1601975 GGTCGCGCTGAGGTGTTTTTAATTTATGTCTTTTTTTTAAAAAAAATCAACTCATAATACAGAGG
66 GGTCACGCTGAGGTATTTTTAATTTATGTCTTTTTTTT--AAAAAATCAACTCATATTACAGAGG
1602040 TGAGTTGAGCCTCGGGTCACGCT
129 TGAGTTGAGCCTCGGGTCACGCT
*
1602063 GAGGTATTTTT-AATTTCTGTCTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC
1 GAGGTATTTTTAAATTTCTGT-TTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
* * * * *
1602126 GGGTCACGCTGAGGTATTTTCAACTTCTGT-TTTTTTTTAAAAAAAATCAACTCATCCTTTTTTT
65 GGGTCACGCTGAGGTATTTTTAATTTATGTCTTTTTTTT--AAAAAATCAACTCA-----TATTA
* * ** * * * ** * *
1602190 TAAAAATCAACTCATAATAC-CGAGGTGAGTTGAGCCT
123 CAGAGGT-GAGT--TGAGCCTCG-GGTCA----CG-CT
* * * *
1602227 CGGGTCACGCTGAGGTATTTTTAATTTCTGTCTTTTTTAAAATCAATTCATAATAC-AGAGGTGA
1 ---G--A-GGT-A--T-TTTTAAATTTCTGT-TTTTTAAAAATCAACTCATAATACGAGAGGTGA
1602291 GTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTC-TTTTTTT-AAAAATCAACTCATA
55 GTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTCTTTTTTTTAAAAAATCAACTCATA
* ** *
1602354 ATACAGAGGTGAGTTGAGCCTTAGGTCACTCT
120 TTACAGAGGTGAGTTGAGCCTCGGGTCACGCT
* * * * *
1602386 GAGGTATTTTT-AATTTATGTCTTTTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC
1 GAGGTATTTTTAAATTTCTGT-TTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
** * * * * *
1602450 GGACCATGCCGAGGTATTTCTTTTAAATTTATG----TTTTTCAAAAAATCAACTAATATTGCGA
65 GGGTCACGCTGAGGTA--T-TTTT-AATTTATGTCTTTTTTTTAAAAAATCAACTCATATTAC-A
* ** * *
1602511 GAGGTGAGTTGAGCCTTGGACCATGCC
125 GAGGTGAGTTGAGCCTCGGGTCACGCT
* * * *
1602538 AAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 GAGGTA--T-TTTTAAATTTCTGTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCC
** * * * * * * *
1602603 TCGGACCATGCCGAGGTATTTCTT--TTAAATTTC-TGTTTTTCAAAAATCAACTCATATTGCGA
63 TCGGGTCACGCTGAGGTATTT-TTAATT-TATGTCTTTTTTTTAAAAAATCAACTCATATTAC-A
*
1602665 GAGGTGAGTTGAGCCTCGGGTCACATGCC
125 GAGGTGAGTTGAGCCTCGGGTCAC--GCT
* * *
1602694 GAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 GAGGTA--T-TTTTAAATTTCTGTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCC
* * * * * * *
1602759 TTGGGTCGCATGCTGAGGTATTTCTT--TTAAATTTC-TGTTTTTCAAAAATCAACTCATATTGC
63 TCGGGT--CACGCTGAGGTATTT-TTAATT-TATGTCTTTTTTTTAAAAAATCAACTCATATTAC
* * * * *
1602821 GAGATGTGAGTTGAGCTTTGGGTTACGCC
124 -AGAGGTGAGTTGAGCCTCGGGTCACGCT
* * * * *
1602850 GAGATATTTTTCAA-TTCATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 GAGGTATTTTTAAATTTC-TGTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1602914 GGG
65 GGG
1602917 GCACATGTCG
Statistics
Matches: 855, Mismatches: 98, Indels: 106
0.81 0.09 0.10
Matches are distributed among these distances:
148 37 0.04
149 86 0.10
150 15 0.02
151 57 0.07
152 162 0.19
153 86 0.10
154 47 0.05
155 60 0.07
156 92 0.11
157 2 0.00
158 77 0.09
159 9 0.01
163 1 0.00
164 9 0.01
166 2 0.00
167 6 0.01
169 1 0.00
170 2 0.00
171 1 0.00
172 13 0.02
173 1 0.00
174 4 0.00
175 85 0.10
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (151 bp):
GAGGTATTTTTAAATTTCTGTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGGTATTTTTAATTTATGTCTTTTTTTTAAAAAATCAACTCATATTACAGAGGTG
AGTTGAGCCTCGGGTCACGCT
Found at i:1602215 original size:102 final size:100
Alignment explanation
Indices: 1602084--1602268 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 100
1602074 AATTTCTGTC
1602084 TTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAA
1 TTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAA
*
1602149 CTTCTGTTTTTTTTTAAAAAAAATCAACTCATCCTT
66 CTTCTG-TCTTTTTTAAAAAAAATCAACTCATCCTT
* *
1602185 TTTTTTAAAAATCAACTCATAATACCGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTA
1 TTTTTT-AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCA
*
1602250 ATTTCTGTCTTTTTTAAAA
65 ACTTCTGTCTTTTTTAAAA
1602269 TCAATTCATA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 17 0.22
102 62 0.78
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (100 bp):
TTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAA
CTTCTGTCTTTTTTAAAAAAAATCAACTCATCCTT
Found at i:1602307 original size:175 final size:175
Alignment explanation
Indices: 1602016--1602343 Score: 602
Period size: 175 Copynumber: 1.9 Consensus size: 175
1602006 TTTTTTTAAA
1602016 AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCT
1 AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCT
1602081 GTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
66 GTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
* *
1602146 CAACTTCTGTTTTTTTTTAAAAAAAATCAACTCATCCTTTTTTTT
131 CAACTTATGTCTTTTTTTAAAAAAAATCAACTCATCCTTTTTTTT
*
1602191 AAAAATCAACTCATAATACCGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCT
1 AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCT
*
1602256 GTCTTTTTTAAAATCAATTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
66 GTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
* *
1602321 TAATTTATGTCTTTTTTTAAAAA
131 CAACTTATGTCTTTTTTTAAAAA
1602344 TCAACTCATA
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 147 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (175 bp):
AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCT
GTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
CAACTTATGTCTTTTTTTAAAAAAAATCAACTCATCCTTTTTTTT
Found at i:1602740 original size:79 final size:79
Alignment explanation
Indices: 1602185--1602934 Score: 853
Period size: 79 Copynumber: 9.8 Consensus size: 79
1602175 ACTCATCCTT
* * * * *
1602185 TTTTTTAAAAATCAACTCATAATAC-CGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTA--T
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602245 -TTTT-AATTTCTG
66 CTTTTAAATTTCTG
** * * * *
1602257 TCTTTTTTAAAATCAATTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATT
1 T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT
* *
1602319 T-TTAATT-TATGTCT-
65 TCTT--TTAAATTTCTG
* * * ** *
1602333 TTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTTAGGTCAC-T-CTGAGGTA--T
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
*
1602393 -TTTT-AATTTATG
66 CTTTTAAATTTCTG
** * *
1602405 TCTTTTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-GGAC-CATGCCGAGGTATT
1 T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT
*
1602468 TCTTTTAAATTTATG
65 TCTTTTAAATTTCTG
* * * *
1602483 TTTTTCAAAAAATCAACTAATATTGCGAGAGGTGAGTTGAGCCT-TGGAC-CATGCCAAGGTATT
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT
1602546 TCTTTTAAATTTCTG
65 TCTTTTAAATTTCTG
*
1602561 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602624 CTTTTAAATTTCTG
66 CTTTTAAATTTCTG
1602638 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602703 CTTTTAAATTTCTG
66 CTTTTAAATTTCTG
* * *
1602717 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGCATGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602782 CTTTTAAATTTCTG
66 CTTTTAAATTTCTG
* * * * *
1602796 TTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCTTTGGGTTAC--GCCGA-G-ATAT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
*
1602857 -TTTTCAA-TTCATG
66 CTTTTAAATTTC-TG
* *
1602870 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602935 TCGATTTTTA
Statistics
Matches: 608, Mismatches: 45, Indels: 44
0.87 0.06 0.06
Matches are distributed among these distances:
71 6 0.01
72 3 0.00
73 86 0.14
74 77 0.13
75 59 0.10
76 7 0.01
77 132 0.22
78 86 0.14
79 152 0.25
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (79 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
CTTTTAAATTTCTG
Found at i:1602891 original size:232 final size:230
Alignment explanation
Indices: 1602185--1602934 Score: 904
Period size: 232 Copynumber: 3.3 Consensus size: 230
1602175 ACTCATCCTT
* * * * *
1602185 TTTTTTAAAAATCAACTCATAATAC-CGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTA--T
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
** * * * *
1602245 -TTTT-AATTTCTGTCTTTTTTAAAATCAATTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT-C
66 CTTTTAAATTTCTGT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCC
* * * * * *
1602306 ACGCTGAGGTATTT-TTAATT-TATGTCT-TTTTTTAAAAATCAACTCATAATAC-AGAGGTGAG
130 ATGCTGAGGTATTTCTT--TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
* * * * *
1602367 TTGAGCCTTAGGTCACTCTGAGGTATTTTTAATTTATG
193 TTGAGCCTTGGGTCACGCCGAGATATTTTTAATTCATG
** * *
1602405 TCTTTTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-GGAC-CATGCCGAGGTATT
1 T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT
* * *
1602468 TCTTTTAAATTTATGTTTTTCAAAAAATCAACTAATATTGCGAGAGGTGAGTTGAGCCTT-GGAC
65 TCTTTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
**
1602532 CATGCCAAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
129 CATGCTGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* ** * *
1602597 TGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTC-TG
194 TGAGCCTTGGGTCACGCCGA-G-ATAT-TTTT-AA-TTCATG
1602638 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602703 CTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGC
66 CTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC-C
*
1602768 ATGCTGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTT
130 ATGCTGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
1602833 GAGCTTTGGGTTACGCCGAGATATTTTTCAATTCATG
195 GAGCCTTGGGTCACGCCGAGATATTTTT-AATTCATG
* *
1602870 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1602935 TCGATTTTTA
Statistics
Matches: 451, Mismatches: 54, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
220 2 0.00
221 24 0.05
222 24 0.05
224 1 0.00
225 8 0.02
226 26 0.06
227 34 0.08
228 24 0.05
229 23 0.05
230 1 0.00
231 5 0.01
232 115 0.25
233 48 0.11
234 40 0.09
235 76 0.17
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (230 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
CTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCCA
TGCTGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTTGGGTCACGCCGAGATATTTTTAATTCATG
Found at i:1603014 original size:75 final size:75
Alignment explanation
Indices: 1602561--1603016 Score: 182
Period size: 79 Copynumber: 6.0 Consensus size: 75
1602551 TAAATTTCTG
* * * * * * *
1602561 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA-TT
** * *
1602624 CTTTTAAATTTCTG
65 C---TCGATTTTTA
* * * * * * *
1602638 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA-TT
** * *
1602703 CTTTTAAATTTCTG
65 C---TCGATTTTTA
* * * * * * * * * *
1602717 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGCATGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA-TT
** * *
1602782 CTTTTAAATTTCTG
65 C---TCGATTTTTA
* * * * * ** ** *
1602796 TTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAG-CTTTGGG-TTACGCCGAGATATTT
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA-TT
* * ** *
1602859 TTCAATTCATG
65 CTCGATTTTTA
* * * * * * * *
1602870 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTC
1602935 TCGATTTTTA
66 TCGATTTTTA
* * * * * *
1602945 TTTTTCGAAGATCAACTCATAATCCAAAAGGTGAGTTGAGTCTCGGGTCGCACGCCGAGCTGTTC
1 TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTC
1603010 TCGATTT
66 TCGATTT
1603017 CTGCTTTTCA
Statistics
Matches: 333, Mismatches: 42, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
74 46 0.14
75 72 0.22
76 8 0.02
77 55 0.17
78 8 0.02
79 144 0.43
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (75 bp):
TTTTTCAAAAATCAACTCATAATCCAAAAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTC
TCGATTTTTA
Found at i:1603248 original size:29 final size:30
Alignment explanation
Indices: 1603189--1603289 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 30
1603179 AATTTTTTTG
** * * *
1603189 CATTTTAACCCCTGTACTTTTTGAAATTTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
*
1603219 CATTTTGACCCC-AAACTTTCTCAAAATTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
*
1603248 CATTTTAACCCCTAAACTTTCTCAAAATAA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
* *
1603278 CGTTTCAACCCC
1 CATTTTAACCCC
1603290 AAAAGTTTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.38
30 37 0.62
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (30 bp):
CATTTTAACCCCTAAACTTTCTCAAAATTA
Found at i:1603790 original size:4 final size:4
Alignment explanation
Indices: 1603781--1603862 Score: 68
Period size: 4 Copynumber: 21.5 Consensus size: 4
1603771 CTGAACGGGG
* *
1603781 AAGA AAGA AAGA AAG- AAG- AAGA AAGA AAAA AAG- AAGA AAAA AGAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA
* *
1603827 AAG- AAGG AAGA AGAAA AAGA AA-A AAGA AA-A AAGA AA
1 AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AA
1603863 AAGAAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
3 18 0.28
4 40 0.62
5 6 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1603836 original size:20 final size:20
Alignment explanation
Indices: 1603786--1603885 Score: 91
Period size: 20 Copynumber: 5.0 Consensus size: 20
1603776 CGGGGAAGAA
*
1603786 AGAAAGAAAGAAGAAGAAAG
1 AGAAAGAAAGAAGAAAAAAG
1603806 A-AAA-AAAGAAGAAAAAAG
1 AGAAAGAAAGAAGAAAAAAG
*
1603824 AGAAAGAAGGAAGAAGAAAA-
1 AGAAAGAAAGAAGAA-AAAAG
* *
1603844 AGAAA-AAAGAAAAAAGAAAA
1 AGAAAGAAAGAAGAAA-AAAG
* *
1603864 AGAAAAAAATAAGAAAATAAG
1 AGAAAGAAAGAAGAAAA-AAG
1603885 A
1 A
1603886 AAATAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.23
19 16 0.24
20 20 0.30
21 15 0.23
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAGAAGAAAAAAG
Found at i:1603841 original size:23 final size:21
Alignment explanation
Indices: 1603781--1603871 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 21
1603771 CTGAACGGGG
*
1603781 AAGAAAGAAAGAAAGAAGAAGA
1 AAGAAA-AAAGAAAGAAGAAAA
1603803 AAG--AAAA-AAAGAAGAAAA
1 AAGAAAAAAGAAAGAAGAAAA
*
1603821 AAGAGAAAGAAGGAAGAAG-AAA
1 AAGA-AAA-AAGAAAGAAGAAAA
*
1603843 AAGAAAAAAGAAAAAAG-AAA
1 AAGAAAAAAGAAAGAAGAAAA
1603863 AAGAAAAAA
1 AAGAAAAAA
1603872 ATAAGAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
18 13 0.22
19 3 0.05
20 21 0.35
21 5 0.08
22 12 0.20
23 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAGAAAGAAGAAAA
Found at i:1603864 original size:8 final size:8
Alignment explanation
Indices: 1603781--1603888 Score: 71
Period size: 8 Copynumber: 12.9 Consensus size: 8
1603771 CTGAACGGGG
*
1603781 AAGAAAGA
1 AAGAAAAA
1603789 AAGAAAGAA
1 AAGAAA-AA
*
1603798 GAAGAAAGA
1 -AAGAAAAA
*
1603807 AA-AAAAG
1 AAGAAAAA
1603814 AAGAAAAA
1 AAGAAAAA
1603822 AGAGAAAGAA
1 A-AGAAA-AA
1603832 GGAAGAAGAAA
1 --AAGAA-AAA
1603843 AAG-AAAA
1 AAGAAAAA
1603850 AAG-AAAA
1 AAGAAAAA
1603857 AAGAAAAA
1 AAGAAAAA
1603865 GAA-AAAAA
1 -AAGAAAAA
*
1603873 TAAGAAAAT
1 -AAGAAAAA
1603882 AAGAAAA
1 AAGAAAA
1603889 TAAATTTTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
7 18 0.22
8 32 0.39
9 16 0.20
10 8 0.10
11 6 0.07
12 2 0.02
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1603870 original size:7 final size:7
Alignment explanation
Indices: 1603784--1603871 Score: 76
Period size: 7 Copynumber: 12.4 Consensus size: 7
1603774 AACGGGGAAG
1603784 AAAGAAA
1 AAAGAAA
1603791 GAAAG-AA
1 -AAAGAAA
*
1603798 GAAGAAA
1 AAAGAAA
1603805 GAAA-AAA
1 -AAAGAAA
1603812 AGAAGAAA
1 A-AAGAAA
1603820 AAAGAGAA
1 AAAGA-AA
*
1603828 AGAAGGAA
1 A-AAGAAA
*
1603836 GAAG-AA
1 AAAGAAA
1603842 AAAGAAA
1 AAAGAAA
1603849 AAAGAAA
1 AAAGAAA
1603856 AAAG-AA
1 AAAGAAA
1603862 AAAGAAA
1 AAAGAAA
1603869 AAA
1 AAA
1603872 ATAAGAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
6 15 0.22
7 34 0.51
8 15 0.22
9 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1604030 original size:23 final size:23
Alignment explanation
Indices: 1604005--1604047 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1603995 AAGCAACACA
1604005 AAAAAAACAGCCCAA-AAGAAAG
1 AAAAAAACAGCCCAAGAAGAAAG
1604027 AAAAAAACAGCCCAAGAAGAA
1 AAAAAAACAGCCCAAGAAGAA
1604048 GCAAGAGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.67, C:0.19, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAACAGCCCAAGAAGAAAG
Found at i:1604755 original size:17 final size:16
Alignment explanation
Indices: 1604711--1604759 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1604701 TTAAAAAAAA
*
1604711 TCGTGTTTCAAAAACTT
1 TCGTGTTTC-AAAATTT
*
1604728 TCATGTCTTCAAAATTT
1 TCGTGT-TTCAAAATTT
1604745 CTCGTGTTTCAAAAT
1 -TCGTGTTTCAAAAT
1604760 AATAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:1604853 original size:20 final size:19
Alignment explanation
Indices: 1604828--1604872 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1604818 TCGTGTTTCT
*
1604828 AAAATTCTTGTATTTAAAAA
1 AAAATTCGTGT-TTTAAAAA
1604848 AAAATTTCGTGTTTTAAAAA
1 AAAA-TTCGTGTTTTAAAAA
1604868 AAAAT
1 AAAAT
1604873 AAAAAGTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAATTCGTGTTTTAAAAA
Found at i:1606296 original size:34 final size:34
Alignment explanation
Indices: 1606258--1606325 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1606248 CTGTTTAGCT
*
1606258 TTTTTTTTTTTTTTTTTTATTTTGGAATAATATA
1 TTTTTTTTTTTTTTTTTTAATTTGGAATAATATA
1606292 TTTTTTTTTTTTTTTTTTAATTTGGAATAATATA
1 TTTTTTTTTTTTTTTTTTAATTTGGAATAATATA
1606326 CTATTTGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (34 bp):
TTTTTTTTTTTTTTTTTTAATTTGGAATAATATA
Found at i:1610467 original size:49 final size:49
Alignment explanation
Indices: 1610344--1610650 Score: 393
Period size: 49 Copynumber: 6.2 Consensus size: 49
1610334 CATAACTGAA
** *
1610344 ATGAATGCAACAAAA-AAAAAATGAAGCATAATTAAAACACCACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACA--ACTTTATTT
* * *
1610394 ATGAATGCAACAAAACAATGAATGAAGCATAAATAAAACAACTCTATGT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTTTATTT
* * *
1610443 ATGAATGCAACAAAATAGTCAATGAAGCATAATTAAAACACCACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACA--ACTTTATTT
* * * * *
1610494 ATGAATGCAACAGAACAATGAATGAAGCATAAATAAAGCAACTCTGTTT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTTTATTT
* *
1610543 ATGAATGCAGCAAAATAATCAATGAAGCATAAATAAAACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTTTATTT
* *
1610592 ATGAATGCAGCGAAACAATCAATGAAGCATAAAT-AAACAAACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAC-AACTTTATTT
1610641 ATGAATGCAA
1 ATGAATGCAA
1610651 GTATGCTTTA
Statistics
Matches: 224, Mismatches: 29, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
48 4 0.02
49 143 0.64
50 15 0.07
51 62 0.28
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (49 bp):
ATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTTTATTT
Found at i:1610472 original size:100 final size:100
Alignment explanation
Indices: 1610344--1610650 Score: 460
Period size: 100 Copynumber: 3.1 Consensus size: 100
1610334 CATAACTGAA
**
1610344 ATGAATGCAACAAAA-AAAAAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAA
1 ATGAATGCAACAAAATAATCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAA
*
1610408 ACAATGAATGAAGCATAAATAAAACAACTCTATGT
66 ACAATGAATGAAGCATAAATAAAACAACTCTATTT
* *
1610443 ATGAATGCAACAAAATAGTCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAGA
1 ATGAATGCAACAAAATAATCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAA
* *
1610508 ACAATGAATGAAGCATAAATAAAGCAACTCTGTTT
66 ACAATGAATGAAGCATAAATAAAACAACTCTATTT
* * * *
1610543 ATGAATGCAGCAAAATAATCAATGAAGCATAAATAAAACA--ACTTTATTTATGAATGCAGCGAA
1 ATGAATGCAACAAAATAATCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAA
* *
1610606 ACAATCAATGAAGCATAAAT-AAACAAACTTTATTT
66 ACAATGAATGAAGCATAAATAAAAC-AACTCTATTT
1610641 ATGAATGCAA
1 ATGAATGCAA
1610651 GTATGCTTTA
Statistics
Matches: 188, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
97 3 0.02
98 56 0.30
99 15 0.08
100 114 0.61
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (100 bp):
ATGAATGCAACAAAATAATCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAA
ACAATGAATGAAGCATAAATAAAACAACTCTATTT
Found at i:1610557 original size:149 final size:147
Alignment explanation
Indices: 1610344--1610650 Score: 409
Period size: 149 Copynumber: 2.1 Consensus size: 147
1610334 CATAACTGAA
* *
1610344 ATGAATGCAACAAAAAAAAAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACAAAA
1 ATGAATGCAACAAAAAAAAAATGAAGCATAAATAAAACA-CACTCTATTTATGAATGCAACAAAA
* * *
1610409 CAATGAATGAAGCATAAATAAAACAACTCTATGTATGAATGCAACAAAATAGTCAATGAAGCATA
65 CAATCAATGAAGCATAAATAAAACAACTCTATGTATGAATGCAACAAAACAATCAATGAAGCATA
* *
1610474 ATTAAAACACCACTTTATTT
130 AAT-AAACA-AACTTTATTT
* ** * * *
1610494 ATGAATGCAACAGAACAATGAATGAAGCATAAATAAAGCA-ACTCTGTTTATGAATGCAGCAAAA
1 ATGAATGCAACA-AAAAAAAAATGAAGCATAAATAAAACACACTCTATTTATGAATGCAACAAAA
* * * * *
1610558 TAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAGCGAAACAATCAATGAAGCATA
65 CAATCAATGAAGCATAAATAAAACAACTCTATGTATGAATGCAACAAAACAATCAATGAAGCATA
1610623 AATAAACAAACTTTATTT
130 AATAAACAAACTTTATTT
1610641 ATGAATGCAA
1 ATGAATGCAA
1610651 GTATGCTTTA
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
147 19 0.14
148 5 0.04
149 80 0.58
150 12 0.09
151 22 0.16
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (147 bp):
ATGAATGCAACAAAAAAAAAATGAAGCATAAATAAAACACACTCTATTTATGAATGCAACAAAAC
AATCAATGAAGCATAAATAAAACAACTCTATGTATGAATGCAACAAAACAATCAATGAAGCATAA
ATAAACAAACTTTATTT
Found at i:1613704 original size:23 final size:24
Alignment explanation
Indices: 1613678--1613738 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
1613668 TTTTTCACTC
1613678 TTTTTTTCTTTTCCCTCATG-TTT
1 TTTTTTTCTTTTCCCTCATGATTT
* *
1613701 TTTTTTTGC-ATTCTCTCATGATTT
1 TTTTTTT-CTTTTCCCTCATGATTT
1613725 TCTCTTTTTCTTTT
1 T-T-TTTTTCTTTT
1613739 GTTGTTACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 16 0.53
24 5 0.17
25 2 0.07
26 7 0.23
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.69
Consensus pattern (24 bp):
TTTTTTTCTTTTCCCTCATGATTT
Found at i:1616521 original size:49 final size:49
Alignment explanation
Indices: 1616426--1616691 Score: 282
Period size: 49 Copynumber: 5.3 Consensus size: 49
1616416 ACAAACAAAG
* * * * *
1616426 AATGAAGCATAATTAAAATACTACTTTAGTTATGAATGCAACAAAATAATG
1 AATGAAGCATAAAT-AAA-ACAACTCTATTTATGAATGCAACAAAATAATC
* *
1616477 AATGAATCATAAATAAAACAACTCTATGTATGAATGCAACAAAATAATC
1 AATGAAGCATAAATAAAACAACTCTATTTATGAATGCAACAAAATAATC
* * * * * *
1616526 AATGAAGCATAATTAAAACACCACTTTATTTATGAATACAATAGAATAATG
1 AATGAAGCATAAATAAAACA--ACTCTATTTATGAATGCAACAAAATAATC
* * * *
1616577 AATGAAGCATAAATAAAGCAACTCTATTTATGAATGTAGCAAAACAATC
1 AATGAAGCATAAATAAAACAACTCTATTTATGAATGCAACAAAATAATC
* * * *
1616626 AATGAAGCATAAATAAAACAACT-TAATATAGGAATGCAGCAAAACAATC
1 AATGAAGCATAAATAAAACAACTCT-ATTTATGAATGCAACAAAATAATC
*
1616675 AATAAAGCATAAATAAA
1 AATGAAGCATAAATAAA
1616692 GCAAATTTGA
Statistics
Matches: 182, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
48 1 0.01
49 125 0.69
50 3 0.02
51 53 0.29
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (49 bp):
AATGAAGCATAAATAAAACAACTCTATTTATGAATGCAACAAAATAATC
Found at i:1616540 original size:100 final size:100
Alignment explanation
Indices: 1616426--1616645 Score: 323
Period size: 100 Copynumber: 2.2 Consensus size: 100
1616416 ACAAACAAAG
* * * *
1616426 AATGAAGCATAATTAAAATACTACTTTAGTTATGAATGCAACAAAATAATGAATGAATCATAAAT
1 AATGAAGCATAATTAAAACACCACTTTAGTTATGAATACAACAAAATAATGAATGAAGCATAAAT
*
1616491 AAAACAACTCTATGTATGAATGCAACAAAATAATC
66 AAAACAACTCTATGTATGAATGCAACAAAACAATC
* * *
1616526 AATGAAGCATAATTAAAACACCACTTTATTTATGAATACAATAGAATAATGAATGAAGCATAAAT
1 AATGAAGCATAATTAAAACACCACTTTAGTTATGAATACAACAAAATAATGAATGAAGCATAAAT
* * * *
1616591 AAAGCAACTCTATTTATGAATGTAGCAAAACAATC
66 AAAACAACTCTATGTATGAATGCAACAAAACAATC
*
1616626 AATGAAGCATAAATAAAACA
1 AATGAAGCATAATTAAAACA
1616646 ACTTAATATA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 107 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.26
Consensus pattern (100 bp):
AATGAAGCATAATTAAAACACCACTTTAGTTATGAATACAACAAAATAATGAATGAAGCATAAAT
AAAACAACTCTATGTATGAATGCAACAAAACAATC
Found at i:1619249 original size:43 final size:45
Alignment explanation
Indices: 1619151--1619269 Score: 135
Period size: 43 Copynumber: 2.8 Consensus size: 45
1619141 CGATTTGAGT
* * * *
1619151 ATTACGTGTAAGACCATGTATGGGACATTGG---CGTTGTATATG
1 ATTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTTGTATATG
1619193 ATTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTTGT-T-TG
1 ATTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTTGTATATG
1619236 ATTACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
1 ATTACATGTAAGACC-CTGTCTGGGACAG-TGGCAT
1619270 TGTACTAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
42 28 0.41
43 32 0.47
44 2 0.03
45 6 0.09
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (45 bp):
ATTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTTGTATATG
Found at i:1631131 original size:16 final size:16
Alignment explanation
Indices: 1631110--1631174 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
1631100 ATTTGATTTG
*
1631110 CTATTACACCCCTATT
1 CTATTACACCCCTAAT
*
1631126 CTATTACACCTCTAAT
1 CTATTACACCCCTAAT
* *
1631142 CCATTACACCTCTAAT
1 CTATTACACCCCTAAT
* * *
1631158 CCAATACACCTCTAAT
1 CTATTACACCCCTAAT
1631174 C
1 C
1631175 CAATACAGCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.32
Consensus pattern (16 bp):
CTATTACACCCCTAAT
Found at i:1631132 original size:45 final size:44
Alignment explanation
Indices: 1631036--1631133 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
1631026 CTATTACACC
* * *
1631036 TCTATTCCATTCAACCAAACACAAGATTACTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACACAAGATTACTATTACACCCCTAT
* *** *
1631080 TCCATTACATTCAACCAAACATTTGATTTGCTATTACACCCCTAT
1 TCTATTACATTCAACCAAACACAAGA-TTACTATTACACCCCTAT
1631125 TCTATTACA
1 TCTATTACA
1631134 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 21 0.48
45 23 0.52
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (44 bp):
TCTATTACATTCAACCAAACACAAGATTACTATTACACCCCTAT
Found at i:1631166 original size:32 final size:32
Alignment explanation
Indices: 1631112--1631181 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1631102 TTGATTTGCT
* * *
1631112 ATTACACCCCTATTCTATTACACCTCTAATCC
1 ATTACACCCCTAATCCAATACACCTCTAATCC
*
1631144 ATTACACCTCTAATCCAATACACCTCTAATCC
1 ATTACACCCCTAATCCAATACACCTCTAATCC
*
1631176 AATACA
1 ATTACA
1631182 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (32 bp):
ATTACACCCCTAATCCAATACACCTCTAATCC
Found at i:1631175 original size:16 final size:16
Alignment explanation
Indices: 1631130--1631181 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
1631120 CCTATTCTAT
*
1631130 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
1631146 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1631162 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1631178 TACA
1 TACA
1631182 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1638362 original size:14 final size:14
Alignment explanation
Indices: 1638343--1638369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1638333 GGCAATTCTC
1638343 AAAGAGTAAGTGGG
1 AAAGAGTAAGTGGG
1638357 AAAGAGTAAGTGG
1 AAAGAGTAAGTGG
1638370 AATTACTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (14 bp):
AAAGAGTAAGTGGG
Found at i:1639839 original size:15 final size:16
Alignment explanation
Indices: 1639802--1639839 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1639792 GTTTTACTAT
1639802 TATTTCAATTTTAATTA
1 TATTT-AATTTTAATTA
*
1639819 TTTTTAATTTT-ATTA
1 TATTTAATTTTAATTA
1639834 TATTTA
1 TATTTA
1639840 GATTCCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 6 0.32
17 4 0.21
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTAATTTTAATTA
Found at i:1641318 original size:17 final size:19
Alignment explanation
Indices: 1641273--1641320 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1641263 ATTTTTTAAA
1641273 TATATATTTATATTAATTT
1 TATATATTTATATTAATTT
1641292 TATTTAATATTTA-A-TAATTT
1 TA--T-ATATTTATATTAATTT
1641312 TATATATTT
1 TATATATTT
1641321 TTTCACTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.23
18 1 0.04
19 2 0.08
20 8 0.31
21 2 0.08
22 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATTTATATTAATTT
Found at i:1642520 original size:46 final size:47
Alignment explanation
Indices: 1642449--1642537 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 47
1642439 GCTGTCAAAG
*
1642449 CTGAAGAGTATGGATCTAGACATGACAATATTAAAGATGTTGGTATA
1 CTGAAGAGTATGGATCTAGACATGACAATATTAAAGATCTTGGTATA
* *
1642496 CTGAAG-GTATGGATTTAGATATGACAATATTAAAGATCTTGG
1 CTGAAGAGTATGGATCTAGACATGACAATATTAAAGATCTTGG
1642538 ACTTGGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 33 0.85
47 6 0.15
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (47 bp):
CTGAAGAGTATGGATCTAGACATGACAATATTAAAGATCTTGGTATA
Found at i:1646901 original size:22 final size:22
Alignment explanation
Indices: 1646859--1646903 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1646849 TGAATTTAAA
* *
1646859 TTACATTCTATTGTATTTATTG
1 TTACATTCTAATGTATATATTG
1646881 TTACATT-TAATGTAATATATTG
1 TTACATTCTAATGT-ATATATTG
1646903 T
1 T
1646904 AACCTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.56
Consensus pattern (22 bp):
TTACATTCTAATGTATATATTG
Found at i:1649708 original size:15 final size:15
Alignment explanation
Indices: 1649685--1649749 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
1649675 AAGGGGAATC
*
1649685 TAAATATAATAAAAT
1 TAAAAATAATAAAAT
1649700 TAAAAATAATTAAAAT
1 TAAAAATAA-TAAAAT
* *
1649716 TGAAATAATAGTAAAAA
1 T-AAA-AATAATAAAAT
*
1649733 TAGAAAATAATTAAAT
1 TA-AAAATAATAAAAT
1649749 T
1 T
1649750 TAATTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 8 0.20
16 17 0.43
17 11 0.28
18 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (15 bp):
TAAAAATAATAAAAT
Found at i:1652673 original size:39 final size:39
Alignment explanation
Indices: 1652574--1652675 Score: 168
Period size: 39 Copynumber: 2.6 Consensus size: 39
1652564 CATATTCACT
* *
1652574 TTTAAGCATATATCACATTACACATATAATCACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATCACATAAAA
*
1652613 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAAAA
*
1652652 TTTAAGCATAAATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
1652676 AAAACATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAAAA
Found at i:1657448 original size:62 final size:59
Alignment explanation
Indices: 1657372--1657488 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
1657362 AAGTGATTAT
* *
1657372 CTTAATATTAAATTTAATTTAATGTTTATCTTGTGGATAAACATTCTATTATTTTAATCAGA
1 CTTAATATTAAATTTAATTTAATATTTATC-T-T-GATAAACATTATATTATTTTAATCAGA
* *
1657434 CTTAATATTTAATTTAATTTAATATTTATCTTGATAAATATTATATTATTTTAAT
1 CTTAATATTAAATTTAATTTAATATTTATCTTGATAAACATTATATTATTTTAAT
1657489 ATTAAAGTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.41
60 1 0.02
61 1 0.02
62 28 0.55
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (59 bp):
CTTAATATTAAATTTAATTTAATATTTATCTTGATAAACATTATATTATTTTAATCAGA
Found at i:1659652 original size:11 final size:10
Alignment explanation
Indices: 1659626--1659660 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1659616 GGTAACATAG
1659626 AATTTTTCAA
1 AATTTTTCAA
1659636 AATTTTTCAA
1 AATTTTTCAA
1659646 AATTTTT--A
1 AATTTTTCAA
1659654 AATTTTT
1 AATTTTT
1659661 GTTCTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (10 bp):
AATTTTTCAA
Found at i:1660973 original size:49 final size:48
Alignment explanation
Indices: 1660909--1661043 Score: 207
Period size: 49 Copynumber: 2.8 Consensus size: 48
1660899 TATCTTGAAT
1660909 TTTAAAAGCTCTTTTAAATAATAATTTAAATTCTATTTAATTATCATTTA
1 TTTAAAA-CTCTTTTAAATAATAA-TTAAATTCTATTTAATTATCATTTA
* * *
1660959 TTTAAAACTCTTTTAAATAATAATTAAATTATGTTTTAATTATTATTTA
1 TTTAAAACTCTTTTAAATAATAATTAAATTCT-ATTTAATTATCATTTA
*
1661008 TCTAAAACTCTTTTAAATAATAATTAAATTCTATTT
1 TTTAAAACTCTTTTAAATAATAATTAAATTCTATTT
1661044 CCTTATTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
48 11 0.14
49 60 0.77
50 7 0.09
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.50
Consensus pattern (48 bp):
TTTAAAACTCTTTTAAATAATAATTAAATTCTATTTAATTATCATTTA
Found at i:1675964 original size:32 final size:32
Alignment explanation
Indices: 1675886--1675964 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
1675876 TGACTATGGC
*
1675886 CGTGTGGGCCACACAGGCTAGGCCAGGTTGGG
1 CGTGTGGGCCACACGGGCTAGGCCAGGTTGGG
**
1675918 CACGTGGGCCACACGGGCTAGGCCAGGTTGGG
1 CGTGTGGGCCACACGGGCTAGGCCAGGTTGGG
*
1675950 TGTGTGGGCCACACG
1 CGTGTGGGCCACACG
1675965 AGCGTGTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.15, C:0.27, G:0.43, T:0.15
Consensus pattern (32 bp):
CGTGTGGGCCACACGGGCTAGGCCAGGTTGGG
Found at i:1683462 original size:24 final size:24
Alignment explanation
Indices: 1683430--1683477 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1683420 TTTTGTAGAG
*
1683430 TTAGTTCTTCACTTCTGAACCAAC
1 TTAGTTCTTCACTTCCGAACCAAC
1683454 TTAGTTCTTCACTTCCGAACCAAC
1 TTAGTTCTTCACTTCCGAACCAAC
1683478 CTAAGCCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (24 bp):
TTAGTTCTTCACTTCCGAACCAAC
Found at i:1685334 original size:39 final size:39
Alignment explanation
Indices: 1685280--1685364 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
1685270 CTTAGTGTTC
* *
1685280 TTGTAGTTAGTTAACACTGTAGCTTAGGTTTATTTGCAT
1 TTGTAGTTAGTTAACACTATAGCTTAGATTTATTTGCAT
1685319 TTGTAGTTAGTTAACACTATAGCTTAGATTTATTTGCAT
1 TTGTAGTTAGTTAACACTATAGCTTAGATTTATTTGCAT
*
1685358 TTTTAGT
1 TTGTAGT
1685365 CCCTGTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (39 bp):
TTGTAGTTAGTTAACACTATAGCTTAGATTTATTTGCAT
Found at i:1691265 original size:12 final size:12
Alignment explanation
Indices: 1691248--1691281 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1691238 AAGTACCTTC
1691248 AATAATAATGAT
1 AATAATAATGAT
*
1691260 AATAATAAAGAT
1 AATAATAATGAT
1691272 AATAA-AATGA
1 AATAATAATGA
1691282 AAACAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (12 bp):
AATAATAATGAT
Found at i:1693379 original size:42 final size:42
Alignment explanation
Indices: 1693333--1693487 Score: 249
Period size: 42 Copynumber: 3.7 Consensus size: 42
1693323 GCGTGTAACC
1693333 CAAGTCAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCT
1 CAAGTCAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCT
* *
1693375 CAAGTCAGTGAGCTACACGAGCTGGGACATAGCCGTGTGTCT
1 CAAGTCAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCT
* * *
1693417 CAAGCCAGTGAGTTACACGGGCTGGGACATGGTCGTGTGTC-
1 CAAGTCAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCT
1693458 CTAAGTCAGTGAGTTACACGGGCTGGGACA
1 C-AAGTCAGTGAGTTACACGGGCTGGGACA
1693488 CGACTGTGTG
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 103 0.99
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.22
Consensus pattern (42 bp):
CAAGTCAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCT
Found at i:1693519 original size:84 final size:83
Alignment explanation
Indices: 1693338--1693504 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 83
1693328 TAACCCAAGT
*
1693338 CAGTGAGTTACACGGGCTGGGACATAGCCGTGTGTCTCAAGTCAGTGAGCTACACGAGCTGGGAC
1 CAGTGAGTCACACGGGCTGGGACATAGCCGTGTGTCTCAAGTCAGTGAGCTACACGAGCTGGGAC
* *
1693403 ATAGCCGTGTGTCTCAAGC
66 AGAGCCGTGTGTCCCAA-C
* * * * *
1693422 CAGTGAGTTACACGGGCTGGGACATGGTCGTGTGTC-CTAAGTCAGTGAGTTACACGGGCTGGGA
1 CAGTGAGTCACACGGGCTGGGACATAGCCGTGTGTCTC-AAGTCAGTGAGCTACACGAGCTGGGA
*
1693486 CACGA-CTGTGTGTCCCAAC
65 CA-GAGCCGTGTGTCCCAAC
1693505 TTTGAAAGTC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
83 2 0.03
84 71 0.96
85 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (83 bp):
CAGTGAGTCACACGGGCTGGGACATAGCCGTGTGTCTCAAGTCAGTGAGCTACACGAGCTGGGAC
AGAGCCGTGTGTCCCAAC
Found at i:1701455 original size:3 final size:3
Alignment explanation
Indices: 1701447--1701485 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1701437 AAAGTAACTT
*
1701447 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA -AGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
1701486 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1705790 original size:16 final size:16
Alignment explanation
Indices: 1705769--1705799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1705759 AATTCATTTA
*
1705769 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
1705785 AATTAAATAATTTTC
1 AATTAAATAATTTTC
1705800 TTAACCGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:1707611 original size:42 final size:41
Alignment explanation
Indices: 1707534--1707648 Score: 133
Period size: 42 Copynumber: 2.8 Consensus size: 41
1707524 AGGTTTGTAC
* * ** *
1707534 TTTAGTTTATCTAGTGATGCACTTACATGCAGGTATGA-TTG
1 TTTAGTTTATCCAATGATGCACTTATGTGCCGGTAT-ATTTG
1707575 TTTAAGTTTATCCAATGATGCACTTATGTGCCGGTATATTTG
1 TTT-AGTTTATCCAATGATGCACTTATGTGCCGGTATATTTG
* *
1707617 TTTCGTTACATCCAATGATGCACTTATGTGCC
1 TTTAGTT-TATCCAATGATGCACTTATGTGCC
1707649 AACATGATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 7 0.11
42 57 0.89
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (41 bp):
TTTAGTTTATCCAATGATGCACTTATGTGCCGGTATATTTG
Found at i:1708851 original size:54 final size:55
Alignment explanation
Indices: 1708784--1708893 Score: 195
Period size: 54 Copynumber: 2.0 Consensus size: 55
1708774 AAATATGAAC
* *
1708784 TCATTGGGGATGTATGTTTGGCTGAAAAATGTGTTTTGGTATGTATATTGGTTGT
1 TCATTGGGGATGTATGTTTGGCTAAAAAATGTGTTTTGGTAAGTATATTGGTTGT
1708839 TCATT-GGGATGTATGTTTGGCTAAAAAATGTGTTTTGGTAAGTATATTGGTTGT
1 TCATTGGGGATGTATGTTTGGCTAAAAAATGTGTTTTGGTAAGTATATTGGTTGT
1708893 T
1 T
1708894 TGGAGCTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 48 0.91
55 5 0.09
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.45
Consensus pattern (55 bp):
TCATTGGGGATGTATGTTTGGCTAAAAAATGTGTTTTGGTAAGTATATTGGTTGT
Found at i:1718202 original size:40 final size:41
Alignment explanation
Indices: 1718138--1718221 Score: 152
Period size: 40 Copynumber: 2.0 Consensus size: 41
1718128 TATCAAAATA
1718138 TATTTCCCAAATTTCTCTCACTCATGACTTTTAAAAGAATGG
1 TATTTCCCAAA-TTCTCTCACTCATGACTTTTAAAAGAATGG
1718180 TATTTCCCAAA-TCTCTCACTCATGACTTTTAAAAGAATGG
1 TATTTCCCAAATTCTCTCACTCATGACTTTTAAAAGAATGG
1718220 TA
1 TA
1718222 ATATTGTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 31 0.74
42 11 0.26
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (41 bp):
TATTTCCCAAATTCTCTCACTCATGACTTTTAAAAGAATGG
Found at i:1723051 original size:9 final size:9
Alignment explanation
Indices: 1723037--1723073 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1723027 TATAGTTTGA
1723037 TATTCGAAT
1 TATTCGAAT
1723046 TATTCGAAT
1 TATTCGAAT
*
1723055 TATTCGAGT
1 TATTCGAAT
1723064 TATTCGAAT
1 TATTCGAAT
1723073 T
1 T
1723074 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1723144 original size:9 final size:9
Alignment explanation
Indices: 1723127--1723166 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
1723117 TCGAGTTGAT
1723127 TCGAATAAC
1 TCGAATAAC
*
1723136 TCGATTAAC
1 TCGAATAAC
1723145 TCGAATAAC
1 TCGAATAAC
1723154 TCGAATAAC
1 TCGAATAAC
1723163 TCGA
1 TCGA
1723167 TTCGTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1724739 original size:21 final size:21
Alignment explanation
Indices: 1724715--1724760 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1724705 GGCTGCAGGG
1724715 CTTCCTCATCTTCATCTTCTT
1 CTTCCTCATCTTCATCTTCTT
*
1724736 CTTCCTCATCTTCATTTTCTT
1 CTTCCTCATCTTCATCTTCTT
1724757 CTTC
1 CTTC
1724761 TTCAACATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.37, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTCCTCATCTTCATCTTCTT
Found at i:1724784 original size:15 final size:15
Alignment explanation
Indices: 1724766--1724838 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 15
1724756 TCTTCTTCAA
1724766 CATCCTCTTCATCCT
1 CATCCTCTTCATCCT
* *
1724781 CATCCTCTCCATCGT
1 CATCCTCTTCATCCT
*
1724796 CATCGTCATCATCATCCT
1 CATC--C-TCTTCATCCT
*
1724814 CGTCCTCGTCCTCATCCT
1 CATCCTC-T--TCATCCT
1724832 CATCCTC
1 CATCCTC
1724839 AGGGTCTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
15 19 0.43
16 1 0.02
17 1 0.02
18 23 0.52
ACGTcount: A:0.14, C:0.47, G:0.05, T:0.34
Consensus pattern (15 bp):
CATCCTCTTCATCCT
Found at i:1724785 original size:6 final size:6
Alignment explanation
Indices: 1724774--1724839 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
1724764 AACATCCTCT
* * * *
1724774 TCATCC TCATCC TC-T-C -CATCG TCATCG TCATCA TCATCC TCGTCC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC
*
1724819 TCGTCC TCATCC TCATCC TCA
1 TCATCC TCATCC TCATCC TCA
1724840 GGGTCTTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 1 0.02
6 48 0.92
ACGTcount: A:0.15, C:0.45, G:0.06, T:0.33
Consensus pattern (6 bp):
TCATCC
Found at i:1726174 original size:18 final size:18
Alignment explanation
Indices: 1726151--1726188 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1726141 TCATATATAT
1726151 ATATATATTTGAACCATA
1 ATATATATTTGAACCATA
1726169 ATATATATTTGAACCATA
1 ATATATATTTGAACCATA
1726187 AT
1 AT
1726189 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATATATTTGAACCATA
Found at i:1727316 original size:10 final size:10
Alignment explanation
Indices: 1727303--1727336 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1727293 ACTTTTTTTA
*
1727303 TTTATAAAAT
1 TTTAAAAAAT
*
1727313 TTTAAAAAAC
1 TTTAAAAAAT
1727323 TTTAAAAAAT
1 TTTAAAAAAT
1727333 TTTA
1 TTTA
1727337 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAAAT
Found at i:1728223 original size:14 final size:15
Alignment explanation
Indices: 1728192--1728239 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1728182 CCAAATGAAA
1728192 AAAAAATAGAGTGAG
1 AAAAAATAGAGTGAG
1728207 AAAAAATATGAG-G-G
1 AAAAAATA-GAGTGAG
*
1728221 AAAAAAT-TAGTGA-
1 AAAAAATAGAGTGAG
1728234 AAAAAA
1 AAAAAA
1728240 AAACTGCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 8 0.28
15 9 0.31
16 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (15 bp):
AAAAAATAGAGTGAG
Found at i:1730513 original size:20 final size:22
Alignment explanation
Indices: 1730469--1730514 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1730459 ATCAATACTT
**
1730469 AAAAAAGATTCTTTTGTTGTTC
1 AAAAAAGATTCTTTTGTTGACC
1730491 AAAAAA-ATTCTTTTG-TGACC
1 AAAAAAGATTCTTTTGTTGACC
1730511 AAAA
1 AAAA
1730515 TAAAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAAAAAGATTCTTTTGTTGACC
Found at i:1731085 original size:17 final size:18
Alignment explanation
Indices: 1731055--1731092 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
1731045 AGAACTTTTT
1731055 ATTTTTTATTTTTATAACA
1 ATTTTTTA-TTTTATAACA
1731074 ATTTTTTA-TTTATAACA
1 ATTTTTTATTTTATAACA
1731091 AT
1 AT
1731093 CAACAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATTTTATAACA
Found at i:1733226 original size:189 final size:187
Alignment explanation
Indices: 1732878--1733255 Score: 491
Period size: 189 Copynumber: 2.0 Consensus size: 187
1732868 CTGGATCGCG
* * *
1732878 ATTATTTTTCGGTGAATTTGGAAAGCCAAGTATTCATTTTGCAATAATCACACAAATTTCAAATA
1 ATTATTTTTCGATGAATTTAGAAAACCAAGTATTCATTTTGCAATAATCACACAAATTTCAAATA
*
1732943 AAAGCTTGTTCTCGGGAATCTAAAAGTGCCGGGTCCTAACTTACTGGTCCTGATATTTTGACTTC
66 AAAGCTTATTCTCGGGAATCTAAAAGTGCCGGGTCCTAACTTACTGGTCCTGATATTTTGACTTC
1733008 TCGAAATAAGAATTTTCAAAAGCAAAAGGCAATATTCGGGTATTTTGAAGATTTAAAAA
131 TC--AATAAGAATTTTCAAAAGCAAAAGGCAATATTCGGGTATTTTGAAGATTTAAAAA
* * * * *
1733067 ATTATTTTTCGATGAATTTAGAAAACCAAGTATTTATTTTGCATTAAAT-TCGCAAATTTTAAAT
1 ATTATTTTTCGATGAATTTAGAAAACCAAGTATTCATTTTGCAAT-AATCACACAAATTTCAAAT
* * **
1733131 AAAAGCTTATTCTTGGGAGT-TCAAGAA-TGTTGGGTCCTAACTTACTGGTCCTGATATTTTGAC
65 AAAAGCTTATTCTCGGGAATCT-AA-AAGTGCCGGGTCCTAACTTACTGGTCCTGATATTTTGAC
1733194 -TC-C-ATAAGAA-TTTCAAAAGCAAAAGGAAAAGGCAATATTCGGGTATTTTGAAGATTTAAAA
128 TTCTCAATAAGAATTTTCAAAAGC------AAAAGGCAATATTCGGGTATTTTGAAGATTTAAAA
1733255 A
187 A
1733256 CATTGTGCCC
Statistics
Matches: 167, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
183 10 0.06
184 7 0.04
187 1 0.01
188 3 0.02
189 141 0.84
190 5 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (187 bp):
ATTATTTTTCGATGAATTTAGAAAACCAAGTATTCATTTTGCAATAATCACACAAATTTCAAATA
AAAGCTTATTCTCGGGAATCTAAAAGTGCCGGGTCCTAACTTACTGGTCCTGATATTTTGACTTC
TCAATAAGAATTTTCAAAAGCAAAAGGCAATATTCGGGTATTTTGAAGATTTAAAAA
Found at i:1745039 original size:44 final size:44
Alignment explanation
Indices: 1744971--1745847 Score: 466
Period size: 44 Copynumber: 19.4 Consensus size: 44
1744961 GTTGAAAGAT
* *
1744971 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAAT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* * * * * *
1745015 ACCAAATCTTGTTTTC-TCATACTGGTGGCGAAGCAGATCGAAGGAAAA
1 AACAGATCTTGTCTTCAT-ATACTGG-CGTGAAGTAGATC-AA--AAAA
* * * * * *
1745063 AGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAGAGAT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* * ** * * *
1745107 ACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAGAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATC-AA-AA-AA
* ***
1745155 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* ** * * *
1745199 AACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGAT-AAAAAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAAAA
** * * ***
1745243 AGTAGATCTTGTATTCATGTACTGGCGTGAAGTAGATCAAAGGT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* ** * * * *
1745287 AACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGACGAAGAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATC-A--AAAAA
* ***
1745335 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* ** * * *
1745379 AACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGAT-AAAAAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAAAA
* * * * *
1745423 AGCAGATCTTGTCTTCATGTACTGGCTTGAAGTAGATCAAAGAT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* * * ** * * *
1745467 ACCAGATCCTGCCTTCCCATACTGGTGGCGAAGCAGATCGACAAAGAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATC-A-AAA-AA
* ** *
1745515 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAGGAT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* * ** * * *
1745559 ACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCTAAGAAGAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATC-AA-AA-AA
* * * ***
1745607 AACATATTTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* * * ** ** * *
1745651 AACATATCTTGCCCTCCCATACTTGTG-GCAAAGCAGATCGACGAATAA
1 AACAGATCTTGTCTTCATATAC-TG-GCGTGAAGTAGATC-A--AAAAA
* * * * *
1745699 AATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
* ** * * * *
1745743 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
1 AACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAAAA
* * * *
1745788 AACGGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAA
1 AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
*
1745832 AGCAGATCTTGTCTTC
1 AACAGATCTTGTCTTC
1745848 CCATACTAAC
Statistics
Matches: 599, Mismatches: 201, Indels: 66
0.69 0.23 0.08
Matches are distributed among these distances:
43 18 0.03
44 262 0.44
45 115 0.19
46 18 0.03
47 64 0.11
48 121 0.20
49 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
AACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAAAA
Found at i:1745130 original size:92 final size:92
Alignment explanation
Indices: 1744966--1745854 Score: 1275
Period size: 92 Copynumber: 9.8 Consensus size: 92
1744956 AGCAGGTTGA
* * * * **
1744966 AAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAAATCTTGTTTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
*
1745031 TCATACTGGTGGCGAAGCAGATCGAAGG
66 CCATACTGGTGGCGAAGCAGATCGAA-G
* * * *
1745059 AA-AAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
1745123 CCATACTGGTGGCGAAGCAGATCGAAG
66 CCATACTGGTGGCGAAGCAGATCGAAG
*
1745150 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
1745215 CCATACTGGTGGCGAAGCAGAT--AA-
66 CCATACTGGTGGCGAAGCAGATCGAAG
** * *
1745239 AA-AAAGTAGATCTTGTATTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
*
1745303 CCATACTGGTGGCGAAGCAGATCGACG
66 CCATACTGGTGGCGAAGCAGATCGAAG
*
1745330 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
1745395 CCATACTGGTGGCGAAGCAGAT--AA-
66 CCATACTGGTGGCGAAGCAGATCGAAG
* * * *
1745419 AA-AAAGCAGATCTTGTCTTCATGTACTGGCTTGAAGTAGATCAAAGATACCAGATCCTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
1745483 CCATACTGGTGGCGAAGCAGATCGACA-
66 CCATACTGGTGGCGAAGCAGATCGA-AG
* *
1745510 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAGGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
*
1745575 CCATACTGGTGGCGAAGCAGATCTAAG
66 CCATACTGGTGGCGAAGCAGATCGAAG
* * * * *
1745602 AAGAAAACATATTTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACATATCTTGCCCTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
* * *
1745667 CCATACTTGTGGCAAAGCAGATCGACG
66 CCATACTGGTGGCGAAGCAGATCGAAG
* * * * *
1745694 AATAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
*
1745759 CCATACTGGTGGCGAAGTAGATC---G
66 CCATACTGGTGGCGAAGCAGATCGAAG
* * *
1745783 AAGAAAACGGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTCTT
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGCCTT
1745847 CCCATACT
65 CCCATACT
1745855 AACAGTGAAG
Statistics
Matches: 723, Mismatches: 62, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
88 161 0.22
89 69 0.10
90 5 0.01
91 9 0.01
92 477 0.66
93 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (92 bp):
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTC
CCATACTGGTGGCGAAGCAGATCGAAG
Found at i:1745317 original size:180 final size:181
Alignment explanation
Indices: 1744966--1745854 Score: 1279
Period size: 180 Copynumber: 4.9 Consensus size: 181
1744956 AGCAGGTTGA
* ** * * **
1744966 AAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAAATCTTGTTTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
* *
1745031 TCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGT
66 CCATACTGGTGGCGAAGCAGAT--AA-GAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGT
* * *
1745096 AGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAG
128 AGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAG
1745150 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
* *
1745215 CCATACTGGTGGCGAAGCAGATAA-AAAAAGTAGATCTTGTATTCATGTACTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGCAGATAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGA
*
1745279 TCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGACG
131 TCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAG
1745330 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
*
1745395 CCATACTGGTGGCGAAGCAGATAA-AAAAAGCAGATCTTGTCTTCATGTACTGGCTTGAAGTAGA
66 CCATACTGGTGGCGAAGCAGATAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGA
* * *
1745459 TCAAAGATACCAGATCCTGCCTTCCCATACTGGTGGCGAAGCAGATCGACA-
131 TCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGA-AG
*
1745510 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AAGGATACCAGATCTTGCCTT
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGG-TAACAGATCTTGCCTT
* * *
1745574 CCCATACTGGTGGCGAAGCAGATCTAAGAAGAAAACATATTTTGTCTTCATGTACTGGCGTGAAG
65 CCCATACTGGTGGCGAAGCAGA--TAAGAA-AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAG
* * * * *
1745639 TAGATCAAAGGTAACATATCTTGCCCTCCCATACTTGTGGCAAAGCAGATCGACG
127 TAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAG
* * * * * *
1745694 AATAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
* * *
1745759 CCATACTGGTGGCGAAGTAGATCGAAG-AAAA-CGGATCTTGTCTTCATGTATTGGCGTGAAGTA
66 CCATACTGGTGGCGAAGCAGAT--AAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTA
* *
1745822 GATCAAA-GAAAGCAGATCTTGTCTTCCCATACT
129 GATCAAAGGTAA-CAGATCTTGCCTTCCCATACT
1745855 AACAGTGAAG
Statistics
Matches: 644, Mismatches: 50, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
179 4 0.01
180 339 0.53
181 53 0.08
182 9 0.01
183 3 0.00
184 233 0.36
185 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (181 bp):
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTC
CCATACTGGTGGCGAAGCAGATAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGA
TCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAG
Found at i:1745524 original size:272 final size:271
Alignment explanation
Indices: 1744965--1745854 Score: 1258
Period size: 272 Copynumber: 3.3 Consensus size: 271
1744955 GAGCAGGTTG
* ** * * **
1744965 AAAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAAATCTTGTTTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTT
* * *
1745030 CTCATACTGGTGGCGAAGCAGATCGAAGGAA-AAAGCAGATCTTATCTTCATGTACTGGCGTGAA
66 CCCATACTGGTGGCGAAGCAGATCGAA-GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAA
* * *
1745094 GTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAGAAAACA
130 GTAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC--A-AA-AAAACA
*
1745159 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGG
191 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTGG
1745224 TGGCGAAGCAGAT--A
256 TGGCGAAGCAGATCGA
** *
1745238 AAA-AAAGTAGATCTTGTATTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTT
*
1745302 CCCATACTGGTGGCGAAGCAGATCGACGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAG
66 CCCATACTGGTGGCGAAGCAGATCGAAGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAG
1745367 TAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGAT-AAAAAAAGCAGATC
131 TAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAAAAA-CAGATC
* * *
1745431 TTGTCTTCATGTACTGGCTTGAAGTAGATCAAAGATACCAGATCCTGCCTTCCCATACTGGTGGC
195 TTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGC
1745496 GAAGCAGATCGA
260 GAAGCAGATCGA
*
1745508 CAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AAGGATACCAGATCTTGCC
1 -AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGG-TAACAGATCTTGCC
* * *
1745572 TTCCCATACTGGTGGCGAAGCAGATCTAAGAAGAAAACATATTTTGTCTTCATGTACTGGCGTGA
64 TTCCCATACTGGTGGCGAAGCAGATCGAAGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGA
* * * * *
1745637 AGTAGATCAAAGGTAACATATCTTGCCCTCCCATACTTGTGGCAAAGCAGATCGACGAATAAAAT
129 AGTAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC-A--AA-AAAAC
* * *
1745702 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG
190 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTG
*
1745767 GTGGCGAAGTAGATCG-
255 GTGGCGAAGCAGATCGA
* * * *
1745783 -AAGAAAACGGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAA-GAAAGCAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAA-CAGATCTTGCCT
1745846 TCCCATACT
65 TCCCATACT
1745855 AACAGTGAAG
Statistics
Matches: 558, Mismatches: 45, Indels: 28
0.88 0.07 0.04
Matches are distributed among these distances:
267 4 0.01
268 78 0.14
269 1 0.00
270 1 0.00
271 10 0.02
272 315 0.56
273 65 0.12
274 3 0.01
276 77 0.14
277 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (271 bp):
AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTT
CCCATACTGGTGGCGAAGCAGATCGAAGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAG
TAGATCAAAGGTAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAAAAACAGATCT
TGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGCG
AAGCAGATCGA
Found at i:1751458 original size:50 final size:50
Alignment explanation
Indices: 1751349--1751574 Score: 231
Period size: 50 Copynumber: 4.4 Consensus size: 50
1751339 ACATTAAGAG
* *
1751349 GATGAGA--TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---A
* * *
1751400 GATTATGAGAGGTCCCATATAATACCATGTTTGGGACATGGCATTGGCACCAA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
** * * *
1751453 GATGAGAGGTTTCATGTTAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
** * *
1751503 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* **
1751553 TATGAGAACTCCCATGTAAGAC
1 GATGAGAGGTCCCATGTAAGAC
1751575 NNNNNNNNNN
Statistics
Matches: 146, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
50 100 0.68
51 1 0.01
53 2 0.01
54 6 0.04
56 37 0.25
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
Found at i:1758904 original size:18 final size:18
Alignment explanation
Indices: 1758861--1758904 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1758851 AACCAATCTA
* *
1758861 AACCCAAGTATCCAACCC
1 AACCCAATTACCCAACCC
1758879 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
1758897 AACCCAAT
1 AACCCAAT
1758905 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:1759045 original size:9 final size:9
Alignment explanation
Indices: 1759031--1759106 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
1759021 GTAGTGATTC
1759031 AATTCGGTT
1 AATTCGGTT
*
1759040 AATTCGGGT
1 AATTCGGTT
*
1759049 AATTCGAG-A
1 AATTCG-GTT
1759058 AATTCGGTT
1 AATTCGGTT
*
1759067 AATTCGGGT
1 AATTCGGTT
*
1759076 AATTCAGTT
1 AATTCGGTT
1759085 AATTCGGTT
1 AATTCGGTT
*
1759094 AATTCAGTT
1 AATTCGGTT
1759103 AATT
1 AATT
1759107 TTTAACTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
8 1 0.02
9 55 0.96
10 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1759106 original size:27 final size:27
Alignment explanation
Indices: 1759031--1759098 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
1759021 GTAGTGATTC
1759031 AATTCGGTTAATTCGGGTAATTCGAGA
1 AATTCGGTTAATTCGGGTAATTCGAGA
*
1759058 AATTCGGTTAATTCGGGTAATTC-AGTT
1 AATTCGGTTAATTCGGGTAATTCGAG-A
1759085 AATTCGGTTAATTC
1 AATTCGGTTAATTC
1759099 AGTTAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTCGAGA
Found at i:1759283 original size:12 final size:12
Alignment explanation
Indices: 1759266--1759290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1759256 TGTTATTTCG
1759266 GGTCGGTTAACC
1 GGTCGGTTAACC
1759278 GGTCGGTTAACC
1 GGTCGGTTAACC
1759290 G
1 G
1759291 ACTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:1760053 original size:12 final size:12
Alignment explanation
Indices: 1760036--1760065 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1760026 TTATTGATAG
1760036 GAGAAAGTAAAT
1 GAGAAAGTAAAT
1760048 GAGAAAGTAAAT
1 GAGAAAGTAAAT
1760060 GAGAAA
1 GAGAAA
1760066 AAGACTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (12 bp):
GAGAAAGTAAAT
Found at i:1760939 original size:31 final size:31
Alignment explanation
Indices: 1760904--1760962 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1760894 TTTAAATGTG
* *
1760904 TACATTTAAATCA-AAATCAAAGTTTCATACA
1 TACATATAAACCACAAAT-AAAGTTTCATACA
*
1760935 TACATATAAACCACAAATTAAGTTTCAT
1 TACATATAAACCACAAATAAAGTTTCAT
1760963 GTGTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.32
Consensus pattern (31 bp):
TACATATAAACCACAAATAAAGTTTCATACA
Found at i:1763088 original size:26 final size:27
Alignment explanation
Indices: 1763059--1763117 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1763049 AGTGAAAAAT
*
1763059 TATTTATATAA-TTTTATTATATATTA
1 TATTTATAAAATTTTTATTATATATTA
* * *
1763085 TATTTTTAAAATTTTTATTTTCTATTA
1 TATTTATAAAATTTTTATTATATATTA
*
1763112 TTTTTA
1 TATTTA
1763118 ATGGTGATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTATAAAATTTTTATTATATATTA
Found at i:1771464 original size:43 final size:43
Alignment explanation
Indices: 1771367--1771521 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
1771357 AGGGTTACCA
* * * *
1771367 AGATTACGTGTAAGACTATATCTAGGATATT-GCATCGATATG
1 AGATTTCGTGTAAGACCATATCTGGGACATTGGCATCGATATG
* *
1771409 AGACTTCGTGTAAGACCATATCTGGGACATTGGCATTGATATG
1 AGATTTCGTGTAAGACCATATCTGGGACATTGGCATCGATATG
* * ** *
1771452 TGATTTCGTGTAAGACAATGGCTGGG-CTATTGGCATCGATACG
1 AGATTTCGTGTAAGACCATATCTGGGAC-ATTGGCATCGATATG
* *
1771495 AGATTAT-ATCTAAGACCATATCTGGGA
1 AGATT-TCGTGTAAGACCATATCTGGGA
1771522 TTGGACATTG
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 27 0.30
43 62 0.69
44 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (43 bp):
AGATTTCGTGTAAGACCATATCTGGGACATTGGCATCGATATG
Found at i:1778005 original size:43 final size:43
Alignment explanation
Indices: 1777940--1778062 Score: 151
Period size: 43 Copynumber: 2.8 Consensus size: 43
1777930 CTAGGATATG
*
1777940 GCATCAATATGAGACTTTGTGTAAGACCATGTCTGGGGC-ATTA
1 GCATCGATATGAGA-TTTGTGTAAGACCATGTCTGGGGCTATTA
* * *
1777983 GCATCGATATGTGATTTGGTGTAAGACCATGGCT-GGGCTATTG
1 GCATCGATATGAGATTT-GTGTAAGACCATGTCTGGGGCTATTA
* *
1778026 GCATCGATATGAGATTATATGTAAGACCATATCTGGG
1 GCATCGATATGAGATT-TGTGTAAGACCATGTCTGGG
1778063 ATATGACATT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 7 0.10
43 58 0.85
44 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (43 bp):
GCATCGATATGAGATTTGTGTAAGACCATGTCTGGGGCTATTA
Found at i:1781527 original size:25 final size:26
Alignment explanation
Indices: 1781479--1781532 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
1781469 AAGGTAGTCT
1781479 TTTCTTTTTTTCTTGTGTTCATTTCA
1 TTTCTTTTTTTCTTGTGTTCATTTCA
1781505 TTTCTTTTTTTCTT-T-TTCGATTTCA
1 TTTCTTTTTTTCTTGTGTTC-ATTTCA
1781530 TTT
1 TTT
1781533 TGTTCAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 3 0.11
25 10 0.37
26 14 0.52
ACGTcount: A:0.07, C:0.15, G:0.06, T:0.72
Consensus pattern (26 bp):
TTTCTTTTTTTCTTGTGTTCATTTCA
Found at i:1797555 original size:15 final size:15
Alignment explanation
Indices: 1797535--1797567 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1797525 ATAGGAATAT
1797535 AATAAAATATTAAAA
1 AATAAAATATTAAAA
1797550 AAT-AAATATTAAAA
1 AATAAAATATTAAAA
1797564 AATA
1 AATA
1797568 GTAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAATATTAAAA
Found at i:1801638 original size:24 final size:24
Alignment explanation
Indices: 1801609--1801658 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1801599 GTTTCTCAGT
1801609 CTCATACTCCTCATTTTCTCCAAA
1 CTCATACTCCTCATTTTCTCCAAA
*
1801633 CTCATATTCCTCATTTTCTCCAAA
1 CTCATACTCCTCATTTTCTCCAAA
1801657 CT
1 CT
1801659 ACTCATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (24 bp):
CTCATACTCCTCATTTTCTCCAAA
Found at i:1812575 original size:17 final size:17
Alignment explanation
Indices: 1812523--1812575 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
1812513 TATGAAAACA
*
1812523 TAATCTTCGAAGATATG
1 TAATCTTAGAAGATATG
*
1812540 TAATCGTAGATATGATATG
1 TAATCTTAGA-A-GATATG
1812559 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
1812576 ATTTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 15 0.48
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:1812575 original size:22 final size:21
Alignment explanation
Indices: 1812547--1812604 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
1812537 ATGTAATCGT
*
1812547 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
1812568 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
1812591 AGATTTGATTTGTA
1 AGATATGATTTGTA
1812605 GATACCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:1817655 original size:17 final size:17
Alignment explanation
Indices: 1817603--1817655 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
1817593 TATGGAAATA
*
1817603 TAATCTTCGAAGATATG
1 TAATCTTAGAAGATATG
* *
1817620 CAATCGTAGATATGATATG
1 TAATCTTAGA-A-GATATG
1817639 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
1817656 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:1817688 original size:22 final size:22
Alignment explanation
Indices: 1817627--1817685 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1817617 ATGCAATCGT
* *
1817627 AGATATGATATGTAATCTTAGA
1 AGATATGATTTGTAATATTAGA
1817649 AGATATGATTTTGTAATATTAG-
1 AGATATGA-TTTGTAATATTAGA
*
1817671 AGATTTGATTTGTAA
1 AGATATGATTTGTAA
1817686 ATACCTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.21
22 15 0.45
23 11 0.33
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (22 bp):
AGATATGATTTGTAATATTAGA
Found at i:1818649 original size:216 final size:216
Alignment explanation
Indices: 1818264--1818702 Score: 621
Period size: 216 Copynumber: 2.0 Consensus size: 216
1818254 AGGTATTTAT
* * *
1818264 ACATGT-TGTCACAGATATTATTACAACTCATGATAGGATCCCACTACTAGGACCCCATTATTTT
1 ACATGTGTGTCACAAATATTATTACAACTCATGATAGGACCCCACTACTAGGACCCCACTATTTT
* * *
1818328 GTCTTGACTCCACTACATCTAGCCTTGACATTCTTTGTCCCTAATATTGACATTCTCAGTGAACT
66 GTCTTGACTCCACTACATCTAGCCTTGACATTCTCTGTCCCTAATACTGACATTCTCAGAGAACT
* * * **
1818393 CCAAGCCTATTGGACACATGTCTATGGAGCACGTGGTCCTTTCTATTCTTGGGGTTAATGATTTG
131 CCAAGCCTATTGGACACATGTCTACGGAGCACGCGGTCCTTTCTATTCTTGGGGCTAACAATTTG
* **
1818458 AGCGGGGTCCATACCTGTTGG
196 AGCGGGCTCCATACCTACTGG
* * *
1818479 ACATGTGTGTCACAAATATTATTATAGCTCATGATAGGACCCCACTACTAGGACTCCACTATTTT
1 ACATGTGTGTCACAAATATTATTACAACTCATGATAGGACCCCACTACTAGGACCCCACTATTTT
* *
1818544 GTCTTGACTCCACTACCTCTAGCCTTGACATTCTCTGTCTCTAATACTGACATTCTCAGCAG-AC
66 GTCTTGACTCCACTACATCTAGCCTTGACATTCTCTGTCCCTAATACTGACATTCTCAG-AGAAC
* * * * * *
1818608 TTCAGGCCTGTTGGACACATGTCTACGGAGTACGCGGTCCTTTCTGTTCTTGGGGCTGACAATTT
130 TCCAAGCCTATTGGACACATGTCTACGGAGCACGCGGTCCTTTCTATTCTTGGGGCTAACAATTT
*
1818673 GAGCGGGCTCTATACCTACTGG
195 GAGCGGGCTCCATACCTACTGG
1818695 ACATGTGT
1 ACATGTGT
1818703 CCGAGTGACT
Statistics
Matches: 196, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
215 6 0.03
216 189 0.96
217 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (216 bp):
ACATGTGTGTCACAAATATTATTACAACTCATGATAGGACCCCACTACTAGGACCCCACTATTTT
GTCTTGACTCCACTACATCTAGCCTTGACATTCTCTGTCCCTAATACTGACATTCTCAGAGAACT
CCAAGCCTATTGGACACATGTCTACGGAGCACGCGGTCCTTTCTATTCTTGGGGCTAACAATTTG
AGCGGGCTCCATACCTACTGG
Found at i:1822053 original size:18 final size:18
Alignment explanation
Indices: 1822010--1822045 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1822000 GAAGATAACT
1822010 AAATAT-AAAATTTTAAA
1 AAATATAAAAATTTTAAA
1822027 AAATATAAAAATTTTAAA
1 AAATATAAAAATTTTAAA
1822045 A
1 A
1822046 TCATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAAAAATTTTAAA
Found at i:1824186 original size:18 final size:19
Alignment explanation
Indices: 1824163--1824206 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1824153 ACTTGATATT
1824163 GAAATGGAAAAT-AAACGA
1 GAAATGGAAAATGAAACGA
* *
1824181 GAAAT-GAAAATGGAATGA
1 GAAATGGAAAATGAAACGA
1824199 GAAATGGA
1 GAAATGGA
1824207 GTACTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.27, T:0.14
Consensus pattern (19 bp):
GAAATGGAAAATGAAACGA
Found at i:1832590 original size:16 final size:16
Alignment explanation
Indices: 1832571--1832601 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1832561 TTGAAAAAGT
1832571 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
1832587 TTTCAAATTTATATG
1 TTTCAAATATATATG
1832602 CTCTAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:1833507 original size:55 final size:55
Alignment explanation
Indices: 1833448--1833684 Score: 240
Period size: 55 Copynumber: 4.3 Consensus size: 55
1833438 CCTAACCGTT
* ** *
1833448 AGGTCAATGGTTGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATA
1 AGGTCAACGGTTGCACCCTCCACAAACATCTCATATTGCATAAACCTGGGTCATA
* * * * * * **
1833503 AGGTCAATGATTGAATCTTCCACAAGCATCTCATATTGCATAAACCTGGGTTGTA
1 AGGTCAACGGTTGCACCCTCCACAAACATCTCATATTGCATAAACCTGGGTCATA
* ** * *
1833558 AGGTCAACGGTTGCACCTTCCACAAACATCTCATATCACGTAAACCTGGGTGATA
1 AGGTCAACGGTTGCACCCTCCACAAACATCTCATATTGCATAAACCTGGGTCATA
** * * * * * * *
1833613 AGGTCAAAAGTTACACCCTCCGCGAGCATCTCTTATTGCATAAACCCGAGTCATA
1 AGGTCAACGGTTGCACCCTCCACAAACATCTCATATTGCATAAACCTGGGTCATA
1833668 AGGTCAACGGTTGCACC
1 AGGTCAACGGTTGCACC
1833685 TCTGGTACAT
Statistics
Matches: 145, Mismatches: 37, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 145 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (55 bp):
AGGTCAACGGTTGCACCCTCCACAAACATCTCATATTGCATAAACCTGGGTCATA
Found at i:1833508 original size:110 final size:110
Alignment explanation
Indices: 1833394--1833684 Score: 246
Period size: 110 Copynumber: 2.6 Consensus size: 110
1833384 TAGGCTGTAG
* * *** * * * *
1833394 GGTCAACGGTTGCACCTTCCGTGAGCATCTCATGTTGCGTAAACCCT-AACCGTTAGGTCAATGG
1 GGTCAACGATTGAACCTTCCACAAGCATCTCATATTGCATAAA-CCTGAACCGTAAGGTCAACGG
1833458 TTGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATAA
65 TTGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATAA
* * ****
1833504 GGTCAATGATTGAATCTTCCACAAGCATCTCATATTGCATAAACCTGGGTTGTAAGGTCAACGGT
1 GGTCAACGATTGAACCTTCCACAAGCATCTCATATTGCATAAACCTGAACCGTAAGGTCAACGGT
* ** * ** **
1833569 TGCACCTTCCACAAACATCTCATATCACGTAAACCTGGGTGATAA
66 TGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATAA
* * * * * * ** *
1833614 GGTCAA-AAGTT-ACACCCTCCGCGAGCATCTCTTATTGCATAAACCCGAGTCATAAGGTCAACG
1 GGTCAACGA-TTGA-ACCTTCCACAAGCATCTCATATTGCATAAACCTGAACCGTAAGGTCAACG
1833677 GTTGCACC
64 GTTGCACC
1833685 TCTGGTACAT
Statistics
Matches: 145, Mismatches: 33, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
109 5 0.03
110 140 0.97
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (110 bp):
GGTCAACGATTGAACCTTCCACAAGCATCTCATATTGCATAAACCTGAACCGTAAGGTCAACGGT
TGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATAA
Found at i:1833685 original size:110 final size:110
Alignment explanation
Indices: 1833448--1833685 Score: 273
Period size: 110 Copynumber: 2.2 Consensus size: 110
1833438 CCTAACCGTT
* * ** ** *
1833448 AGGTCAATGGTTGCACCCTCCACAAACATCTCATATTGCATAAATTTGGGCCATAAGGTCAATGA
1 AGGTCAACGGTTGCACCTTCCACAAACATCTCATATCACATAAACCTGGGCCATAAGGTCAAAGA
* * * * **
1833513 TTGAATCTTCCACAAGCATCTCATATTGCATAAACCTGGGTTGTA
66 TTGAACCCTCCACAAGCATCTCATATTGCATAAACCCGAGTCATA
* **
1833558 AGGTCAACGGTTGCACCTTCCACAAACATCTCATATCACGTAAACCTGGGTGATAAGGTCAAA-A
1 AGGTCAACGGTTGCACCTTCCACAAACATCTCATATCACATAAACCTGGGCCATAAGGTCAAAGA
* * *
1833622 GTT-ACACCCTCCGCGAGCATCTCTTATTGCATAAACCCGAGTCATA
66 -TTGA-ACCCTCCACAAGCATCTCATATTGCATAAACCCGAGTCATA
1833668 AGGTCAACGGTTGCACCT
1 AGGTCAACGGTTGCACCT
1833686 CTGGTACATT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
109 2 0.02
110 105 0.98
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (110 bp):
AGGTCAACGGTTGCACCTTCCACAAACATCTCATATCACATAAACCTGGGCCATAAGGTCAAAGA
TTGAACCCTCCACAAGCATCTCATATTGCATAAACCCGAGTCATA
Found at i:1839111 original size:16 final size:16
Alignment explanation
Indices: 1839090--1839120 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1839080 AAAGTTTATT
1839090 TGGTTTATTCACACTC
1 TGGTTTATTCACACTC
1839106 TGGTTTATTCACACT
1 TGGTTTATTCACACT
1839121 AAGGTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (16 bp):
TGGTTTATTCACACTC
Found at i:1841045 original size:9 final size:9
Alignment explanation
Indices: 1841031--1841079 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
1841021 TCACTCAAAT
1841031 TCAATTCTC
1 TCAATTCTC
*
1841040 TCAATTCTT
1 TCAATTCTC
1841049 TCTAA-TCTC
1 TC-AATTCTC
*
1841058 TCAACTCTC
1 TCAATTCTC
*
1841067 TTAATTCTC
1 TCAATTCTC
1841076 TCAA
1 TCAA
1841080 ATTTCTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 2 0.06
9 29 0.88
10 2 0.06
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (9 bp):
TCAATTCTC
Found at i:1843263 original size:22 final size:23
Alignment explanation
Indices: 1843238--1843287 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1843228 ACCGTCGTCG
1843238 GCCACTAG-ACATCGCCATCACA
1 GCCACTAGAACATCGCCATCACA
* * *
1843260 GCCAC-CGAACGTCGCCATCGCA
1 GCCACTAGAACATCGCCATCACA
1843282 GCCACT
1 GCCACT
1843288 GGCACCACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.26, C:0.44, G:0.18, T:0.12
Consensus pattern (23 bp):
GCCACTAGAACATCGCCATCACA
Found at i:1844793 original size:16 final size:16
Alignment explanation
Indices: 1844772--1844802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1844762 CTATGCATGC
*
1844772 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
1844788 AAAATACAAAAGACA
1 AAAATACAAAAGACA
1844803 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:1847024 original size:16 final size:16
Alignment explanation
Indices: 1847003--1847033 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1846993 CTATGCATGC
*
1847003 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
1847019 AAAATACAAAAGACA
1 AAAATACAAAAGACA
1847034 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:1848621 original size:16 final size:15
Alignment explanation
Indices: 1848594--1848632 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1848584 TAAACAAATT
1848594 AGAAAGAAAAGAAAGAA
1 AGAAA-AAAAGAAAG-A
1848611 AGAAAAAAAGAAAGA
1 AGAAAAAAAGAAAGA
1848626 AGAAAAA
1 AGAAAAA
1848633 TAAAGAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 9 0.41
17 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAGA
Found at i:1848631 original size:13 final size:12
Alignment explanation
Indices: 1848594--1848638 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
1848584 TAAACAAATT
1848594 AGAAAGAAAAGAA
1 AGAAAGAAAA-AA
1848607 AGAAAGAAAAAA
1 AGAAAGAAAAAA
1848619 AGAAAGAAGAAAA
1 AGAAAGAA-AAAA
*
1848632 ATAAAGA
1 AGAAAGA
1848639 GACTCACGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:1851336 original size:27 final size:27
Alignment explanation
Indices: 1851304--1851755 Score: 496
Period size: 27 Copynumber: 16.4 Consensus size: 27
1851294 AGACCCTAAA
*
1851304 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
**
1851331 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
1851358 ATAGGGTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
1851385 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * * * *
1851412 ATAAGATAAAATGATCAAAACACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* **
1851439 ATAGGGTAAAATAACCGAAATACCCTAATAG
1 ATAGGGTAAAATGACCGAAATACCC----CC
*
1851470 ATAAGGGTAAAATGACTGAAATACCCCC
1 AT-AGGGTAAAATGACCGAAATACCCCC
** * *
1851498 ATAGAGTAAAGGTAAAATGATTGAAATACCTCT
1 AT--AG----GGTAAAATGACCGAAATACCCCC
*
1851531 ATAGGGTAAAATGACCGAAATA-CCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
1851557 ATAAGGTAAAATGACTGAAATA-CCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
1851583 ATAGGGTAGAATGACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
1851610 ATAGGGTAAAATGACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
1851637 ATAGGATAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
1851664 ATAGAGTAAAATGACCAAAATACCTCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
1851691 ATAGGGTAAAATGACCAAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
1851718 ATAAGGT-AAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
1851744 ATAGGGTAAAAT
1 ATAGGGTAAAAT
1851756 AACTGTTATA
Statistics
Matches: 358, Mismatches: 55, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
26 65 0.18
27 242 0.68
28 2 0.01
29 2 0.01
31 4 0.01
32 21 0.06
33 22 0.06
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:1851540 original size:33 final size:33
Alignment explanation
Indices: 1851443--1851527 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
1851433 ACCCTCATAG
* * ** *
1851443 GGTAAAATAACCGAAATACCCTAATAGA-TAAG
1 GGTAAAATGACTGAAATACCCCCATAGAGTAAA
1851475 GGTAAAATGACTGAAATACCCCCATAGAGTAAA
1 GGTAAAATGACTGAAATACCCCCATAGAGTAAA
*
1851508 GGTAAAATGATTGAAATACC
1 GGTAAAATGACTGAAATACC
1851528 TCTATAGGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 24 0.52
33 22 0.48
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (33 bp):
GGTAAAATGACTGAAATACCCCCATAGAGTAAA
Found at i:1853801 original size:25 final size:24
Alignment explanation
Indices: 1853756--1853810 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
1853746 GTCATTTGGG
* *
1853756 TTACCGATTTCAGCTCTTATGAGC
1 TTACCGATCTCAGCTCGTATGAGC
1853780 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGAT-CTCAGCTCGTATGAGC
1853805 TTACCG
1 TTACCG
1853811 TTATTTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (24 bp):
TTACCGATCTCAGCTCGTATGAGC
Found at i:1853820 original size:25 final size:25
Alignment explanation
Indices: 1853762--1853846 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
1853752 TGGGTTACCG
* *
1853762 ATTTCAGCTCTTATGAGCTTACCGAT
1 ATTT-AGCTCGTATGAGCTTACCGTT
* *
1853788 ACTCAGCTCGTATGAGCTTACCGTT
1 ATTTAGCTCGTATGAGCTTACCGTT
* * *
1853813 ATTTAGCTCAG-AGGAGCTTACCATA
1 ATTTAGCTC-GTATGAGCTTACCGTT
1853838 ATTTAGCTC
1 ATTTAGCTC
1853847 AGAGGAGCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
25 46 0.94
26 3 0.06
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (25 bp):
ATTTAGCTCGTATGAGCTTACCGTT
Found at i:1853847 original size:25 final size:25
Alignment explanation
Indices: 1853801--1853858 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1853791 CAGCTCGTAT
* *
1853801 GAGCTTACCGTTATTTAGCTCAGAG
1 GAGCTTACCATAATTTAGCTCAGAG
1853826 GAGCTTACCATAATTTAGCTCAGAG
1 GAGCTTACCATAATTTAGCTCAGAG
1853851 GAGCTTAC
1 GAGCTTAC
1853859 TATTTACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (25 bp):
GAGCTTACCATAATTTAGCTCAGAG
Found at i:1870394 original size:26 final size:26
Alignment explanation
Indices: 1870336--1870387 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1870326 CCCTCACACC
* * *
1870336 AATATTGCAGCATAGCTGCCAGTAGT
1 AATAATGCAGCAAAGCTGCCAATAGT
1870362 AATAATGCAGCAAAGCTGCCAATAGT
1 AATAATGCAGCAAAGCTGCCAATAGT
1870388 CGAAATGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (26 bp):
AATAATGCAGCAAAGCTGCCAATAGT
Found at i:1870431 original size:22 final size:22
Alignment explanation
Indices: 1870401--1870452 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1870391 AATGGCTAAG
* * *
1870401 AGCCGTAAACAGGATAGCTATA
1 AGCCATAAACAGAATAGCTACA
* *
1870423 AGCTATAAACAGAATGGCTACA
1 AGCCATAAACAGAATAGCTACA
1870445 AGCCATAA
1 AGCCATAA
1870453 GTATAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAGAATAGCTACA
Found at i:1870514 original size:32 final size:32
Alignment explanation
Indices: 1870478--1870677 Score: 119
Period size: 32 Copynumber: 6.3 Consensus size: 32
1870468 TGGCACAAAG
*
1870478 CCATCAGTAGCAGTGATATGATCGACACACAA
1 CCATCAGTAACAGTGATATGATCGACACACAA
* * *
1870510 CCATCAGTAACGGTAATATGATCGGCACA-AA
1 CCATCAGTAACAGTGATATGATCGACACACAA
* * * *
1870541 GCCATCAATAGCAGTGATAT-ATC-AGTACACAG
1 -CCATCAGTAACAGTGATATGATCGA-CACACAA
* * *
1870573 CCATCAGTAACAGTGAAATGATC-AGCACATAG
1 CCATCAGTAACAGTGATATGATCGA-CACACAA
* * * *
1870605 CCATTAGTAAC-GATAATATGATTGGCACA-AA
1 CCATCAGTAACAG-TGATATGATCGACACACAA
* * *
1870636 GTCATCAGTAACGGT-ATTATGATCGGCACA-AA
1 -CCATCAGTAACAGTGA-TATGATCGACACACAA
1870668 GCCATCAGTA
1 -CCATCAGTA
1870678 GCATCGCAGC
Statistics
Matches: 133, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
31 27 0.20
32 105 0.79
33 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
CCATCAGTAACAGTGATATGATCGACACACAA
Found at i:1870559 original size:64 final size:64
Alignment explanation
Indices: 1870458--1870680 Score: 240
Period size: 64 Copynumber: 3.5 Consensus size: 64
1870448 CATAAGTATA
* *
1870458 GTAATGTGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACG
* * * *
1870522 GTAATATGATCGGCACAAAGCCATCAATAGCAGTGATAT-ATC-AGTACACAGCCATCAGTAACA
1 GTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGA-CACACAACCATCAGTAACG
* * * * * * * *
1870585 GTGAA-ATGATCAGCACATAGCCATTAGTAAC-GATAATATGATTGGCACA-AAGTCATCAGTAA
1 GT-AATATGATCGGCACAAAGCCATCAGTAGCAG-TGATATGATCGACACACAA-CCATCAGTAA
1870647 CG
63 CG
*
1870649 GTATTATGATCGGCACAAAGCCATCAGTAGCA
1 GTAATATGATCGGCACAAAGCCATCAGTAGCA
1870681 TCGCAGCAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
62 2 0.02
63 49 0.38
64 77 0.60
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (64 bp):
GTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACG
Found at i:1870709 original size:26 final size:26
Alignment explanation
Indices: 1870680--1870733 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
1870670 CATCAGTAGC
1870680 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
* * * * *
1870706 ATCGTAGTAAAGTTGCCAGTAATAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
1870732 AT
1 AT
1870734 ATGTGGCAAA
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:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:1870751 original size:27 final size:27
Alignment explanation
Indices: 1870721--1870777 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1870711 AGTAAAGTTG
*
1870721 CCAGTAATAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTGAT-TGTGGCAAAGCCA
*
1870748 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAAAGCCA
1870775 CCA
1 CCA
1870778 ATACAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAAAGCCA
Found at i:1870923 original size:24 final size:23
Alignment explanation
Indices: 1870849--1870921 Score: 101
Period size: 24 Copynumber: 3.1 Consensus size: 23
1870839 CCATGCTCAG
*
1870849 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATTTAAA-CACAGACA
*
1870873 AATCAGTCATACTAAACACAGACA
1 AATCAGTCAT-TTAAACACAGACA
*
1870897 AATCAGTCATTTAACCACAGACA
1 AATCAGTCATTTAAACACAGACA
1870920 AA
1 AA
1870922 ATAATCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 13 0.30
24 28 0.64
25 3 0.07
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.19
Consensus pattern (23 bp):
AATCAGTCATTTAAACACAGACA
Found at i:1871259 original size:27 final size:27
Alignment explanation
Indices: 1870952--1871272 Score: 291
Period size: 27 Copynumber: 12.0 Consensus size: 27
1870942 GGCAAAAATA
* * *
1870952 GTCA-TTTACCCA-CCAGGGCATTACG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
1870977 GTCATTTTACCC-TAC-AGGGGTATTACG
1 GTCATTTTACCCAT-CGA-GGGTATTTCG
*
1871004 GTCATTTTACCC-TAC-AGGGGAATTAT-G
1 GTCATTTTACCCAT-CGA-GGGTATT-TCG
* * * **
1871031 GTTATTTTACCTTATAG-GGGTATTTTA
1 GTCATTTTACC-CATCGAGGGTATTTCG
1871058 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
1871085 GTCATTCTACCCATCGAGGATATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
1871112 GTTATTTTACCCTAT-AAGGGTATTTCA
1 GTCATTTTACCC-ATCGAGGGTATTTCG
* *
1871139 GTCATTCTACCTATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* **
1871166 GTCATTTTACCCTTTAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
1871193 GTCATTTTACTCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
1871220 ATCATTCTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
1871247 GTTATTTTACCCATCGAGGGTATTTC
1 GTCATTTTACCCATCGAGGGTATTTC
1871273 AGCTCAGATA
Statistics
Matches: 242, Mismatches: 42, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.02
26 14 0.06
27 221 0.91
28 2 0.01
29 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:1873130 original size:22 final size:22
Alignment explanation
Indices: 1873104--1873148 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1873094 TGTTGATGAC
1873104 ATGTTAATAGTAGCCAAAGATG
1 ATGTTAATAGTAGCCAAAGATG
1873126 ATGTTAATAGTAGCCAAAGATG
1 ATGTTAATAGTAGCCAAAGATG
1873148 A
1 A
1873149 AGGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (22 bp):
ATGTTAATAGTAGCCAAAGATG
Found at i:1874210 original size:5 final size:5
Alignment explanation
Indices: 1874200--1874234 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1874190 AATTCATGTT
*
1874200 AATAA AATAA AATAA AATAA AATACA AGTAA AATA
1 AATAA AATAA AATAA AATAA AATA-A AATAA AATA
1874235 TGTATAGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1882821 original size:39 final size:39
Alignment explanation
Indices: 1882773--1882881 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 39
1882763 TTTTTTCCTT
* * *
1882773 ATACTATTACACCTCTATTCCATTCAACCAAACACAAGA
1 ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
1882812 ATACCATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGA
1 ATACCATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGA
*
1882856 ATTACCTATTATGCCTCTATTCCATT
1 A-TACC-ATTACGCCTCTATTCCATT
1882882 ACGCATCTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
39 13 0.22
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.39
45 4 0.07
46 9 0.15
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (39 bp):
ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
Found at i:1882856 original size:44 final size:46
Alignment explanation
Indices: 1882789--1882881 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
1882779 TTACACCTCT
*
1882789 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
*
1882833 ATTCCATTCAACCAAACAAAAGAATTACCTATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1882879 ATT
1 ATT
1882882 ACGCATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:1884314 original size:19 final size:19
Alignment explanation
Indices: 1884290--1884329 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1884280 TAGGGACATG
1884290 GAAGCAGAAAAGCAAAAGA
1 GAAGCAGAAAAGCAAAAGA
1884309 GAAGCAGAAAAGCAAAAGA
1 GAAGCAGAAAAGCAAAAGA
1884328 GA
1 GA
1884330 GGGATATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (19 bp):
GAAGCAGAAAAGCAAAAGA
Found at i:1886289 original size:15 final size:15
Alignment explanation
Indices: 1886269--1886297 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1886259 TTCTTTCCCC
1886269 CTTCTTCTTCTTCCT
1 CTTCTTCTTCTTCCT
1886284 CTTCTTCTTCTTCC
1 CTTCTTCTTCTTCC
1886298 CTAACCCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTCTTCTTCTTCCT
Done.