Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 26
Found at i:1538112 original size:57 final size:51
Alignment explanation
Indices: 1538022--1538137 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 51
1538012 TATGTATTTG
*
1538022 TATGTATATATTTGATTTTTTTATAATAATTAACTTGCTTTTATAATAATT
1 TATGTATATATTTGATTTTTTTATAATAATTAACTTGATTTTATAATAATT
*
1538073 TATGTATATATTTGATTTTATAATATTTAACTTAATTAACTTGATTTTATAATAATT
1 TATGTATATATTTGATTTT-T--T-TATAA--TAATTAACTTGATTTTATAATAATT
1538130 TATGTATA
1 TATGTATA
1538138 ATAATTAACT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
51 19 0.33
52 1 0.02
54 1 0.02
55 4 0.07
57 32 0.56
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (51 bp):
TATGTATATATTTGATTTTTTTATAATAATTAACTTGATTTTATAATAATT
Found at i:1538143 original size:34 final size:33
Alignment explanation
Indices: 1538047--1538170 Score: 133
Period size: 34 Copynumber: 4.0 Consensus size: 33
1538037 TTTTTTTATA
*
1538047 ATAATTAACTTGCTTTTATAATAATTTATGTAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
1538080 AT-A-T---TTGATTTTATAAT-ATTTA---ACT
1 ATAATTAACTTGATTTTATAATAATTTATGTA-T
1538105 -TAATTAACTTGATTTTATAATAATTTATGTAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
* *
1538137 AATAATTAACTTTATTTTATAATCATTTATGTAT
1 -ATAATTAACTTGATTTTATAATAATTTATGTAT
1538171 TTTTTAGTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 23
0.75 0.03 0.23
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 1 0.01
27 5 0.07
28 12 0.16
29 13 0.17
30 5 0.07
31 1 0.01
32 2 0.03
33 3 0.04
34 30 0.39
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (33 bp):
ATAATTAACTTGATTTTATAATAATTTATGTAT
Found at i:1538151 original size:29 final size:29
Alignment explanation
Indices: 1538060--1538143 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
1538050 ATTAACTTGC
*
1538060 TTTTATAATAATTTATGTAT-ATATTTGA
1 TTTTATAATAATTTATGTATAATAATTGA
**
1538088 TTTTATAAT-ATTTAACT-TAATTAACTTGA
1 TTTTATAATAATTTATGTATAA-TAA-TTGA
1538117 TTTTATAATAATTTATGTATAATAATT
1 TTTTATAATAATTTATGTATAATAATT
1538144 AACTTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 7 0.15
28 11 0.24
29 15 0.33
30 9 0.20
31 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (29 bp):
TTTTATAATAATTTATGTATAATAATTGA
Found at i:1538182 original size:24 final size:23
Alignment explanation
Indices: 1538154--1538199 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1538144 AACTTTATTT
*
1538154 TATAATCATTTATGTATTTTTTAG
1 TATAATAATTTATGT-TTTTTTAG
1538178 TATAATAATTTATGTTTTTTTA
1 TATAATAATTTATGTTTTTTTA
1538200 AGTTTGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TATAATAATTTATGTTTTTTTAG
Found at i:1539289 original size:19 final size:19
Alignment explanation
Indices: 1539237--1539302 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1539227 CAAAATTATA
*
1539237 AAATTATAA-AAAAGAAA-T
1 AAATTA-AATAAAATAAATT
*
1539255 AAATATAAAT-AAATAACTT
1 AAAT-TAAATAAAATAAATT
*
1539274 AATTTAAATAAAATAAATT
1 AAATTAAATAAAATAAATT
1539293 AAATTAAATA
1 AAATTAAATA
1539303 TTATTATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAATTAAATAAAATAAATT
Found at i:1539308 original size:15 final size:14
Alignment explanation
Indices: 1539251--1539301 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1539241 TATAAAAAAG
1539251 AAATAAATATAAA-T
1 AAATAAAT-TAAATT
* *
1539265 AAATAACTTAATTT
1 AAATAAATTAAATT
*
1539279 AAATAAAATAAATT
1 AAATAAATTAAATT
1539293 AAATTAAAT
1 AAA-TAAAT
1539302 ATTATTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 3 0.10
14 22 0.76
15 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAATTAAATT
Found at i:1541037 original size:20 final size:20
Alignment explanation
Indices: 1541000--1541076 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
1540990 TTTAACTTTA
* *
1541000 TTCTCTTCT-TCTTGTTTCT
1 TTCTCTTTTCTCTTCTTTCT
1541019 TTCTCTTTTCTCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
1541039 TTCTCTTTTCTCTTCTTTC-
1 TTCTCTTTTCTCTTCTTTCT
*
1541058 TTCTCTCCTTCT-TTCTTTC
1 TTCTCT-TTTCTCTTCTTTC
1541077 ACTCCCGGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 21 0.40
20 32 0.60
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (20 bp):
TTCTCTTTTCTCTTCTTTCT
Found at i:1541048 original size:27 final size:28
Alignment explanation
Indices: 1541000--1541061 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1540990 TTTAACTTTA
*
1541000 TTCTCTTC-TTCTTGTTTCTTTCTCTT-
1 TTCTCTTCTTTCTTGTCTCTTTCTCTTC
1541026 TTCTCTTCTTTCTT-TCTCTTTTCTCTTC
1 TTCTCTTCTTTCTTGTCTC-TTTCTCTTC
1541054 TT-TCTTCT
1 TTCTCTTCT
1541062 CTCCTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 11 0.34
27 19 0.59
28 2 0.06
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (28 bp):
TTCTCTTCTTTCTTGTCTCTTTCTCTTC
Found at i:1541069 original size:27 final size:27
Alignment explanation
Indices: 1541018--1541069 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1541008 TTCTTGTTTC
* *
1541018 TTTCTCTTTTCTCTTCTTTCTTTCTCT
1 TTTCTCTTTTCTCTTCTCTCCTTCTCT
1541045 TTTCTCTTCTT-TCTTCTCTCCTTCT
1 TTTCTCTT-TTCTCTTCTCTCCTTCT
1541070 TTCTTTCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTCTCTTTTCTCTTCTCTCCTTCTCT
Found at i:1541376 original size:19 final size:18
Alignment explanation
Indices: 1541327--1541378 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1541317 CTCAACATGA
*
1541327 CAGCAGCACATGGGGTGG
1 CAGCAGCGCATGGGGTGG
*
1541345 CAGTAGCGCATGGGGTGG
1 CAGCAGCGCATGGGGTGG
*
1541363 CAGCAGTTGCATGGGG
1 CAGCAG-CGCATGGGG
1541379 CATGCAAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.15
Consensus pattern (18 bp):
CAGCAGCGCATGGGGTGG
Found at i:1542596 original size:13 final size:13
Alignment explanation
Indices: 1542575--1542635 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1542565 ATTTTGTTAG
1542575 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1542588 TATTGTA-TTATT
1 TATTTTATTTAAT
*
1542600 TAATTTT-TTTTAT
1 T-ATTTTATTTAAT
1542613 TATTTTATTTAAT
1 TATTTTATTTAAT
1542626 TATTTTATTT
1 TATTTTATTT
1542636 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.26
13 29 0.74
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1542611 original size:30 final size:30
Alignment explanation
Indices: 1542577--1542639 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1542567 TTTGTTAGTA
1542577 TTTTATT-TAATTATTGT-ATTATTTAATTTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTTT
* *
1542607 TTTTATTATTTTATTTAATTATTTTATTTT
1 TTTTATTATATTATTTAATTATTTAATTTT
1542637 TTT
1 TTT
1542640 ACAGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 27 0.93
31 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (30 bp):
TTTTATTATATTATTTAATTATTTAATTTT
Found at i:1542612 original size:22 final size:22
Alignment explanation
Indices: 1542587--1542631 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1542577 TTTTATTTAA
* *
1542587 TTATTGTATTATTTAATTTTTT
1 TTATTATATTATTTAATTATTT
*
1542609 TTATTATTTTATTTAATTATTT
1 TTATTATATTATTTAATTATTT
1542631 T
1 T
1542632 ATTTTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTATATTATTTAATTATTT
Found at i:1542615 original size:17 final size:17
Alignment explanation
Indices: 1542579--1542623 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1542569 TGTTAGTATT
1542579 TTATTTAA-TTATTGTA
1 TTATTTAATTTATTGTA
* *
1542595 TTATTTAATTTTTTTTA
1 TTATTTAATTTATTGTA
*
1542612 TTATTTTATTTA
1 TTATTTAATTTA
1542624 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTAATTTATTGTA
Found at i:1542910 original size:13 final size:13
Alignment explanation
Indices: 1542892--1542951 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1542882 AACTGTAAAA
1542892 AAATAAAATAATT
1 AAATAAAATAATT
1542905 AAATAAAATAA-T
1 AAATAAAATAATT
*
1542917 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
1542930 -AATACAATAATT
1 AAATAAAATAATT
1542942 AAATAAAATA
1 AAATAAAATA
1542952 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.10
12 13 0.32
13 23 0.57
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1542911 original size:21 final size:21
Alignment explanation
Indices: 1542887--1542931 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1542877 TTTATAACTG
*
1542887 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAAAAATTAAA
*
1542908 TAAAATAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
1542929 TAA
1 TAA
1542932 TACAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATTAAA
Found at i:1542924 original size:16 final size:16
Alignment explanation
Indices: 1542887--1542947 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
1542877 TTTATAACTG
1542887 TAAAAAAATAAAATAA
1 TAAAAAAATAAAATAA
*
1542903 T---TAAATAAAATAA
1 TAAAAAAATAAAATAA
*
1542916 TAAAAAAATTAAATAA
1 TAAAAAAATAAAATAA
* * *
1542932 TACAATAATTAAATAA
1 TAAAAAAATAAAATAA
1542948 AATACTAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 12 0.32
16 25 0.68
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAAATAAAATAA
Found at i:1542945 original size:21 final size:21
Alignment explanation
Indices: 1542887--1542939 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1542877 TTTATAACTG
* *
1542887 TAAAAAAATAAAATAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
1542908 TAAAATAATAAAAAAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
1542929 TAATACAATAA
1 TAAAACAATAA
1542940 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAACAATAAAAAAATTAAA
Found at i:1542950 original size:21 final size:20
Alignment explanation
Indices: 1542887--1542951 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
1542877 TTTATAACTG
*
1542887 TAAAAAAATAAAATAATTAAA
1 TAAAATAAT-AAATAATTAAA
1542908 TAAAATAAT-AA-AA--AAA
1 TAAAATAATAAATAATTAAA
*
1542924 TTAAATAATACAATAATTAAA
1 TAAAATAATA-AATAATTAAA
1542945 TAAAATA
1 TAAAATA
1542952 CTAACAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 11 0.31
18 4 0.11
19 4 0.11
21 17 0.47
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAATAAATAATTAAA
Found at i:1544276 original size:18 final size:21
Alignment explanation
Indices: 1544253--1544292 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
1544243 ATAAAATTCA
1544253 TATAATC-TTT-TTT-TATAT
1 TATAATCATTTATTTGTATAT
1544271 TATAATCATTTATTTGTATAT
1 TATAATCATTTATTTGTATAT
1544292 T
1 T
1544293 TATTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 3 0.16
21 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TATAATCATTTATTTGTATAT
Found at i:1551145 original size:2 final size:2
Alignment explanation
Indices: 1551138--1551169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1551128 CCTTTTCATG
1551138 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
1551170 GATTCATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1560589 original size:20 final size:21
Alignment explanation
Indices: 1560564--1560608 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1560554 GGATAAATAC
1560564 TTATTTAGACC-TTCAATTTT
1 TTATTTAGACCTTTCAATTTT
* * *
1560584 TTATTTTGCCCTTTCCATTTT
1 TTATTTAGACCTTTCAATTTT
1560605 TTAT
1 TTAT
1560609 CGTTAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTTAGACCTTTCAATTTT
Found at i:1584570 original size:16 final size:17
Alignment explanation
Indices: 1584539--1584571 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1584529 ATTTACATGC
*
1584539 TAAAATATATATTTTTA
1 TAAAATATATAATTTTA
1584556 TAAAAT-TATAATTTTA
1 TAAAATATATAATTTTA
1584572 GTCCCTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAATATATAATTTTA
Found at i:1586860 original size:193 final size:193
Alignment explanation
Indices: 1586531--1586925 Score: 783
Period size: 193 Copynumber: 2.1 Consensus size: 193
1586521 AAGTTCTCCC
1586531 TGATTGGTCCTCCCCAACCAACACCCAGAAAACAAAAGAACACCTACAAGAGAGGCTACCTTCTT
1 TGATTGGTCCTCCCCAACCAACACCCAGAAAACAAAAGAACACCTACAAGAGAGGCTACCTTCTT
1586596 CCTCTCCGAGTCTCTTCGTCTTGTCCTAACAAGAGAGAGAGAGAGAGCTTGTAATCGGCCATGGA
66 CCTCTCCGAGTCTCTTCGTCTTGTCCTAACAAGAGAGAGAGAGAGAGCTTGTAATCGGCCATGGA
1586661 TTTCTCCGAAGAATGTGAAAACTTCGTTTACGTTGCCAAGCTCGCTGAACAAGCCGAACGATT
131 TTTCTCCGAAGAATGTGAAAACTTCGTTTACGTTGCCAAGCTCGCTGAACAAGCCGAACGATT
1586724 TGATTGGTCCTCCCCAACCAACACCCAGAAAACAAAAGAACACCTACAAGAGAGGCTACCTTCTT
1 TGATTGGTCCTCCCCAACCAACACCCAGAAAACAAAAGAACACCTACAAGAGAGGCTACCTTCTT
1586789 CCTCTCCGAGTCTCTTCGTCTTGTCCTAACAAGAGAGAGAGAGAGAGCTTGTAATCGGCCATGGA
66 CCTCTCCGAGTCTCTTCGTCTTGTCCTAACAAGAGAGAGAGAGAGAGCTTGTAATCGGCCATGGA
1586854 TTTCTCCGAAGAATGTGAAAACTTCGTTTACGTTGCCAAGCTCGCTGAACAAGCCGAACGATT
131 TTTCTCCGAAGAATGTGAAAACTTCGTTTACGTTGCCAAGCTCGCTGAACAAGCCGAACGATT
1586917 TGA-TGGTCC
1 TGATTGGTCC
1586926 GATCTAACCA
Statistics
Matches: 202, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
192 6 0.03
193 196 0.97
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (193 bp):
TGATTGGTCCTCCCCAACCAACACCCAGAAAACAAAAGAACACCTACAAGAGAGGCTACCTTCTT
CCTCTCCGAGTCTCTTCGTCTTGTCCTAACAAGAGAGAGAGAGAGAGCTTGTAATCGGCCATGGA
TTTCTCCGAAGAATGTGAAAACTTCGTTTACGTTGCCAAGCTCGCTGAACAAGCCGAACGATT
Found at i:1594169 original size:17 final size:17
Alignment explanation
Indices: 1594147--1594180 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1594137 AACATTTGGT
* *
1594147 TAAAAATAGACTTAAAA
1 TAAAAAAAGAATTAAAA
1594164 TAAAAAAAGAATTAAAA
1 TAAAAAAAGAATTAAAA
1594181 GAATATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAAAAAAGAATTAAAA
Found at i:1597052 original size:53 final size:53
Alignment explanation
Indices: 1596989--1597096 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1596979 GATTAATGCA
1596989 ATTAATAACCATATCCGGAAGGGCAACTCCAAAAGATGGTGATTAGAGTTTTT
1 ATTAATAACCATATCCGGAAGGGCAACTCCAAAAGATGGTGATTAGAGTTTTT
1597042 ATTAATAACCATATCCGGAAGGGCAACTCCAAAAGATGGTGATTAGAGTTTTT
1 ATTAATAACCATATCCGGAAGGGCAACTCCAAAAGATGGTGATTAGAGTTTTT
1597095 AT
1 AT
1597097 AAAATTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (53 bp):
ATTAATAACCATATCCGGAAGGGCAACTCCAAAAGATGGTGATTAGAGTTTTT
Found at i:1597919 original size:70 final size:70
Alignment explanation
Indices: 1597806--1598006 Score: 325
Period size: 70 Copynumber: 2.9 Consensus size: 70
1597796 TAGAAGTCAA
* * * * *
1597806 TTGGGATGCTCTTCTTTGTTTCTTAGTCATGTGTGATTGTTTTGTTTTCATATTTTTACTCTTTA
1 TTGGGATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCCTATTTTTACTCTTTA
1597871 GACTT
66 GACTT
*
1597876 TTGGGATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCCTATTTTTACTCCTTA
1 TTGGGATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCCTATTTTTACTCTTTA
1597941 GACTT
66 GACTT
*
1597946 TTGGGATGCTCTTCTATGTTTCTTAGCCATGT-GGATT-TTTTGTTCTCCTATTTTTGCTCTT
1 TTGGGATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCCTATTTTTACTCTT
1598007 CTATGCTCTT
Statistics
Matches: 123, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 22 0.18
69 5 0.04
70 96 0.78
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.54
Consensus pattern (70 bp):
TTGGGATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCCTATTTTTACTCTTTA
GACTT
Found at i:1600663 original size:18 final size:18
Alignment explanation
Indices: 1600642--1600681 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1600632 AATTTTTTAA
1600642 TAAAAAATATAAAAAATT
1 TAAAAAATATAAAAAATT
* * *
1600660 TAAAATATATGAAAATTT
1 TAAAAAATATAAAAAATT
1600678 TAAA
1 TAAA
1600682 TTTTATCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAAAATATAAAAAATT
Found at i:1600666 original size:16 final size:17
Alignment explanation
Indices: 1600645--1600682 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1600635 TTTTTAATAA
1600645 AAAATATA-AAAAATTT
1 AAAATATATAAAAATTT
*
1600661 AAAATATATGAAAATTT
1 AAAATATATAAAAATTT
*
1600678 TAAAT
1 AAAAT
1600683 TTTATCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATATATAAAAATTT
Found at i:1601682 original size:184 final size:183
Alignment explanation
Indices: 1601338--1601770 Score: 607
Period size: 184 Copynumber: 2.4 Consensus size: 183
1601328 GAAATATTGT
* * *
1601338 CATGTTATATTGTTATATATCGATACATTTTTATAAAGTATCGATATTTTATAAGCGCTATTACT
1 CATGTTATATTGTTATATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGTTATTACT
* * *
1601403 ACTTTTCTTTTAAATTCCAAAAGTATTGATACTTATTTGAATAGAATCGATACTTTCAACATATT
66 ACTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTAAATAGAATCGATACTTTCAACATATC
** * * **
1601468 CAGTAGCGCTTTACCGGTTTTGTTATAATGAAACCGGTTTTGTCATATTTTTA
131 CAGTAGAACTTTACAGGTTTTGTCATAATGAAACCAATTTTGTCATATTTTTA
* * * * * **
1601521 CCTGTTATATTGTTATTTATCTATATATTTTTTTTAAAGTATCGATACTTTATAGGAATTATTAC
1 CATGTTATATTGTTATATATCGATACA-TTTTTATAAAGTATCGATACTTTATAGGCGTTATTAC
** * * *
1601586 TGTTTTTCTTTTAAATTCTAAAAGTGTCGATATTTATTTAAAT-GAAATCGATACTTTCAACATA
65 TACTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTAAATAG-AATCGATACTTTCAACATA
*
1601650 TCCGGTAGAACTTTACAGGTTTTGTCATAATGAAACCAATTTTGTCATATTTTTA
129 TCCAGTAGAACTTTACAGGTTTTGTCATAATGAAACCAATTTTGTCATATTTTTA
*
1601705 CATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGTTATTACT
1 CATGTTATATTGTTATATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGTTATTACT
1601770 A
66 A
1601771 TTATAATAAT
Statistics
Matches: 215, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
183 59 0.27
184 156 0.73
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (183 bp):
CATGTTATATTGTTATATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGTTATTACT
ACTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTAAATAGAATCGATACTTTCAACATATC
CAGTAGAACTTTACAGGTTTTGTCATAATGAAACCAATTTTGTCATATTTTTA
Found at i:1601887 original size:74 final size:74
Alignment explanation
Indices: 1601782--1602078 Score: 336
Period size: 74 Copynumber: 4.0 Consensus size: 74
1601772 TATAATAATG
* * *
1601782 AAATCGATACGTATTTTAATGTAATAAGTAGCGGCTATTTTTTTTTACCGTTTACATTATTAACA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGGCTA-TTTTTTTTACCGTTTACATTATTAACA
*
1601847 ACCTTC-AAA
65 ACATTCAAAA
* * *
1601856 AAATCGGTAGGTAGTTTATTGTAATAGGTAGC-AC-ATTTTTTTT---GTTTACATTATTAACAA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGGCTATTTTTTTTACCGTTTACATTATTAACAA
*
1601916 CCTTCAAAA
66 CATTCAAAA
* * *
1601925 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTGTTTTTTTTTTTTACTGTTTACATTATTA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCG---G-CTATTTTTTTTACCGTTTACATTATTA
*
1601990 GCAACATTCAAAA
62 ACAACATTCAAAA
* ** * * * *
1602003 AAATCGGTAGGTACTTTAATGTAATATATACCGTCTATTTTTTTTACCGTTTATATTATTACCAA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGGCTATTTTTTTTACCGTTTACATTATTAACAA
1602068 CATTCAAAA
66 CATTCAAAA
1602077 AA
1 AA
1602079 TTCGATATTT
Statistics
Matches: 190, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
68 22 0.12
69 33 0.17
71 8 0.04
72 1 0.01
73 1 0.01
74 64 0.34
75 8 0.04
78 53 0.28
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (74 bp):
AAATCGGTAGGTATTTTAATGTAATAGGTAGCGGCTATTTTTTTTACCGTTTACATTATTAACAA
CATTCAAAA
Found at i:1601948 original size:69 final size:71
Alignment explanation
Indices: 1601782--1602078 Score: 285
Period size: 78 Copynumber: 4.0 Consensus size: 71
1601772 TATAATAATG
* * * *
1601782 AAATCGATACGTATTTTAATGTAATAAGTAGCGGCTATTTTTTTTTACCGTTTACATTATTAACA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGACTA-TTTTTTTT---GTTTACATTATTAACA
1601847 ACCTTC-AAA
62 ACCTTCAAAA
* *
1601856 AAATCGGTAGGTAGTTTATTGTAATAGGTAGC-AC-ATTTTTTTTGTTTACATTATTAACAACCT
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTGTTTACATTATTAACAACCT
1601919 TCAAAA
66 TCAAAA
* *
1601925 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTGTTTTTTTTTTTTACTGTTTACATTATTA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGAC-----TATTTTTTT--TGTTTACATTATTA
* *
1601990 GCAACATTCAAAA
59 ACAACCTTCAAAA
* ** * * * *
1602003 AAATCGGTAGGTACTTTAATGTAATATATACCGTCTATTTTTTTTACCGTTTATATTATTACCAA
1 AAATCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTT---GTTTACATTATTAACAA
*
1602068 CATTCAAAA
63 CCTTCAAAA
1602077 AA
1 AA
1602079 TTCGATATTT
Statistics
Matches: 190, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
68 22 0.12
69 33 0.17
70 1 0.01
71 9 0.05
72 1 0.01
73 9 0.05
74 53 0.28
76 7 0.04
78 55 0.29
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (71 bp):
AAATCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTGTTTACATTATTAACAACCT
TCAAAA
Found at i:1607199 original size:3 final size:3
Alignment explanation
Indices: 1607191--1607215 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1607181 ATATTTTGAT
1607191 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1607216 AGTGTTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1607440 original size:18 final size:17
Alignment explanation
Indices: 1607414--1607502 Score: 88
Period size: 18 Copynumber: 5.1 Consensus size: 17
1607404 AATTCTAAAC
1607414 ATTTACAGTTATCAGAT
1 ATTTACAGTTATCAGAT
* *
1607431 GATTTTCAGTTATCATAT
1 -ATTTACAGTTATCAGAT
*
1607449 GATTTACAGTTATTAGAT
1 -ATTTACAGTTATCAGAT
* ** *
1607467 AATTACAAATATCATAT
1 ATTTACAGTTATCAGAT
1607484 ATTTTACAGTTATCAGAT
1 A-TTTACAGTTATCAGAT
1607502 A
1 A
1607503 CAAATTAATA
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
17 13 0.23
18 43 0.77
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (17 bp):
ATTTACAGTTATCAGAT
Found at i:1607750 original size:144 final size:144
Alignment explanation
Indices: 1607490--1607787 Score: 560
Period size: 144 Copynumber: 2.1 Consensus size: 144
1607480 ATATATTTTA
1607490 CAGTTATCAGATACAAATTAATAAATGATTTTACGATGATAAATATAAGCCCATTGTATGTTGCA
1 CAGTTATCAGATACAAATTAATAAATGATTTTACGATGATAAATATAAGCCCATTGTATGTTGCA
*
1607555 TTGAGAGTCGTATGTACATTTGGCATGCTATTGAGGAGTACTTACCAGTTCATCTTTGGTACATT
66 TTGAGAGTCGTAGGTACATTTGGCATGCTATTGAGGAGTACTTACCAGTTCATCTTTGGTACATT
*
1607620 TGTGTATCAATGTT
131 AGTGTATCAATGTT
* *
1607634 CAGTTATCAGATACAGATTAATAAATGATTTTACGATGATAAATATAAGTCCATTGTATGTTGCA
1 CAGTTATCAGATACAAATTAATAAATGATTTTACGATGATAAATATAAGCCCATTGTATGTTGCA
1607699 TTGAGAGTCGTAGGTACATTTGGCATGCTATTGAGGAGTACTTACCAGTTCATCTTTGGTACATT
66 TTGAGAGTCGTAGGTACATTTGGCATGCTATTGAGGAGTACTTACCAGTTCATCTTTGGTACATT
1607764 AGTGTATCAATGTT
131 AGTGTATCAATGTT
1607778 CAGTTATCAG
1 CAGTTATCAG
1607788 TTATTAGTTC
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 150 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (144 bp):
CAGTTATCAGATACAAATTAATAAATGATTTTACGATGATAAATATAAGCCCATTGTATGTTGCA
TTGAGAGTCGTAGGTACATTTGGCATGCTATTGAGGAGTACTTACCAGTTCATCTTTGGTACATT
AGTGTATCAATGTT
Found at i:1609659 original size:16 final size:16
Alignment explanation
Indices: 1609638--1609694 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
1609628 TAAATCTAAC
1609638 AATAATAATT-AATAAT
1 AATAATAATTAAAT-AT
* *
1609654 ATTAATGATTAAATAT
1 AATAATAATTAAATAT
1609670 AATAATAATTAAATAT
1 AATAATAATTAAATAT
1609686 AATATATAA
1 AATA-ATAA
1609695 ATATAGCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 28 0.80
17 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATAATAATTAAATAT
Found at i:1609671 original size:29 final size:29
Alignment explanation
Indices: 1609638--1609699 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 29
1609628 TAAATCTAAC
1609638 AATAATAATTAATAATATTAATGAT-TAAATAT
1 AATAATAATT-A-AATA-TAAT-ATATAAATAT
1609670 AATAATAATTAAATATAATATATAAATAT
1 AATAATAATTAAATATAATATATAAATAT
1609699 A
1 A
1609700 GCAATGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 2 0.07
29 12 0.41
30 4 0.14
31 1 0.03
32 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
AATAATAATTAAATATAATATATAAATAT
Found at i:1609811 original size:16 final size:15
Alignment explanation
Indices: 1609802--1609882 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 15
1609792 TAATAATAAT
*
1609802 AATAATTAATAATATG
1 AATAATTAA-AATATA
*
1609818 AATTATTAAATATAATA
1 AATAATTAAA-AT-ATA
1609835 AATAATTAAAATAT-
1 AATAATTAAAATATA
1609849 AATAATATATAAATAT-
1 AATAAT-TA-AAATATA
* *
1609865 AGTAATTAAAATAGA
1 AATAATTAAAATATA
1609880 AAT
1 AAT
1609883 TTTATAAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
14 11 0.20
15 9 0.17
16 23 0.43
17 11 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
AATAATTAAAATATA
Found at i:1609855 original size:26 final size:27
Alignment explanation
Indices: 1609794--1609863 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
1609784 AATAAATCTA
* * *
1609794 ATAATAATAATAATTAATAATATGAATT
1 ATAATAAT-ATAATAAATAATATAAAAT
*
1609822 ATTA-AATATAATAAATAAT-TAAAAT
1 ATAATAATATAATAAATAATATAAAAT
1609847 ATAATAATAT-ATAAATA
1 ATAATAATATAATAAATA
1609864 TAGTAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 14 0.39
26 16 0.44
27 3 0.08
28 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
ATAATAATATAATAAATAATATAAAAT
Found at i:1609916 original size:161 final size:156
Alignment explanation
Indices: 1609617--1609917 Score: 410
Period size: 161 Copynumber: 1.9 Consensus size: 156
1609607 ATGAAATGAA
*
1609617 ATTATAATAAATAAATCTAACAATAATAATTAATAATATTAATGATTAAATATAATAATAATTAA
1 ATTATAATAAATAAATCTAACAATAATAATTAATAATATGAATGATTAAATATAATAATAATTAA
* *
1609682 ATATAATATATAAATATAGCAATGAAAATAGAAATTTTATAAAAAAAAATAATTGTAATATGTTT
66 ATATAATATATAAATATAGCAATGAAAATAGAAATTTTAT--AAAAAAATAATTATAATATGATT
1609747 TGTAAATTTTGAAATAATGAAAATTTAT
129 TGTAAATTTTGAAATAATGAAAATTTAT
* * *
1609775 ATTATGATAAATAAATCTAATAATAATAATAATTAATAATATGAATTATTAAATATAATAAATAA
1 ATTATAATAAATAAATC---TAACAATAATAATTAATAATATGAATGATTAAATATAAT-AATAA
* * *
1609840 TTAAAATATAATAATATATAAATATAGTAATTAAAATAGAAATTTTAT-AAAGAATAATTATAAT
62 TT--AA-AT-ATAATATATAAATATAGCAATGAAAATAGAAATTTTATAAAAAAATAATTATAAT
1609904 AT-ATTT-TAAATTTT
123 ATGATTTGTAAATTTT
1609918 TTGAAATGAA
Statistics
Matches: 126, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
158 16 0.13
161 44 0.35
162 10 0.08
163 16 0.13
164 2 0.02
165 2 0.02
166 36 0.29
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (156 bp):
ATTATAATAAATAAATCTAACAATAATAATTAATAATATGAATGATTAAATATAATAATAATTAA
ATATAATATATAAATATAGCAATGAAAATAGAAATTTTATAAAAAAATAATTATAATATGATTTG
TAAATTTTGAAATAATGAAAATTTAT
Found at i:1625167 original size:144 final size:142
Alignment explanation
Indices: 1624923--1625214 Score: 484
Period size: 144 Copynumber: 2.0 Consensus size: 142
1624913 TTAAAAGTGC
*
1624923 ATTTTTAAATGGTTTTATAAAGAAGATGTATGTGGAACACCTCCAGTTTTGAAGATTCAAAATTT
1 ATTTTTAAATGGTTTTATAAAGAAGACGTATGTGGAACACCTCCAGTTTTGAAGATTCAAAATTT
*
1624988 CCAGATTATGTTTTAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCGTAGAGCTTGGTATG
66 CCAGATTATGTTTTAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTGGTATG
1625053 AAAGATTGTC-A
131 AAAGATTGTCAA
1625064 ATTTTTAAATGGTTTTTATAAAG-AGAAGCGTATGTGGAACAACCTCCAGTTTTTGAAGATTCAA
1 ATTTTTAAATGG-TTTTATAAAGAAG-A-CGTATGTGGAAC-ACCTCCAG-TTTTGAAGATTCAA
1625128 AATTT-CAGATTATGTTTTTAAATTGACAAAGCTC-TTATGGTTTAAAACAAGCTCCTAGAGCTT
61 AATTTCCAGATTATG-TTTTAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTT
1625191 GGTATGAAAGATTGTCAA
125 GGTATGAAAGATTGTCAA
1625209 ATTTTT
1 ATTTTT
1625215 TTGAAAAAGG
Statistics
Matches: 142, Mismatches: 2, Indels: 10
0.92 0.01 0.06
Matches are distributed among these distances:
141 14 0.10
142 11 0.08
143 11 0.08
144 61 0.43
145 45 0.32
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (142 bp):
ATTTTTAAATGGTTTTATAAAGAAGACGTATGTGGAACACCTCCAGTTTTGAAGATTCAAAATTT
CCAGATTATGTTTTAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTGGTATG
AAAGATTGTCAA
Found at i:1626511 original size:417 final size:406
Alignment explanation
Indices: 1625715--1626539 Score: 1492
Period size: 417 Copynumber: 2.0 Consensus size: 406
1625705 TACCTTAAGG
1625715 ACACTCCTAGTTTATGACTTTGGTATCCTAGAGACTCTAGTTTTAGCTTGCATGATTTCTCAATA
1 ACACTCCTAGTTTATGACTTTGGTATCCTAGAGACTCTAGTTTTAGCTTGCATGATTTCTCAATA
1625780 CGGATTATGGAGGATGCAAATAGATAGGAAAAGCACCTCCGTACTTGCCAATTCCTAGGAACTAT
66 CGGATTATGGAGGATGCAAATAGATAGGAAAAGCACCTCCGTACTTGCCAATTCCTAGGAACTAT
1625845 GCTAATTCTTGGTTTCCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCGGAATACAT
131 GCTAATTCTTGGTTTCCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCGGAATACAT
*
1625910 TTCAACCAGGATTTTGTGCACAAGTTTTATGGATAAAACAATTTTTGATTATGGAATTGAAGTAA
196 TTCAACCAGGATTTTGTGCACAAGTTTTATGGATAAAACAATTCTTGATTATGGAATTGAAGTAA
1625975 GTATCATTCCTATCAAGTGTGACATATAGTGCTATTCGTCTCACTAAAAATCCCATCCAATACTC
261 GTATCATTCCTATCAAGTGTGACATATAGTGCTATTCGTCTCACTAAAAATCCCATCCAATACTC
1626040 TAGAACTAAACACATTAAAATTAGACATCACTTCATTAGAGACATGTCGCTAAGGAAGATGTAGT
326 TAGAACTAAACACATTAAAATTAGACATCACTTCATTAGAGACATGTCGCTAAGGAAGATGTAGT
1626105 TCTAGAA-TTGTTGAT
391 TCTAGAATTTGTTGAT
1626120 ACACTCCTAGTTTATGACTTTGGTATCCTAGAGACTCTAGTTTTAGCTTGCATGATTTCTCAGAT
1 ACACTCCTAGTTTATGACTTTGGTATCCTAGAGACTCTAGTTTTAGCTTGCATGATTTCTCA-AT
1626185 ACGGATTATGGAGGATGCAAATTAGATAGGAAAAGCACCTCCGATACTTGCCAATTCCTAGGAAC
65 ACGGATTATGGAGGATGCAAA-TAGATAGGAAAAGCACCTCCG-TACTTGCCAATTCCTAGGAAC
1626250 TATGCTAATTTCTTGGTTTCCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCGGAAT
128 TATGCTAA-TTCTTGGTTTCCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCGGAAT
*
1626315 ACATTTCAGCCAGGAGTTGTTGTGCACAAGTTTTATGGATGAAACAACAACTTCTTGATTATGGA
192 ACATTTCAACCAGGA-TT-TTGTGCACAAGTTTTATGGAT--AA-AACAA-TTCTTGATTATGGA
1626380 ATTGAAGTAAGTATCATTCCTATCAAGTGTGACAATATTAGTGCTATTCGTCTCACTAAAAATCC
251 ATTGAAGTAAGTATCATTCCTATCAAGTGTGAC-ATA-TAGTGCTATTCGTCTCACTAAAAATCC
*
1626445 CATCCAATACTCTAGAACTAAACATATT-AAATTAGACATCACTTCATTAGAGACCATGTCGCTA
314 CATCCAATACTCTAGAACTAAACACATTAAAATTAGACATCACTTCATTAGAGA-CATGTCGCTA
1626509 AGGAAGATGTAGTTCTAGAATTTGTTGAT
378 AGGAAGATGTAGTTCTAGAATTTGTTGAT
1626538 AC
1 AC
1626540 TTTGCACCAA
Statistics
Matches: 403, Mismatches: 3, Indels: 15
0.96 0.01 0.04
Matches are distributed among these distances:
405 62 0.15
406 23 0.06
407 21 0.05
408 29 0.07
409 70 0.17
410 2 0.00
411 21 0.05
413 2 0.00
414 5 0.01
415 46 0.11
416 28 0.07
417 84 0.21
418 10 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (406 bp):
ACACTCCTAGTTTATGACTTTGGTATCCTAGAGACTCTAGTTTTAGCTTGCATGATTTCTCAATA
CGGATTATGGAGGATGCAAATAGATAGGAAAAGCACCTCCGTACTTGCCAATTCCTAGGAACTAT
GCTAATTCTTGGTTTCCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCGGAATACAT
TTCAACCAGGATTTTGTGCACAAGTTTTATGGATAAAACAATTCTTGATTATGGAATTGAAGTAA
GTATCATTCCTATCAAGTGTGACATATAGTGCTATTCGTCTCACTAAAAATCCCATCCAATACTC
TAGAACTAAACACATTAAAATTAGACATCACTTCATTAGAGACATGTCGCTAAGGAAGATGTAGT
TCTAGAATTTGTTGAT
Found at i:1629473 original size:20 final size:20
Alignment explanation
Indices: 1629448--1629496 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1629438 AGAGATGTAC
1629448 CGATGCACTAGTCCATGCAT
1 CGATGCACTAGTCCATGCAT
1629468 CGATGCACTAGTCCATGCAT
1 CGATGCACTAGTCCATGCAT
*
1629488 CAATGCACT
1 CGATGCACT
1629497 CTCAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (20 bp):
CGATGCACTAGTCCATGCAT
Found at i:1634697 original size:29 final size:29
Alignment explanation
Indices: 1634653--1634764 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
1634643 AACGGGGGGT
*
1634653 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
1634682 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
1634711 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
1634740 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
1634765 TACCCCACGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.20, C:0.44, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:1634807 original size:30 final size:30
Alignment explanation
Indices: 1634771--1634880 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
1634761 GACCTACCCC
1634771 ACGACCTCCATGCACGCCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* * *
1634801 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
*
1634831 ACGACCTCCATGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
1634861 ACGACCTCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCA
1634881 GCTCGCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCATGCACGCCCA
Found at i:1635518 original size:21 final size:21
Alignment explanation
Indices: 1635493--1635536 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1635483 AATTTACTTA
1635493 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1635514 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1635535 AT
1 AT
1635537 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1635544 original size:28 final size:28
Alignment explanation
Indices: 1635513--1635566 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1635503 TAGTATAAAT
*
1635513 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
1635541 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
1635567 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:1638688 original size:59 final size:58
Alignment explanation
Indices: 1638618--1639090 Score: 688
Period size: 59 Copynumber: 8.3 Consensus size: 58
1638608 GTATTTATAA
*
1638618 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT-ATGATTTGATAGTAAT
1638677 GATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAAT
1638736 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT-ATGATTTGATAGTAAT
*
1638795 GATTTAGTAATGATTAGTAATAATGAAATTATTAATT-A-TGTATGATTTGATAGT-AT
1 GATTTAGTAATGATTAGTAATAATGAAATTATT-ATTAATTTTATGATTTGATAGTAAT
*
1638851 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAAT
*
1638911 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAAT
*
1638971 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT-T-A-ATGAT--T--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAAT
* * *
1639022 GA--TAGTAATGATTAGTAATAAT-AATTTATTATT-ATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAAT
1639076 GATTTAGTAATGATT
1 GATTTAGTAATGATT
1639091 TGATAGTAAT
Statistics
Matches: 386, Mismatches: 9, Indels: 41
0.89 0.02 0.09
Matches are distributed among these distances:
47 4 0.01
48 11 0.03
49 21 0.05
50 4 0.01
51 3 0.01
52 1 0.00
53 1 0.00
54 3 0.01
55 7 0.02
56 47 0.12
57 15 0.04
58 18 0.05
59 132 0.34
60 119 0.31
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (58 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAAT
Found at i:1638753 original size:21 final size:20
Alignment explanation
Indices: 1638729--1638816 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
1638719 TATGATTTGA
1638729 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
1638750 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
1638768 TATTAAT-TTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
1638788 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
1638809 TAGTAATA
1 TAGTAATA
1638817 ATGAAATTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 15
0.64 0.16 0.20
Matches are distributed among these distances:
18 13 0.27
19 1 0.02
20 12 0.25
21 17 0.35
22 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:1638813 original size:10 final size:11
Alignment explanation
Indices: 1638670--1638815 Score: 59
Period size: 11 Copynumber: 12.6 Consensus size: 11
1638660 AATGATTTGA
1638670 TAGTAATGATT
1 TAGTAATGATT
1638681 TAGTAATGATT
1 TAGTAATGATT
* *
1638692 AGTAATAATGAAT
1 --TAGTAATGATT
* * *
1638705 TA-TTATTAAT
1 TAGTAATGATT
1638715 TATGT-ATGATTT
1 TA-GTAATGA-TT
1638727 GATAGTAATGATT
1 --TAGTAATGATT
1638740 TAGTAATGATT
1 TAGTAATGATT
* *
1638751 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
1638765 TATTATTAATT
1 TAGTAATGATT
1638776 T--TAATGATTT
1 TAGTAATGA-TT
1638786 GATAGTAATGATT
1 --TAGTAATGATT
1638799 TAGTAATGA-T
1 TAGTAATGATT
1638809 TAGTAAT
1 TAGTAAT
1638816 AATGAAATTA
Statistics
Matches: 105, Mismatches: 14, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
9 4 0.04
10 18 0.17
11 39 0.37
12 8 0.08
13 22 0.21
14 14 0.13
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1638830 original size:25 final size:25
Alignment explanation
Indices: 1638772--1638884 Score: 61
Period size: 25 Copynumber: 4.3 Consensus size: 25
1638762 AATTATTATT
* *
1638772 AATT-TTAATGATTTGATAGTAATG
1 AATTATTAATGATTAGATAATAATG
* *
1638796 ATTTAGTAATGATTAG-TAATAATG
1 AATTATTAATGATTAGATAATAATG
* *
1638820 AAATTATTAATTATGTATGATTTGATAGTATG
1 -AATTATTAATGAT-TA-GA--TAATA--ATG
* *
1638852 ACTTAGTAATGATTAG-TAATAATG
1 AATTATTAATGATTAGATAATAATG
1638876 AAATTATTA
1 -AATTATTA
1638885 TTAATTATGT
Statistics
Matches: 65, Mismatches: 14, Indels: 19
0.66 0.14 0.19
Matches are distributed among these distances:
24 13 0.20
25 25 0.38
26 6 0.09
27 1 0.02
29 1 0.02
30 6 0.09
31 10 0.15
32 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (25 bp):
AATTATTAATGATTAGATAATAATG
Found at i:1638939 original size:60 final size:60
Alignment explanation
Indices: 1638618--1639040 Score: 706
Period size: 59 Copynumber: 7.2 Consensus size: 60
1638608 GTATTTATAA
*
1638618 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATT-T-TAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1638677 GATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1638736 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1638795 GATTTAGTAATGATTAGTAATAATG-AA--ATTATTAATTATGTATGATTTGATAGT-AT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
1638851 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
1638911 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
1638971 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1639031 GA-TTAGTAAT
1 GATTTAGTAAT
1639041 AATAATTTAT
Statistics
Matches: 349, Mismatches: 4, Indels: 22
0.93 0.01 0.06
Matches are distributed among these distances:
56 36 0.10
57 16 0.05
58 18 0.05
59 145 0.42
60 134 0.38
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:1639032 original size:14 final size:14
Alignment explanation
Indices: 1639013--1639105 Score: 68
Period size: 14 Copynumber: 6.6 Consensus size: 14
1639003 TATTAATTTT
1639013 TAATGATTTGATAG
1 TAATGATTTGATAG
* *
1639027 TAATGATTAG-TAA
1 TAATGATTTGATAG
* * *
1639040 TAATAATTTATTATTATT
1 TAATGA-TT-TGA-TA-G
*
1639058 TAATGATTTGATAT
1 TAATGATTTGATAG
1639072 TAATGA-TT--TAG
1 TAATGATTTGATAG
1639083 TAATGATTTGATAG
1 TAATGATTTGATAG
1639097 TAATGATTT
1 TAATGATTT
1639106 ACGACTTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
11 8 0.13
12 2 0.03
13 9 0.15
14 30 0.48
15 2 0.03
16 2 0.03
17 4 0.06
18 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1639066 original size:45 final size:48
Alignment explanation
Indices: 1638975--1639086 Score: 167
Period size: 45 Copynumber: 2.4 Consensus size: 48
1638965 AGTAATGATT
1638975 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGA
*
1639024 TAGTAATGATTAGTAATAAT-AATTTATTATT-A-TTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
*
1639069 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
1639087 GATTTGATAG
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
45 21 0.35
46 8 0.13
47 1 0.02
48 10 0.17
49 20 0.33
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
Found at i:1639087 original size:25 final size:25
Alignment explanation
Indices: 1639058--1639106 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1639048 TATTATTATT
*
1639058 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
1639083 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
1639107 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:1639189 original size:7 final size:7
Alignment explanation
Indices: 1639177--1639203 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1639167 ATTTTTGGTT
1639177 CAATGAA
1 CAATGAA
1639184 CAATGAA
1 CAATGAA
1639191 CAATGAA
1 CAATGAA
1639198 CAATGA
1 CAATGA
1639204 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:1639331 original size:14 final size:13
Alignment explanation
Indices: 1639312--1639376 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
1639302 TTTAAATATT
1639312 TAATGATTTGATAC
1 TAATGATTT-ATAC
1639326 TAATGA-TT-TAC
1 TAATGATTTATAC
*
1639337 TAAT--TAT-TAC
1 TAATGATTTATAC
1639347 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
1639361 TAATTATTTGATAC
1 TAATGATTT-ATAC
1639375 TA
1 TA
1639377 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:1639348 original size:10 final size:11
Alignment explanation
Indices: 1639323--1639356 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1639313 AATGATTTGA
1639323 TACTAATGATT
1 TACTAATGATT
*
1639334 TACTAATTA-T
1 TACTAATGATT
1639344 TACTAATGATT
1 TACTAATGATT
1639355 TA
1 TA
1639357 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:1639366 original size:21 final size:21
Alignment explanation
Indices: 1639323--1639366 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1639313 AATGATTTGA
* *
1639323 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
1639344 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
1639365 TA
1 TA
1639367 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:1639383 original size:17 final size:17
Alignment explanation
Indices: 1639361--1639393 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1639351 GATTTAATAC
1639361 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
1639378 TAATTATTTGATACTA
1 TAATTATTTGATACTA
1639394 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:1641590 original size:32 final size:33
Alignment explanation
Indices: 1641516--1641596 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
1641506 ACCAACCCTT
*
1641516 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTATATAACTA
1641548 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTT-A-TATAACTA
*
1641581 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
1641597 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 22 0.50
34 2 0.05
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTTATATAACTA
Found at i:1641602 original size:12 final size:12
Alignment explanation
Indices: 1641577--1641629 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1641567 TTTTTCATTA
*
1641577 TAATATACT-AC
1 TAATAAACTAAC
*
1641588 TAATAAACTTAC
1 TAATAAACTAAC
1641600 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
1641614 TAATAAACTAAC
1 TAATAAACTAAC
1641626 TAAT
1 TAAT
1641630 TTTTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:1641746 original size:45 final size:48
Alignment explanation
Indices: 1641658--1641748 Score: 136
Period size: 45 Copynumber: 2.0 Consensus size: 48
1641648 CAACAAACAA
1641658 ATATAACTTAACTATTTAACTAACAAAAACTAATTAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAATAATTTTTTTT
*
1641706 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAATAATTTTTT
1641749 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
44 2 0.05
45 21 0.51
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAATAATTTTTTTT
Found at i:1641756 original size:47 final size:47
Alignment explanation
Indices: 1641658--1641761 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 47
1641648 CAACAAACAA
*
1641658 ATATAACTTAACTATTTAACTAACAAAAACTAATTAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAATAATTTTTTCT
*
1641706 ATATAACTAACTA-TTAAC-AA-AACAAACTAATTAATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAATAATTTTTT--CT
1641753 ATATAACTA
1 ATATAACTA
1641762 TCAAACATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
44 2 0.04
45 21 0.41
46 5 0.10
47 16 0.31
48 7 0.14
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAATAATTTTTTCT
Found at i:1641817 original size:41 final size:40
Alignment explanation
Indices: 1641729--1641817 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1641719 TTAACAAAAC
* *
1641729 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1641770 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
1641811 AAACTAA
1 AAACTAA
1641818 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:1641882 original size:16 final size:18
Alignment explanation
Indices: 1641853--1641891 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1641843 ACTAATTAAC
*
1641853 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
1641871 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
1641887 ATTTA
1 ATTTA
1641892 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:1642174 original size:50 final size:48
Alignment explanation
Indices: 1642103--1642211 Score: 177
Period size: 49 Copynumber: 2.3 Consensus size: 48
1642093 TAGGATCACA
*
1642103 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
1642152 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1642200 TGGC-TGCATGCA
1 TGGCATGCATGCA
1642212 TGGTCTGCAG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
47 8 0.14
48 5 0.09
49 32 0.55
50 13 0.22
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:1642383 original size:19 final size:19
Alignment explanation
Indices: 1642359--1642396 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1642349 TATATGGCTT
1642359 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
1642378 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
1642397 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:1642439 original size:29 final size:29
Alignment explanation
Indices: 1642406--1642509 Score: 199
Period size: 29 Copynumber: 3.6 Consensus size: 29
1642396 GTGAGTATAT
1642406 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1642435 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1642464 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
*
1642493 GGCGTACATGGCGACCT
1 GGCGTGCATGGCGACCT
1642510 ACCCCCGTTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTGGTTGGTCGCCG
Found at i:1644193 original size:3 final size:3
Alignment explanation
Indices: 1644185--1644267 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
1644175 TTTATTCATC
* * *
1644185 TTA TTA TTA TTA TTA ATA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1644233 TTA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
1644268 CAAACAGGCC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 62 0.91
4 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1644705 original size:14 final size:14
Alignment explanation
Indices: 1644686--1644729 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
1644676 CCGAACCTGA
1644686 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
*
1644700 AAAAAAGAAAGAAG
1 AAAAAAAAAAGAAG
*
1644714 ACAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
1644728 AA
1 AA
1644730 CAGAGAGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:1646460 original size:18 final size:18
Alignment explanation
Indices: 1646419--1646461 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1646409 AATTTTTATA
1646419 TTTATTTATTATTTTCAT
1 TTTATTTATTATTTTCAT
**
1646437 AATATTTA-TATGTTTCAT
1 TTTATTTATTAT-TTTCAT
1646455 TTTATTT
1 TTTATTT
1646462 TATTTGCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTTTCAT
Found at i:1646476 original size:15 final size:13
Alignment explanation
Indices: 1646456--1646493 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1646446 ATGTTTCATT
1646456 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
1646471 TTATTTTATTTCA
1 TTATTTTATTTCA
1646484 TTA-TTTATTT
1 TTATTTTATTT
1646494 TTCTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:1658729 original size:83 final size:83
Alignment explanation
Indices: 1658238--1658728 Score: 907
Period size: 83 Copynumber: 5.9 Consensus size: 83
1658228 TATCTTAGTC
1658238 CAAA-CATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
1658302 TAATCTGGTTTG-GCAGAA
66 TGATCTGGTTTGAG-AGAA
1658320 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
1658385 TGATCTGGTTTGAGAGAC
66 TGATCTGGTTTGAGAGAA
1658403 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1658468 TGATCTGGTTTGAGAGAA
66 TGATCTGGTTTGAGAGAA
1658486 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1658551 TGATCTGGTTTGAGAGAA
66 TGATCTGGTTTGAGAGAA
1658569 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
1658634 TGATCTAGTTTG-GCAGAA
66 TGATCTGGTTTGAG-AGAA
*
1658652 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1658717 TGATCTGGTTTG
66 TGATCTGGTTTG
1658729 GTAAGAACTA
Statistics
Matches: 400, Mismatches: 6, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
82 5 0.01
83 394 0.99
84 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (83 bp):
CAAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGAGAGAA
Found at i:1659612 original size:112 final size:112
Alignment explanation
Indices: 1659456--1660126 Score: 978
Period size: 112 Copynumber: 6.0 Consensus size: 112
1659446 TCAAAGATTT
*
1659456 AAATCCATCA-TTCGATGGATCAACATTTT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCCATCACTT-GATGGATCAGC-TTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* ** *
1659519 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTGCTT
64 AGAAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
1659568 AAATTCATC-CTTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCAC-TTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
1659632 GAAGGAAGAAAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
1659680 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1659745 AAGGAAGAAAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
1659792 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1659857 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** * *
1659904 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
1659969 AAGGAAGAAGAAGTTCATAATGATAAGAATTTGTTTAACCTCTTAC-C
66 AAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
1660016 TGAATTCATCAATTGATGGATTATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGA
1 -AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGA
* * *
1660079 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
64 AGAAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1660127 ATAATTCTAT
Statistics
Matches: 518, Mismatches: 33, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
111 5 0.01
112 445 0.86
113 68 0.13
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1660365 original size:3 final size:3
Alignment explanation
Indices: 1660357--1660439 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
1660347 TTTATTCATC
* * * *
1660357 TTA TTA TTA TTA TTA ATA TTA TTA TAA TTA TTA TTA TTA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1660405 TTA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
1660440 CAAACAGGCC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 62 0.91
4 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1660880 original size:21 final size:21
Alignment explanation
Indices: 1660856--1660900 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1660846 ACCCGAACCT
*
1660856 GAAAAAAAAAAGAAGAAAAAA
1 GAAAAAAAAAAGAAAAAAAAA
* * *
1660877 GAAAGAAGACAGAAAAAAAAA
1 GAAAAAAAAAAGAAAAAAAAA
1660898 GAA
1 GAA
1660901 GAACAGAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAAAGAAAAAAAAA
Found at i:1660892 original size:17 final size:16
Alignment explanation
Indices: 1660859--1660907 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
1660849 CGAACCTGAA
1660859 AAAAAAAAGAAGA-A-
1 AAAAAAAAGAAGACAG
*
1660873 AAAAGAAAGAAGACAG
1 AAAAAAAAGAAGACAG
1660889 AAAAAAAAAGAAGAACAG
1 -AAAAAAAAGAAG-ACAG
1660907 A
1 A
1660908 GAGACAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 12 0.41
15 1 0.03
17 12 0.41
18 4 0.14
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAGACAG
Found at i:1667016 original size:31 final size:31
Alignment explanation
Indices: 1666978--1667045 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1666968 GAATTCTGGA
1666978 CACCAGTTGATCGATACTAATAAACAAATCC
1 CACCAGTTGATCGATACTAATAAACAAATCC
*
1667009 CACCAGTTGATCGATACTTATAAACAAATCC
1 CACCAGTTGATCGATACTAATAAACAAATCC
1667040 CACCAG
1 CACCAG
1667046 ATTCGAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (31 bp):
CACCAGTTGATCGATACTAATAAACAAATCC
Found at i:1667591 original size:95 final size:96
Alignment explanation
Indices: 1667427--1667599 Score: 312
Period size: 95 Copynumber: 1.8 Consensus size: 96
1667417 ATGCTTTCAG
* *
1667427 CCATGCAAGAGCTCTTAACTTTGTAATAAAAAACAAATCCTTCATACTTGCAGATTTTCCTTCGA
1 CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
1667492 AAATTATATCATTTCTTATCAACTAGATACT
66 AAATTATATCATTTCTTATCAACTAGATACT
*
1667523 CCATGCAAAAGCTCTTAACTTTTTAAT-AAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
1 CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
1667587 AAATTATATCATT
66 AAATTATATCATT
1667600 GATACTCCAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 49 0.66
96 25 0.34
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (96 bp):
CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
AAATTATATCATTTCTTATCAACTAGATACT
Found at i:1669942 original size:18 final size:19
Alignment explanation
Indices: 1669918--1669964 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
1669908 GATTACGATT
1669918 TCATTTTGAAAAAATTGGA
1 TCATTTTGAAAAAATTGGA
1669937 -CATTTTGAAAAAATTGGA
1 TCATTTTGAAAAAATTGGA
*
1669955 TGATTTTGAA
1 TCATTTTGAA
1669965 TTGATTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (19 bp):
TCATTTTGAAAAAATTGGA
Found at i:1672695 original size:3 final size:3
Alignment explanation
Indices: 1672682--1672735 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
1672672 ATATATGTAC
*
1672682 ATA ATTA ATA ATA ATA A-A CAAA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA
1672729 ATA ATA A
1 ATA ATA A
1672736 AAAGACCCGG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
2 1 0.02
3 38 0.83
4 7 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1673000 original size:40 final size:40
Alignment explanation
Indices: 1672882--1673003 Score: 113
Period size: 40 Copynumber: 3.0 Consensus size: 40
1672872 TTGGTTGTTG
*
1672882 GGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCGTCTAA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCT-G--GTC-AA
* ** * * **
1672926 AGG-TGACAAGGTTTC-TACATGATGAGGAAATCTGGTCAA
1 GGGATGACACTG-CTCATACATGATGAAGAGTTCTGGTCAA
1672965 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCA
1673004 TCTTTAGGAG
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
39 6 0.10
40 29 0.48
42 1 0.02
43 20 0.33
44 4 0.07
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAA
Found at i:1673167 original size:133 final size:134
Alignment explanation
Indices: 1672940--1673278 Score: 475
Period size: 133 Copynumber: 2.5 Consensus size: 134
1672930 GACAAGGTTT
* * * *
1672940 CTACATGATGAGGAAATCTGGTCAAGGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
*
1673005 CTTTAGGAGGAGTGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTA-GGATGACACG
66 CTTTAGGAGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACACG
1673069 GCTC
131 GCTC
* * *
1673073 CTACGTGATGAGGAGGTCTGGTCAGGGGATGGCACTGCTCATACGTGATGAAGAGTTCTGGCCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
* * * *
1673138 CTTTAGGTAGG-GAGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACAT
66 CTTTAGG-AGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACAC
1673202 GGCTC
130 GGCTC
* * * * * * *
1673207 CTACATGATGAGGAGATCTGGTCAGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
*
1673272 CTCTAGG
66 CTTTAGG
1673279 GATAATGGTT
Statistics
Matches: 181, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
133 105 0.58
134 76 0.42
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
CTTTAGGAGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACACG
GCTC
Found at i:1673641 original size:66 final size:62
Alignment explanation
Indices: 1673458--1673634 Score: 185
Period size: 66 Copynumber: 2.8 Consensus size: 62
1673448 CAAAAGCAAC
* * * * **
1673458 TGTCTCAAAAGAGACAAAATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAGGGAAT
1 TGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAGGGAAT
** ** * *
1673519 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGTGTTTCATGGGAA
1 TGTCTCAAAAGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGTGTTT-A-GGG-A
1673584 AT
61 AT
*
1673586 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1673635 TTTGTTTTGT
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
61 17 0.18
62 13 0.14
63 8 0.09
64 5 0.05
65 2 0.02
66 28 0.30
67 20 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (62 bp):
TGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAGGGAAT
Found at i:1673966 original size:15 final size:15
Alignment explanation
Indices: 1673948--1673976 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1673938 TTGTTTTAAG
1673948 AGAAAATGTTTCAAT
1 AGAAAATGTTTCAAT
1673963 AGAAAATGTTTCAA
1 AGAAAATGTTTCAA
1673977 GTGAAACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (15 bp):
AGAAAATGTTTCAAT
Found at i:1673982 original size:15 final size:15
Alignment explanation
Indices: 1673939--1673982 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1673929 AAGATGATCT
* *
1673939 TGTTTTAAGAGAAAA
1 TGTTTCAAGTGAAAA
1673954 TGTTTCAA-TAGAAAA
1 TGTTTCAAGT-GAAAA
1673969 TGTTTCAAGTGAAA
1 TGTTTCAAGTGAAA
1673983 CGACTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 24 0.96
16 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (15 bp):
TGTTTCAAGTGAAAA
Found at i:1674174 original size:64 final size:65
Alignment explanation
Indices: 1674104--1674225 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 65
1674094 GGGTAGTTTT
*
1674104 AAAAGAAATTGTCTC-GAGAGACAAAATTTTATTT-CAAAGGAAACAAACTCAAAGATTTTTTCT
1 AAAAGAAATTGTCTCAGAGAGACAAAAATTTATTTCCAAA-GAAACAAACTCAAAGATTTTTTCT
1674167 C
65 C
* * *
1674168 AAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTCCAAAGAAATATACTCAAAGAT
1 AAAAGAAATTGTCTC-AGAGAGACAAAAATTTATTTCCAAAGAAACAAACTCAAAGAT
1674226 GGATTACATC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
64 15 0.29
66 32 0.63
67 4 0.08
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (65 bp):
AAAAGAAATTGTCTCAGAGAGACAAAAATTTATTTCCAAAGAAACAAACTCAAAGATTTTTTCTC
Found at i:1674317 original size:118 final size:119
Alignment explanation
Indices: 1674129--1674344 Score: 303
Period size: 118 Copynumber: 1.8 Consensus size: 119
1674119 GAGAGACAAA
*
1674129 ATTTTATTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAA
1 ATTTTATTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCTCAAGAGAGACAA
*
1674194 AAATTTGTTTCCAAAGAAATATACTCAAAGATGGATTACATCTTAAGTGAGACG
66 AAATTTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACG
* * * **
1674248 ATTTT-TTTCAAAGGAGACAATCTCAAAGGTTGGTTTT-TCATTAGAAACTGTCTCAAGAGAGAC
1 ATTTTATTTCAAAGGAAACAAACTCAAAGATT--TTTTCTCAAAAGAAACTGTCTCAAGAGAGAC
* **
1674311 -ACAATTTGTTTTTAAAGAAATAAACTCAAAGATG
64 AAAAATTTGTTTCCAAAGAAATAAACTCAAAGATG
1674345 ATTTTGTTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
118 53 0.62
119 28 0.33
120 4 0.05
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (119 bp):
ATTTTATTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCTCAAGAGAGACAA
AAATTTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACG
Found at i:1674455 original size:27 final size:27
Alignment explanation
Indices: 1674319--1674455 Score: 94
Period size: 27 Copynumber: 5.2 Consensus size: 27
1674309 ACACAATTTG
* *
1674319 TTTTTAA-AGAAATAAACTCAAAGATGAT
1 TTTTTAAGAGAAACAGACTCAAAGAT--T
1674347 TTTGTTAAGAGAAACAGACTCAAAGATT
1 TTT-TTAAGAGAAACAGACTCAAAGATT
*** *
1674375 TTTTTTTTATG-AACAGACTCAAAAATT
1 TTTTTAAGA-GAAACAGACTCAAAGATT
1674402 TGTTTTAAGAG----AGA--CAAA-ATT
1 T-TTTTAAGAGAAACAGACTCAAAGATT
*
1674423 CATTTTAAGAGAAACAGACTCAAAGATT
1 -TTTTTAAGAGAAACAGACTCAAAGATT
1674451 TTTTT
1 TTTTT
1674456 CTCAAAAGAA
Statistics
Matches: 86, Mismatches: 11, Indels: 25
0.70 0.09 0.20
Matches are distributed among these distances:
21 12 0.14
22 4 0.05
24 3 0.03
25 3 0.03
27 28 0.33
28 16 0.19
29 4 0.05
30 16 0.19
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (27 bp):
TTTTTAAGAGAAACAGACTCAAAGATT
Found at i:1674518 original size:28 final size:27
Alignment explanation
Indices: 1674482--1674590 Score: 87
Period size: 28 Copynumber: 3.8 Consensus size: 27
1674472 TCAAGAGAGA
* *
1674482 CAAAAATTTGTTTCCAAAGAAATAGACT
1 CAAAGATTTGTTTCAAAAGAAATA-ACT
1674510 CAAAGATTTG-TTCAAAAAAAAGAAATAACT
1 CAAAGATTTGTTTC----AAAAGAAATAACT
* *
1674540 CAAAGATTTTTATTTAAAAGGAACA-AACT
1 CAAAGATTTGT-TTCAAAA-GAA-ATAACT
*
1674569 CAAAGATTTGTTTCAAGAGAAA
1 CAAAGATTTGTTTCAAAAGAAA
1674591 CTGTCTCGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
26 1 0.02
27 6 0.09
28 18 0.27
29 17 0.26
30 13 0.20
31 9 0.14
32 2 0.03
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.28
Consensus pattern (27 bp):
CAAAGATTTGTTTCAAAAGAAATAACT
Found at i:1674983 original size:103 final size:103
Alignment explanation
Indices: 1674813--1675054 Score: 360
Period size: 103 Copynumber: 2.3 Consensus size: 103
1674803 ATTATGAATG
*
1674813 AAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAGAAACAACAATCTCAATTGAGATTAATATT
1 AAAATGTCTCAAGCGAGATG-AATTTGTTTT--AAGAAACAACAATCTCAAGTGAGATTAATATT
* *
1674878 GTTTTAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGG-A
63 GTTTCAAGTGAAGCAAATTCAAAATTTGTATATCAAAGGAA
* *
1674918 AAAATGTCTAAAGCGAGATGAAGTTTGTTTTAAGAAACAACAATCTCAAGTGAGATTAATTTTGT
1 AAAATGTCTCAAGCGAGATGAA-TTTGTTTTAAGAAACAACAATCTCAAGTGAGATTAATATTGT
* *
1674983 TTCAAGTGAAGCAAATTCGAAATTTGTATATGAAAGGAA
65 TTCAAGTGAAGCAAATTCAAAATTTGTATATCAAAGGAA
*
1675022 AAAATGTCTCAAGCGAGACGCAATTTGTTTTAA
1 AAAATGTCTCAAGCGAGATG-AATTTGTTTTAA
1675055 ATTTCTCAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
103 65 0.52
104 31 0.25
105 29 0.23
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (103 bp):
AAAATGTCTCAAGCGAGATGAATTTGTTTTAAGAAACAACAATCTCAAGTGAGATTAATATTGTT
TCAAGTGAAGCAAATTCAAAATTTGTATATCAAAGGAA
Found at i:1675511 original size:4 final size:4
Alignment explanation
Indices: 1675494--1675558 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
1675484 TTTCATGTGT
* *
1675494 TATG TATA TATG TATG TATG TATGGG T-TG -ATG TATG TTTG TATG TATG
1 TATG TATG TATG TATG TATG TAT--G TATG TATG TATG TATG TATG TATG
1675542 TATG TAT- TGATG TATG T
1 TATG TATG T-ATG TATG T
1675559 TTTCTTGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 4 0.08
4 43 0.84
5 2 0.04
6 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1675535 original size:28 final size:28
Alignment explanation
Indices: 1675495--1675560 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
1675485 TTCATGTGTT
* * *
1675495 ATGTATATATGTATGTATGTATGGGTTG
1 ATGTATGTTTGTATGTATGTATGGATTG
*
1675523 ATGTATGTTTGTATGTATGTATGTATTG
1 ATGTATGTTTGTATGTATGTATGGATTG
1675551 ATGTATGTTT
1 ATGTATGTTT
1675561 TCTTGATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (28 bp):
ATGTATGTTTGTATGTATGTATGGATTG
Found at i:1676653 original size:42 final size:42
Alignment explanation
Indices: 1676564--1676662 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
1676554 AGTCAGGAGA
1676564 CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
1 CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
* * * * *
1676606 TTCTTTGT-TGTTGTTTTTTTTCCTTTGTTTTTTTCTTTG-TTT
1 CTCTTTGTCTG-TGTTCTTTGTCCTCT-TTTTGTTCTTTGCTTT
* *
1676648 CTCTTTTTCTTTGTT
1 CTCTTTGTCTGTGTT
1676663 TTAATTGGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 32 0.70
43 12 0.26
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (42 bp):
CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
Found at i:1676655 original size:32 final size:30
Alignment explanation
Indices: 1676577--1676655 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
1676567 TTTGTCTGTG
*
1676577 TTCTTTG-TCCTCTTTTTGTTCTTTGCTTT
1 TTCTTTGTTTCTCTTTTTGTTCTTTGCTTT
* * *
1676606 TTCTTTGTTGT-TGTTTTTTTTCCTTTGTTTTT
1 TTCTTTGTT-TCTCTTTTTGTT-CTTTG-CTTT
1676638 TTCTTTGTTTCTCTTTTT
1 TTCTTTGTTTCTCTTTTT
1676656 CTTTGTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 6 0.15
32 18 0.45
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (30 bp):
TTCTTTGTTTCTCTTTTTGTTCTTTGCTTT
Found at i:1677364 original size:46 final size:45
Alignment explanation
Indices: 1677272--1677365 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
1677262 ATAAATGCAG
* * * *
1677272 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
1677317 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
1677363 TGT
1 TGT
1677366 CAAAATTTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:1682501 original size:3 final size:3
Alignment explanation
Indices: 1682488--1682538 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
1682478 TATATGTAAC
*
1682488 ATA ATTA ATA ATA ATA ATA A-A CAAA ATA ATA ATAA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A ATA ATA ATA ATA
1682535 ATA A
1 ATA A
1682539 AAAGACCCGG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
2 1 0.02
3 35 0.81
4 7 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1683485 original size:2 final size:2
Alignment explanation
Indices: 1683478--1683509 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1683468 TGTAGTAAGA
1683478 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
1683510 GAAATTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1684206 original size:35 final size:35
Alignment explanation
Indices: 1684160--1684235 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
1684150 CATAAACAAT
*
1684160 TTCCTGGTTGGTCATGGGTGACTAGCGCCAGTATA
1 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
1684195 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
1 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
1684230 TTCCTG
1 TTCCTG
1684236 CAAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (35 bp):
TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
Found at i:1686670 original size:13 final size:13
Alignment explanation
Indices: 1686654--1686680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1686644 TATCTAGTTG
1686654 ACATGTATATTAA
1 ACATGTATATTAA
1686667 ACATGTATATTAA
1 ACATGTATATTAA
1686680 A
1 A
1686681 TATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ACATGTATATTAA
Found at i:1687062 original size:16 final size:16
Alignment explanation
Indices: 1687041--1687071 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1687031 TCTAGTTTTT
1687041 CCGAGTACCCGGTTAC
1 CCGAGTACCCGGTTAC
1687057 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
1687072 GTTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:1687289 original size:15 final size:15
Alignment explanation
Indices: 1687269--1687325 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1687259 AATCAGGTAT
1687269 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
** *
1687284 CGGGTACCCGCAAAATT
1 CGGGTACCCG-ATTA-C
1687301 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
1687316 CGGGTACCCG
1 CGGGTACCCG
1687326 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1687337 original size:17 final size:16
Alignment explanation
Indices: 1687269--1687337 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
1687259 AATCAGGTAT
**
1687269 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
1687284 CGGGTACCCGCAAAATT
1 CGGGTACCCG-AAAATC
**
1687301 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
1687316 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
1687333 CGGGT
1 CGGGT
1687338 CGGGACACAG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:1687337 original size:32 final size:32
Alignment explanation
Indices: 1687269--1687337 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1687259 AATCAGGTAT
*
1687269 CGGGTACCCGATTACCGGGTACCCGCAAAATT
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
1687301 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1687333 CGGGT
1 CGGGT
1687338 CGGGACACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:1687395 original size:15 final size:16
Alignment explanation
Indices: 1687363--1687417 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
1687353 GAAATCGTCG
*
1687363 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
1687380 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
1687395 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
1687411 ACCCGGA
1 ACCCGGA
1687418 TTTGCACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 12 0.35
17 8 0.24
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:1688012 original size:15 final size:15
Alignment explanation
Indices: 1687992--1688024 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1687982 GGTGAATTAT
*
1687992 TTTGAATTTAAATAA
1 TTTGAATTTAAACAA
1688007 TTTGAATTTAAACAA
1 TTTGAATTTAAACAA
1688022 TTT
1 TTT
1688025 CAATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTGAATTTAAACAA
Found at i:1688448 original size:77 final size:76
Alignment explanation
Indices: 1688281--1688537 Score: 313
Period size: 77 Copynumber: 3.4 Consensus size: 76
1688271 TTGTGAGTAA
* * * *
1688281 CCATTTTATTAATAAAAATATTAGCATTCTAGATCGTAATTTA-TTATTAGTGAATCATGATATT
1 CCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGATATT
*
1688345 CTTAGGTGCAAC
66 CTTA-GCGCAAC
* * * *
1688357 CCATTTTATGAATAAATATATTAACATTCAAGATCGTAACTTATTTCTTAGTGAACCATGACATT
1 CCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGATATT
*
1688422 CTTGAGCGCTAC
66 CTT-AGCGCAAC
* * * * *
1688434 CCATTTTGTTAATAAAAATATTAACATTCCAGATAGCAATTTATTTCTTACTGAACCATGATATT
1 CCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGATATT
* *
1688499 CTTAAGCACAAT
66 CTT-AGCGCAAC
1688511 CCATTTTATT-A-AAAAATATTAACATTC
1 CCATTTTATTAATAAAAATATTAACATTC
1688538 CAAATTACAA
Statistics
Matches: 155, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
75 16 0.10
76 39 0.25
77 99 0.64
78 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (76 bp):
CCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGATATT
CTTAGCGCAAC
Found at i:1688602 original size:2 final size:2
Alignment explanation
Indices: 1688595--1688640 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1688585 CCGTACTTCT
1688595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1688637 -A TA T
1 TA TA T
1688641 TTTCAATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1688861 original size:76 final size:76
Alignment explanation
Indices: 1688725--1688874 Score: 176
Period size: 76 Copynumber: 2.0 Consensus size: 76
1688715 TATAACTCAT
** * * * * *
1688725 TTTATTATTAAAAATATTAAGATTCTAGATCGCAATCTATTTATTAGTGAACCACGACATTCTTG
1 TTTATTAAAAAAAATATTAACATTCTAGATCACAACCTATTTATTAGTGAACCACAACATTATTG
*
1688790 GGCGCAACCTA
66 GACGCAACCTA
* ***
1688801 TTTATTAAAAAAAATATTAACATTAC-ATATCACAACCTATTTATTAGTGAACTGTAACATTATT
1 TTTATTAAAAAAAATATTAACATT-CTAGATCACAACCTATTTATTAGTGAACCACAACATTATT
1688865 GGACGCAACC
65 GGACGCAACC
1688875 GTAATTCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 60 0.98
77 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (76 bp):
TTTATTAAAAAAAATATTAACATTCTAGATCACAACCTATTTATTAGTGAACCACAACATTATTG
GACGCAACCTA
Found at i:1688987 original size:258 final size:260
Alignment explanation
Indices: 1688625--1689181 Score: 754
Period size: 258 Copynumber: 2.2 Consensus size: 260
1688615 TATATATATA
* * * *
1688625 TATATATAT-ATAATATTTTCAATTTTTAACTTATTTT-TTATCGTGGTAAAATCCAAAGTTTCA
1 TATATATATCATAACATTTTCAATTTTTAACTTATTTTCTTATCGTCGTAAAATACAAAGTTCCA
* * * *
1688688 CTAACTTAACTTTGATATCATTTTAGGTATAACTCATTTTATTATTAAAAATATTAAGATTCTAG
66 CTAACTTAAATTTGATAACATTTTAGGGATAACTCATTTTATTATT-AAAATATTAAAATTCTAG
* * *
1688753 ATCGCAATCTATTTATTAGTGAACCACGACATTCTTGGGCGCAACCTA-TTTATTAAAAAAAATA
130 ATCGCAACCCATTTATTAGTGAACCACGACATTCTTGGGCACAACCTATTTTATTAAAAAAAATA
* **
1688817 TTAACATTACATATCACAACCTATTTATTAGTGAACTGTAACATTATTGGACGCAACCGTAATTC
195 TTAACATTACAGATCACAACCTATTTATTAGTGAACCATAACATTATTGGACGCAACCGTAATTC
1688882 -
260 T
*
1688882 T-TATATATCATAACATTTTCAATTTTTAACTTATTTTCTTATCGTACG-AAAATACAATGTTCC
1 TATATATATCATAACATTTTCAATTTTTAACTTATTTTCTTATCGT-CGTAAAATACAAAGTTCC
* *
1688945 A-TCAACTTAAATTCTGATAACATTTTAGGCGA-ACCT-ATTTTATTATTAAAATATTAAAATTG
65 ACT-AACTTAAATT-TGATAACATTTTAGG-GATAACTCATTTTATTATTAAAATATTAAAATTC
* * *
1689007 TAGATCTCAACCCATTTATTAGTGAACCATGACATTCTTGGGCACAACCTATTTTATTAATAAAA
127 TAGATCGCAACCCATTTATTAGTGAACCACGACATTCTTGGGCACAACCTATTTTATTAAAAAAA
* * * * * * *
1689072 GTATTAACATTACAGATCGCAACTTATTTCTTAGTGAACCATAATATTATTGGACGTAACCGTAT
192 ATATTAACATTACAGATCACAACCTATTTATTAGTGAACCATAACATTATTGGACGCAACCGTAA
1689137 TTCT
257 TTCT
1689141 TATATATATTCATAACATTTTCAATTTTTAACTTATTTTCT
1 TATATATA-TCATAACATTTTCAATTTTTAACTTATTTTCT
1689182 CACGTGACGT
Statistics
Matches: 263, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
256 7 0.03
257 88 0.33
258 110 0.42
259 19 0.07
260 7 0.03
261 32 0.12
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (260 bp):
TATATATATCATAACATTTTCAATTTTTAACTTATTTTCTTATCGTCGTAAAATACAAAGTTCCA
CTAACTTAAATTTGATAACATTTTAGGGATAACTCATTTTATTATTAAAATATTAAAATTCTAGA
TCGCAACCCATTTATTAGTGAACCACGACATTCTTGGGCACAACCTATTTTATTAAAAAAAATAT
TAACATTACAGATCACAACCTATTTATTAGTGAACCATAACATTATTGGACGCAACCGTAATTCT
Found at i:1698594 original size:22 final size:22
Alignment explanation
Indices: 1698568--1698633 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
1698558 TTAATTTTTA
1698568 TTTAACTAGCAGCGATATTAAT
1 TTTAACTAGCAGCGATATTAAT
1698590 TTTAACTAGCAGCGATATT-AT
1 TTTAACTAGCAGCGATATTAAT
*
1698611 TTTAA-TAACAGCGATATTAAT
1 TTTAACTAGCAGCGATATTAAT
1698632 TT
1 TT
1698634 AACAGGCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 12 0.29
21 11 0.26
22 19 0.45
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTAACTAGCAGCGATATTAAT
Found at i:1700397 original size:16 final size:16
Alignment explanation
Indices: 1700376--1700406 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1700366 ACTATTCACA
*
1700376 GAATAGTGAATTTCGT
1 GAATAGTGAAATTCGT
1700392 GAATAGTGAAATTCG
1 GAATAGTGAAATTCG
1700407 GTCGGCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
GAATAGTGAAATTCGT
Found at i:1711893 original size:19 final size:20
Alignment explanation
Indices: 1711813--1711905 Score: 98
Period size: 21 Copynumber: 4.6 Consensus size: 20
1711803 TTCTAAACTT
**
1711813 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
1711833 AAAACCGCAACACGAAAAATG
1 AAAATCGCAACGCG-AAAATG
** *
1711854 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGCGA-AAATG
1711875 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
1711894 AAAATCGCAACG
1 AAAATCGCAACG
1711906 AGATAATCGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.28
20 13 0.21
21 31 0.51
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1711904 original size:40 final size:40
Alignment explanation
Indices: 1711813--1711908 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
1711803 TTCTAAACTT
1711813 AAAATCGCAAC-ATGAAAATGAAAACCGCAACACGAAAAATG
1 AAAATCGCAACGA-GAAAATGAAAACCGCAACACG-AAAATG
** * *
1711854 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAACCGCAACACGAAAATG
1711894 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
1711909 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 18 0.38
41 11 0.23
42 18 0.38
ACGTcount: A:0.51, C:0.20, G:0.19, T:0.10
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAACCGCAACACGAAAATG
Found at i:1712021 original size:20 final size:19
Alignment explanation
Indices: 1711931--1712029 Score: 126
Period size: 20 Copynumber: 5.1 Consensus size: 19
1711921 GAAACCAAAA
*
1711931 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1711950 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
1711969 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1711988 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
*
1712008 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1712028 TC
1 TC
1712030 AACCAAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.49
20 36 0.51
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1713866 original size:17 final size:17
Alignment explanation
Indices: 1713836--1713868 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1713826 GTTGCTGCCA
1713836 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
1713853 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
1713869 AAGTTAGTAT
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:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:1713909 original size:94 final size:93
Alignment explanation
Indices: 1713722--1714097 Score: 589
Period size: 94 Copynumber: 4.1 Consensus size: 93
1713712 TAGATTGCTT
* *
1713722 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1713783 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
1713812 AGTAAATTTATTTGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1713877 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1713906 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1713971 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
1714000 AGTAAATTTGTTCGTTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
1714065 AGTTGTCTTTGTTTTGTCATTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1714093 AGTAA
1 AGTAA
1714098 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 33 0.12
92 3 0.01
93 28 0.10
94 204 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1714279 original size:52 final size:53
Alignment explanation
Indices: 1714217--1714337 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 53
1714207 GAAACTATAA
1714217 TCGCGTTGCGATTTTCATTTCGCATTGCG-ATTCTCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGTATTCTCTCGTTACGATTTTCATT
* * *
1714269 TCGCGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCG----T-ATTCTCTCGTTACGATTTTCATT
*
1714327 TCGTGTTGCGA
1 TCGCGTTGCGA
1714338 CAGTCATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
52 27 0.46
58 32 0.54
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (53 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGTATTCTCTCGTTACGATTTTCATT
Found at i:1714316 original size:20 final size:19
Alignment explanation
Indices: 1714217--1714337 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
1714207 GAAACTATAA
1714217 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1714236 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1714250 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1714269 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
1714288 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1714307 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
*
1714327 TCGTGTTGCGA
1 TCGCGTTGCGA
1714338 CAGTCATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 8 0.09
16 3 0.04
17 3 0.04
19 53 0.62
20 18 0.21
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.