Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 174 of 770
Found at i:51999264 original size:24 final size:24
Alignment explanation
Indices: 51999165--51999273 Score: 157
Period size: 24 Copynumber: 4.5 Consensus size: 24
51999155 AATCTCAAAT
*
51999165 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
51999189 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATA
*
51999213 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
** *
51999237 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCG-ATTTACTATA
51999261 GCACTATGTGTGC
1 GCACTATGTGTGC
51999274 AACGTTTGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
24 73 0.94
25 5 0.06
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATA
Found at i:52000786 original size:203 final size:203
Alignment explanation
Indices: 52000433--52000803 Score: 706
Period size: 203 Copynumber: 1.8 Consensus size: 203
52000423 TTTCAGGACA
52000433 AAACTGGTTTTCGAGTTTTGGAACTCAAGATATGATTTTTAAAGTGACAGTGACGCAGTTAGCCG
1 AAACTGGTTTTCGAGTTTTGGAACTCAAGATATGATTTTTAAAGTGACAGTGACGCAGTTAGCCG
*
52000498 ACTGCTTGGAAAAATTTTAAAATGGACTGTAAAAGTGAATGGTTTAAGCCGTTAGCCCCTCGTGT
66 ACTGCCTGGAAAAATTTTAAAATGGACTGTAAAAGTGAATGGTTTAAGCCGTTAGCCCCTCGTGT
*
52000563 CCGATTCCGGCAGCGGACTCGGGTACGGGGCGTTACAAGAAGATTGTTTGGCTGAAAGCTAGGAA
131 CCGAATCCGGCAGCGGACTCGGGTACGGGGCGTTACAAGAAGATTGTTTGGCTGAAAGCTAGGAA
52000628 AAATTACG
196 AAATTACG
52000636 AAACTGGTTTTCGAGTTTTGGAACTCAAGATATGATTTTTAAAGTGACAGTGACGCAGTTAGCCG
1 AAACTGGTTTTCGAGTTTTGGAACTCAAGATATGATTTTTAAAGTGACAGTGACGCAGTTAGCCG
*
52000701 ACTGCCTGGAAAAATTTTAAAATGGACTGTAAAAGTGAATGGTTTAAGCCGTTAGCCTCTCGTGT
66 ACTGCCTGGAAAAATTTTAAAATGGACTGTAAAAGTGAATGGTTTAAGCCGTTAGCCCCTCGTGT
*
52000766 CCGAATCCGGCAGTGGACTCGGGTACGGGGCGTTACAA
131 CCGAATCCGGCAGCGGACTCGGGTACGGGGCGTTACAA
52000804 TTTTATTGGT
Statistics
Matches: 164, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
203 164 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (203 bp):
AAACTGGTTTTCGAGTTTTGGAACTCAAGATATGATTTTTAAAGTGACAGTGACGCAGTTAGCCG
ACTGCCTGGAAAAATTTTAAAATGGACTGTAAAAGTGAATGGTTTAAGCCGTTAGCCCCTCGTGT
CCGAATCCGGCAGCGGACTCGGGTACGGGGCGTTACAAGAAGATTGTTTGGCTGAAAGCTAGGAA
AAATTACG
Found at i:52007255 original size:24 final size:24
Alignment explanation
Indices: 52007223--52007307 Score: 118
Period size: 24 Copynumber: 3.5 Consensus size: 24
52007213 AATCTCAAAT
52007223 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATA
*
52007247 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
** *
52007271 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCG-ATTTACTATA
52007295 GCACTATGTGTGC
1 GCACTATGTGTGC
52007308 AACGTTTGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 50 0.91
25 5 0.09
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATA
Found at i:52027987 original size:30 final size:30
Alignment explanation
Indices: 52027953--52028013 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52027943 TCCTTAACTC
52027953 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52027983 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52028013 A
1 A
52028014 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52035452 original size:39 final size:39
Alignment explanation
Indices: 52035335--52035516 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
52035325 TCGTTCAAAC
* * * ** * **
52035335 GCCTTCGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
* * * *
52035374 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
52035414 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52035453 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52035492 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
52035517 CTCGAACATT
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
39 96 0.77
40 28 0.23
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:52040225 original size:40 final size:40
Alignment explanation
Indices: 52040078--52040242 Score: 145
Period size: 40 Copynumber: 4.1 Consensus size: 40
52040068 AATACAACCA
* * *
52040078 GATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGCCCG
1 GATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGCCCG
* ** *
52040118 GATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGCCCG
* * * * *
52040158 GATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 GATATAATCACCAGCACAAATGCCTTCGGGTCTTAGCCCG
** * * *
52040198 GATATAATTTCCAGCATAAATGTCTTCGGGACTTAGCCCG
1 GATATAATCACCAGCACAAATGCCTTCGGGTCTTAGCCCG
52040238 GATAT
1 GATAT
52040243 CATTCAATTG
Statistics
Matches: 101, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
GATATAATCACCAGCACAAATGCCTTCGGGTCTTAGCCCG
Found at i:52042670 original size:47 final size:47
Alignment explanation
Indices: 52042600--52043129 Score: 907
Period size: 47 Copynumber: 11.3 Consensus size: 47
52042590 TCCTTCGGGA
* * * *
52042600 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
52042647 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
52042694 CGTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
52042741 CGTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
52042788 CTTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
52042835 CTTATCACATATATACACATTCACATTCATCGCATTGGCCATTAGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
52042882 CTTATCACATATATACACATTCACATTCCTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
52042929 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
52042976 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
52043023 CTTATCACATATATACATATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
52043070 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
52043117 TTTACCACATATA
1 CTTATCACATATA
52043130 CATATCTTAT
Statistics
Matches: 461, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 461 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
Found at i:52045261 original size:19 final size:19
Alignment explanation
Indices: 52045237--52045273 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52045227 GGATGAACAC
52045237 TTTTCTTCCTTTCTTTTTT
1 TTTTCTTCCTTTCTTTTTT
* *
52045256 TTTTCTTTCTTTGTTTTT
1 TTTTCTTCCTTTCTTTTT
52045274 GTTTCTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTCTTCCTTTCTTTTTT
Found at i:52052013 original size:40 final size:40
Alignment explanation
Indices: 52051864--52052030 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
52051854 CGGAATACAA
* *
52051864 CCGGATATAACCA-CATGCACGAATGCC-TCGGGTCTTAGC
1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGC
* ** *
52051903 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
52051943 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
** * * *
52051983 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
52052023 CCGGATAT
1 CCGGATAT
52052031 CATTCAATTG
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 21 0.20
40 81 0.78
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52053286 original size:20 final size:20
Alignment explanation
Indices: 52053261--52053298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52053251 GGATGAACAC
52053261 TTTTCTTCCTTTCTTTTTTT
1 TTTTCTTCCTTTCTTTTTTT
* *
52053281 TTTTCTTTCTTTGTTTTT
1 TTTTCTTCCTTTCTTTTT
52053299 GTTTCTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTCCTTTCTTTTTTT
Found at i:52053288 original size:16 final size:18
Alignment explanation
Indices: 52053269--52053304 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
52053259 ACTTTTCTTC
52053269 CTTTCTTT-TTTTT-TTT
1 CTTTCTTTGTTTTTGTTT
52053285 CTTTCTTTGTTTTTGTTT
1 CTTTCTTTGTTTTTGTTT
52053303 CT
1 CT
52053305 CTCATGTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (18 bp):
CTTTCTTTGTTTTTGTTT
Found at i:52058385 original size:39 final size:39
Alignment explanation
Indices: 52058330--52058441 Score: 156
Period size: 38 Copynumber: 2.9 Consensus size: 39
52058320 ATGGTAAACC
** *
52058330 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAA-T
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
52058369 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
52058408 CGCACAATTGCC-TCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
52058442 TCGAACATTC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 38 0.58
39 27 0.42
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.22
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:52062976 original size:12 final size:11
Alignment explanation
Indices: 52062953--52062992 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
52062943 CATAAATCAC
52062953 TTTTTTTT--A
1 TTTTTTTTGAA
52062962 TTTTTTTTCGAA
1 TTTTTTTT-GAA
52062974 TTTTTTTTGAA
1 TTTTTTTTGAA
52062985 TTTTTTTT
1 TTTTTTTT
52062993 AACTTGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.29
11 11 0.39
12 9 0.32
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:52063225 original size:14 final size:14
Alignment explanation
Indices: 52063208--52063247 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52063198 CGAATGGAAT
*
52063208 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
52063222 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
52063236 GATACGAACAAA
1 GGTAGGAACAAA
52063248 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:52065764 original size:15 final size:15
Alignment explanation
Indices: 52065744--52065791 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52065734 TCAAAGATGG
52065744 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
52065759 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
52065774 -TTTATGGATATAAA
1 GTTTATGGATATGAA
52065788 GTTT
1 GTTT
52065792 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:52065771 original size:29 final size:29
Alignment explanation
Indices: 52065738--52065797 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
52065728 AAGGATTCAA
* *
52065738 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
52065767 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
52065796 AG
1 AG
52065798 GTTTGGTTAT
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:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:52068200 original size:13 final size:13
Alignment explanation
Indices: 52068182--52068210 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52068172 AATAGTTGTG
52068182 TGTTATTTAATTA
1 TGTTATTTAATTA
52068195 TGTTATTTAATTA
1 TGTTATTTAATTA
52068208 TGT
1 TGT
52068211 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:52069742 original size:14 final size:14
Alignment explanation
Indices: 52069723--52069767 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52069713 AACTCATCTT
*
52069723 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
52069737 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
52069750 AATTTAATTTAATG
1 AGTTTAATTTAATG
52069764 AGTT
1 AGTT
52069768 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:52070776 original size:29 final size:29
Alignment explanation
Indices: 52070744--52070803 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
52070734 ATAACCAAAC
* * *
52070744 CTACAAAAACTTTATATCTATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
52070773 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
52070802 CT
1 CT
52070804 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:52071975 original size:18 final size:18
Alignment explanation
Indices: 52071952--52072001 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
52071942 GAAAGAAAAA
*
52071952 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
52071970 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
52071988 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
52072002 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:52071978 original size:24 final size:24
Alignment explanation
Indices: 52071945--52072021 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
52071935 AAGAAATGAA
52071945 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
52071969 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
52071993 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
52072017 AGAAA
1 AGAAA
52072022 GAATGTGAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:52074480 original size:14 final size:14
Alignment explanation
Indices: 52074461--52074505 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52074451 AACTCATCTT
*
52074461 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
52074475 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
52074488 AATTTAATTTAATG
1 AGTTTAATTTAATG
52074502 AGTT
1 AGTT
52074506 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:52075518 original size:29 final size:29
Alignment explanation
Indices: 52075485--52075544 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
52075475 ATAACCAAAC
* *
52075485 CTACA-AAAACTTTATATCCATAAATCCAT
1 CTACATAAAA-TTCATATCCATAAACCCAT
52075514 CTACATAAAATTCATATCCATAAACCCAT
1 CTACATAAAATTCATATCCATAAACCCAT
52075543 CT
1 CT
52075545 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACATAAAATTCATATCCATAAACCCAT
Found at i:52078183 original size:18 final size:17
Alignment explanation
Indices: 52078156--52078203 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
52078146 AATCTTACAA
* *
52078156 TCTTTCTCTTTTTTGTTT
1 TCTTTTTCTTTTTTG-TG
**
52078174 TCTTTTTCTTTCATGTG
1 TCTTTTTCTTTTTTGTG
52078191 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
52078204 CTATTTCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (17 bp):
TCTTTTTCTTTTTTGTG
Found at i:52080327 original size:19 final size:19
Alignment explanation
Indices: 52080300--52080392 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 19
52080290 TTATTCCAAC
*
52080300 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
52080319 AACTTAATTAACTAACATG
1 AACTTAATTAACTAAGATG
* * * *
52080338 AA--TAATTTATTCCA-A-C
1 AACTTAATTAACT-AAGATG
52080354 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
52080373 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
52080392 A
1 A
52080393 GTAATTTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 2 0.03
17 9 0.16
18 9 0.16
19 38 0.66
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:52080350 original size:54 final size:54
Alignment explanation
Indices: 52080290--52080418 Score: 204
Period size: 54 Copynumber: 2.4 Consensus size: 54
52080280 CATCATTAAA
* *
52080290 TTATTCCAACAACTAAATTAACTAAGATGAACTTAATTAACTAACATGAATAAT
1 TTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
* *
52080344 TTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
* *
52080398 TTATTCTAGCAACTTAATTAA
1 TTATTCCAACAACTTAATTAA
52080419 TTAAACTAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (54 bp):
TTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
Found at i:52081852 original size:17 final size:17
Alignment explanation
Indices: 52081830--52081864 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52081820 GTTCGGGGCA
*
52081830 TAAAAAAAATTTACTTT
1 TAAAAAAAATTTAATTT
*
52081847 TAAAAAAATTTTAATTT
1 TAAAAAAAATTTAATTT
52081864 T
1 T
52081865 CTCACATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAAAAATTTAATTT
Found at i:52083168 original size:54 final size:53
Alignment explanation
Indices: 52083031--52083180 Score: 174
Period size: 53 Copynumber: 2.8 Consensus size: 53
52083021 CTTTCCTTTT
* * ** *
52083031 TAAACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATACTTGCCTTA
1 TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATACTTGCCTTA
* * * * * *
52083084 TGAACTCACCATTGCCATGCCTTTGCATGGTCTTACATGATTTCCTTGCCTTG
1 TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATACTTGCCTTA
* *
52083137 TAAAACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGATAT
1 T-AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATAT
52083181 CCCTTAAACC
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 43 0.54
54 36 0.46
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (53 bp):
TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATACTTGCCTTA
Found at i:52086364 original size:19 final size:19
Alignment explanation
Indices: 52086340--52086432 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
52086330 AATAAATTAC
*
52086340 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
52086359 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * *
52086378 TGC-T-GGAATAAATT-A-T
1 T-CATCTTAGTTAATTAAGT
* *
52086394 TCATGTTAGTAAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
52086413 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
52086432 T
1 T
52086433 GCTGGAATAA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 8 0.14
18 7 0.12
19 38 0.66
20 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:52086391 original size:54 final size:54
Alignment explanation
Indices: 52086314--52086442 Score: 213
Period size: 54 Copynumber: 2.4 Consensus size: 54
52086304 CTTAGTTTAA
* *
52086314 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
* *
52086368 TTAATTAAGTTGCTGGAATAAATTATTCATGTTAGTAAATTAAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
*
52086422 TTAATTTAGTTGCTGGAATAA
1 TTAATTAAGTTGCTGGAATAA
52086443 TCTAATAATG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (54 bp):
TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
Found at i:52086514 original size:9 final size:9
Alignment explanation
Indices: 52086500--52086537 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
52086490 AAGTTAAGTT
52086500 TTTAATATG
1 TTTAATATG
52086509 TTTAATATG
1 TTTAATATG
*
52086518 TTTAAATGTG
1 TTT-AATATG
52086528 TTTAATATG
1 TTTAATATG
52086537 T
1 T
52086538 CTGCTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (9 bp):
TTTAATATG
Found at i:52088618 original size:36 final size:36
Alignment explanation
Indices: 52088541--52088638 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
52088531 GAAAGGAAGC
* * *
52088541 AAGAAAAAGAAATTGAGAGAAGAAAAAAAGAAGTGA
1 AAGAAAAAGAAATAGAAAAAAGAAAAAAAGAAGTGA
* * *
52088577 TAGAAAATGAAATAGAAAAAAGAAAAAGAGACA-TGA
1 AAGAAAAAGAAATAGAAAAAAGAAAAAAAGA-AGTGA
52088613 AAGAAAAAGAAA-ATGAAAAAGAGAAA
1 AAGAAAAAGAAATA-GAAAAA-AGAAA
52088639 GATTGTGAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 1 0.02
36 44 0.86
37 6 0.12
ACGTcount: A:0.69, C:0.01, G:0.21, T:0.08
Consensus pattern (36 bp):
AAGAAAAAGAAATAGAAAAAAGAAAAAAAGAAGTGA
Found at i:52088789 original size:15 final size:14
Alignment explanation
Indices: 52088769--52088813 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
52088759 AGAGAGCCTA
52088769 AAAAAGAAACAAGTG
1 AAAAAGAAA-AAGTG
*
52088784 AAAAAGATGAAAGTG
1 AAAAAGA-AAAAGTG
*
52088799 AACAAGAAAAAGTG
1 AAAAAGAAAAAGTG
52088813 A
1 A
52088814 GGATTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 18 0.69
16 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.22, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAAAGTG
Found at i:52092500 original size:18 final size:17
Alignment explanation
Indices: 52092487--52092560 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 17
52092477 AAAAAGAGTG
52092487 TGAAAGAAAAAAAGAAA
1 TGAAAGAAAAAAAGAAA
* *
52092504 TGAAAGAAAAAGAG-CA
1 TGAAAGAAAAAAAGAAA
52092520 TGAAAGAGAGCAAAAAGAAA
1 TGAAAGA-A--AAAAAGAAA
52092540 GTG--AGAAAAAGAA-AAA
1 -TGAAAGAAAAA-AAGAAA
52092556 TGAAA
1 TGAAA
52092561 TTGAAAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
15 2 0.04
16 14 0.31
17 17 0.38
18 1 0.02
19 8 0.18
20 1 0.02
21 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.07
Consensus pattern (17 bp):
TGAAAGAAAAAAAGAAA
Found at i:52092513 original size:15 final size:16
Alignment explanation
Indices: 52092476--52092526 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
52092466 TAATAAAATC
**
52092476 GAAAAAGAGTGTGAAA
1 GAAAAAGAGAATGAAA
*
52092492 GAAAAAAAGAAATGAAA
1 GAAAAAGAG-AATGAAA
*
52092509 GAAAAAGAGCATGAAA
1 GAAAAAGAGAATGAAA
52092525 GA
1 GA
52092527 GAGCAAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (16 bp):
GAAAAAGAGAATGAAA
Found at i:52092514 original size:33 final size:34
Alignment explanation
Indices: 52092476--52092551 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 34
52092466 TAATAAAATC
**
52092476 GAAAAAGAGTGTGAAAGA-A-AAAAAGAAA-TGAAA
1 GAAAAAGAGCATGAAAGAGACAAAAAGAAAGTG--A
52092509 GAAAAAGAGCATGAAAGAGAGCAAAAAGAAAGTGA
1 GAAAAAGAGCATGAAAGAGA-CAAAAAGAAAGTGA
52092544 GAAAAAGA
1 GAAAAAGA
52092552 AAAATGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 16 0.43
34 1 0.03
35 9 0.24
36 9 0.24
37 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.26, T:0.07
Consensus pattern (34 bp):
GAAAAAGAGCATGAAAGAGACAAAAAGAAAGTGA
Found at i:52092550 original size:14 final size:15
Alignment explanation
Indices: 52092521--52092553 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52092511 AAAAGAGCAT
52092521 GAAAGAGAGCAAAAA
1 GAAAGAGAGCAAAAA
*
52092536 GAAAGTGAG-AAAAA
1 GAAAGAGAGCAAAAA
52092550 GAAA
1 GAAA
52092554 AATGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.27, T:0.03
Consensus pattern (15 bp):
GAAAGAGAGCAAAAA
Found at i:52094431 original size:30 final size:31
Alignment explanation
Indices: 52094397--52094493 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
52094387 AGCTCACTCC
*
52094397 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
52094427 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
52094457 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
52094487 TAGCTCA
1 TAGCTCA
52094494 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:52104322 original size:19 final size:18
Alignment explanation
Indices: 52104282--52104340 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
52104272 TATCATTAAG
* *
52104282 TGTTTAATGTGTTTTATG
1 TGTTTAATGTGTTTAATA
52104300 TGTTTAAATGTGTTTAATA
1 TGTTT-AATGTGTTTAATA
52104319 TG-TT--TGT-TTTAATA
1 TGTTTAATGTGTTTAATA
52104333 TGTTTAAT
1 TGTTTAAT
52104341 TTCAGGTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 9 0.26
15 5 0.14
17 1 0.03
18 7 0.20
19 13 0.37
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (18 bp):
TGTTTAATGTGTTTAATA
Found at i:52104340 original size:9 final size:9
Alignment explanation
Indices: 52104277--52104323 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
52104267 GTTCGTATCA
52104277 TTAA-GTGT
1 TTAATGTGT
52104285 TTAATGTGT
1 TTAATGTGT
*
52104294 TTTATGTGT
1 TTAATGTGT
52104303 TTAAATGTGT
1 TT-AATGTGT
*
52104313 TTAATATGT
1 TTAATGTGT
52104322 TT
1 TT
52104324 GTTTTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 4 0.12
9 22 0.65
10 8 0.24
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.57
Consensus pattern (9 bp):
TTAATGTGT
Found at i:52108777 original size:20 final size:18
Alignment explanation
Indices: 52108752--52108809 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
52108742 AATGGAATTG
52108752 AGCTCAAACGAGCTGGAGTA
1 AGCTCAAA-GAGCTGGAG-A
* *
52108772 AGCTCAAGTGAGCTGAACGA
1 AGCTCAA-AGAGCTGGA-GA
*
52108792 AGCTCAGAGAGCTGGAGA
1 AGCTCAAAGAGCTGGAGA
52108810 TGAGTTGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.06
19 7 0.23
20 21 0.68
21 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.33, T:0.14
Consensus pattern (18 bp):
AGCTCAAAGAGCTGGAGA
Found at i:52111906 original size:12 final size:12
Alignment explanation
Indices: 52111898--52111922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52111888 TTTGAAAAGC
52111898 AAAAAGAAAATG
1 AAAAAGAAAATG
52111910 AAAAAGAAAATG
1 AAAAAGAAAATG
52111922 A
1 A
52111923 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:52111919 original size:18 final size:18
Alignment explanation
Indices: 52111892--52111948 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
52111882 AAAGCCTTTG
*
52111892 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
52111911 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
52111929 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
52111946 AAA
1 AAA
52111949 TCGAGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 5 0.16
18 22 0.69
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:52111932 original size:30 final size:30
Alignment explanation
Indices: 52111898--52111954 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
52111888 TTTGAAAAGC
52111898 AAAAAGAAAATGAAAAAGAAAAT-GAGATTG
1 AAAAAGAAAATG-AAAAGAAAATCGAGATTG
*
52111928 AAAAAGAGAATGAAAAGAAAATCGAGA
1 AAAAAGAAAATGAAAAGAAAATCGAGA
52111955 AAATGAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAGAAAATCGAGATTG
Found at i:52115093 original size:24 final size:24
Alignment explanation
Indices: 52115050--52115096 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
52115040 CTACTTTGAC
** *
52115050 TTCATTAATTTTTTATTTAATAAG
1 TTCATTAATTAGTTAATTAATAAG
52115074 TTCATTAATTAGTTAATTAATAA
1 TTCATTAATTAGTTAATTAATAA
52115097 ACCACATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TTCATTAATTAGTTAATTAATAAG
Found at i:52118073 original size:30 final size:30
Alignment explanation
Indices: 52118039--52118135 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
52118029 TAAACTAAAA
52118039 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
52118069 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
52118099 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
52118129 TGAGCTA
1 TGAGCTA
52118136 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:52118761 original size:18 final size:19
Alignment explanation
Indices: 52118740--52118802 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
52118730 ATACTCACTC
52118740 TCTTTTTCAATTTTC-TTT
1 TCTTTTTCAATTTTCTTTT
**
52118758 TCTTGATCAA-TTTCTTTT
1 TCTTTTTCAATTTTCTTTT
52118776 TCTTTTTCAA-TTTCGTTTT
1 TCTTTTTCAATTTTC-TTTT
*
52118795 TATTTTTC
1 TCTTTTTC
52118803 TCACTTTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
17 4 0.11
18 23 0.61
19 11 0.29
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (19 bp):
TCTTTTTCAATTTTCTTTT
Found at i:52120210 original size:11 final size:9
Alignment explanation
Indices: 52120172--52120197 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52120162 GAAGAAGAAA
52120172 TCAAAAAAT
1 TCAAAAAAT
52120181 TCAAAAAAT
1 TCAAAAAAT
52120190 TCAAAAAA
1 TCAAAAAA
52120198 AATTCATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
TCAAAAAAT
Found at i:52121187 original size:18 final size:17
Alignment explanation
Indices: 52121162--52121207 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
52121152 TCATCTTGTA
52121162 AAGAAAAAGAGAT-TGAG
1 AAGAAAAAGA-ATGTGAG
*
52121179 AGTGAAAAAGAATGTGAG
1 A-AGAAAAAGAATGTGAG
52121197 AAGAAAAAGAA
1 AAGAAAAAGAA
52121208 AATTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (17 bp):
AAGAAAAAGAATGTGAG
Found at i:52123075 original size:19 final size:19
Alignment explanation
Indices: 52123051--52123087 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52123041 TACTACAGCA
52123051 ATTTAAGTTGTCTTAGTTC
1 ATTTAAGTTGTCTTAGTTC
*
52123070 ATTTAATTTGTCTTAGTT
1 ATTTAAGTTGTCTTAGTT
52123088 TAATGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (19 bp):
ATTTAAGTTGTCTTAGTTC
Found at i:52125855 original size:27 final size:26
Alignment explanation
Indices: 52125811--52125862 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
52125801 CTCGCTGCAA
*
52125811 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
52125838 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
52125863 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:52130144 original size:30 final size:30
Alignment explanation
Indices: 52130110--52130170 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52130100 TCCTTAACTC
52130110 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52130140 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52130170 A
1 A
52130171 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52134567 original size:30 final size:30
Alignment explanation
Indices: 52134533--52134593 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52134523 TCCTTAACTC
52134533 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52134563 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52134593 A
1 A
52134594 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52150282 original size:53 final size:53
Alignment explanation
Indices: 52150225--52150653 Score: 490
Period size: 53 Copynumber: 8.1 Consensus size: 53
52150215 TGATTTATAA
* * *
52150225 AATTACCGAAATA-CCCTGTAAGGTACAATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATA-CCCTGTAAGGTAG
* * * *
52150278 AATTACCAAAATACCCTTGCAGGGTAGAATTACTAAAATA-CCTAGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCT-GTAAGGTAG
* * *
52150331 AATTACTG-AATACCCCTGTAGAGTAAAATTACTGAAATACCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
* *
52150383 AATTACCGAAATACCCTTGTAGGGTA-AATTATTGAAATACCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
** * * *
52150435 AATTATTGAAATACCCCTATATGGTAGAATTACTGAAATACCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
* * * ** *
52150488 AATTATCGAAATATCCCTGTAAGGTAGAATTACCAAAATACCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
* * *
52150541 AATTACCGAAATACCCCTGTAGGGTAGAATTACCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATA-CCCTGTAAGGTAG
** * * * ** *
52150595 AATTATTGAAATA-CCCTGTAGGGTAGAATTACCGAGATACCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
52150647 AATTACC
1 AATTACC
52150654 ATTTTTCCCC
Statistics
Matches: 327, Mismatches: 43, Indels: 13
0.85 0.11 0.03
Matches are distributed among these distances:
52 106 0.32
53 175 0.54
54 46 0.14
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (53 bp):
AATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
Found at i:52150644 original size:26 final size:27
Alignment explanation
Indices: 52150225--52150653 Score: 448
Period size: 26 Copynumber: 16.3 Consensus size: 27
52150215 TGATTTATAA
* *
52150225 AATTACCGAAATA-CCCTGTAAGGTAC
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
52150251 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
52150278 AATTACCAAAATACCCTTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
52150305 AATTACTAAAATA--CCTAGTAAGGTAG
1 AATTACCGAAATACCCCT-GTAGGGTAG
* * *
52150331 AATTACTG-AATACCCCTGTAGAGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
52150357 AATTACTGAAATA-CCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
52150383 AATTACCGAAATACCCTTGTAGGGTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
52150409 AATTATTGAAATA-CCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
52150435 AATTATTGAAATACCCCTATATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
52150462 AATTACTGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
52150488 AATTATCGAAATATCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
52150515 AATTACCAAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
52150541 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
52150568 AATTACCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
52150595 AATTATTGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
52150621 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
52150647 AATTACC
1 AATTACC
52150654 ATTTTTCCCC
Statistics
Matches: 346, Mismatches: 47, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.05
26 171 0.49
27 159 0.46
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:52151087 original size:25 final size:25
Alignment explanation
Indices: 52151084--52151154 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
52151074 CTATCTGATA
52151084 CTGATTCTGATTTTGATTCTGTTAC
1 CTGATTCTGATTTTGATTCTGTTAC
52151109 CTGATTCTGATTTTGATTCTGTTAC
1 CTGATTCTGATTTTGATTCTGTTAC
*
52151134 CTAATTCTGATTTTGATTCTG
1 CTGATTCTGATTTTGATTCTG
52151155 ATTCTAGTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.52
Consensus pattern (25 bp):
CTGATTCTGATTTTGATTCTGTTAC
Found at i:52151094 original size:31 final size:31
Alignment explanation
Indices: 52151056--52151126 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
52151046 TTGCATTCAC
*
52151056 ATTCTGATTTTGATTCTGCTATCTGATACTG
1 ATTCTGATTTTGATTCTGCTACCTGATACTG
* *
52151087 ATTCTGATTTTGATTCTGTTACCTGATTCTG
1 ATTCTGATTTTGATTCTGCTACCTGATACTG
*
52151118 ATTTTGATT
1 ATTCTGATT
52151127 CTGTTACCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGCTACCTGATACTG
Found at i:52151095 original size:6 final size:6
Alignment explanation
Indices: 52151056--52151168 Score: 88
Period size: 6 Copynumber: 18.3 Consensus size: 6
52151046 TTGCATTCAC
* * * *
52151056 ATTCTG ATTTTG ATTCTG CTATCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
52151105 -TTACCTG ATTCTG ATTTTG ATTCTG -TTACCTA ATTCTG ATTTTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
52151155 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
52151169 AATGTTTCTT
Statistics
Matches: 84, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 5 0.06
6 64 0.76
7 11 0.13
8 4 0.05
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:52151115 original size:13 final size:13
Alignment explanation
Indices: 52151097--52151142 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
52151087 ATTCTGATTT
52151097 TGATTCTGTTACC
1 TGATTCTGTTACC
*
52151110 TGATTCTGATT--T
1 TGATTCTG-TTACC
52151122 TGATTCTGTTACC
1 TGATTCTGTTACC
*
52151135 TAATTCTG
1 TGATTCTG
52151143 ATTTTGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 8 0.30
13 15 0.56
14 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (13 bp):
TGATTCTGTTACC
Found at i:52151144 original size:31 final size:28
Alignment explanation
Indices: 52151056--52151154 Score: 111
Period size: 25 Copynumber: 3.6 Consensus size: 28
52151046 TTGCATTCAC
*
52151056 ATTCTGATTTTGATTCTGCTATCTGATACTG
1 ATTCTGATTTTGATTCTGTTA-CT-AT-CTG
52151087 ATTCTGATTTTGATTCTGTTAC---CTG
1 ATTCTGATTTTGATTCTGTTACTATCTG
*
52151112 ATTCTGATTTTGATTCTGTTAC---CTA
1 ATTCTGATTTTGATTCTGTTACTATCTG
52151137 ATTCTGATTTTGATTCTG
1 ATTCTGATTTTGATTCTG
52151155 ATTCTAGTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
25 45 0.68
30 1 0.02
31 20 0.30
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (28 bp):
ATTCTGATTTTGATTCTGTTACTATCTG
Found at i:52151157 original size:31 final size:30
Alignment explanation
Indices: 52151060--52151159 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
52151050 ATTCACATTC
* * *
52151060 TGATTTTGATTCTGCTATCTGATACTGATT
1 TGATTTTGATTCTGTTACCTGATTCTGATT
52151090 CTGATTTTGATTCTGTTACCTGATTC-----
1 -TGATTTTGATTCTGTTACCTGATTCTGATT
*
52151116 TGATTTTGATTCTGTTACCTAATTCTGATTT
1 TGATTTTGATTCTGTTACCTGATTCTGA-TT
*
52151147 TGATTCTGATTCT
1 TGATTTTGATTCT
52151160 AGTTCTGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
25 24 0.41
31 34 0.59
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (30 bp):
TGATTTTGATTCTGTTACCTGATTCTGATT
Found at i:52154779 original size:28 final size:28
Alignment explanation
Indices: 52154747--52154802 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
52154737 ATAATCTTGA
52154747 TTAGCCACACCAATAGCTAATCATTCTC
1 TTAGCCACACCAATAGCTAATCATTCTC
*
52154775 TTAGCCACTCCAATAGCTAATCATTCTC
1 TTAGCCACACCAATAGCTAATCATTCTC
52154803 AAACATTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.30
Consensus pattern (28 bp):
TTAGCCACACCAATAGCTAATCATTCTC
Found at i:52159719 original size:24 final size:24
Alignment explanation
Indices: 52159669--52159722 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
52159659 AATTGAATTT
*
52159669 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
52159693 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
52159717 GCACAC
1 GCACAC
52159723 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:52165803 original size:16 final size:16
Alignment explanation
Indices: 52165782--52165816 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52165772 GCAAATCTCA
*
52165782 AAATGCCGAAAAGTCG
1 AAATGCCGAAAAGCCG
52165798 AAATGCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
52165814 AAA
1 AAA
52165817 GTTTGGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.09
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:52166082 original size:29 final size:28
Alignment explanation
Indices: 52166050--52166123 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
52166040 TTGGGGGCCG
52166050 ATGGGCCATATGAATGTGATTTAGGCCTA
1 ATGGGCCATATGAATGTGA-TTAGGCCTA
* *
52166079 ATGGGCCATATGAATGAGATTGGGCCTA
1 ATGGGCCATATGAATGTGATTAGGCCTA
* * *
52166107 GTGGACCATATGCATGT
1 ATGGGCCATATGAATGT
52166124 ATGTAGACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (28 bp):
ATGGGCCATATGAATGTGATTAGGCCTA
Found at i:52166115 original size:28 final size:27
Alignment explanation
Indices: 52166029--52166123 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 27
52166019 ATTGCATGAC
*
52166029 TATGAATGTGATTGGGGGCCGATGGGCCA
1 TATGAATGTGATT--GGGCCTATGGGCCA
*
52166058 TATGAATGTGATTTAGGCCTAATGGGCCA
1 TATGAATGTGA-TTGGGCCT-ATGGGCCA
* *
52166087 TATGAATGAGATTGGGCCTAGTGGACCA
1 TATGAATGTGATTGGGCCTA-TGGGCCA
*
52166115 TATGCATGT
1 TATGAATGT
52166124 ATGTAGACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 24 0.43
29 29 0.52
30 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (27 bp):
TATGAATGTGATTGGGCCTATGGGCCA
Found at i:52167896 original size:77 final size:77
Alignment explanation
Indices: 52167769--52167952 Score: 305
Period size: 77 Copynumber: 2.4 Consensus size: 77
52167759 TATAAGATGA
* *
52167769 TATACCGATTTGGCTTCGGACCATGCATATCGGATGAGTTGGCTTCGGGCCATGATATTAGCACT
1 TATACCGATTTGGCTTCGGGCCATGCATATCGAATGAGTTGGCTTCGGGCCATGATATTAGCACT
*
52167834 TCGGGTGTGAGT
66 TCGGGTGTGACT
*
52167846 TATACCGATTTGGCTTCGGGCCATGCATATTGAATGAGTTGGCTTCGGGCCATGATATTAGCACT
1 TATACCGATTTGGCTTCGGGCCATGCATATCGAATGAGTTGGCTTCGGGCCATGATATTAGCACT
52167911 TCGGGTGTGACT
66 TCGGGTGTGACT
** *
52167923 TATACAAATTTGGCTTTGGGCCATGCATAT
1 TATACCGATTTGGCTTCGGGCCATGCATAT
52167953 AGGATGTTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 100 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (77 bp):
TATACCGATTTGGCTTCGGGCCATGCATATCGAATGAGTTGGCTTCGGGCCATGATATTAGCACT
TCGGGTGTGACT
Found at i:52167990 original size:77 final size:77
Alignment explanation
Indices: 52167776--52167977 Score: 296
Period size: 77 Copynumber: 2.6 Consensus size: 77
52167766 TGATATACCG
* *
52167776 ATTTGGCTTCGGACCATGCATATCGGATGAGTTGGCTTCGGGCCATGATATTAGCACTTCGGGTG
1 ATTTGGCTTCGGGCCATGCATATAGGATGAGTTGGCTTCGGGCCATGATATTAGCACTTCGGGTG
* **
52167841 TGAGTTATACCG
66 TGACTTATACAA
* *
52167853 ATTTGGCTTCGGGCCATGCATATTGAATGAGTTGGCTTCGGGCCATGATATTAGCACTTCGGGTG
1 ATTTGGCTTCGGGCCATGCATATAGGATGAGTTGGCTTCGGGCCATGATATTAGCACTTCGGGTG
52167918 TGACTTATACAA
66 TGACTTATACAA
* ** **
52167930 ATTTGGCTTTGGGCCATGCATATAGGATGTTTTGGCTTTAGGCCATGA
1 ATTTGGCTTCGGGCCATGCATATAGGATGAGTTGGCTTCGGGCCATGA
52167978 AAATAGTTCT
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 112 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (77 bp):
ATTTGGCTTCGGGCCATGCATATAGGATGAGTTGGCTTCGGGCCATGATATTAGCACTTCGGGTG
TGACTTATACAA
Found at i:52170499 original size:40 final size:41
Alignment explanation
Indices: 52170411--52170507 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
52170401 TAAATCAGTA
*
52170411 TCGCACACTTAGTGCC-TTCTATAGCCGAAGCTATGCCAAC
1 TCGCACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAAC
* **
52170451 TCGCACACTTAGTGCCATT-TATAGCTGAAGCTATATTAAAC
1 TCGCACACTTAGTGCCATTCTATAGCCGAAGCTAT-GCAAAC
*
52170492 -CGTACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
52170508 ATCATAGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 45 0.90
41 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAAC
Found at i:52177028 original size:43 final size:43
Alignment explanation
Indices: 52176842--52177040 Score: 240
Period size: 43 Copynumber: 4.6 Consensus size: 43
52176832 ATATCATACA
* * **
52176842 ATGCCAACGTCCCAAACATGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
* * * *
52176885 AT-CCCACTGTCCCAAACAG-GGTCTTACTCATAAACACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACATAATCACATATCG
* * *
52176928 ATGCCAACATCCTAGACGTGGTCTTACCCATAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
* *
52176971 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
*
52177014 ATGCCAACGTCCCAGATGTGGTCTTAC
1 ATGCCAACGTCCCAGACGTGGTCTTAC
52177041 TCGCACACTT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.04
43 125 0.93
44 4 0.03
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
Found at i:52184251 original size:65 final size:65
Alignment explanation
Indices: 52184147--52184277 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
52184137 CCTCTAGGGT
*
52184147 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATATTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
*
52184212 TAAGGTTGACCTGAATGCATATTTGACTGTTACTATTTACTGTATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATATTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
52184277 T
1 T
52184278 GCATGGGACT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATATTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
Found at i:52187010 original size:49 final size:48
Alignment explanation
Indices: 52186957--52187277 Score: 477
Period size: 49 Copynumber: 6.7 Consensus size: 48
52186947 GATTCTACAC
* *
52186957 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTAT-AATATGTGATAAGGCCTAATGGCCGATGT
*
52187006 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCGATGT
*
52187055 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCGATGT
*
52187104 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCGATGT
*
52187153 GATGAATGTGAAAGTGTAT-ATATGTGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
* * * * *
52187200 GATGAATGTGAAAGTGTAT-ATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
*
52187247 GATGGATGTGAAAGTGTATAA-ATGTGATAAG
1 GATGAATGTGAAAGTGTATAATATGTGATAAG
52187278 TCCCGAAGGG
Statistics
Matches: 256, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 97 0.38
48 2 0.01
49 157 0.61
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (48 bp):
GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
Found at i:52190767 original size:40 final size:39
Alignment explanation
Indices: 52190712--52190915 Score: 203
Period size: 40 Copynumber: 5.1 Consensus size: 39
52190702 TGAATGAAAC
* * *
52190712 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
* * *
52190752 CCGGGCTAAGACCCGAAGGCATTCGTACGAGTTGTTAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* *
52190792 CCAGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * * *
52190832 CCGGGCTAAGACCTGAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGT--TATAT
* * **
52190872 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
52190912 CCGG
1 CCGG
52190916 TTAGATTCCG
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 132 0.96
41 2 0.01
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:52190850 original size:80 final size:79
Alignment explanation
Indices: 52190715--52190915 Score: 233
Period size: 80 Copynumber: 2.5 Consensus size: 79
52190705 ATGAAACCCG
* *
52190715 GGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGACCCGAAGGCATTCGTA
1 GGCTAAGACCCGAAGGCA-TTGTGCTAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTCGTA
* ***
52190779 CGAGTTGTTAAATCCA
64 CAAGTTACCAAATCCA
* * * *
52190795 GGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCTGAAGGCATTTGTGC
1 GGCTAAGACCCGAAGGCATT-GTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTCGTAC
*
52190860 AAGTTACCAAATCCG
65 AAGTTACCAAATCCA
* * *
52190875 GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGG
1 GGCTAAGACCCGAAGGC-ATTGTGCTAGTTGTTATATCCGG
52190916 TTAGATTCCG
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
79 2 0.02
80 96 0.93
81 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
GGCTAAGACCCGAAGGCATTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTCGTACA
AGTTACCAAATCCA
Found at i:52193948 original size:68 final size:67
Alignment explanation
Indices: 52193876--52194025 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
52193866 CATCATGTGT
* * * *
52193876 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
52193938 ATGTAG
62 ATGTAG
** * *
52193944 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
52194009 AG
66 AG
52194011 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
52194026 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:52193981 original size:64 final size:64
Alignment explanation
Indices: 52193900--52194083 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
52193890 AGACATTATG
* *
52193900 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
52193964 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
52194029 AA
63 AA
* * * *
52194031 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
52194084 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:52196921 original size:63 final size:64
Alignment explanation
Indices: 52196740--52196922 Score: 203
Period size: 63 Copynumber: 2.8 Consensus size: 64
52196730 ATATAGTTCG
* * * *
52196740 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACA-TATATCCCGT
52196802 A
64 A
* * * *
52196803 GCTCTCTTGTCTACATGGTGTCCTTCACTTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCG
52196868 TA
63 TA
* *
52196870 GCT-TCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACAT
52196923 CATAATGTCT
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 46 0.46
66 39 0.39
67 12 0.12
68 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:52197688 original size:30 final size:30
Alignment explanation
Indices: 52197654--52197714 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52197644 TCCTTAACTC
52197654 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52197684 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52197714 A
1 A
52197715 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52214802 original size:15 final size:17
Alignment explanation
Indices: 52214782--52214821 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
52214772 GAGAGACGAA
52214782 AAAAAGAAAT-G-AAAG
1 AAAAAGAAATCGAAAAG
52214797 AAAAAGAAATCGAAAAAG
1 AAAAAGAAATCG-AAAAG
52214815 AAAAAGA
1 AAAAAGA
52214822 GAGTGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 1 0.05
18 11 0.50
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAGAAATCGAAAAG
Found at i:52216791 original size:27 final size:27
Alignment explanation
Indices: 52216761--52216848 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
52216751 TAAAATAATC
52216761 ATTTTACCCTATAGGGGTATTTCAGTA
1 ATTTTACCCTATAGGGGTATTTCAGTA
* * *
52216788 ATTTTACACTACAAGGGTATTTC-GATA
1 ATTTTACCCTATAGGGGTATTTCAG-TA
**
52216815 ATTTTA-CAAACT-GAGGGTATTTCAGTA
1 ATTTTACCCTA-TAG-GGGTATTTCAGTA
52216842 ATTTTAC
1 ATTTTAC
52216849 AAGTCGAGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.04
27 45 0.94
28 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATAGGGGTATTTCAGTA
Found at i:52216819 original size:54 final size:54
Alignment explanation
Indices: 52216775--52216931 Score: 173
Period size: 54 Copynumber: 2.9 Consensus size: 54
52216765 TACCCTATAG
52216775 GGGTATTTCAGTAATTTTAC-ACTACAAGGGTATTTCGATAATTTTACAAACTGA
1 GGGTATTTCAGTAATTTTACAACT-CAAGGGTATTTCGATAATTTTACAAACTGA
* * * *
52216829 GGGTATTTCAGTAATTTTACAAGTCGAGGGTATTTCGATAATTTCACAAA-TCA
1 GGGTATTTCAGTAATTTTACAACTCAAGGGTATTTCGATAATTTTACAAACTGA
* *
52216882 GGAGTATGTC-GTTAATTTTACAAC-C-CGGGATATTTC-AGTAATTTTACAAA
1 GG-GTATTTCAG-TAATTTTACAACTCAAGGG-TATTTCGA-TAATTTTACAAA
52216932 TCAGAGGCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
52 4 0.04
53 23 0.26
54 61 0.68
55 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAACTCAAGGGTATTTCGATAATTTTACAAACTGA
Found at i:52216849 original size:27 final size:27
Alignment explanation
Indices: 52216775--52216931 Score: 121
Period size: 27 Copynumber: 5.9 Consensus size: 27
52216765 TACCCTATAG
* *
52216775 GGGTATTTC-AGTAATTTTACACTAC-AA
1 GGGTATTTCGA-TAATTTTACA-AACTGA
52216802 GGGTATTTCGATAATTTTACAAACTGA
1 GGGTATTTCGATAATTTTACAAACTGA
*
52216829 GGGTATTTC-AGTAATTTTAC-AAGTCGA
1 GGGTATTTCGA-TAATTTTACAAACT-GA
* *
52216856 GGGTATTTCGATAATTTCACAAA-TCA
1 GGGTATTTCGATAATTTTACAAACTGA
* * * *
52216882 GGAGTATGTCGTTAATTTTACAACCCG-
1 GG-GTATTTCGATAATTTTACAAACTGA
*
52216909 GGATATTTC-AGTAATTTTACAAA
1 GGGTATTTCGA-TAATTTTACAAA
52216932 TCAGAGGCTT
Statistics
Matches: 106, Mismatches: 15, Indels: 19
0.76 0.11 0.14
Matches are distributed among these distances:
26 25 0.24
27 77 0.73
28 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAACTGA
Found at i:52217144 original size:17 final size:17
Alignment explanation
Indices: 52217122--52217154 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52217112 TATCCGTGTG
52217122 GGCCCAC-GAGCCCATTA
1 GGCCCACTG-GCCCATTA
52217139 GGCCCACTGGCCCATT
1 GGCCCACTGGCCCATT
52217155 TTGACCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.15
Consensus pattern (17 bp):
GGCCCACTGGCCCATTA
Found at i:52226856 original size:17 final size:18
Alignment explanation
Indices: 52226823--52226863 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
52226813 AACGGACTTA
52226823 AACATTTACAACAACACAT
1 AACATTTAC-ACAACACAT
52226842 AACATTTAC-CAACACAT
1 AACATTTACACAACACAT
52226859 AACAT
1 AACAT
52226864 CATCAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (18 bp):
AACATTTACACAACACAT
Found at i:52229741 original size:15 final size:15
Alignment explanation
Indices: 52229718--52229757 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
52229708 CAAGCCTAGA
52229718 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
52229733 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
52229748 ATAAGGAAAT
1 ATAAGGAAAT
52229758 ACCATTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:52231628 original size:40 final size:39
Alignment explanation
Indices: 52231563--52231766 Score: 221
Period size: 40 Copynumber: 5.1 Consensus size: 39
52231553 TTCGGAACAA
* *
52231563 CCGGATATAACCAC-ACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAA-CACTA-GCACAAATGCCTTCGGGTCTTAGC
* * *
52231603 CCGGACATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* *
52231643 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
52231683 CCGGATATAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
52231723 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGC
52231763 CCGG
1 CCGG
52231767 GTATCATTCA
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 139 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52231921 original size:64 final size:64
Alignment explanation
Indices: 52231853--52232041 Score: 142
Period size: 64 Copynumber: 3.0 Consensus size: 64
52231843 GAACACAAAC
52231853 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
* * * * *** * *** * ** * *
52231917 ATATCAATA--ATCATTACACATCCATATTTCATTTTC-GTTA-C--T--AAGGCTCAAACACAA
1 ATATCACTAGCATAATTGC-CTTCGGGACTT-A-GCCCGGGTACCATTCAAATACTCATACACAC
*
52231974 AC
63 AT
52231976 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
52232040 AT
1 AT
52232042 GTCAATAATC
Statistics
Matches: 80, Mismatches: 34, Indels: 22
0.59 0.25 0.16
Matches are distributed among these distances:
58 1 0.01
59 24 0.30
60 7 0.09
61 7 0.09
62 7 0.09
63 7 0.09
64 26 0.32
65 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (64 bp):
ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
Found at i:52231954 original size:123 final size:123
Alignment explanation
Indices: 52231735--52232073 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
52231725 GGATATAATT
* * * * * * *
52231735 ACTAGCATAAATGTCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATAAATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
52231800 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
52231858 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
52231923 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
52231981 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
52232046 ATAATCATTACACATCCATATTTCATTT
66 ATAATCATTACACATCCATATTTCATTT
52232074 CACATAATTC
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (123 bp):
ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:52237668 original size:47 final size:49
Alignment explanation
Indices: 52237553--52237821 Score: 172
Period size: 46 Copynumber: 5.7 Consensus size: 49
52237543 GGGTAAGGTT
* * * *
52237553 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-TCTCATATCTAAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
* * * * *
52237600 TCGATGCCATGCCCCAAACATGGTCTTACACTAACTATCATCTCGTA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
* * * * *
52237648 CCGATG-CATGTCCTAGACAT-GTTTTACACTGGCT-TACGTGTCG-AGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCGAAGG
* * * *
52237694 CCAATG-CATTTCCTAGACAT-GTCTTACACTAGC-ACTCATCTC-AATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTCGAAGG
* ** * * **
52237740 CCAATGCCATGTCCCAGACATGGTCTTACACGGGCTCTC-T-TAGTGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCG-AAGG
*
52237788 CCGATG-CAGGTCCCAGACAT-GTCTTACACTAGCT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
52237822 CACAATAACC
Statistics
Matches: 173, Mismatches: 37, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
45 2 0.01
46 71 0.41
47 67 0.39
48 25 0.14
49 8 0.05
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
Found at i:52244003 original size:20 final size:21
Alignment explanation
Indices: 52243978--52244017 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52243968 CACTTGACAC
52243978 AAGGGC-ACACGCCCATGTGG
1 AAGGGCAACACGCCCATGTGG
*
52243998 AAGGGCAACACGCCCGTGTG
1 AAGGGCAACACGCCCATGTG
52244018 ACCATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (21 bp):
AAGGGCAACACGCCCATGTGG
Found at i:52245250 original size:46 final size:46
Alignment explanation
Indices: 52245184--52245295 Score: 120
Period size: 46 Copynumber: 2.4 Consensus size: 46
52245174 AATGCCTTGC
* * *
52245184 CCCAAACATGGTCTTACACTGAC-TATCATCTCGTA-ACTGATGCATGT
1 CCCAGACAT-GTCTTACACTGACTTA-CATCTCG-AGACCGATGCATCT
* * * *
52245231 CTCAGACATGTCTTACACTGCCTTACGTCTCGAGGCCGATGCATCT
1 CCCAGACATGTCTTACACTGACTTACATCTCGAGACCGATGCATCT
52245277 CCCAGACATGTCTTACACT
1 CCCAGACATGTCTTACACT
52245296 AGCACTCGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 1 0.02
46 45 0.82
47 9 0.16
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (46 bp):
CCCAGACATGTCTTACACTGACTTACATCTCGAGACCGATGCATCT
Found at i:52245306 original size:46 final size:46
Alignment explanation
Indices: 52245222--52245341 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
52245212 TCTCGTAACT
*
52245222 GATGCATGTCTCAGACATGTCTTACACTGCCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGCCTTACGTCTCGAGGCC
* * *
52245268 GATGCATCTCCCAGACATGTCTTACACTAGCAC-T-CGTCTCGATGCT
1 GATGCATGTCCCAGACATGTCTTACACT-GC-CTTACGTCTCGAGGCC
* *
52245314 GATGCCATGTTCCAAACATGGTCTTACA
1 GATG-CATGTCCCAGACAT-GTCTTACA
52245342 TGGGCTCTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
46 40 0.63
47 14 0.22
48 9 0.14
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGCCTTACGTCTCGAGGCC
Found at i:52255389 original size:42 final size:41
Alignment explanation
Indices: 52255342--52255512 Score: 249
Period size: 40 Copynumber: 4.2 Consensus size: 41
52255332 CTCGATATAA
*
52255342 TATATATATATCTGGGTTAAATCCCGCAGGCTTCATGCTGG
1 TATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGG
*
52255383 TA-ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
1 TATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGG
*
52255423 TA-ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
1 TATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGG
**
52255463 TAATATATATATCCGGGTTAAATCCTACAGGCTT-AGTGCTGG
1 T-ATATATATATCCGGGTTAAATCCCGCAGGCTTCA-TGCTGG
52255505 TACTATAT
1 TA-TATAT
52255513 CCGGACTTAG
Statistics
Matches: 121, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
40 77 0.64
41 4 0.03
42 40 0.33
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (41 bp):
TATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGG
Found at i:52255452 original size:80 final size:82
Alignment explanation
Indices: 52255345--52255512 Score: 268
Period size: 82 Copynumber: 2.1 Consensus size: 82
52255335 GATATAATAT
* *
52255345 ATATATATCTGGGTTAAATCCCGCAGGCTTCATGCTGGT-A-ATATATATCCGGGTTAAATCCCG
1 ATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATATATCCGGGTTAAATCCCA
*
52255408 CAGGCTTCGTGCTGGTA
66 CAGGCTTAGTGCTGGTA
* *
52255425 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATATATCCGGGTTAAATCCTA
1 ATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATATATCCGGGTTAAATCCCA
52255490 CAGGCTTAGTGCTGGTA
66 CAGGCTTAGTGCTGGTA
*
52255507 CTATAT
1 ATATAT
52255513 CCGGACTTAG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 37 0.46
81 1 0.01
82 42 0.52
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (82 bp):
ATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATATATCCGGGTTAAATCCCA
CAGGCTTAGTGCTGGTA
Found at i:52262379 original size:2 final size:2
Alignment explanation
Indices: 52262372--52262396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52262362 TCAGCTATGT
52262372 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52262397 TGAAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52263151 original size:40 final size:40
Alignment explanation
Indices: 52263098--52263219 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
52263088 GATATAATAT
* *
52263098 ATATATATCCGGGTTAAATCCCACAGGTTTCGTGCTGGTA
1 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
52263138 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
1 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
* *
52263178 ATATATATCTGGGTTAAATCCTGCAGGCTTCGTGCTGGTA
1 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
52263218 AT
1 AT
52263220 GTAACACCCC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (40 bp):
ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
Found at i:52264320 original size:46 final size:46
Alignment explanation
Indices: 52264252--52264388 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
52264242 TATATATACA
* * * *
52264252 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
52264298 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
52264344 TAACTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
52264389 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:52264422 original size:47 final size:47
Alignment explanation
Indices: 52264362--52264552 Score: 294
Period size: 47 Copynumber: 4.1 Consensus size: 47
52264352 ACACATTTCG
* * * **
52264362 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
52264409 CATTGGCCATTCGGCCTTATCTCA-TTATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
52264455 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
52264502 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
52264549 CATT
1 CATT
52264553 AAAATCCTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
46 43 0.32
47 91 0.68
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:52264464 original size:93 final size:94
Alignment explanation
Indices: 52264362--52264553 Score: 296
Period size: 93 Copynumber: 2.1 Consensus size: 94
52264352 ACACATTTCG
* *
52264362 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
52264427 ATCTCA-TTATGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATTCATCA
* * * *
52264455 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
52264520 ATCACACATACGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATTCATCA
52264549 CATTA
1 CATTA
52264554 AAATCCTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 64 0.73
94 24 0.27
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (94 bp):
CATTAGCCATTCGGCCTTACCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATTCATCA
Found at i:52264504 original size:23 final size:23
Alignment explanation
Indices: 52264477--52264551 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
52264467 GGCCTTATCG
52264477 CACATACGCATGTTCACATTCAT
1 CACATACGCATGTTCACATTCAT
** * *
52264500 CACATTGGCCA--TTCGGCCTT-AT
1 CACATACG-CATGTTC-ACATTCAT
52264522 CACACATACGCATGTTCACATTCAT
1 --CACATACGCATGTTCACATTCAT
52264547 CACAT
1 CACAT
52264552 TAAAATCCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 16 0.43
24 11 0.30
25 5 0.14
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29
Consensus pattern (23 bp):
CACATACGCATGTTCACATTCAT
Found at i:52266624 original size:40 final size:40
Alignment explanation
Indices: 52266580--52266746 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
52266570 CGGAATATAA
*
52266580 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
52266620 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
52266660 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
52266700 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
52266739 CCGGATAT
1 CCGGATAT
52266747 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52268440 original size:13 final size:13
Alignment explanation
Indices: 52268422--52268450 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52268412 CATTCGGGGT
52268422 CACAACTCTCCCC
1 CACAACTCTCCCC
52268435 CACAACTCTCCCC
1 CACAACTCTCCCC
52268448 CAC
1 CAC
52268451 TCAAGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.62, G:0.00, T:0.14
Consensus pattern (13 bp):
CACAACTCTCCCC
Found at i:52276092 original size:12 final size:12
Alignment explanation
Indices: 52276072--52276107 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
52276062 TGGGATATGC
*
52276072 AATGTATGAATG
1 AATGCATGAATG
52276084 AATGCATGAATG
1 AATGCATGAATG
52276096 AATGCATGAATG
1 AATGCATGAATG
52276108 TCAAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:52278135 original size:2 final size:2
Alignment explanation
Indices: 52278076--52278118 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
52278066 GGTATTTAAA
*
52278076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
52278118 A
1 A
52278119 GTATTTAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52278704 original size:37 final size:33
Alignment explanation
Indices: 52278671--52278762 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 33
52278661 GGTTTCTTAG
*
52278671 TTTTTTTTTGGGGGGTTAGGTTTTTCTTTTTTCTTT
1 TTTTTTTTTGGAGGGTTAGG-TTTT-TTTTTTC-TT
**
52278707 TTTCTTTTTTTTAGGGTTAGGTTTTTTTTTTC-T
1 TTT-TTTTTTGGAGGGTTAGGTTTTTTTTTTCTT
52278740 TTTTTTTTT---GGGTTAGGTTTTTT
1 TTTTTTTTTGGAGGGTTAGGTTTTTT
52278763 GGGGGGCTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 14 0.27
32 6 0.12
33 4 0.08
35 7 0.13
36 7 0.13
37 14 0.27
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.72
Consensus pattern (33 bp):
TTTTTTTTTGGAGGGTTAGGTTTTTTTTTTCTT
Found at i:52278707 original size:6 final size:7
Alignment explanation
Indices: 52278691--52278716 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52278681 GGGGGTTAGG
52278691 TTTTTCT
1 TTTTTCT
52278698 TTTTTCT
1 TTTTTCT
52278705 TTTTTCT
1 TTTTTCT
52278712 TTTTT
1 TTTTT
52278717 TTAGGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:52278742 original size:28 final size:29
Alignment explanation
Indices: 52278699--52278762 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
52278689 GGTTTTTCTT
52278699 TTTTCTTTTTTC-TTTTTTTTAGGGTTAGG
1 TTTT-TTTTTTCTTTTTTTTTAGGGTTAGG
*
52278728 TTTTTTTTTTCTTTTTTTTTTGGGTTAGG
1 TTTTTTTTTTCTTTTTTTTTAGGGTTAGG
52278757 TTTTTT
1 TTTTTT
52278763 GGGGGGCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.05, C:0.05, G:0.16, T:0.75
Consensus pattern (29 bp):
TTTTTTTTTTCTTTTTTTTTAGGGTTAGG
Found at i:52282901 original size:22 final size:24
Alignment explanation
Indices: 52282859--52282902 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
52282849 TAACTAAGTT
52282859 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
52282883 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
52282903 TCTTACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:52283657 original size:19 final size:22
Alignment explanation
Indices: 52283617--52283659 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
52283607 TTCATTAATT
52283617 TAATAATATAATATCAATTAAA
1 TAATAATATAATATCAATTAAA
52283639 TAATAATA-AATAT-AA-TAAA
1 TAATAATATAATATCAATTAAA
52283658 TA
1 TA
52283660 TCTATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 5 0.24
22 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAATATAATATCAATTAAA
Found at i:52283869 original size:17 final size:18
Alignment explanation
Indices: 52283849--52283882 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52283839 ATTACAATTG
52283849 TACAAATATA-ATTTTTT
1 TACAAATATATATTTTTT
*
52283866 TACACATATATATTTTT
1 TACAAATATATATTTTT
52283883 ATTATCATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TACAAATATATATTTTTT
Found at i:52283939 original size:11 final size:12
Alignment explanation
Indices: 52283917--52283972 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 12
52283907 AATTTGTTTC
52283917 ATAATATATAAT
1 ATAATATATAAT
52283929 ATAAT-TATAAT
1 ATAATATATAAT
52283940 ATAATCA-ATTAAT
1 ATAAT-ATA-TAAT
*
52283953 AATAATATAAAAT
1 -ATAATATATAAT
52283966 AT-ATATA
1 ATAATATA
52283973 CCTAAGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 16 0.42
12 8 0.21
13 8 0.21
14 6 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:52287103 original size:56 final size:56
Alignment explanation
Indices: 52287035--52287146 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
52287025 AAAAACGCAC
** **
52287035 AGAACCAAAGGAAGCAGCCAAAAATGATGATTGGAGCTGTCAATCAGAGGAAATAA
1 AGAACCAAAGGAAGCAGCCAAAAACAATGATCAGAGCTGTCAATCAGAGGAAATAA
* * * *
52287091 AGAACTAAAGGAAGCAGCCAGAAACAATGATCAGAGCTGTTAATCATAGGAAATAA
1 AGAACCAAAGGAAGCAGCCAAAAACAATGATCAGAGCTGTCAATCAGAGGAAATAA
52287147 CTGGCAATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.15
Consensus pattern (56 bp):
AGAACCAAAGGAAGCAGCCAAAAACAATGATCAGAGCTGTCAATCAGAGGAAATAA
Found at i:52291043 original size:128 final size:127
Alignment explanation
Indices: 52290807--52291101 Score: 385
Period size: 128 Copynumber: 2.3 Consensus size: 127
52290797 AGCACGGCAA
* * * * **
52290807 GGCACGATTCCTCGAATTTCCAAACATTGGACATTGCCTTGCTTTAGAATTTTTAAAACACGAGG
1 GGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTACTTTAAAATTTAAAAAACACGAGG
* *
52290872 GAAATTCTAAAGGAATATTCAATTATTTTGAACAAACTGGAAATCAAAAC-CTAGCACGATAG
66 GAAATTCTAAAGGAATATTCAATTACTTTGAACAAACGGGAAATCAAAACTC-AGCACGATAG
* * * * * *
52290934 GGCACGATTCCCCAAATTTCTAAACGTTGAACATTGTCTTATTTTAAAATTTGAAAAAATACGAG
1 GGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTACTTTAAAATTT-AAAAAACACGAG
* * **
52290999 TGAAATTCTAAAGGAATATTCGATTACTTTGAACAAACGGGAAATTGAAACTCAGCACGATAG
65 GGAAATTCTAAAGGAATATTCAATTACTTTGAACAAACGGGAAATCAAAACTCAGCACGATAG
**
52291062 GGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTT
1 GGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTT
52291102 CGTTTTAAGG
Statistics
Matches: 142, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
127 43 0.30
128 98 0.69
129 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (127 bp):
GGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTACTTTAAAATTTAAAAAACACGAGG
GAAATTCTAAAGGAATATTCAATTACTTTGAACAAACGGGAAATCAAAACTCAGCACGATAG
Found at i:52291800 original size:24 final size:25
Alignment explanation
Indices: 52291766--52291820 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
52291756 GGAAATAAGT
*
52291766 TATATACATAATAGATTTAAAA-AACA
1 TATATATA-AATA-ATTTAAAACAACA
52291792 TATATATAAATAATTTAAAACAAC-
1 TATATATAAATAATTTAAAACAACA
52291816 TATAT
1 TATAT
52291821 GAAAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 13 0.48
25 7 0.26
26 7 0.26
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (25 bp):
TATATATAAATAATTTAAAACAACA
Found at i:52293790 original size:45 final size:45
Alignment explanation
Indices: 52293732--52293980 Score: 193
Period size: 45 Copynumber: 5.5 Consensus size: 45
52293722 ACTTCGATTG
* *
52293732 GCTCCATTGCAACTTTAGGGAGATAAGATCTGCTAACTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTTAGTCT
* *
52293777 GCTCCACTACAACTTCAGGGAGATAAGATCTTCTAACTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTTAGTCT
* * * * * *
52293822 GTTCCATTGCAATTTTAGGGAGATAAGAAT-TGGGTAATTTTA-TCCT
1 GCTCCACTGCAACTTCAGGGAGATAAG-ATCT-GCTAACTTTAGT-CT
* * ** *** *
52293868 ACTCTACTGCAACTTCAGAAAGATAAGGAT-TG-GGGC-TTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATCTGCTAACTTTAG-TCT
* * * *
52293912 GCTACACTGCAACTTTAGGGAGATAAGATCTGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTTAGTCT
* * *
52293957 GCTCTACTACAACTTCAAGGAGAT
1 GCTCCACTGCAACTTCAGGGAGAT
52293981 GAGACTTGCT
Statistics
Matches: 154, Mismatches: 41, Indels: 18
0.72 0.19 0.08
Matches are distributed among these distances:
43 5 0.03
44 24 0.16
45 90 0.58
46 34 0.22
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTTAGTCT
Found at i:52293846 original size:90 final size:89
Alignment explanation
Indices: 52293686--52293980 Score: 260
Period size: 90 Copynumber: 3.3 Consensus size: 89
52293676 ATTTTTTATC
* * * * *
52293686 CTGCTTTACTGCAACTTCAGAGAGATAAGGATT-GTGACTTCGAT-TGGCTCCATTGCAACTTTA
1 CTGCTCTACTACAACTTCAGGGAGATAAGGATTCG-AACTTAGATCT-GCTCCATTGCAACTTTA
52293749 GGGAGATAAGATCTGCTAACTTTAGT
64 GGGAGATAAGATCTGCTAACTTTAGT
* * * *
52293775 CTGCTCCACTACAACTTCAGGGAGATAA-GATCTTCTAACTTTAG-TCTGTTCCATTGCAATTTT
1 CTGCTCTACTACAACTTCAGGGAGATAAGGA--TTCGAAC-TTAGATCTGCTCCATTGCAACTTT
* *
52293838 AGGGAGATAAGAAT-TGGGTAATTTTA-T
63 AGGGAGATAAG-ATCT-GCTAACTTTAGT
* * ** * ** * * *
52293865 CCTACTCTACTGCAACTTCAGAAAGATAAGGATTGGGGCTTCGATCTGCTACACTGCAACTTTAG
1 -CTGCTCTACTACAACTTCAGGGAGATAAGGATTCGAACTTAGATCTGCTCCATTGCAACTTTAG
* *
52293930 GGAGATAAGATCTGCTATCTTCAGT
65 GGAGATAAGATCTGCTAACTTTAGT
*
52293955 CTGCTCTACTACAACTTCAAGGAGAT
1 CTGCTCTACTACAACTTCAGGGAGAT
52293981 GAGACTTGCT
Statistics
Matches: 160, Mismatches: 34, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
88 2 0.01
89 56 0.35
90 63 0.39
91 37 0.23
92 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (89 bp):
CTGCTCTACTACAACTTCAGGGAGATAAGGATTCGAACTTAGATCTGCTCCATTGCAACTTTAGG
GAGATAAGATCTGCTAACTTTAGT
Found at i:52294016 original size:44 final size:45
Alignment explanation
Indices: 52293917--52294036 Score: 111
Period size: 44 Copynumber: 2.7 Consensus size: 45
52293907 GATCTGCTAC
* * ** *
52293917 ACTGCAACTTTAGGGAGATAAGATCTGCTATCTTCAGTCTGCTCT
1 ACTGCAACTTCAAGGAGATAAGATCTGCTATCTTCAACCTACTCT
* * *
52293962 ACTACAACTTCAAGGAGATGAGA-CTTGCTA-CTTCAACCTACTTT
1 ACTGCAACTTCAAGGAGATAAGATC-TGCTATCTTCAACCTACTCT
* *
52294006 ACTGCAACTTC-AGAGAGATAAGGTTTGCTAT
1 ACTGCAACTTCAAG-GAGATAAGATCTGCTAT
52294037 GATAACTTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.03
44 33 0.56
45 24 0.41
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
ACTGCAACTTCAAGGAGATAAGATCTGCTATCTTCAACCTACTCT
Found at i:52305531 original size:127 final size:128
Alignment explanation
Indices: 52305338--52305660 Score: 459
Period size: 128 Copynumber: 2.5 Consensus size: 128
52305328 TATTTAGTCC
* * * * *
52305338 AACGAAAAACCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGGACATTGC
1 AACGGAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGC
* ** *
52305403 CTTGCTTTAGAATTT-TTAAAACACGAGGGAAATTCTAAAGGAATATTCAATTATTTTGAACA
66 CTTACTTTAGAATTTGAAAAAACACGAGGGAAATTCTAAAGGAATATTCAATTACTTTGAACA
* * * * *
52305465 AACTGAAAATCGAAACGCAGTACGATAGGGCACGATTCCCCGAACTTCCAAACGTTGAACATTGC
1 AACGGAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGC
* * *
52305530 CTTATTTTAGAATTTGAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTACTTTGAACA
66 CTTACTTTAGAATTTGAAAAAACACGAGGGAAATTCTAAAGGAATATTCAATTACTTTGAACA
* **
52305593 AACGGGAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGC
1 AACGGAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGC
52305658 CTT
66 CTT
52305661 TGTTTTAAGG
Statistics
Matches: 170, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
127 68 0.40
128 102 0.60
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (128 bp):
AACGGAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGC
CTTACTTTAGAATTTGAAAAAACACGAGGGAAATTCTAAAGGAATATTCAATTACTTTGAACA
Found at i:52306356 original size:24 final size:24
Alignment explanation
Indices: 52306322--52306375 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
52306312 GGAAATAAGT
*
52306322 TATATACATAATAGATTTAAAAAACA
1 TATATATA-AATA-ATTTAAAAAACA
*
52306348 TATATATAAATAATTTAAACAAC-
1 TATATATAAATAATTTAAAAAACA
52306371 TATAT
1 TATAT
52306376 GAAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 10 0.38
25 4 0.15
26 7 0.27
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
TATATATAAATAATTTAAAAAACA
Found at i:52308518 original size:2 final size:2
Alignment explanation
Indices: 52308511--52308546 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52308501 GTAGAAAAAC
52308511 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52308547 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.