Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_pilon, whole genome shotgun sequence
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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 17
Found at i:1096816 original size:20 final size:21
Alignment explanation
Indices: 1096791--1096839 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1096781 AATTCCTTTG
1096791 TTGCATTTACATTTTGCAT-T
1 TTGCATTTACATTTTGCATCT
**
1096811 TTGCATTCCCATTTTGCATCT
1 TTGCATTTACATTTTGCATCT
1096832 TTGCATTT
1 TTGCATTT
1096840 GTATGAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (21 bp):
TTGCATTTACATTTTGCATCT
Found at i:1096835 original size:28 final size:29
Alignment explanation
Indices: 1096795--1096866 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
1096785 CCTTTGTTGC
* **
1096795 ATTTACAT-TTTGCATTTTGCATTCCCAT
1 ATTTGCATCTTTGCATTTTGCATGACCAT
* *
1096823 -TTTGCATCTTTGCA-TTTGTATGAGCAT
1 ATTTGCATCTTTGCATTTTGCATGACCAT
1096850 ATTTGCATCTTTGCATT
1 ATTTGCATCTTTGCATT
1096867 AGCATCTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.42
28 20 0.56
29 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.50
Consensus pattern (29 bp):
ATTTGCATCTTTGCATTTTGCATGACCAT
Found at i:1098193 original size:17 final size:16
Alignment explanation
Indices: 1098149--1098202 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
1098139 GAGATATAAA
*
1098149 AAAAAATAAAAAAAAAG
1 AAAAAA-AAAAAAAATG
* *
1098166 CAAAAACAAAAAAATG
1 AAAAAAAAAAAAAATG
1098182 AAAGAAAAAAAAAAAT-
1 AAA-AAAAAAAAAAATG
1098198 AAAAA
1 AAAAA
1098203 TGAGTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 13 0.42
17 16 0.52
ACGTcount: A:0.85, C:0.04, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAAAAAATG
Found at i:1098212 original size:34 final size:32
Alignment explanation
Indices: 1098156--1098288 Score: 112
Period size: 32 Copynumber: 4.1 Consensus size: 32
1098146 AAAAAAAAAT
*
1098156 AAAAAAA-AAGCAAAAACA-AAAAAATGAAAGAA
1 AAAAAAAGAAG-AAAAAGAGAAAAAA-GAAAGAA
* *
1098188 AAAAAAA-AATAAAAATGAGTAAAAAAGAAAAACA
1 AAAAAAAGAAGAAAAA-GAG-AAAAAAGAAAGA-A
*
1098222 AAGAAAAAGAAGAAAAAGAGAAAAAAGAAAGAG
1 AA-AAAAAGAAGAAAAAGAGAAAAAAGAAAGAA
* * *
1098255 AAAAACAGTAGAAAAAGA-AAAAAAAAATAGAA
1 AAAAAAAGAAGAAAAAGAGAAAAAAGAA-AGAA
1098287 AA
1 AA
1098289 TAGACAGATC
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
31 13 0.15
32 29 0.35
33 7 0.08
34 20 0.24
35 8 0.10
36 7 0.08
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.05
Consensus pattern (32 bp):
AAAAAAAGAAGAAAAAGAGAAAAAAGAAAGAA
Found at i:1098224 original size:10 final size:9
Alignment explanation
Indices: 1098147--1098279 Score: 74
Period size: 9 Copynumber: 13.9 Consensus size: 9
1098137 AAGAGATATA
*
1098147 AAAAAAAATA
1 AAAAAAAA-G
1098157 AAAAAAAAG
1 AAAAAAAAG
1098166 CAAAAACAAA-
1 -AAAAA-AAAG
*
1098176 AAAATGAAAG
1 AAAA-AAAAG
1098186 AAAAAAAA-
1 AAAAAAAAG
1098194 AAATAAAAATG
1 AAA-AAAAA-G
*
1098205 AGTAAAAAAG
1 A-AAAAAAAG
1098215 AAAAACAAAG
1 AAAAA-AAAG
*
1098225 AAAAAGAAG
1 AAAAAAAAG
1098234 AAAAAGAGAA-
1 AAAAA-A-AAG
*
1098244 AAAAGAAAG
1 AAAAAAAAG
*
1098253 AGAAAAACAG
1 A-AAAAAAAG
* *
1098263 TAGAAAAAG
1 AAAAAAAAG
1098272 AAAAAAAA
1 AAAAAAAA
1098280 AATAGAAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
8 5 0.05
9 40 0.42
10 38 0.40
11 11 0.12
12 1 0.01
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1098228 original size:9 final size:8
Alignment explanation
Indices: 1098148--1098278 Score: 65
Period size: 8 Copynumber: 15.9 Consensus size: 8
1098138 AGAGATATAA
*
1098148 AAAAAAAT
1 AAAAAAAG
1098156 AAAAAAA-
1 AAAAAAAG
*
1098163 AAGCAAAAAC
1 AA--AAAAAG
1098173 AAAAAAATG
1 AAAAAAA-G
1098182 AAAGAAAA-
1 AAA-AAAAG
*
1098190 AAAAAAAT
1 AAAAAAAG
*
1098198 AAAAATGAG
1 AAAAA-AAG
*
1098207 TAAAAAAG
1 AAAAAAAG
1098215 AAAAACAA-
1 AAAAA-AAG
*
1098223 AGAAAAAG
1 AAAAAAAG
1098231 AAGAAAAAG
1 AA-AAAAAG
1098240 AGAAAAAAG
1 A-AAAAAAG
*
1098249 --AAAGAG
1 AAAAAAAG
*
1098255 AAAAACAG
1 AAAAAAAG
*
1098263 TAGAAAAAG
1 -AAAAAAAG
1098272 AAAAAAA
1 AAAAAAA
1098279 AAATAGAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
6 5 0.05
7 8 0.08
8 42 0.44
9 34 0.35
10 7 0.07
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1098236 original size:19 final size:20
Alignment explanation
Indices: 1098208--1098278 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 20
1098198 AAAAATGAGT
1098208 AAAA-AAGAAAAACA-AAGA
1 AAAAGAAGAAAAACAGAAGA
*
1098226 AAAAGAAGAAAAAGAGAA-A
1 AAAAGAAGAAAAACAGAAGA
* *
1098245 AAAGAAAGAGAAAAACAGTAGA
1 AAA-AGA-AGAAAAACAGAAGA
1098267 AAAAGAA-AAAAA
1 AAAAGAAGAAAAA
1098279 AAATAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 4 0.09
19 18 0.42
20 5 0.12
21 12 0.28
22 4 0.09
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAAGAAGAAAAACAGAAGA
Found at i:1098248 original size:24 final size:23
Alignment explanation
Indices: 1098130--1098281 Score: 89
Period size: 24 Copynumber: 6.3 Consensus size: 23
1098120 GACAACAGAG
*
1098130 AGAAAAGAAGAGATATAAAA-AAAA
1 AGAAAAAAAGAGA-A-AAAAGAAAA
* * *
1098154 ATAAAAAAAAAGCAAAAACAAAAAA
1 AGAAAAAAAGAG-AAAAA-AGAAAA
*
1098179 ATGAAAGAAAA-A-AAAAAATAAAA
1 A-GAAA-AAAAGAGAAAAAAGAAAA
*
1098202 ATGAGTAAAAAAGAAAAACAAAGAAAA
1 A-GA--AAAAAAGAGAAA-AAAGAAAA
*
1098229 AGAAGAAAAAGAGAAAAAAGAAAG
1 AGAA-AAAAAGAGAAAAAAGAAAA
*
1098253 AGAAAAACAGTAG-AAAAAGAAAA
1 AGAAAAAAAG-AGAAAAAAGAAAA
1098276 A-AAAAA
1 AGAAAAA
1098282 TAGAAAATAG
Statistics
Matches: 106, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.05
23 27 0.25
24 34 0.32
25 19 0.18
26 9 0.08
27 12 0.11
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (23 bp):
AGAAAAAAAGAGAAAAAAGAAAA
Found at i:1098259 original size:30 final size:29
Alignment explanation
Indices: 1098156--1098288 Score: 82
Period size: 31 Copynumber: 4.6 Consensus size: 29
1098146 AAAAAAAAAT
* *
1098156 AAAAAAAAAGCA-AAAACAAAAAAATGAAAGA
1 AAAAAAAAAG-AGAAAACAGAAGAA--AAAGA
*
1098187 AAAAAAAAA-ATAAAA-ATG-AGTAAAAA-A
1 AAAAAAAAAGAGAAAACA-GAAG-AAAAAGA
* *
1098214 GAAAAACAA-AGAAAA-AGAAGAAAAAGA
1 AAAAAAAAAGAGAAAACAGAAGAAAAAGA
*
1098241 GAAAAAAGAAAGAGAAAAACAGTAGAAAAAGA
1 -AAAAAA-AAAGAG-AAAACAGAAGAAAAAGA
*
1098273 AAAAAAAAATAGAAAA
1 AAAAAAAAAGAGAAAA
1098289 TAGACAGATC
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.07
27 17 0.20
28 8 0.10
29 9 0.11
30 13 0.16
31 19 0.23
32 11 0.13
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAGAGAAAACAGAAGAAAAAGA
Found at i:1100372 original size:106 final size:108
Alignment explanation
Indices: 1100219--1100569 Score: 412
Period size: 106 Copynumber: 3.3 Consensus size: 108
1100209 TGTTTTTAGG
* *
1100219 AACTAATTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGAAATTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
* *
1100284 GATTTTTAGAAGTTTCTTGATGATTTTTAATTGAATTTTAAGA
66 GATTTTTAGAAGTTTCTTGATGATTTTCAAATGAATTTTAAGA
* * * * * * * *
1100327 AACTAAGTCCGATATTCA-AAGTTTCTTG-TTATTTTTAAACGAGCTTTTAAAAAAACTAAATCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
* *
1100390 G-TTTTTCAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
66 GATTTTT-AGAAGTTTCTTGATGATTTTCAAATGAATTTT-AAGA
* * *
1100434 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA--TTTCAAAGAAGTTAAGCCC
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
* * *
1100497 GATTTTCA-AGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
66 GATTTTTAGA-AGTTTCTTGATGATTTTCAAATGAATTT-TAAGA
* *
1100540 AACTAAGTCTAATTTT-GGAAGTTTCTTGAT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGAT
1100570 TATGATCTTT
Statistics
Matches: 204, Mismatches: 32, Indels: 17
0.81 0.13 0.07
Matches are distributed among these distances:
105 18 0.09
106 91 0.45
107 54 0.26
108 29 0.14
109 12 0.06
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (108 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
GATTTTTAGAAGTTTCTTGATGATTTTCAAATGAATTTTAAGA
Found at i:1100512 original size:53 final size:54
Alignment explanation
Indices: 1100219--1100569 Score: 374
Period size: 53 Copynumber: 6.6 Consensus size: 54
1100209 TGTTTTTAGG
* *
1100219 AACTAATTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG-TTTCAAAGA
* * * * *
1100274 AATTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAATTGAATTT-TAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTCAAAGA
* * * * * *
1100327 AACTAAGTCCGATATTCA-AAGTTTCTTG-TTATTTTTAAACGAGCTTTTAAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG-TTTCAAAGA
* * * * *
1100380 AACTAAATCTGTTTTTCAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTCAAAGA
1100434 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA-TTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTCAAAGA
** * * * * * *
1100487 AGTTAAGCCCGATTTTCA-AGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
1 AACTAAGTCTGATTTTCAGA-AGTTTCTTGATGATTTTTAAATGAGTTTCAAAGA
* *
1100540 AACTAAGTCTAATTTT-GGAAGTTTCTTGAT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGAT
1100570 TATGATCTTT
Statistics
Matches: 244, Mismatches: 45, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
51 11 0.05
52 34 0.14
53 87 0.36
54 61 0.25
55 51 0.21
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (54 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTCAAAGA
Found at i:1100545 original size:160 final size:161
Alignment explanation
Indices: 1100219--1100568 Score: 429
Period size: 160 Copynumber: 2.2 Consensus size: 161
1100209 TGTTTTTAGG
* * * * *
1100219 AACTAATTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGAAATTAAGTCT
1 AACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTCAAAGAAACTAAGTCT
* * * *
1100284 GATTTTTAGAAGTTTCTTGATGATTTTTAATTGAATTTTAAGAAACTAAGTCCGATATTCAAAGT
66 GATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTAAAGAAACTAAGCCCGATATTCAAAGT
* * * *
1100349 TTCTTGTTATTTTTAAACGAGCTTTTAAAAA
131 TTCTTGATATTTTCAAACGAGATTTGAAAAA
* *
1100380 AACTAAATCTGTTTTTCAGAAGTTTCTTGACGATTTTCAAATGAG-TTTTAAAGAAACTAAGTCT
1 AACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTCAAAGAAACTAAGTCT
** * *
1100444 GATTTTCAGAAGTTTCTTGATGATTTTTAAATG-ATTTCAAAGAAGTTAAGCCCGATTTTCAAGG
66 GATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTT-AAAGAAACTAAGCCCGATATTCAA-A
* * *
1100508 GTTTCTTGATGTTTTCAAATGA-ATTTGAAAGA
129 GTTTCTTGATATTTTCAAACGAGATTTGAAAAA
* * *
1100540 AACTAAGTCTAATTTT-GGAAGTTTCTTGA
1 AACTAAATCTGATTTTCAGAAGTTTCTTGA
1100569 TTATGATCTT
Statistics
Matches: 161, Mismatches: 26, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
159 16 0.10
160 86 0.53
161 59 0.37
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.42
Consensus pattern (161 bp):
AACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTCAAAGAAACTAAGTCT
GATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTAAAGAAACTAAGCCCGATATTCAAAGT
TTCTTGATATTTTCAAACGAGATTTGAAAAA
Found at i:1100616 original size:99 final size:106
Alignment explanation
Indices: 1100219--1100618 Score: 300
Period size: 106 Copynumber: 3.8 Consensus size: 106
1100209 TGTTTTTAGG
* * * * * * *
1100219 AACTAATTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGAAATTAAGTCT
1 AACTAAGTCTAATTTTCAGAAGTTTCTT-ATGATTTATAAATGA--TTTCAAAGAAACTAAGCCC
* * * * *
1100284 GATTTT-TAGAAGTTTCTTGATGATTTTTAATTGAATTT-TAAGA
63 GATTTTCAAG-GGTTTCTTGATGATTTTCAAATGAATTTGAAAGA
** * * * * * * * ** *
1100327 AACTAAGTCCGATATTCA-AAGTTTCTTGTTATTTTTAAACGAGCTTTTAAAAAAACTAAATCTG
1 AACTAAGTCTAATTTTCAGAAGTTTCTTATGATTTATAAATGA--TTTCAAAGAAACTAAGCCCG
* * * * *
1100391 TTTTTC-AGAAGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
64 ATTTTCAAG-GGTTTCTTGATGATTTTCAAATGAATTTGAAAGA
* * **
1100434 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGATTTCAAAGAAGTTAAGCCCGA
1 AACTAAGTCTAATTTTCAGAAGTTTCTT-ATGATTTATAAATGATTTCAAAGAAACTAAGCCCGA
1100499 TTTTCAAGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
65 TTTTCAAGGGTTTCTTGATGATTTTCAAATGAATTTGAAAGA
* * * * **
1100540 AACTAAGTCTAATTTT-GGAAGTTTC-T-TGA-TTAT-GAT-CTTTCTAAGAAACTAAGCTTGAT
1 AACTAAGTCTAATTTTCAGAAGTTTCTTATGATTTATAAATGATTTCAAAGAAACTAAGCCCGAT
1100599 TTTCAAGGGTTTCTTGATGA
66 TTTCAAGGGTTTCTTGATGA
1100619 GTAAGTCCTT
Statistics
Matches: 242, Mismatches: 44, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
99 36 0.15
100 2 0.01
101 3 0.01
102 3 0.01
104 1 0.00
105 8 0.03
106 94 0.39
107 57 0.24
108 26 0.11
109 12 0.05
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (106 bp):
AACTAAGTCTAATTTTCAGAAGTTTCTTATGATTTATAAATGATTTCAAAGAAACTAAGCCCGAT
TTTCAAGGGTTTCTTGATGATTTTCAAATGAATTTGAAAGA
Found at i:1100687 original size:20 final size:20
Alignment explanation
Indices: 1100662--1100726 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1100652 GAATGATGTG
*
1100662 TAAGTCCTTCGAGCCATCTA
1 TAAGTCATTCGAGCCATCTA
* * **
1100682 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCATTCGAGCCATCT-A
*
1100703 TAAGTCATTCGAGCCATCCA
1 TAAGTCATTCGAGCCATCTA
1100723 TAAG
1 TAAG
1100727 ACCTCGGGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
TAAGTCATTCGAGCCATCTA
Found at i:1100717 original size:41 final size:41
Alignment explanation
Indices: 1100613--1100726 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 41
1100603 AAGGGTTTCT
* *
1100613 TGATGAGTAAGTCCTTCGGGCCAT-TAGTAAGTCTTTTGAGAA
1 TGATGA-TAAGTCCTTCGAGCCATCTA-TAAGTCTTTCGAGAA
*
1100655 TGATGTGTAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGCAA
1 TGATG-ATAAGTCCTTCGAGCCATCTATAAGTCTTTCGAG-AA
* *
1100698 -GATGATAAGTCATTCGAGCCATCCATAAG
1 TGATGATAAGTCCTTCGAGCCATCTATAAG
1100727 ACCTCGGGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 22 0.35
42 37 0.59
43 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGAA
Found at i:1100803 original size:51 final size:51
Alignment explanation
Indices: 1100738--1100844 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 51
1100728 CCTCGGGTAA
*
1100738 GATGTTTCAAATGAA-TTTT-AGAAACTAAGCCTGATTTTAAGAGGTTTCTT
1 GATGTTTCAAATGAATTTTTAAGAAACTAAGCCTAATTTT-AGAGGTTTCTT
* * *
1100788 GATGTTTTTAAATGAATTTTTGAAAGAAGCTAAGCCTAATTTTAGGGGTTTCTT
1 GATG-TTTCAAATGAATTTTT--AAGAAACTAAGCCTAATTTTAGAGGTTTCTT
1100842 GAT
1 GAT
1100845 AACTGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
50 4 0.08
51 10 0.21
52 4 0.08
54 13 0.27
55 17 0.35
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (51 bp):
GATGTTTCAAATGAATTTTTAAGAAACTAAGCCTAATTTTAGAGGTTTCTT
Found at i:1100870 original size:55 final size:55
Alignment explanation
Indices: 1100757--1100871 Score: 135
Period size: 55 Copynumber: 2.1 Consensus size: 55
1100747 AATGAATTTT
* * *** *
1100757 AGAAACTAAGCCTGATTTTAAGAGGTTTCTTGATGTTTTTAAATGAATTTTTGAA
1 AGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGTAAATGAATTTTTGAA
*
1100812 AGAAGCTAAGCCTAATTTT-AGGGGTTTCTTGATAACTGTAAATGAATCTTTTTG-A
1 AGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGTAAATGAA--TTTTTGAA
1100867 AGAAG
1 AGAAG
1100872 AAAAAAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
54 22 0.43
55 23 0.45
56 6 0.12
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (55 bp):
AGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGTAAATGAATTTTTGAA
Found at i:1101991 original size:138 final size:138
Alignment explanation
Indices: 1101548--1102036 Score: 576
Period size: 138 Copynumber: 3.6 Consensus size: 138
1101538 GGGTAAACCA
* **
1101548 ATCAACATTTCCAATGGAGAGTTCATAATGAG-A-AACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCAT
** *
1101611 AATGAGAAGAACTCATTCACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGAAACACCTCA
66 AATGAGAAGAACTTGTTCACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGAAACACCTCA
1101676 CTCGAGGG
131 CTCGAGGG
* *
1101684 ATTAACATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAG-TCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAGAAGTTCA
* * ** *
1101748 TAATAAGAA-AACTTGTTCGACCTATCA-CTTGATTC--CG-GTAT----TTCGAATCAGTGACG
65 TAATGAGAAGAACTTGTTC-ACCT-T-AGCTTGATTCATCGCATATGGAGTT-GAATCAGAAACA
* **
1101804 CCTCGCTTAAGGG
126 CCTCACTCGAGGG
* * **
1101817 AAT-GATATTT-CAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
1 -ATCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTC
*
1101880 ATAATGAGAAGAA-TTGTTCAACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGCAACACC
64 ATAATGAGAAGAACTTGTTC-ACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGAAACACC
1101944 TCACTCGAGGG
128 TCACTCGAGGG
*
1101955 ATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-AAAAGGGAGAAGAAGTTCA
* *
1102020 TAATCAGAAGAGCTTGT
65 TAATGAGAAGAACTTGT
1102037 GAGTTCATAA
Statistics
Matches: 293, Mismatches: 37, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
131 1 0.00
132 26 0.09
133 76 0.26
134 6 0.02
135 3 0.01
136 32 0.11
137 12 0.04
138 81 0.28
139 51 0.17
140 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (138 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGAAACACCTCA
CTCGAGGG
Found at i:1102092 original size:63 final size:64
Alignment explanation
Indices: 1101973--1102099 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 64
1101963 TTCTAGTGGA
1101973 GAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATCAGAAGAGCTTGT
1 GAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATCAGAAGAGCTTGT
* * * * *
1102037 GAGTTCATAATGAGAAGAACTC-TCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGATCTTGT
1 GAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATCAGAAGAGCTTGT
1102100 TCGACCTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 36 0.62
64 22 0.38
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (64 bp):
GAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATCAGAAGAGCTTGT
Found at i:1103364 original size:25 final size:24
Alignment explanation
Indices: 1103335--1103402 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
1103325 TATGTGTTAC
1103335 GTATTTATTTTATGTATATTATTAT
1 GTATTTATTTTATGTATATTA-TAT
*
1103360 GTATTTATTTTACGTATATTATAT
1 GTATTTATTTTATGTATATTATAT
* *
1103384 ATATATTACTTTAT-TATAT
1 GTAT-TTATTTTATGTATAT
1103403 ATTTTATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 11 0.29
25 27 0.71
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (24 bp):
GTATTTATTTTATGTATATTATAT
Found at i:1103410 original size:22 final size:21
Alignment explanation
Indices: 1103353--1103415 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
1103343 TTTATGTATA
* *
1103353 TTATTATGTATTTATTTTACGT
1 TTATTATATATTTATATTAC-T
*
1103375 ATATTATATA--TATATTACT
1 TTATTATATATTTATATTACT
*
1103394 TTATTATATATTTTATAATACT
1 TTATTATATA-TTTATATTACT
1103416 ACATATATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 10 0.30
20 7 0.21
22 16 0.48
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (21 bp):
TTATTATATATTTATATTACT
Found at i:1104642 original size:16 final size:16
Alignment explanation
Indices: 1104621--1104652 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1104611 CCTTGAAACC
*
1104621 ATTATTTATTGGTTAT
1 ATTATTAATTGGTTAT
1104637 ATTATTAATTGGTTAT
1 ATTATTAATTGGTTAT
1104653 TATTGGTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
ATTATTAATTGGTTAT
Found at i:1107864 original size:20 final size:20
Alignment explanation
Indices: 1107839--1107891 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1107829 GACCAACAAA
1107839 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
1107859 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
1107879 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1107892 AGTCAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:1107902 original size:20 final size:20
Alignment explanation
Indices: 1107879--1107957 Score: 51
Period size: 20 Copynumber: 4.0 Consensus size: 20
1107869 AGTTTCCAAT
1107879 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*** *
1107899 TTCGCGTTGCGAATTTGT-AAA
1 TTCGCAACGCGAA--AGTCAAA
*
1107920 -TCGCAACAC-AGAAGTCAAA
1 TTCGCAACGCGA-AAGTCAAA
1107939 TTCG--ACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1107957 T
1 T
1107958 GTTTTTACGC
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
18 14 0.33
19 5 0.12
20 19 0.44
21 3 0.07
22 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:1108104 original size:22 final size:22
Alignment explanation
Indices: 1108079--1108135 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1108069 CACTCTCTAT
* *
1108079 GACGACATCTGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCC
*
1108101 GACGAAATCCGTCCCCATTTCC
1 GACGAAATCCGTCCCCATCTCC
1108123 GACGAAATCCGTC
1 GACGAAATCCGTC
1108136 TTTCTCCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (22 bp):
GACGAAATCCGTCCCCATCTCC
Found at i:1110137 original size:21 final size:21
Alignment explanation
Indices: 1110111--1110163 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1110101 GTTAGGGGAA
*
1110111 TTACGTGAAGAGGTCGGTGCT
1 TTACGTGAAGAGGTCGGTACT
* *
1110132 TTACGTCATGAGGTCGGTACT
1 TTACGTGAAGAGGTCGGTACT
1110153 TTACGTGAAGA
1 TTACGTGAAGA
1110164 TAATGGTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (21 bp):
TTACGTGAAGAGGTCGGTACT
Found at i:1110640 original size:21 final size:20
Alignment explanation
Indices: 1110611--1110675 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1110601 ATCATCATTG
*
1110611 AAGAAGCCCATCCCACCGTTC
1 AAGAGGCCCA-CCCACCGTTC
*
1110632 AAGAGGCCC-CCGTCATCGTTC
1 AAGAGGCCCACC--CACCGTTC
*
1110653 AAGAGGTCCCACCCGCCGTTC
1 AAGAGG-CCCACCCACCGTTC
1110674 AA
1 AA
1110676 AAGCCCGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.06
21 29 0.81
22 3 0.08
23 2 0.06
ACGTcount: A:0.25, C:0.40, G:0.20, T:0.15
Consensus pattern (20 bp):
AAGAGGCCCACCCACCGTTC
Found at i:1112220 original size:20 final size:20
Alignment explanation
Indices: 1112197--1112239 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1112187 GATTTTCGGT
1112197 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
1112217 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
1112237 TTG
1 TTG
1112240 ATCGCAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:1112467 original size:39 final size:39
Alignment explanation
Indices: 1112413--1112499 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1112403 TCAAGTTGTA
1112413 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATCTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATCTG
* *
1112452 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATCTG
1112491 GATTTTGAT
1 GATTTTGAT
1112500 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATCTG
Found at i:1112761 original size:11 final size:11
Alignment explanation
Indices: 1112745--1112771 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1112735 TTATACATAC
1112745 AATGTTCAAAT
1 AATGTTCAAAT
1112756 AATGTTCAAAT
1 AATGTTCAAAT
1112767 AATGT
1 AATGT
1112772 ACCCATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:1112789 original size:25 final size:25
Alignment explanation
Indices: 1112756--1112811 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
1112746 ATGTTCAAAT
* *
1112756 AATGTTCAAATAATGTACCCATAAC
1 AATGTTCAAATAACGTACCCACAAC
1112781 AATGTTCAAATAACGTACCCACAAC
1 AATGTTCAAATAACGTACCCACAAC
1112806 AATGTT
1 AATGTT
1112812 TAATTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (25 bp):
AATGTTCAAATAACGTACCCACAAC
Found at i:1112939 original size:20 final size:20
Alignment explanation
Indices: 1112914--1112977 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
1112904 GTTTGCGATT
1112914 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
1112934 TCGCGTTGCGAATTTGTCTT
1 TCGCGTTGCGAATTTGACTA
* * *
1112954 TTGCGTTGTGAACTTGACTA
1 TCGCGTTGCGAATTTGACTA
1112974 TCGC
1 TCGC
1112978 AACGCTTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:1113324 original size:18 final size:18
Alignment explanation
Indices: 1113301--1113336 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1113291 AAGCCGGTTG
*
1113301 TGATTGGGATTTTGATTT
1 TGATTGAGATTTTGATTT
1113319 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
1113337 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:1116364 original size:16 final size:15
Alignment explanation
Indices: 1116342--1116380 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1116332 GAAATCATTG
1116342 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1116358 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1116373 AAAAATTA
1 AAAAATTA
1116381 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1116555 original size:20 final size:20
Alignment explanation
Indices: 1116517--1116665 Score: 92
Period size: 20 Copynumber: 7.5 Consensus size: 20
1116507 CAAAACATTT
**
1116517 GTGTTGCGAAACT-AAATTC
1 GTGTTGCGAATTTGAAATTC
*
1116536 GTGTTGTGAATTTGAAATTC
1 GTGTTGCGAATTTGAAATTC
* *
1116556 -AGTTGCAAATTTGAAATTTC
1 GTGTTGCGAATTTGAAA-TTC
* ** *
1116576 GCGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGAAATTC
* *
1116596 GTGTTGTGAATTTG-ACTATC
1 GTGTTGCGAATTTGAAAT-TC
* *
1116616 GCGTTGCGAATTTG-ACTTC
1 GTGTTGCGAATTTGAAATTC
*
1116635 TGTGTTGCG-ATTTACAAATTC
1 -GTGTTGCGAATTT-GAAATTC
*
1116656 GCGTTGCGAA
1 GTGTTGCGAA
1116666 ATTGGAAACT
Statistics
Matches: 100, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
19 30 0.30
20 53 0.53
21 17 0.17
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (20 bp):
GTGTTGCGAATTTGAAATTC
Found at i:1116658 original size:40 final size:41
Alignment explanation
Indices: 1116557--1116665 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 41
1116547 TTGAAATTCA
* *
1116557 GTTGCAAATTTGA-AATTTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAA-TTCGCGTTGCGAATTTGACTTCTGT
* *
1116598 GTTGTGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGT
1116638 GTTGCG-ATTT-ACAAATTCGCGTTGCGAA
1 GTTGCGAATTTGAC-AATTCGCGTTGCGAA
1116666 ATTGGAAACT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 40 0.68
41 11 0.19
42 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (41 bp):
GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGT
Found at i:1116705 original size:20 final size:19
Alignment explanation
Indices: 1116652--1116705 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1116642 CGATTTACAA
1116652 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** * *
1116671 AAACTGAGTTACGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
1116691 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
1116706 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:1120305 original size:28 final size:28
Alignment explanation
Indices: 1120265--1120323 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1120255 ACATGTTTAA
*
1120265 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
1120293 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
1120321 AAG
1 AAG
1120324 GAAAGATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:1120565 original size:86 final size:86
Alignment explanation
Indices: 1120457--1120668 Score: 363
Period size: 88 Copynumber: 2.5 Consensus size: 86
1120447 ATTGAACGAA
1120457 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
* *
1120522 ATCAAACACGCTCATAAACTC
66 ATCAAACAAGCCCATAAACTC
*
1120543 AATATTTAGCCATTGTTTTTTTTCTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
1 AATATTTAGCCACTG-TTTTTTT-TTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
1120608 CAATCAAACAAGCCCATAAACTC
64 CAATCAAACAAGCCCATAAACTC
*
1120631 AATATTTAGCCACT-ATTTTTTTTCATCAAACTAAGTTT
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTT
1120669 TCCAGAGTGT
Statistics
Matches: 119, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
85 17 0.14
86 20 0.17
87 7 0.06
88 75 0.63
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (86 bp):
AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
ATCAAACAAGCCCATAAACTC
Found at i:1122276 original size:29 final size:29
Alignment explanation
Indices: 1122243--1122328 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
1122233 AAATTACTTG
**
1122243 ATAATGATATTTTTCGTGAATCAAATATA
1 ATAATGATATTTTTCACGAATCAAATATA
1122272 ATAATGATATTTTTCACGAATCAAATATA
1 ATAATGATATTTTTCACGAATCAAATATA
*
1122301 ATAATGATATTTTTTACGAATCAAATAT
1 ATAATGATATTTTTCACGAATCAAATAT
1122329 CTCAATATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
ATAATGATATTTTTCACGAATCAAATATA
Found at i:1124291 original size:33 final size:35
Alignment explanation
Indices: 1124218--1124291 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1124208 AAAATAGTCC
*
1124218 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
* *
1124253 TCAATTTCATTCTAAACCCTAA-TTCTAAA-TAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1124286 TCAATT
1 TCAATT
1124292 CAATTCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 10 0.28
34 6 0.17
35 20 0.56
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
Found at i:1125275 original size:27 final size:28
Alignment explanation
Indices: 1125245--1125305 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1125235 TAGTTGATAA
* *
1125245 ATATTTTAAAAGAAAATTTAA-GATTAT
1 ATATTTTAAAACAAAATTTAATAATTAT
* *
1125272 ATATTTTTAAACTAAATTTAATAATTAT
1 ATATTTTAAAACAAAATTTAATAATTAT
1125300 AT-TTTT
1 ATATTTT
1125306 CATATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (28 bp):
ATATTTTAAAACAAAATTTAATAATTAT
Found at i:1125408 original size:16 final size:18
Alignment explanation
Indices: 1125382--1125414 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1125372 ATTTCTTATT
1125382 AAAAATAAAAT-ATTCAA
1 AAAAATAAAATGATTCAA
1125399 AAAAAT-AAATGATTCA
1 AAAAATAAAATGATTCA
1125415 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAATAAAATGATTCAA
Found at i:1126194 original size:18 final size:20
Alignment explanation
Indices: 1126171--1126207 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1126161 ATTATTACTT
1126171 AAAATATT-ATTTT-TTATA
1 AAAATATTAATTTTGTTATA
1126189 AAAATATTAATTTTGTTAT
1 AAAATATTAATTTTGTTAT
1126208 CTAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AAAATATTAATTTTGTTATA
Found at i:1126312 original size:32 final size:32
Alignment explanation
Indices: 1126275--1126343 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
1126265 AAAAAATAAT
1126275 ATTTTAAATAACATTTTATCAAAAATGTTAAC
1 ATTTTAAATAACATTTTATCAAAAATGTTAAC
1126307 ATTTTAAATAACATTTTATCAAAAATGTTAAC
1 ATTTTAAATAACATTTTATCAAAAATGTTAAC
1126339 ATTTT
1 ATTTT
1126344 TGATAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (32 bp):
ATTTTAAATAACATTTTATCAAAAATGTTAAC
Found at i:1126353 original size:21 final size:20
Alignment explanation
Indices: 1126283--1126343 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
1126273 ATATTTTAAA
1126283 TAACATTTTATCAAAAATGT
1 TAACATTTTATCAAAAATGT
1126303 TAACA-TTT-T---AAA---
1 TAACATTTTATCAAAAATGT
1126315 TAACATTTTATCAAAAATGT
1 TAACATTTTATCAAAAATGT
1126335 TAACATTTT
1 TAACATTTT
1126344 TGATAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
12 5 0.15
13 3 0.09
14 1 0.03
15 3 0.09
17 3 0.09
18 1 0.03
19 3 0.09
20 14 0.42
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (20 bp):
TAACATTTTATCAAAAATGT
Found at i:1129587 original size:32 final size:31
Alignment explanation
Indices: 1129546--1129607 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1129536 CTAAATAAAC
* *
1129546 ATAAAAAACT-TTATTTATTTTATTTTATTTA
1 ATAAAAAACTCATATTT-TTTTATATTATTTA
1129577 ATAAATAAACTCATATTTTTTTATATTATTT
1 ATAAA-AAACTCATATTTTTTTATATTATTT
1129608 TATTTGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 17 0.63
33 5 0.19
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (31 bp):
ATAAAAAACTCATATTTTTTTATATTATTTA
Found at i:1132774 original size:16 final size:15
Alignment explanation
Indices: 1132754--1132797 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 15
1132744 TAAGGTATAT
1132754 TTTATAATATTTTAC
1 TTTATAATATTTTAC
1132769 TTT-T-AT-TTTTAC
1 TTTATAATATTTTAC
1132781 TTTATTAATATTTTAC
1 TTTA-TAATATTTTAC
1132797 T
1 T
1132798 AATATAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
14 2 0.08
15 5 0.20
16 7 0.28
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATAATATTTTAC
Found at i:1132988 original size:108 final size:110
Alignment explanation
Indices: 1132857--1133059 Score: 340
Period size: 108 Copynumber: 1.9 Consensus size: 110
1132847 GATGGAAATC
*
1132857 ATATCTCTACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAA-TTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
*
1132921 TATTTAGTTT-TT-ATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTTATTCA-TTAATGCATGATTATTATATTAATAATTAA
* *
1132965 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1133030 TAATTAGTTTATTCATTAATGCATGATTAT
66 TAATTAGTTTATTCATTAATGCATGATTAT
1133060 AAGATTAAGA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
108 47 0.53
109 23 0.26
110 17 0.19
111 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (110 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTTATTCATTAATGCATGATTATTATATTAATAATTAA
Found at i:1134593 original size:17 final size:18
Alignment explanation
Indices: 1134563--1134600 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1134553 CCCAAAACCA
1134563 CGCAACCATATATGATGC
1 CGCAACCATATATGATGC
1134581 CGCAACC-TATATGATGC
1 CGCAACCATATATGATGC
1134598 CGC
1 CGC
1134601 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (18 bp):
CGCAACCATATATGATGC
Found at i:1135145 original size:26 final size:24
Alignment explanation
Indices: 1135073--1135145 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1135063 TTTTATTTGT
1135073 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
1135098 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1135121 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1135146 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1135270 original size:28 final size:27
Alignment explanation
Indices: 1135221--1135275 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1135211 GTTATCATTT
1135221 AATTTAATATTGTTATTAGTTTGTTTAA
1 AATTTAATATTGTTATTAGTTT-TTTAA
1135249 AATTTAATAATTGTGT-TT-GTTTTTTAA
1 AATTTAAT-ATTGT-TATTAGTTTTTTAA
1135276 TCTTCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 7 0.28
30 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (27 bp):
AATTTAATATTGTTATTAGTTTTTTAA
Found at i:1136472 original size:158 final size:158
Alignment explanation
Indices: 1136176--1136489 Score: 612
Period size: 158 Copynumber: 2.0 Consensus size: 158
1136166 GGCATGATGG
1136176 GGCATATCACTTCAGAGTCCAAGTTGGGATGATCTTGGTTGACCCCTCCAGCACAACATGTGTGA
1 GGCATATCACTTCAGAGTCCAAGTTGGGATGATCTTGGTTGACCCCTCCAGCACAACATGTGTGA
1136241 GGACCGTTGTATTCTGTTAGTTCCCATCTGTTGTTTTCCTCTTCCTCTCCTCTTCGATACGCGAA
66 GGACCGTTGTATTCTGTTAGTTCCCATCTGTTGTTTTCCTCTTCCTCTCCTCTTCGATACGCGAA
1136306 CCATCCAATTGCATCCGTTTTCGCGCTT
131 CCATCCAATTGCATCCGTTTTCGCGCTT
1136334 GGCATATCACTTCAGAGTCCAAGTT-GGATGATCTTGGTTGACCCCTCCAGCACAACATGTGTGA
1 GGCATATCACTTCAGAGTCCAAGTTGGGATGATCTTGGTTGACCCCTCCAGCACAACATGTGTGA
1136398 GGACCGTTGTATTCTGTTAGTTCCCATCTGTTGTTTTTCCTCTTCCTCTCCTCTTCGATACGCGA
66 GGACCGTTGTATTCTGTTAGTTCCCATCTGTTG-TTTTCCTCTTCCTCTCCTCTTCGATACGCGA
1136463 ACCATCCAATTGCATCCGTTTTCGCGC
130 ACCATCCAATTGCATCCGTTTTCGCGC
1136490 AGGGCACAAT
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
157 72 0.46
158 83 0.54
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (158 bp):
GGCATATCACTTCAGAGTCCAAGTTGGGATGATCTTGGTTGACCCCTCCAGCACAACATGTGTGA
GGACCGTTGTATTCTGTTAGTTCCCATCTGTTGTTTTCCTCTTCCTCTCCTCTTCGATACGCGAA
CCATCCAATTGCATCCGTTTTCGCGCTT
Found at i:1138271 original size:50 final size:51
Alignment explanation
Indices: 1138191--1138314 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 51
1138181 CCCTACGTGG
* * * **
1138191 CGTATAGCGCGCTGCAGGGGCCGCGATATA-CCCATGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGATATACCCCACGTGGCGCCAAATCAC
* * *
1138241 CGTATAGCACGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGATATACCCCACGTGGCGCCAAATCAC
*
1138292 CGTATAACGCGGTGCAGGGGGCG
1 CGTATAGCGCGGTGCAGGGGGCG
1138315 AGCTTTACTA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 26 0.41
51 37 0.59
ACGTcount: A:0.19, C:0.31, G:0.35, T:0.15
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGATATACCCCACGTGGCGCCAAATCAC
Found at i:1139525 original size:23 final size:23
Alignment explanation
Indices: 1139493--1139545 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1139483 GATAGATACT
1139493 TTATAATAAGCACTACCTATTACA
1 TTAT-ATAAGCACTACCTATTACA
**
1139517 TTATATAAGTGCTACCTATTACA
1 TTATATAAGCACTACCTATTACA
*
1139540 TCATAT
1 TTATAT
1139546 TTTTACCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TTATATAAGCACTACCTATTACA
Found at i:1139978 original size:21 final size:21
Alignment explanation
Indices: 1139948--1140022 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1139938 GATAGATACT
* *
1139948 TTACAATATAAGCACTACCTA
1 TTACATTATAAACACTACCTA
*
1139969 TTACATTATATAAAAGCTACCTA
1 TTACATTATA-AACA-CTACCTA
*
1139992 TTACATTATAAACGCTACCTA
1 TTACATTATAAACACTACCTA
1140013 TTACATTATA
1 TTACATTATA
1140023 TTTTTTACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 26 0.55
22 4 0.09
23 17 0.36
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (21 bp):
TTACATTATAAACACTACCTA
Found at i:1139988 original size:23 final size:23
Alignment explanation
Indices: 1139962--1140023 Score: 101
Period size: 21 Copynumber: 2.8 Consensus size: 23
1139952 AATATAAGCA
1139962 CTACCTATTACATTATATAAAAG
1 CTACCTATTACATTATATAAAAG
*
1139985 CTACCTATTACA-T-TATAAACG
1 CTACCTATTACATTATATAAAAG
1140006 CTACCTATTACATTATAT
1 CTACCTATTACATTATAT
1140024 TTTTTACCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 19 0.53
22 2 0.06
23 15 0.42
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (23 bp):
CTACCTATTACATTATATAAAAG
Found at i:1140461 original size:23 final size:23
Alignment explanation
Indices: 1140433--1140505 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1140423 GATACTTTAC
1140433 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
1140456 ATATAAACACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
1140479 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
1140502 ATAT
1 ATAT
1140506 TTTACCTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:1140519 original size:478 final size:483
Alignment explanation
Indices: 1139493--1140840 Score: 2231
Period size: 478 Copynumber: 2.8 Consensus size: 483
1139483 GATAGATACT
* *
1139493 TTATAATAAGCACTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTA
1 TTAT-ATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC-ATTA
*
1139558 TATTGAAAGTGTTCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAA-TTATG
64 TATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATG
*
1139622 TTTCAA-TTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTGC
129 TTTCAATTTTTTTAATAG--TTTCATGTTTTCCACCTACAATATTAATTTAATAA-TTTCTTTGC
*
1139686 ACAAAAAATTATTTTATTGTTTTGATA-TTTATAAAATAATATTTAGAATTTAAATTTAACAATA
191 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
1139750 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTG--TTTAATTTAATAATAATATA
256 TTAACCAAAGATAATAATAAATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
1139813 TATTGTAACGT-AAAAATAAATCATTATA--CCTATAA-TACTAAATTAATATCTTAAAACTCAC
319 TATTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
1139874 TCAAAAGATAACCTTAAATTAATGTTTACCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAG
384 TCAAAAGATAACCTTAAATTAATGTTTACCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAG
1139939 ATAGATACTTTACAATATAAGCACTACCTATTACA
449 ATAGATACTTTACAATATAAGCACTACCTATTACA
*
1139974 TTATATAAA-AGCTACCTATTACATTATA-AA-CGCTACCTATTACATTATATTTTTTACCTATT
1 TTATATAAACA-CTACCTATTACATTATATAAGCGCTACCTATTACATCATA-TTTTTACC-ATT
1140036 ATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTAT
63 ATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTAT
*
1140101 GTTTCAATTTTTTTAACAGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCTTTGCAC
128 GTTTCAATTTTTTTAATAGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCTTTGCAC
1140166 -AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
193 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
1140230 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATATT
258 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATATT
*
1140295 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTTACTCAA
323 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
* * *
1140360 AAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACAC-TTTATAAAAAGGATAG
388 AAGATAACCTTAAATTAATGTTTACCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAG
1140424 ATACTTTAC-ATATAAGCACTACCTATTACA
453 ATACTTTACAATATAAGCACTACCTATTACA
1140454 TTATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATA-TTTTACC-TTATA
1 TTATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCATTATA
1140517 TTGAAAGTGTCCATAC-TTTTATAAAAATGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
66 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* *
1140580 T-AATTTTTTTTAATAGTGTTTCATGTTTTCCACCTGCAATATTAATTTAATAATTTCATTTACA
131 TCAA-TTTTTTTAATA--GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC-TTTGCA
* *
1140644 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTA-TTAAATTTAACAATAT
192 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
1140708 TAACCAAAGATAATAATAAATATGT-ATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
257 TAACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATAT
* *
1140772 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTATTA-CTT-AAACTCACTCA
322 TGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
1140835 AAAGAT
387 AAAGAT
1140841 GTACATACCT
Statistics
Matches: 826, Mismatches: 22, Indels: 43
0.93 0.02 0.05
Matches are distributed among these distances:
475 2 0.00
476 67 0.08
477 48 0.06
478 266 0.32
479 172 0.21
480 130 0.16
481 48 0.06
482 93 0.11
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (483 bp):
TTATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCATTATA
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCTTTGCACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATATTGTA
ACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
ATAACCTTAAATTAATGTTTACCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATA
CTTTACAATATAAGCACTACCTATTACA
Found at i:1143626 original size:181 final size:183
Alignment explanation
Indices: 1143304--1143879 Score: 928
Period size: 184 Copynumber: 3.1 Consensus size: 183
1143294 TACTTAAAAT
1143304 TACCGACACAATATTAAAAAGTGTCGATATAGGTTTGTAGACCTATTCGCTCATAAAACCGGTAT
1 TACCGACACAATATTAAAAAGTGTCGATATAGG-TTGTAGACCTATTCGCTCATAAAACCGGTAT
*
1143369 ATTTATACCGGTTATATTACAAAAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAA
65 ATTTATACCGGTTATATTAC---AAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAA
1143434 ATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
127 ATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
1143491 TACCGACACAATATTAAAAAAT-T-GATATAGGTTGTAGACATATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
1143554 TTTATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* * *
1143619 CGACACTTTGTGACAAGGTATCGACACATTTTTCTTCCAATCTGGATATAAAG
131 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
1143672 TACCGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
1143737 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
*
1143802 --TCGACACTTTTTGA-AATGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
1143856 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
1143880 GAAAACTTTA
Statistics
Matches: 364, Mismatches: 19, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
181 116 0.32
182 1 0.00
183 94 0.26
184 119 0.33
185 8 0.02
186 5 0.01
187 21 0.06
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:1145086 original size:6 final size:6
Alignment explanation
Indices: 1145076--1145159 Score: 84
Period size: 6 Copynumber: 14.5 Consensus size: 6
1145066 CTTGTTTGGA
* * *
1145076 TCATCA TCATCG TCAT-- -CATCT TCATCG TCATCG TCATCT TCATCG
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
* * * *
1145121 TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCA
1145160 GCTTCATCTT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
3 3 0.05
6 60 0.95
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (6 bp):
TCATCG
Found at i:1145093 original size:12 final size:12
Alignment explanation
Indices: 1145076--1145159 Score: 102
Period size: 12 Copynumber: 7.2 Consensus size: 12
1145066 CTTGTTTGGA
1145076 TCATCATCATCG
1 TCATCATCATCG
1145088 TCATCATC-T--
1 TCATCATCATCG
*
1145097 TCATCGTCATCG
1 TCATCATCATCG
*
1145109 TCATCTTCATCG
1 TCATCATCATCG
* *
1145121 TCAGCTTCATCG
1 TCATCATCATCG
1145133 TCATCATCATCG
1 TCATCATCATCG
*
1145145 TCATCTTCATCG
1 TCATCATCATCG
1145157 TCA
1 TCA
1145160 GCTTCATCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
9 7 0.11
10 1 0.02
11 1 0.02
12 54 0.86
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:1145112 original size:18 final size:18
Alignment explanation
Indices: 1145091--1145172 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1145081 ATCATCGTCA
*
1145091 TCATCTTCATCGTCATCG
1 TCATCTTCATCGTCAGCG
*
1145109 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCG
* * *
1145127 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCG
*
1145145 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCG
1145163 TCATCTTCAT
1 TCATCTTCAT
1145173 TGACCGCTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCG
Found at i:1145164 original size:12 final size:12
Alignment explanation
Indices: 1145091--1145172 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
1145081 ATCATCGTCA
* *
1145091 TCATCTTCATCG
1 TCATCGTCATCT
1145103 TCATCGTCATCT
1 TCATCGTCATCT
*
1145115 TCATCGTCAGCT
1 TCATCGTCATCT
*
1145127 TCATCGTCATCA
1 TCATCGTCATCT
1145139 TCATCGTCATCT
1 TCATCGTCATCT
*
1145151 TCATCGTCAGCT
1 TCATCGTCATCT
*
1145163 TCATCTTCAT
1 TCATCGTCAT
1145173 TGACCGCTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1146774 original size:20 final size:20
Alignment explanation
Indices: 1146749--1146786 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1146739 GATGTTTATG
*
1146749 GGATCGACATTTTTTTATAT
1 GGATCGACACTTTTTTATAT
1146769 GGATCGACACTTTTTTAT
1 GGATCGACACTTTTTTAT
1146787 TGTTGCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (20 bp):
GGATCGACACTTTTTTATAT
Found at i:1147056 original size:200 final size:200
Alignment explanation
Indices: 1146646--1147806 Score: 1926
Period size: 200 Copynumber: 5.8 Consensus size: 200
1146636 AACATTAAAC
* * * *
1146646 AGTGTCGATACATTA--TATACCAATTTTCTCATAAAACCGGTATACTTGTACCGGTTAGATT-A
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
1146708 AAAA-TACCTATTAC-TTATACTTATGGGTTTCGATGTTTATGGGATCGACA-TTTTTTTATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
1146770 GATCGACACTTTTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGGCACAA
131 GATCGACAC---TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAA
*
1146835 ACTAAAAAA
193 ACT-ACAAA
* *
1146844 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1146909 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGA-ATCTTTTTATATAT
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACA-CTTTTTATATAT
1146973 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
1147038 TACAAA
195 TACAAA
*
1147044 AGTGTCGACACATTA-TTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1147108 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * * *
1147173 GATCGACACTTTATGGTTGCAGCATGTTTGCCATTCATTATGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
1147238 AAAAAA
196 -ACAAA
*
1147244 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1147309 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACATTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
1147374 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1147439 ACAAA
196 ACAAA
*
1147444 AGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
1147509 AAAATTACGTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
1147574 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1147639 ACAAA
196 ACAAA
* * *
1147644 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGCACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
1147709 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
1147774 GATCGACACTTTATGGTTGCA-CCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1147807 ATGTAAATTT
Statistics
Matches: 910, Mismatches: 43, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
198 14 0.02
199 181 0.20
200 422 0.46
201 230 0.25
202 10 0.01
203 33 0.04
204 20 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:1149699 original size:33 final size:33
Alignment explanation
Indices: 1149662--1149727 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1149652 CCATCTAATA
*
1149662 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1149695 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1149728 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1149786 original size:21 final size:21
Alignment explanation
Indices: 1149761--1149825 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1149751 CCCCTTATGC
* *
1149761 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1149782 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1149803 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1149824 CT
1 CT
1149826 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1152049 original size:17 final size:18
Alignment explanation
Indices: 1152027--1152069 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1152017 ATATATCCGG
1152027 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1152044 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1152064 TATCAT
1 TATCAT
1152070 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1152087 original size:20 final size:19
Alignment explanation
Indices: 1152032--1152078 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1152022 TCCGGTATCA
1152032 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1152051 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1152072 TTTTACC
1 TTTTACC
1152079 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1152401 original size:180 final size:181
Alignment explanation
Indices: 1152008--1152469 Score: 676
Period size: 180 Copynumber: 2.6 Consensus size: 181
1151998 GAAAGTATAA
* * *
1152008 ACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATT
1 ACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATAGT
* * * *
1152073 TTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTATAGGCGCTAA
66 TTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAA
*
1152138 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTATCG
131 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTACCG
* *
1152189 AAACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTTTATCATA-T
1 ACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATAGT
* * * **
1152253 TTTACCTGGTATATTGTTTTGGATCGATACATTTTTTAAAAG-ATCGACACTTTATAGGATTTAA
66 TTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAA
*
1152317 AACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAGTACCG
131 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTACCG
* * * * ** *
1152369 ACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTTTGTCATAGT
1 ACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATAGT
* *
1152434 TTTACTTGTTATATCGTTTTGGATCGACACATTTTT
66 TTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1152470 AATTTGGATC
Statistics
Matches: 251, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
179 58 0.23
180 101 0.40
181 92 0.37
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
ACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATAGT
TTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAA
AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTACCG
Found at i:1155542 original size:89 final size:91
Alignment explanation
Indices: 1155291--1155655 Score: 650
Period size: 92 Copynumber: 4.0 Consensus size: 91
1155281 TTCCAAAAGG
1155291 TATATATA-TATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTA-TTTCTTAGA
1 TATATATATTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGA
1155354 TGAAAAATCTGAAAGAACATTCAGAT
66 TGAAAAATCTGAAAGAACATTCAGAT
1155380 TATATATATTTTATAAACATTTTGTTATCGATATTCTTG-TTCATTATAGTATTGTATTTTCTTA
1 TATATATA--TTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTA
1155444 GATGAAAAATCTGAAAGAACATTCAGAT
64 GATGAAAAATCTGAAAGAACATTCAGAT
1155472 TATATATA-TATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTC-TAGA
1 TATATATATTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGA
1155535 TGAAAAATCTGAAAGAACATTCAGATT
66 TGAAAAATCTGAAAGAACATTCAGA-T
1155562 ATATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTA
1 -TATATATA-TTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTA
1155627 GATGAAAAATCTGAAAGAACATTCAGAT
64 GATGAAAAATCTGAAAGAACATTCAGAT
1155655 T
1 T
1155656 TGGAAAGTTG
Statistics
Matches: 266, Mismatches: 0, Indels: 17
0.94 0.00 0.06
Matches are distributed among these distances:
89 65 0.24
90 23 0.09
91 25 0.09
92 72 0.27
93 52 0.20
94 29 0.11
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (91 bp):
TATATATATTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGA
TGAAAAATCTGAAAGAACATTCAGAT
Found at i:1155631 original size:183 final size:181
Alignment explanation
Indices: 1155291--1155655 Score: 696
Period size: 181 Copynumber: 2.0 Consensus size: 181
1155281 TTCCAAAAGG
1155291 TATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTCTTAGATG
1 TATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTCTTAGATG
1155356 AAAAATCTGAAAGAACATTCAGATTATATATATTTTATAAACATTTTGTTATCGATATTCTTGTT
66 AAAAATCTGAAAGAACATTCAGATTATATATATTTTATAAACATTTTGTTATCGATATTCTTGTT
1155421 CATTATAGTATTGTATTTTCTTAGATGAAAAATCTGAAAGAACATTCAGAT
131 CATTATAGTATTGTATTTTCTTAGATGAAAAATCTGAAAGAACATTCAGAT
1155472 TATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTT-TCTAGAT
1 TATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTCT-TAGAT
1155536 GAAAAATCTGAAAGAACATTCAGATTATATATATATTTATAAACATTTTGTTATCGATATTCTTG
65 GAAAAATCTGAAAGAACATTCAGATTATATATAT-TTTATAAACATTTTGTTATCGATATTCTTG
1155601 TTTCATTATAGTATTGTATTTTCTTAGATGAAAAATCTGAAAGAACATTCAGAT
129 -TTCATTATAGTATTGTATTTTCTTAGATGAAAAATCTGAAAGAACATTCAGAT
1155655 T
1 T
1155656 TGGAAAGTTG
Statistics
Matches: 181, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
180 1 0.01
181 96 0.53
182 30 0.17
183 54 0.30
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (181 bp):
TATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTCTTAGATG
AAAAATCTGAAAGAACATTCAGATTATATATATTTTATAAACATTTTGTTATCGATATTCTTGTT
CATTATAGTATTGTATTTTCTTAGATGAAAAATCTGAAAGAACATTCAGAT
Found at i:1157372 original size:3 final size:3
Alignment explanation
Indices: 1157364--1157402 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1157354 CACCCATTTA
1157364 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1157403 GAGAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1161690 original size:21 final size:21
Alignment explanation
Indices: 1161666--1161709 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161656 TCATAAAACC
1161666 CTACAGTGGCATATGAAACGA
1 CTACAGTGGCATATGAAACGA
* * * *
1161687 CTACGGTGTCATCTGAACCGA
1 CTACAGTGGCATATGAAACGA
1161708 CT
1 CT
1161710 GTGTACCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
CTACAGTGGCATATGAAACGA
Found at i:1163336 original size:15 final size:15
Alignment explanation
Indices: 1163316--1163362 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1163306 TGCAAAAAGT
* *
1163316 AATAAAATTTAGTAA
1 AATAAAATATAATAA
1163331 AATAAAATATAATAA
1 AATAAAATATAATAA
*
1163346 AATAATAAAATAATAA
1 AATAA-AATATAATAA
1163362 A
1 A
1163363 CTCTTAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAAAATATAATAA
Found at i:1163352 original size:8 final size:8
Alignment explanation
Indices: 1163328--1163362 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1163318 TAAAATTTAG
1163328 TAAAATAA
1 TAAAATAA
*
1163336 -AATATAA
1 TAAAATAA
1163343 TAAAATAA
1 TAAAATAA
1163351 TAAAATAA
1 TAAAATAA
1163359 TAAA
1 TAAA
1163363 CTCTTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:1163746 original size:101 final size:101
Alignment explanation
Indices: 1163589--1163798 Score: 287
Period size: 101 Copynumber: 2.1 Consensus size: 101
1163579 AATGATTTGT
* * *
1163589 GCCTTCTAGCATGTGTCAGAATCCCATCGAAGGTGCGCTTGAGGATCTACATTTTACCCCCGTGG
1 GCCTTCTAGCATGTGTCAGAATCCCATCAAAGGCGCGCTTGAGGATCTACACTTTACCCCCGTGG
* *
1163654 CACCAGCTCGAAC-AGAAGGCGCGATTGATGATCCGC
66 CACCAGCTAGAACGA-AAGGCACGATTGATGATCCGC
* * ***
1163690 GCCTTCTAGCATGTGTCAGAATCCCATCAAAGGCGCGCTTGAGTATTTGTGCTTTACCCCCGTGG
1 GCCTTCTAGCATGTGTCAGAATCCCATCAAAGGCGCGCTTGAGGATCTACACTTTACCCCCGTGG
* **
1163755 CGCCAGCTAGAACGAAAGGCACTCTTGATGATCCGC
66 CACCAGCTAGAACGAAAGGCACGATTGATGATCCGC
1163791 GCCTTCTA
1 GCCTTCTA
1163799 TCCACGTGTG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 94 0.99
102 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (101 bp):
GCCTTCTAGCATGTGTCAGAATCCCATCAAAGGCGCGCTTGAGGATCTACACTTTACCCCCGTGG
CACCAGCTAGAACGAAAGGCACGATTGATGATCCGC
Found at i:1164145 original size:39 final size:39
Alignment explanation
Indices: 1164084--1164189 Score: 153
Period size: 39 Copynumber: 2.7 Consensus size: 39
1164074 TTTTATTCAT
*
1164084 TTATTT-ATTAAACG-AACGAACATGAGCAAGATTTTGTG
1 TTATTTAATTAAA-GAAACGAACATGAACAAGATTTTGTG
* *
1164122 TTATTTAATTAAAGAAACAAACATGAACAAGATTTTTTG
1 TTATTTAATTAAAGAAACGAACATGAACAAGATTTTGTG
*
1164161 TTATTTAATTAAAGAAACGAACACGAACA
1 TTATTTAATTAAAGAAACGAACATGAACA
1164190 GAGGACTCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
38 7 0.11
39 54 0.89
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (39 bp):
TTATTTAATTAAAGAAACGAACATGAACAAGATTTTGTG
Found at i:1164446 original size:10 final size:10
Alignment explanation
Indices: 1164431--1164506 Score: 62
Period size: 10 Copynumber: 6.9 Consensus size: 10
1164421 AAAAAATATT
1164431 TTCGTTTATG
1 TTCGTTTATG
**
1164441 TTCGTTTACA
1 TTCGTTTATG
1164451 TTCGTTTATG
1 TTCGTTTATG
*
1164461 TTCATTTATTTTG
1 TTCGTTTA---TG
1164474 TTCGTTTACATTCG
1 TTCGTTT--A-T-G
1164488 TTCGTTTATG
1 TTCGTTTATG
1164498 TTCGTTTAT
1 TTCGTTTAT
1164507 TTGTGTTTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 33 0.61
11 1 0.02
12 1 0.02
13 10 0.19
14 8 0.15
15 1 0.02
ACGTcount: A:0.13, C:0.13, G:0.14, T:0.59
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:1173490 original size:18 final size:18
Alignment explanation
Indices: 1173461--1173522 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
1173451 GTACGTACCT
* *
1173461 TCATTATCACCACCATGA
1 TCATCATCACCACCATCA
*
1173479 TCATCA-CTACCACCACCA
1 TCATCATC-ACCACCATCA
*
1173497 TCATCATCACCATCATCA
1 TCATCATCACCACCATCA
1173515 TCATCATC
1 TCATCATC
1173523 GTCACTTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 35 0.95
19 1 0.03
ACGTcount: A:0.32, C:0.40, G:0.02, T:0.26
Consensus pattern (18 bp):
TCATCATCACCACCATCA
Found at i:1173509 original size:12 final size:12
Alignment explanation
Indices: 1173492--1173522 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1173482 TCACTACCAC
1173492 CACCATCATCAT
1 CACCATCATCAT
1173504 CACCATCATCAT
1 CACCATCATCAT
*
1173516 CATCATC
1 CACCATC
1173523 GTCACTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (12 bp):
CACCATCATCAT
Found at i:1179434 original size:20 final size:20
Alignment explanation
Indices: 1179409--1179449 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1179399 TAAGCATCCC
1179409 TTAGAAGTTCTCCCGCATCT
1 TTAGAAGTTCTCCCGCATCT
*
1179429 TTAGAAGTTCTCCTGCATCT
1 TTAGAAGTTCTCCCGCATCT
1179449 T
1 T
1179450 GTGACAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (20 bp):
TTAGAAGTTCTCCCGCATCT
Found at i:1180531 original size:33 final size:33
Alignment explanation
Indices: 1180494--1180582 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
1180484 AGAAATCTAA
* * *
1180494 CCATCACGAGAACCATGTACAGATGGA-ATCTGG
1 CCATCATGAGAACCATGCACAGATGGAGA-ATGG
*
1180527 CCATCATGAGAACTATGCACAGATGGAGAATGG
1 CCATCATGAGAACCATGCACAGATGGAGAATGG
*
1180560 CCATAATGAGAACCATGCACAGA
1 CCATCATGAGAACCATGCACAGA
1180583 CAAAGACGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (33 bp):
CCATCATGAGAACCATGCACAGATGGAGAATGG
Found at i:1184267 original size:13 final size:13
Alignment explanation
Indices: 1184249--1184273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184239 TGGTGAAAAC
1184249 GCTATGGAGGAAT
1 GCTATGGAGGAAT
1184262 GCTATGGAGGAA
1 GCTATGGAGGAA
1184274 CCATGGCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
GCTATGGAGGAAT
Found at i:1185559 original size:4 final size:4
Alignment explanation
Indices: 1185534--1185591 Score: 98
Period size: 4 Copynumber: 14.5 Consensus size: 4
1185524 CACTATATAT
* *
1185534 ATAC ATAA ATAC ATAA ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1185582 ATAC ATAC AT
1 ATAC ATAC AT
1185592 GTCATTATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1185985 original size:18 final size:18
Alignment explanation
Indices: 1185964--1186029 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
1185954 ATTTGTCCTA
*
1185964 AAGGATCACTATGTCCCG
1 AAGGACCACTATGTCCCG
*
1185982 AAGGACCACTGATTGTTCCG
1 AAGGACCACT-A-TGTCCCG
*
1186002 AAGAACCACTATGTCCCG
1 AAGGACCACTATGTCCCG
1186020 AAGGACCACT
1 AAGGACCACT
1186030 GATAATCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 24 0.59
19 2 0.05
20 15 0.37
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (18 bp):
AAGGACCACTATGTCCCG
Found at i:1187486 original size:19 final size:19
Alignment explanation
Indices: 1187462--1187513 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1187452 TTTAAGTGGG
1187462 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1187481 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1187500 TGCATCGATGCACT
1 TGCATCGATGCACT
1187514 AATTGTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:1191284 original size:18 final size:18
Alignment explanation
Indices: 1191261--1191333 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
1191251 ACTGAATATT
* *
1191261 TGTCCCAAATGACCACTA
1 TGTCCCGAAGGACCACTA
1191279 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1191298 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
1191317 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1191334 GTTTGTCCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1191308 original size:20 final size:20
Alignment explanation
Indices: 1191260--1191356 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
1191250 CACTGAATAT
* *
1191260 TTGTCCCAAATGACCACT-A
1 TTGTCCCGAAGGACCACTGA
1191279 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
1191298 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
1191317 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
* *
1191336 TTGTCCTGAATGACCACTGA
1 TTGTCCCGAAGGACCACTGA
1191356 T
1 T
1191357 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 30 0.47
19 2 0.03
20 32 0.50
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:1191352 original size:38 final size:37
Alignment explanation
Indices: 1191259--1191353 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 37
1191249 GCACTGAATA
*
1191259 TTTGTCCCAAATGACCACTATGTCCCGAAGGACCACTG
1 TTTGT-CCGAATGACCACTATGTCCCGAAGGACCACTG
*
1191297 ATTGTTCCGAA-GAACCACTATGTCCCGAAGGACCACTG
1 TTTG-TCCGAATG-ACCACTATGTCCCGAAGGACCACTG
1191335 TTTGTCCTGAATGACCACT
1 TTTGTCC-GAATGACCACT
1191354 GATAATCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 4 0.08
38 44 0.88
39 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
TTTGTCCGAATGACCACTATGTCCCGAAGGACCACTG
Found at i:1193775 original size:105 final size:105
Alignment explanation
Indices: 1193593--1193801 Score: 418
Period size: 105 Copynumber: 2.0 Consensus size: 105
1193583 ATGTTACAAC
1193593 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1193658 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
66 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
1193698 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1193763 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTC
66 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTC
1193802 TTATTTATGC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (105 bp):
TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
Found at i:1195819 original size:21 final size:21
Alignment explanation
Indices: 1195777--1195821 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1195767 AAAGAAAAAA
* *
1195777 ATCTGATCCCGATATTTGGAT
1 ATCTGATCCCGAAATTTAGAT
1195798 ATCTGAT-CCGAAATTTCAGAT
1 ATCTGATCCCGAAATTT-AGAT
1195819 ATC
1 ATC
1195822 CGAATTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCTGATCCCGAAATTTAGAT
Found at i:1195844 original size:15 final size:16
Alignment explanation
Indices: 1195803--1195838 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1195793 TGGATATCTG
*
1195803 ATCCGAAATTTCAGAT
1 ATCCGAATTTTCAGAT
*
1195819 ATCCGAATTTTCGGAT
1 ATCCGAATTTTCAGAT
1195835 ATCC
1 ATCC
1195839 TATTTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (16 bp):
ATCCGAATTTTCAGAT
Found at i:1198403 original size:16 final size:17
Alignment explanation
Indices: 1198376--1198409 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1198366 ATTTTCATTC
1198376 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1198393 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
1198409 T
1 T
1198410 GACATCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:1202181 original size:29 final size:29
Alignment explanation
Indices: 1202146--1202205 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1202136 TTTATAGGTT
1202146 GATCTCTATAGTCGCATGGAGCACACGGC
1 GATCTCTATAGTCGCATGGAGCACACGGC
* * *
1202175 GATCTCTATGGTCGTATGGAGCATACGGC
1 GATCTCTATAGTCGCATGGAGCACACGGC
1202204 GA
1 GA
1202206 CCTACCTAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (29 bp):
GATCTCTATAGTCGCATGGAGCACACGGC
Found at i:1202800 original size:21 final size:21
Alignment explanation
Indices: 1202767--1202964 Score: 203
Period size: 21 Copynumber: 9.5 Consensus size: 21
1202757 ATTTCCAGAT
* *
1202767 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1202788 TCACAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1202809 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1202830 TCGCAATGCG-ACTATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
1202850 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
1202871 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1202892 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
1202912 TCGTAATGCGATAGTCT--ACTA
1 TCGCAATGCGA-ACT-TGGACTA
1202933 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1202954 TCGCAATGCGA
1 TCGCAATGCGA
1202965 TTTACATATT
Statistics
Matches: 147, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.22
21 111 0.76
22 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1202920 original size:41 final size:43
Alignment explanation
Indices: 1202784--1202964 Score: 159
Period size: 41 Copynumber: 4.3 Consensus size: 43
1202774 GCGAACTTCG
* *
1202784 ACTATCACAATGCGAACT-TGGACTATCGCAATGCGAACT-TGG
1 ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAA-TATGT
* *
1202826 ACTATCGCAATGCG-ACTATGTA-AATCGCAATGCG-ATA-GT
1 ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
1202865 CGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT
1 --ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
* * ** *
1202909 A-AATCGTAATGCG-A-TAGTCTACTATCGCAATGCGAACT-TGG
1 ACTATCGCAATGCGAACTA-TGGACTATCGCAATGCGAA-TATGT
1202950 ACTATCGCAATGCGA
1 ACTATCGCAATGCGA
1202965 TTTACATATT
Statistics
Matches: 113, Mismatches: 13, Indels: 25
0.75 0.09 0.17
Matches are distributed among these distances:
39 3 0.03
40 2 0.02
41 61 0.54
42 42 0.37
43 3 0.03
44 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (43 bp):
ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
Found at i:1202936 original size:83 final size:83
Alignment explanation
Indices: 1202767--1202964 Score: 242
Period size: 83 Copynumber: 2.4 Consensus size: 83
1202757 ATTTCCAGAT
* * * *
1202767 TCGCAACGCGAACTTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACAATC
*
1202832 GCAATGCGACTATGTAAA
66 GCAATGCGACTATCTAAA
*
1202850 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGA-ACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACAA
* *
1202912 TCGTAATGCGA-TAGTCTACTA
64 TCGCAATGCGACTA-TCTA-AA
* *
1202933 TCGCAATGCGAACTTGGACTATCGCAATGCGA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGA
1202965 TTTACATATT
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
81 2 0.02
82 16 0.16
83 81 0.81
84 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (83 bp):
TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACAATC
GCAATGCGACTATCTAAA
Found at i:1202989 original size:62 final size:61
Alignment explanation
Indices: 1202804--1202965 Score: 288
Period size: 62 Copynumber: 2.6 Consensus size: 61
1202794 TGCGAACTTG
1202804 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGACTATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGA-TATGTAAATCGCAATGCGATAGTC
*
1202866 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCG-ATATGTAAATCGCAATGCGATAGTC
*
1202928 TACTATCGCAATGCGAACTTGGACTATCGCAATGCGAT
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAT
1202966 TTACATATTC
Statistics
Matches: 97, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
61 2 0.02
62 94 0.97
63 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (61 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGATATGTAAATCGCAATGCGATAGTC
Found at i:1203002 original size:21 final size:21
Alignment explanation
Indices: 1202973--1203013 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202963 GATTTACATA
1202973 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1202994 TTCGTATTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
1203014 AATTGCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1203758 original size:21 final size:21
Alignment explanation
Indices: 1203733--1203877 Score: 163
Period size: 21 Copynumber: 6.8 Consensus size: 21
1203723 ATTTTGGACT
1203733 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1203754 ATCGCAATGCGAACTTTGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
1203775 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1203796 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1203817 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1203838 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1203859 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1203878 CTATCGCAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
19 19 0.18
21 55 0.53
23 30 0.29
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1203832 original size:63 final size:63
Alignment explanation
Indices: 1203733--1203877 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
1203723 ATTTTGGACT
* * *
1203733 ATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTTGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1203796 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1203859 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1203878 CTATCGCAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 67 0.87
65 10 0.13
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:1204331 original size:15 final size:16
Alignment explanation
Indices: 1204311--1204341 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1204301 CCGAATTCAG
1204311 TGCCCAATTTT-TTGA
1 TGCCCAATTTTGTTGA
1204326 TGCCCAATTTTGTTGA
1 TGCCCAATTTTGTTGA
1204342 AAATGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (16 bp):
TGCCCAATTTTGTTGA
Found at i:1205433 original size:15 final size:15
Alignment explanation
Indices: 1205409--1205440 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1205399 TGACAGATCG
*
1205409 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1205424 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1205439 AA
1 AA
1205441 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1208758 original size:15 final size:15
Alignment explanation
Indices: 1208738--1208768 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1208728 GGGCACCGAA
1208738 TTTGGTGCCCAATTT
1 TTTGGTGCCCAATTT
1208753 TTTGGTGCCCAATTT
1 TTTGGTGCCCAATTT
1208768 T
1 T
1208769 GTTAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TTTGGTGCCCAATTT
Found at i:1219901 original size:21 final size:23
Alignment explanation
Indices: 1219872--1219916 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
1219862 TTTTTATTTG
1219872 AATTCTTTAAATA-ACATT-TAA
1 AATTCTTTAAATACACATTATAA
* *
1219893 AATTTTTTATATACACATTATAA
1 AATTCTTTAAATACACATTATAA
1219916 A
1 A
1219917 TATAATTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 5 0.25
23 4 0.20
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTCTTTAAATACACATTATAA
Found at i:1220111 original size:19 final size:19
Alignment explanation
Indices: 1220089--1220129 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1220079 TTGTAAACTC
1220089 GTTGAAGCTGGTTTTCAGT
1 GTTGAAGCTGGTTTTCAGT
1220108 GTTGAAGCTGGTTTTCAGT
1 GTTGAAGCTGGTTTTCAGT
1220127 GTT
1 GTT
1220130 AAACCAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.32, T:0.44
Consensus pattern (19 bp):
GTTGAAGCTGGTTTTCAGT
Found at i:1233728 original size:45 final size:43
Alignment explanation
Indices: 1233677--1233827 Score: 176
Period size: 45 Copynumber: 3.3 Consensus size: 43
1233667 TGAAAATTTT
*
1233677 ATGAAATTGAAAAAAAAATAGAGGCCTTAATTGTAAAGGTAGAA
1 ATGAAATTGAAAAAAAAATAG-GGCCTTAATTATAAAGGTAGAA
* *
1233721 ATCGAAATTGAAAAAAAAATTAGGGCCTCAATTATAAAGGTATAA
1 AT-GAAATTGAAAAAAAAA-TAGGGCCTTAATTATAAAGGTAGAA
* * *
1233766 TTGAGATTGAAAAAAACACTTATGGGCCTTAATTATAAAGGTAGAA
1 ATGAAATTGAAAAAAA-A-ATA-GGGCCTTAATTATAAAGGTAGAA
*
1233812 AGTGAGATTGAAAAAA
1 A-TGAAATTGAAAAAA
1233828 CTTAAGGGGC
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
44 15 0.16
45 39 0.42
46 24 0.26
47 14 0.15
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGAAATTGAAAAAAAAATAGGGCCTTAATTATAAAGGTAGAA
Found at i:1233775 original size:44 final size:42
Alignment explanation
Indices: 1233682--1233990 Score: 245
Period size: 41 Copynumber: 7.1 Consensus size: 42
1233672 ATTTTATGAA
* * * *
1233682 ATTGAAAAAAAAATAGAGGCCTTAATTGTAAAGGTAGAAA-TCGAA
1 ATTG-AAAAAAATTAG-GGCCTCAATTATAAAGGTA-AAAGT-GAG
* *
1233727 ATTGAAAAAAAAATTAGGGCCTCAATTATAAAGGTATAATTGAG
1 ATTG--AAAAAAATTAGGGCCTCAATTATAAAGGTAAAAGTGAG
*
1233771 ATTGAAAAAAACACTTATGGGCCTTAATTATAAAGGTAGAAAGTGAG
1 ATTG-AAAAAA-A-TTA-GGGCCTCAATTATAAAGGTA-AAAGTGAG
* * *
1233818 ATTGAAAAAACTTAAGGGGCTCAATTATAAAGTTAAAAAGTGAG
1 ATTGAAAAAAATT-AGGGCCTCAATTATAAAGGT-AAAAGTGAG
* * *
1233862 ATT-AAAAAAATTAGAGCCTCAATTATAAAGTTAAAAGGTGGG
1 ATTGAAAAAAATTAGGGCCTCAATTATAAAGGTAAAA-GTGAG
**
1233904 ATT--AAAAAATTAGGGACCTCAATTATAAAGGTAAAA-AAATG
1 ATTGAAAAAAATTAGGG-CCTCAATTATAAAGGTAAAAGTGA-G
* * * *
1233945 ATTG--AAAAATTAGAGACTTCAATTATAAAGATAAAAATGAG
1 ATTGAAAAAAATTAG-GGCCTCAATTATAAAGGTAAAAGTGAG
1233986 ATTGA
1 ATTGA
1233991 TTATGACCTC
Statistics
Matches: 223, Mismatches: 26, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
41 51 0.23
42 46 0.21
43 15 0.07
44 38 0.17
45 27 0.12
46 36 0.16
47 10 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (42 bp):
ATTGAAAAAAATTAGGGCCTCAATTATAAAGGTAAAAGTGAG
Found at i:1233862 original size:91 final size:84
Alignment explanation
Indices: 1233687--1233990 Score: 255
Period size: 91 Copynumber: 3.5 Consensus size: 84
1233677 ATGAAATTGA
* * *
1233687 AAAAAAAATAGAGGCCTTAATTGTAAAGGTAGAAA-TCGAAATTGAAAAAAAAATTAGGGCCTCA
1 AAAAAAATTAG-GGCCTTAATTATAAAGGTAGAAAGT-GAGATTG---AAAAAATTAGGGCCTCA
* *
1233751 ATTATAAAGGT-ATAATTGAGATT
61 ATTATAAAGGTAAAAAGTGAGATT
*
1233774 GAAAAAAACACTTATGGGCCTTAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGGCT
1 --AAAAAA-A-TTA-GGGCCTTAATTATAAAGGTAGAAAGTGAGATTGAAAAAA-TT-AGGGCCT
*
1233839 CAATTATAAAGTTAAAAAGTGAGATT
59 CAATTATAAAGGTAAAAAGTGAGATT
* * * *
1233865 AAAAAAATTAGAGCCTCAATTATAAAGTTA-AAAGGTGGGATT-AAAAAATTAGGGACCTCAATT
1 AAAAAAATTAGGGCCTTAATTATAAAGGTAGAAA-GTGAGATTGAAAAAATTAGGG-CCTCAATT
*
1233928 ATAAAGGTAAAAA--AATGATT
64 ATAAAGGTAAAAAGTGA-GATT
* * * * *
1233948 -GAAAAATTAGAGACTTCAATTATAAAGATA-AAAATGAGATTGA
1 AAAAAAATTAGGGCCTT-AATTATAAAGGTAGAAAGTGAGATTGA
1233991 TTATGACCTC
Statistics
Matches: 183, Mismatches: 20, Indels: 30
0.79 0.09 0.13
Matches are distributed among these distances:
82 20 0.11
83 24 0.13
84 21 0.11
85 9 0.05
86 24 0.13
87 3 0.02
88 7 0.04
89 14 0.08
90 19 0.10
91 40 0.22
92 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (84 bp):
AAAAAAATTAGGGCCTTAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGGCCTCAATTAT
AAAGGTAAAAAGTGAGATT
Found at i:1233884 original size:42 final size:42
Alignment explanation
Indices: 1233733--1233988 Score: 236
Period size: 42 Copynumber: 6.0 Consensus size: 42
1233723 CGAAATTGAA
* *
1233733 AAAAAAATTAGGGCCTCAATTATAAAGGT-ATAATTGAGATT
1 AAAAAAATTAGGGCCTCAATTATAAAGGTAAAAAGTGAGATT
* *
1233774 GAAAAAAACACTTATGGGCCTTAATTATAAAGGTAGAAAGTGAGATT
1 --AAAAAA-A-TTA-GGGCCTCAATTATAAAGGTAAAAAGTGAGATT
* * *
1233821 GAAAAAACTTAAGGGGCTCAATTATAAAGTTAAAAAGTGAGATT
1 -AAAAAAATT-AGGGCCTCAATTATAAAGGTAAAAAGTGAGATT
* * * *
1233865 AAAAAAATTAGAGCCTCAATTATAAAGTTAAAAGGTGGGATT
1 AAAAAAATTAGGGCCTCAATTATAAAGGTAAAAAGTGAGATT
*
1233907 -AAAAAATTAGGGACCTCAATTATAAAGGTAAAAA--AATGATT
1 AAAAAAATTAGGG-CCTCAATTATAAAGGTAAAAAGTGA-GATT
* * * *
1233948 -GAAAAATTAGAGACTTCAATTATAAAGATAAAAA-TGAGATT
1 AAAAAAATTAG-GGCCTCAATTATAAAGGTAAAAAGTGAGATT
1233989 GATTATGACC
Statistics
Matches: 179, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
41 47 0.26
42 50 0.28
43 14 0.08
44 31 0.17
45 4 0.02
46 24 0.13
47 9 0.05
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAAAATTAGGGCCTCAATTATAAAGGTAAAAAGTGAGATT
Found at i:1234693 original size:25 final size:21
Alignment explanation
Indices: 1234641--1234685 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1234631 ATCATTGAGA
1234641 ATTCATTGATTTATTTATTAG
1 ATTCATTGATTTATTTATTAG
1234662 ATTCATTGATTTATTTATTAG
1 ATTCATTGATTTATTTATTAG
1234683 ATT
1 ATT
1234686 GATTCATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (21 bp):
ATTCATTGATTTATTTATTAG
Found at i:1236035 original size:20 final size:20
Alignment explanation
Indices: 1236010--1236047 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1236000 TTCTTCGATA
1236010 AATTAAAAGATG-AATATTTT
1 AATT-AAAGATGAAATATTTT
1236030 AATTAAAGATGAAATATT
1 AATTAAAGATGAAATATT
1236048 AATAGAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTAAAGATGAAATATTTT
Found at i:1236257 original size:2 final size:2
Alignment explanation
Indices: 1236250--1236307 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1236240 TGTTATTAGC
1236250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1236292 AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT
1236308 TGAAACAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1239298 original size:20 final size:21
Alignment explanation
Indices: 1239253--1239306 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
1239243 ATACTCAGGA
1239253 AAGTATTGATACTGAAGACCAG
1 AAGTATTGATACTGAAGA-CAG
*
1239275 AAGTATTGATACTTAAGA-AG
1 AAGTATTGATACTGAAGACAG
*
1239295 AAGTATCGATAC
1 AAGTATTGATAC
1239307 CAATCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (21 bp):
AAGTATTGATACTGAAGACAG
Found at i:1239363 original size:20 final size:21
Alignment explanation
Indices: 1239338--1239389 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1239328 AATGAGTTAG
1239338 TAGTATCGATACCCAGA-GGT
1 TAGTATCGATACCCAGAGGGT
*
1239358 TAGTATCAATA-CCAGAGGGT
1 TAGTATCGATACCCAGAGGGT
* *
1239378 CAGTATTGATAC
1 TAGTATCGATAC
1239390 TGAACAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (21 bp):
TAGTATCGATACCCAGAGGGT
Found at i:1242227 original size:14 final size:13
Alignment explanation
Indices: 1242199--1242232 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1242189 TTTTTTTAAA
*
1242199 TTTAAACTATTTT
1 TTTAAAATATTTT
1242212 TTTAAAATATTTT
1 TTTAAAATATTTT
1242225 TTTAAAAT
1 TTTAAAAT
1242233 CTGAACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAAATATTTT
Found at i:1247975 original size:155 final size:155
Alignment explanation
Indices: 1247770--1248079 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
1247760 ATTGGAAAGG
1247770 ACAACAATCGAAGACAAGTGCTTAGTACCTGTAGGGCCAAACCGTAACCACCATTGACGTCTTGT
1 ACAACAATCGAAGACAAGTGCTTAGTACCTGTAGGGCCAAACCGTAACCACCATTGACGTCTTGT
1247835 TCAAAATAAAGTAACTGGAATTTTACATTAATAAAACAGTCAGTTACAATATGTCTGACAAAGTG
66 TCAAAATAAAGTAACTGGAATTTTACATTAATAAAACAGTCAGTTACAATATGTCTGACAAAGTG
1247900 CCACATAGAAGAGATGCATACCCAT
131 CCACATAGAAGAGATGCATACCCAT
1247925 ACAACAATCGAAGACAAGTGCTTAGTACCTGTAGGGCCAAACCGTAACCACCATTGACGTCTTGT
1 ACAACAATCGAAGACAAGTGCTTAGTACCTGTAGGGCCAAACCGTAACCACCATTGACGTCTTGT
1247990 TCAAAATAAAGTAACTGGAATTTTACATTAATAAAACAGTCAGTTACAATATGTCTGACAAAGTG
66 TCAAAATAAAGTAACTGGAATTTTACATTAATAAAACAGTCAGTTACAATATGTCTGACAAAGTG
1248055 CCACATAGAAGAGATGCATACCCAT
131 CCACATAGAAGAGATGCATACCCAT
1248080 GAGCAATGGT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (155 bp):
ACAACAATCGAAGACAAGTGCTTAGTACCTGTAGGGCCAAACCGTAACCACCATTGACGTCTTGT
TCAAAATAAAGTAACTGGAATTTTACATTAATAAAACAGTCAGTTACAATATGTCTGACAAAGTG
CCACATAGAAGAGATGCATACCCAT
Found at i:1253652 original size:187 final size:187
Alignment explanation
Indices: 1253337--1253710 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
1253327 ATTTGGGAAG
1253337 CAATTGCGCATTTGGACGGCAATAAAGCACCAGGCCCAGATGGTCTGAATTTAGGGTTTTTCAAG
1 CAATTGCGCATTTGGACGGCAATAAAGCACCAGGCCCAGATGGTCTGAATTTAGGGTTTTTCAAG
1253402 AAGTTTTGGGGAAATTTGAAAGAAGACTTGGTGTTGTTTTTTAGAGAATTTCATCAAGGGAAAGT
66 AAGTTTTGGGGAAATTTGAAAGAAGACTTGGTGTTGTTTTTTAGAGAATTTCATCAAGGGAAAGT
1253467 ATGGGACTCGGAGGTGAACCATTCTTTTATCTCTCTCATTCCAAAGAGGGTGAATCC
131 ATGGGACTCGGAGGTGAACCATTCTTTTATCTCTCTCATTCCAAAGAGGGTGAATCC
1253524 CAATTGCGCATTTGGACGGCAATAAAGCACCAGGCCCAGATGGTCTGAATTTAGGGTTTTTCAAG
1 CAATTGCGCATTTGGACGGCAATAAAGCACCAGGCCCAGATGGTCTGAATTTAGGGTTTTTCAAG
1253589 AAGTTTTGGGGAAATTTGAAAGAAGACTTGGTGTTGTTTTTTAGAGAATTTCATCAAGGGAAAGT
66 AAGTTTTGGGGAAATTTGAAAGAAGACTTGGTGTTGTTTTTTAGAGAATTTCATCAAGGGAAAGT
1253654 ATGGGACTCGGAGGTGAACCATTCTTTTATCTCTCTCATTCCAAAGAGGGTGAATCC
131 ATGGGACTCGGAGGTGAACCATTCTTTTATCTCTCTCATTCCAAAGAGGGTGAATCC
1253711 AGAGGAGCTA
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (187 bp):
CAATTGCGCATTTGGACGGCAATAAAGCACCAGGCCCAGATGGTCTGAATTTAGGGTTTTTCAAG
AAGTTTTGGGGAAATTTGAAAGAAGACTTGGTGTTGTTTTTTAGAGAATTTCATCAAGGGAAAGT
ATGGGACTCGGAGGTGAACCATTCTTTTATCTCTCTCATTCCAAAGAGGGTGAATCC
Done.