Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 54 of 279
Found at i:18160027 original size:20 final size:20
Alignment explanation
Indices: 18160004--18160059 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
18159994 GAAACGTACG
18160004 TACATAATATATATACATAA
1 TACATAATATATATACATAA
18160024 TACATTAA-ATATATACATAA
1 TACA-TAATATATATACATAA
*
18160044 TATATAAATATATATA
1 TACAT-AATATATATA
18160060 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 21 0.66
21 10 0.31
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
TACATAATATATATACATAA
Found at i:18160060 original size:17 final size:17
Alignment explanation
Indices: 18160014--18160068 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
18160004 TACATAATAT
* *
18160014 ATATACATAATACATTAA
1 ATATATATAATATA-TAA
18160032 ATATATACATAATATATAA
1 ATATAT--ATAATATATAA
*
18160051 ATATATATAATATTTAA
1 ATATATATAATATATAA
18160068 A
1 A
18160069 AAATATGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.34
18 5 0.16
19 9 0.28
20 7 0.22
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATAATATATAA
Found at i:18161938 original size:44 final size:44
Alignment explanation
Indices: 18161873--18162333 Score: 283
Period size: 44 Copynumber: 10.6 Consensus size: 44
18161863 CAGCTTGTGA
* * * ** *
18161873 CCCTATTGCTTAGGAGCTTAAGGCCCATCA-CTTCTGATATGTTT
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTC-GATCTGTTT
** ** * * *
18161917 CCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGCCTGCTA
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGA-TCTGTTT
* * ** ** * *
18161960 CCCTACTGCTTAGGTGGTTAAGGTCTGT-AAATTCG-GCTTGTTA
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATC-TGTTT
* * *
18162003 CCCTAC-GACTTAGGAGGTTAA-AGCCCATTACCTTCGATCTGTTT
1 CCCTACTG-CTTAGGGGGTTAAGA-TCCATCACCTTCGATCTGTTT
* * *
18162047 CCCTACTACTTAAGGGGTTAAAATCCATCACCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
* * ** * * * * *
18162091 CCTTACTGCTTAGAGGGTTAAGATCTGTAACTTTAG-CCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
* * ** * *
18162134 CTCTACTGCTTAGGGGTTTAAGGCCCATCATCTTTGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
* *
18162178 CCCTACTGCTTAGGGTGTTAAGATCCATCATCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
* ** * ** * * *
18162222 CCCTACTGCTTAAGGGGTTAAGATCTGTAAATTTAG-CCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
* ** * *
18162265 CCCTACTGCTTAGGGGTTTAAGGCCCTTCACCTTCGATTTGTTT
1 CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
*
18162309 CCCAACTGCTTAGGGGGTTAAGATC
1 CCCTACTGCTTAGGGGGTTAAGATC
18162334 TGTAAATTCA
Statistics
Matches: 316, Mismatches: 89, Indels: 24
0.74 0.21 0.06
Matches are distributed among these distances:
42 3 0.01
43 120 0.38
44 191 0.60
45 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (44 bp):
CCCTACTGCTTAGGGGGTTAAGATCCATCACCTTCGATCTGTTT
Found at i:18162132 original size:87 final size:88
Alignment explanation
Indices: 18162041--18162242 Score: 223
Period size: 87 Copynumber: 2.3 Consensus size: 88
18162031 TACCTTCGAT
* * *
18162041 CTGTTTCCCTACTACTTAAGGGGTTAAAATCCATCACCTTCGATCTGTTTCCTTACTGCTTAGAG
1 CTGTTTCCCTACTGCTTAAGGGGTTAAAACCCATCACCTTCGATCTGTTTCCCTACTGCTTAG-G
**
18162106 G-GTTAAGATCTGTAA-CTTTAG-C
65 GTGTTAAGATCCATAATC-TTAGAC
* * ** * *
18162128 CTGTTACTCTACTGCTT-AGGGGTTTAAGGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAAGGGG-TTAAAACCCATCACCTTCGATCTGTTTCCCTACTGCTTAGG
* * *
18162192 GTGTTAAGATCCATCATCTTCGAT
65 GTGTTAAGATCCATAATCTTAGAC
18162216 CTGTTTCCCTACTGCTTAAGGGGTTAA
1 CTGTTTCCCTACTGCTTAAGGGGTTAA
18162243 GATCTGTAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
86 7 0.07
87 62 0.66
88 20 0.21
89 5 0.05
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (88 bp):
CTGTTTCCCTACTGCTTAAGGGGTTAAAACCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
TGTTAAGATCCATAATCTTAGAC
Found at i:18162263 original size:87 final size:87
Alignment explanation
Indices: 18162172--18162373 Score: 289
Period size: 87 Copynumber: 2.3 Consensus size: 87
18162162 CATCTTTGAT
* * * *
18162172 CTGTTTCCCTACTGCTTA-GGGTGTTAAGATCCATCATCTTCGATCTGTTTCCCTACTGCTTAAG
1 CTGTTACCCTACTGCTTAGGGGT-TTAAGACCCATCACCTTCGATCTGTTTCCCAACTGCTTAAG
*
18162236 GGGTTAAGATCTGTAAATTTAGC
65 GGGTTAAGATCTGTAAATTCAGC
* * * *
18162259 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCACCTTCGATTTGTTTCCCAACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCATCACCTTCGATCTGTTTCCCAACTGCTTAAGG
18162324 GGTTAAGATCTGTAAATTCAGC
66 GGTTAAGATCTGTAAATTCAGC
**
18162346 CTGTTACCCTACTATTTAGGGGTTTAAG
1 CTGTTACCCTACTGCTTAGGGGTTTAAG
18162374 GCTTGTGAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 99 0.96
88 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (87 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGACCCATCACCTTCGATCTGTTTCCCAACTGCTTAAGG
GGTTAAGATCTGTAAATTCAGC
Found at i:18162330 original size:131 final size:130
Alignment explanation
Indices: 18161849--18162333 Score: 557
Period size: 131 Copynumber: 3.7 Consensus size: 130
18161839 CAAGGAGAAG
* * * * * * * *
18161849 AGATTTGTAATTTTCAGCTTGTGACCCTATTGCTTAGGAGCTTAAGGCCCATCA-CTTCTGATAT
1 AGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTC-GATCT
** * * * *
18161913 GTTTCCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGCCTGCTACCCTACTGCTTAGGTG
64 GTTTCCCTACTGCTTAGGGGGTTAAGATCCATCAACTTCGA-TCTGTTTCCCTACTGCTTAGG-G
18161976 GTTA
127 GTTA
* ** * * *
18161980 AGGTCTGTAAATTCGGCTTGTTACCCTAC-GACTTAGGAGG-TTAAAGCCCATTACCTTCGATCT
1 AGATCTGTAAATTTAGCCTGTTACCCTACTG-CTTAGG-GGTTTAAGGCCCATCACCTTCGATCT
* * * * *
18162043 GTTTCCCTACTACTTAAGGGGTTAAAATCCATCACCTTCGATCTGTTTCCTTACTGCTTAGAGGG
64 GTTTCCCTACTGCTTAGGGGGTTAAGATCCATCAACTTCGATCTGTTTCCCTACTGCTTAG-GGG
18162108 TTA
128 TTA
* * * *
18162111 AGATCTGTAACTTTAGCCTGTTACTCTACTGCTTAGGGGTTTAAGGCCCATCATCTTTGATCTGT
1 AGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGT
* *
18162176 TTCCCTACTGCTTAGGGTGTTAAGATCCATCATCTTCGATCTGTTTCCCTACTGCTTAAGGGGTT
66 TTCCCTACTGCTTAGGGGGTTAAGATCCATCAACTTCGATCTGTTTCCCTACTGCTT-AGGGGTT
18162241 A
130 A
* *
18162242 AGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCACCTTCGATTTGT
1 AGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGT
*
18162307 TTCCCAACTGCTTAGGGGGTTAAGATC
66 TTCCCTACTGCTTAGGGGGTTAAGATC
18162334 TGTAAATTCA
Statistics
Matches: 299, Mismatches: 46, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
129 1 0.00
130 62 0.21
131 231 0.77
132 5 0.02
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (130 bp):
AGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGT
TTCCCTACTGCTTAGGGGGTTAAGATCCATCAACTTCGATCTGTTTCCCTACTGCTTAGGGGTTA
Found at i:18162558 original size:66 final size:66
Alignment explanation
Indices: 18162441--18162568 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
18162431 TGCTTATGTT
* * *
18162441 AAATGATTAGGATACTGTAATCGAAATAAATCGAATGCTCCTAACTAGATGTGTTATGAATGTTT
1 AAATAATTAGGATACTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTGTTATGAATGTTT
18162506 C
66 C
* * * * *
18162507 AAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTGGATGTGTTATGAATG
1 AAATAATTAGGATACTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTGTTATGAATG
18162569 ATATATGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (66 bp):
AAATAATTAGGATACTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTGTTATGAATGTTT
C
Found at i:18166015 original size:79 final size:78
Alignment explanation
Indices: 18165913--18166135 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
18165903 GCTCCTCGTT
* *
18165913 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
18165978 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
18165993 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
18166057 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
18166071 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
18166134 GA
63 GA
18166136 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:18166030 original size:39 final size:40
Alignment explanation
Indices: 18165913--18166135 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
18165903 GCTCCTCGTT
* *
18165913 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
18165953 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
18165993 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
18166032 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
18166071 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
18166112 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18166136 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:18173934 original size:40 final size:40
Alignment explanation
Indices: 18173890--18174151 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
18173880 GCTCCTCGTT
* *
18173890 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
18173930 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
18173970 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
18174009 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
18174048 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
18174087 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
18174128 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18174152 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:18178255 original size:9 final size:10
Alignment explanation
Indices: 18178242--18178287 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
18178232 GGGAAAGTCT
18178242 AATGCAAAT-
1 AATGCAAATG
18178251 AATGC-AATG
1 AATGCAAATG
18178260 CAATGCAAATG
1 -AATGCAAATG
*
18178271 CATG-AAATG
1 AATGCAAATG
18178280 AATGCAAA
1 AATGCAAA
18178288 ATAAAGGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 3 0.10
9 13 0.42
10 11 0.35
11 4 0.13
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (10 bp):
AATGCAAATG
Found at i:18178266 original size:19 final size:19
Alignment explanation
Indices: 18178242--18178287 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18178232 GGGAAAGTCT
*
18178242 AATGCAAAT-AATGCAATG
1 AATGCAAATGAATGAAATG
*
18178260 CAATGCAAATGCATGAAATG
1 -AATGCAAATGAATGAAATG
18178280 AATGCAAA
1 AATGCAAA
18178288 ATAAAGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (19 bp):
AATGCAAATGAATGAAATG
Found at i:18180535 original size:3 final size:3
Alignment explanation
Indices: 18180527--18180564 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18180517 AGTAATACAG
18180527 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18180565 GTGATATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18181053 original size:41 final size:42
Alignment explanation
Indices: 18180981--18181074 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 42
18180971 CGTACATAAT
* *
18180981 ATATATACATAATACATTAAATATATACATAATATG-TAAAA
1 ATATATATATAATACATTAAAAATATACATAATATGATAAAA
* * **
18181022 ATATATATATAATA-TTTAAAAAATATGCATAATATGATATTA
1 ATATATATATAATACATT-AAAAATATACATAATATGATAAAA
18181064 ATATATATATA
1 ATATATATATA
18181075 TGTAATATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.04
41 29 0.64
42 14 0.31
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (42 bp):
ATATATATATAATACATTAAAAATATACATAATATGATAAAA
Found at i:18181838 original size:13 final size:13
Alignment explanation
Indices: 18181817--18181846 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18181807 CGAAAGGTAT
*
18181817 TATTTTTTTTGTA
1 TATTCTTTTTGTA
18181830 TATTCTTTTTGTA
1 TATTCTTTTTGTA
18181843 TATT
1 TATT
18181847 TTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (13 bp):
TATTCTTTTTGTA
Found at i:18181853 original size:22 final size:23
Alignment explanation
Indices: 18181836--18181878 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
18181826 TGTATATTCT
18181836 TTTTG-TATATTTTATATATATA
1 TTTTGATATATTTTATATATATA
18181858 TTTTGATATATTTTA-ATATAT
1 TTTTGATATATTTTATATATAT
18181879 GAATGAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (23 bp):
TTTTGATATATTTTATATATATA
Found at i:18181855 original size:24 final size:23
Alignment explanation
Indices: 18181836--18181878 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
18181826 TGTATATTCT
18181836 TTTTG-TATATTTT-ATATATATA
1 TTTTGATATATTTTAATATAT-TA
18181858 TTTTGATATATTTTAATATAT
1 TTTTGATATATTTTAATATAT
18181879 GAATGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (23 bp):
TTTTGATATATTTTAATATATTA
Found at i:18184830 original size:9 final size:9
Alignment explanation
Indices: 18184812--18184885 Score: 51
Period size: 10 Copynumber: 7.7 Consensus size: 9
18184802 AGTGATTTCT
18184812 TAAAAATTA
1 TAAAAATTA
*
18184821 TAAAATTTA
1 TAAAAATTA
18184830 TTTAAAAATTA
1 --TAAAAATTA
18184841 TAAAAAATTA
1 T-AAAAATTA
*
18184851 TAAATGATTA
1 TAAA-AATTA
**
18184861 TTAATTATT-
1 -TAAAAATTA
18184870 TAAAAATTAA
1 TAAAAATT-A
18184880 TAAAAA
1 TAAAAA
18184886 ATATTATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.12
9 12 0.24
10 22 0.43
11 11 0.22
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (9 bp):
TAAAAATTA
Found at i:18185183 original size:11 final size:10
Alignment explanation
Indices: 18185091--18185183 Score: 52
Period size: 11 Copynumber: 9.4 Consensus size: 10
18185081 ATATGTGTAT
18185091 ATAATTTTT-
1 ATAATTTTTA
*
18185100 ATAAATTTTA
1 ATAATTTTTA
18185110 ATAA--TTTA
1 ATAATTTTTA
* *
18185118 A-ATTTTATTT
1 ATAATTT-TTA
* *
18185128 AGAATTCTTA
1 ATAATTTTTA
*
18185138 ATCAATTTTAA
1 AT-AATTTTTA
*
18185149 ATAATTTTTTT
1 ATAA-TTTTTA
18185160 ATAATTTTT-
1 ATAATTTTTA
18185169 ATAATTATTTA
1 ATAATT-TTTA
18185180 ATAA
1 ATAA
18185184 ATCAATCTTG
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
7 1 0.02
8 5 0.08
9 15 0.23
10 20 0.31
11 23 0.36
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:18185183 original size:20 final size:21
Alignment explanation
Indices: 18185135--18185183 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
18185125 TTTAGAATTC
*
18185135 TTAATCAATTTTAAATAATTTT
1 TTAAT-AATTTTAAATAATTAT
* *
18185157 TTTATAATTTT-TATAATTAT
1 TTAATAATTTTAAATAATTAT
18185177 TTAATAA
1 TTAATAA
18185184 ATCAATCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.57
21 6 0.26
22 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATAATTTTAAATAATTAT
Found at i:18185286 original size:11 final size:10
Alignment explanation
Indices: 18185262--18185307 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
18185252 TCAATGTTAT
18185262 TTTTAATAAA
1 TTTTAATAAA
*
18185272 TTTAAATAAA
1 TTTTAATAAA
18185282 TTTT-ATAAA
1 TTTTAATAAA
*
18185291 TTCTTAATAAT
1 TT-TTAATAAA
18185302 TTTTAA
1 TTTTAA
18185308 ATAATTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 7 0.23
10 18 0.58
11 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:18185291 original size:19 final size:19
Alignment explanation
Indices: 18185262--18185309 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
18185252 TCAATGTTAT
18185262 TTTTAATAAATT-TAAATAAA
1 TTTT-ATAAATTCTAAAT-AA
*
18185282 TTTTATAAATTCTTAATAA
1 TTTTATAAATTCTAAATAA
18185301 TTTT-TAAAT
1 TTTTATAAAT
18185310 AATTTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 13 0.50
20 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTATAAATTCTAAATAA
Found at i:18187663 original size:19 final size:19
Alignment explanation
Indices: 18187639--18187681 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18187629 AATTATTTAT
18187639 TAAATT-TAATTAGAATATG
1 TAAATTCTAATTA-AATATG
* *
18187658 TAAATTCTATTTAAATATT
1 TAAATTCTAATTAAATATG
18187677 TAAAT
1 TAAAT
18187682 ATAACAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
TAAATTCTAATTAAATATG
Found at i:18187677 original size:41 final size:41
Alignment explanation
Indices: 18187619--18187761 Score: 125
Period size: 41 Copynumber: 3.5 Consensus size: 41
18187609 ATTTCTAAGT
*
18187619 AATTA-ATATTAATTATTTATTAAATTTAATTAGAATATGTA
1 AATTATAT-TTAAATATTTATTAAATTTAATTAGAATATGTA
* **
18187660 AATTCTATTTAAATATTTA--AATATAACAATTA-AATATTTGT-
1 AATTATATTTAAATATTTATTAA-AT-TTAATTAGAATA--TGTA
* * *
18187701 AATTAGATATTGAATATTTATTAAATTTAATTAGAATATATA
1 AATTATAT-TTAAATATTTATTAAATTTAATTAGAATATGTA
*
18187743 AACTATATTTAAATATTTA
1 AATTATATTTAAATATTTA
18187762 AATATAATAA
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
39 2 0.03
40 6 0.08
41 37 0.47
42 26 0.33
43 6 0.08
44 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (41 bp):
AATTATATTTAAATATTTATTAAATTTAATTAGAATATGTA
Found at i:18187720 original size:83 final size:82
Alignment explanation
Indices: 18187617--18187794 Score: 286
Period size: 83 Copynumber: 2.1 Consensus size: 82
18187607 ACATTTCTAA
* * *
18187617 GTAATTAATATTAATTATTTATTAAATTTAATTAGAATATGTAAATTCTATTTAAATATTTAAAT
1 GTAATTAATATTAATTATTTATTAAATTTAATTAGAATATATAAACTATATTTAAATATTTAAAT
18187682 ATAACAATTAAATATTT
66 ATAACAATTAAATATTT
18187699 GTAATTAGATATTGAA-TATTTATTAAATTTAATTAGAATATATAAACTATATTTAAATATTTAA
1 GTAATTA-ATATT-AATTATTTATTAAATTTAATTAGAATATATAAACTATATTTAAATATTTAA
*
18187763 ATATAATAATTAAATATTT
64 ATATAACAATTAAATATTT
18187782 GTAATTAAATATT
1 GTAATT-AATATT
18187795 TGGAAGAAGA
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
82 7 0.08
83 79 0.89
84 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (82 bp):
GTAATTAATATTAATTATTTATTAAATTTAATTAGAATATATAAACTATATTTAAATATTTAAAT
ATAACAATTAAATATTT
Found at i:18187777 original size:21 final size:21
Alignment explanation
Indices: 18187668--18187781 Score: 80
Period size: 21 Copynumber: 5.5 Consensus size: 21
18187658 TAAATTCTAT
*
18187668 TTAAATATTTAAATATAACAA
1 TTAAATATTTAAATATAATAA
*
18187689 TTAAATATTTGTAAT-TAGAT-A
1 TTAAATATTT-AAATATA-ATAA
* *
18187710 TTGAATATTTATTAA-AT-TTAA
1 TTAAATATTTA--AATATAATAA
*
18187731 TTAGAATATATAAACTAT-AT--
1 TTA-AATATTTAAA-TATAATAA
18187751 TTAAATATTTAAATATAATAA
1 TTAAATATTTAAATATAATAA
18187772 TTAAATATTT
1 TTAAATATTT
18187782 GTAATTAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 24
0.69 0.09 0.23
Matches are distributed among these distances:
18 3 0.04
19 11 0.15
20 6 0.08
21 35 0.49
22 17 0.24
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAATATTTAAATATAATAA
Found at i:18187788 original size:14 final size:14
Alignment explanation
Indices: 18187769--18187796 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18187759 TTAAATATAA
18187769 TAATTAAATATTTG
1 TAATTAAATATTTG
18187783 TAATTAAATATTTG
1 TAATTAAATATTTG
18187797 GAAGAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TAATTAAATATTTG
Found at i:18188511 original size:23 final size:23
Alignment explanation
Indices: 18188465--18188520 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
18188455 AAAGGGTTTG
18188465 ATTTTATTATTTGATAGGTTTAAT
1 ATTTTATTATTTGATA-GTTTAAT
18188489 -TTTTATTATTTGATA-TTAATAAT
1 ATTTTATTATTTGATAGTT--TAAT
18188512 ATTTT-TTAT
1 ATTTTATTAT
18188521 AAATTGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
23 23 0.79
24 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
ATTTTATTATTTGATAGTTTAAT
Found at i:18189804 original size:43 final size:43
Alignment explanation
Indices: 18189743--18189829 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
18189733 GTTCCGAGCT
18189743 AGTGAGAAGTCTTTGTTTAAAAGCTAACTAAATAAAAACTCTA
1 AGTGAGAAGTCTTTGTTTAAAAGCTAACTAAATAAAAACTCTA
18189786 AGTGAGAAGTCTTTGTTTAAAAGCTAACTAAATAAAAACTCTA
1 AGTGAGAAGTCTTTGTTTAAAAGCTAACTAAATAAAAACTCTA
18189829 A
1 A
18189830 CTCTTTGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (43 bp):
AGTGAGAAGTCTTTGTTTAAAAGCTAACTAAATAAAAACTCTA
Found at i:18199558 original size:16 final size:15
Alignment explanation
Indices: 18199533--18199562 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18199523 AAAATAATTC
18199533 TTCATGAATAAAATG
1 TTCATGAATAAAATG
18199548 TTCATTGAATAAAAT
1 TTCA-TGAATAAAAT
18199563 ATTTATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (15 bp):
TTCATGAATAAAATG
Found at i:18200534 original size:20 final size:18
Alignment explanation
Indices: 18200484--18200535 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 18
18200474 CAATGAATAA
18200484 GTTCACCAATAGATACAATT
1 GTTCA-CAA-AGATACAATT
18200504 GTTCA-AAAGATACAATT
1 GTTCACAAAGATACAATT
18200521 GTTCATCAAGAGATA
1 GTTCA-CAA-AGATA
18200536 GAACATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
19 2 0.07
20 10 0.34
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (18 bp):
GTTCACAAAGATACAATT
Found at i:18208155 original size:20 final size:21
Alignment explanation
Indices: 18208103--18208155 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
18208093 AATTAAAAAT
18208103 AATAAAATTTAATTAGTTATAA
1 AATAAAA-TTAATTAGTTATAA
* ** *
18208125 AATTATTTTAATTA-TTATTA
1 AATAAAATTAATTAGTTATAA
18208145 AATAAAATTAA
1 AATAAAATTAA
18208156 AAATCATATC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAAAATTAATTAGTTATAA
Found at i:18208523 original size:8 final size:8
Alignment explanation
Indices: 18208510--18208613 Score: 57
Period size: 8 Copynumber: 11.9 Consensus size: 8
18208500 ATATTTTCTC
18208510 ATAAAAAT
1 ATAAAAAT
18208518 ATAAAAAAAT
1 AT--AAAAAT
18208528 CATAAAAA-
1 -ATAAAAAT
*
18208536 ATTAAAAT
1 ATAAAAAT
18208544 ATTAAAATTGAT
1 A-TAAAA---AT
**
18208556 ATAAACTT
1 ATAAAAAT
*
18208564 ATAAATATT
1 ATAAA-AAT
18208573 ATAAAAAT
1 ATAAAAAT
*
18208581 ATGAAAAT
1 ATAAAAAT
*
18208589 CTAATAAATT
1 ATAA-AAA-T
18208599 ATAAAAAT
1 ATAAAAAT
18208607 ATAAAAA
1 ATAAAAA
18208614 ATTAATAAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
7 6 0.08
8 28 0.37
9 22 0.29
10 10 0.13
11 6 0.08
12 3 0.04
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (8 bp):
ATAAAAAT
Found at i:18208550 original size:26 final size:26
Alignment explanation
Indices: 18208513--18208618 Score: 87
Period size: 26 Copynumber: 4.1 Consensus size: 26
18208503 TTTTCTCATA
*
18208513 AAAATA-TAAAAAAATCATAAAAAATT
1 AAAATATTATAAAAAT-ATAAAAAATT
* * *
18208539 AAAATA-T-TAAAATTGATATAAACTT
1 AAAATATTATAAAAAT-ATAAAAAATT
*
18208564 ATAAATATTATAAAAATAT-GAAAATCT
1 A-AAATATTATAAAAATATAAAAAAT-T
18208591 AATAA-ATTATAAAAATATAAAAAATT
1 AA-AATATTATAAAAATATAAAAAATT
18208617 AA
1 AA
18208619 TAAGTCTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
25 14 0.22
26 33 0.51
27 12 0.18
28 6 0.09
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAATATTATAAAAATATAAAAAATT
Found at i:18209015 original size:17 final size:17
Alignment explanation
Indices: 18208993--18209026 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18208983 GTTCAATTAA
* *
18208993 ATAAAATATTAAAAAAT
1 ATAAAACATAAAAAAAT
18209010 ATAAAACATAAAAAAAT
1 ATAAAACATAAAAAAAT
18209027 GTATTAAAAA
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:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAACATAAAAAAAT
Found at i:18213964 original size:17 final size:17
Alignment explanation
Indices: 18213929--18213976 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
18213919 ATTGAGAAAT
18213929 AAAAAGAAATCAA-AAAAG
1 AAAAAGAAA--AAGAAAAG
**
18213947 AAATTGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
18213964 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
18213977 GAAACAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 2 0.08
17 16 0.64
18 7 0.28
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:18213974 original size:30 final size:30
Alignment explanation
Indices: 18213912--18213976 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
18213902 AACGAATTTT
*
18213912 AAAAGAAATTGAGAAATAAAAAGAAATCAA
1 AAAAGAAATTGAGAAATAAAAAGAAAACAA
18213942 AAAAGAAATTGA-AAA-AGAAAAGAAAA-AGA
1 AAAAGAAATTGAGAAATA-AAAAGAAAACA-A
18213971 AAAAGA
1 AAAAGA
18213977 GAAACAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.06
29 18 0.56
30 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (30 bp):
AAAAGAAATTGAGAAATAAAAAGAAAACAA
Found at i:18218783 original size:8 final size:8
Alignment explanation
Indices: 18218731--18218824 Score: 55
Period size: 8 Copynumber: 10.5 Consensus size: 8
18218721 AAAATTTTAA
18218731 ATATATTTT
1 ATAT-TTTT
*
18218740 ATTAATTTT
1 A-TATTTTT
18218749 ATATTTTTT
1 ATA-TTTTT
18218758 ATAATTTATT
1 AT-ATTT-TT
*
18218768 AGATTTTT
1 ATATTTTT
18218776 ATATTTTT
1 ATATTTTT
18218784 ATAATATTTAGT
1 AT-AT-TTT--T
18218796 AATATTTTT
1 -ATATTTTT
18218805 AT-TTATTT
1 ATATT-TTT
*
18218813 ATAATTTT
1 ATATTTTT
18218821 ATAT
1 ATAT
18218825 CAATTTTCAC
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
7 2 0.03
8 26 0.38
9 23 0.34
10 9 0.13
11 3 0.04
12 3 0.04
13 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
ATATTTTT
Found at i:18219793 original size:18 final size:18
Alignment explanation
Indices: 18219772--18219807 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18219762 AAATAAAATA
*
18219772 TTAAAAATTATAAACTTT
1 TTAAAAATTAAAAACTTT
18219790 TTAAAAATTAAAAACTTT
1 TTAAAAATTAAAAACTTT
18219808 CGTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAAATTAAAAACTTT
Found at i:18220122 original size:37 final size:37
Alignment explanation
Indices: 18220080--18220154 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
18220070 GAGATAAGTA
18220080 TATTTTACATAAAATCTCAAGAAAATAGTCTTTTACG
1 TATTTTACATAAAATCTCAAGAAAATAGTCTTTTACG
* *
18220117 TATTTTACATCAAATCTCAAGATAATAGTCTTTTACG
1 TATTTTACATAAAATCTCAAGAAAATAGTCTTTTACG
18220154 T
1 T
18220155 TTGTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (37 bp):
TATTTTACATAAAATCTCAAGAAAATAGTCTTTTACG
Found at i:18221404 original size:3 final size:3
Alignment explanation
Indices: 18221396--18221439 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
18221386 GTTTGTTTTC
18221396 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
18221440 AATTTCATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18222157 original size:13 final size:13
Alignment explanation
Indices: 18222136--18222182 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
18222126 AGGCAAAAAA
18222136 AAATTTAAAATTT
1 AAATTTAAAATTT
*
18222149 -AATTTTAAATTT
1 AAATTTAAAATTT
*
18222161 AAATTTACAATTT
1 AAATTTAAAATTT
18222174 AAACTTTAA
1 AAA-TTTAA
18222183 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:18222161 original size:6 final size:6
Alignment explanation
Indices: 18222136--18222182 Score: 58
Period size: 6 Copynumber: 7.3 Consensus size: 6
18222126 AGGCAAAAAA
*
18222136 AAATTT AAAATTT AATTTT AAATTT AAATTT ACAATTT AAACTTT AA
1 AAATTT -AAATTT AAATTT AAATTT AAATTT A-AATTT AAA-TTT AA
18222183 TTTTTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 19 0.53
7 17 0.47
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:18227117 original size:40 final size:41
Alignment explanation
Indices: 18227033--18227217 Score: 229
Period size: 40 Copynumber: 4.6 Consensus size: 41
18227023 TCGAATGATG
* * *
18227033 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
* *
18227073 TCCGGACTAAGACCCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
18227113 TCCGGGCTAAG-CCCGAAGGAATTGGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
18227152 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
18227192 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18227218 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 36 0.29
40 81 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:18227239 original size:79 final size:78
Alignment explanation
Indices: 18227070--18227240 Score: 202
Period size: 79 Copynumber: 2.2 Consensus size: 78
18227060 CTAAGTGACC
* *
18227070 ATATCCGGACTAAGACCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGAAT
1 ATATCCGG-TTAAGACCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGAAT
**
18227135 TGGTGCGAGTTACT
65 TGGAACGAGTTACT
* * * *
18227149 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGC
1 ATATCC-GGTTAAGACCCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGA
*
18227213 ATTTGAACGAG-TAGCT
63 ATTGGAACGAGTTA-CT
18227229 ATATCCGGTTAA
1 ATATCCGGTTAA
18227241 ATTCTGAAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 51 0.65
80 25 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
ATATCCGGTTAAGACCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGAATT
GGAACGAGTTACT
Found at i:18236179 original size:47 final size:47
Alignment explanation
Indices: 18236128--18236474 Score: 534
Period size: 47 Copynumber: 7.3 Consensus size: 47
18236118 GTGAATGTAC
18236128 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
18236175 ATATATGTGATAAGG-CTGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCT-AATGGCCAATGTGATGAATGTGAAAGTG--T
*
18236224 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
*
18236271 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--T
*
18236320 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
* *
18236367 ATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
* * * * * *
18236414 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
*
18236461 ATAAATGTGATAAG
1 ATATATGTGATAAG
18236475 TCCCGAAGGG
Statistics
Matches: 277, Mismatches: 17, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
46 2 0.01
47 185 0.67
49 88 0.32
50 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGT
Found at i:18236183 original size:96 final size:96
Alignment explanation
Indices: 18236116--18236474 Score: 546
Period size: 96 Copynumber: 3.8 Consensus size: 96
18236106 GATAATTGTG
* *
18236116 ATGTG-AA-TGTACATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
18236179 ATGTGATAAGGCTGAATGGCCAATGTGATGA
66 ATGTGATAAGGCAGAATGGCCAATGTGATGA
18236210 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
18236275 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCAGAATGGCCAATGTGATGA
18236306 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* ** *
18236371 ATGTGATGAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCAGAATGGCCAATGTGATGA
* * * * * * * *
18236402 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
18236465 ATGTGATAAG
66 ATGTGATAAG
18236475 TCCCGAAGGG
Statistics
Matches: 248, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
94 58 0.23
95 2 0.01
96 188 0.76
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCAGAATGGCCAATGTGATGA
Found at i:18236263 original size:143 final size:141
Alignment explanation
Indices: 18236128--18236474 Score: 561
Period size: 143 Copynumber: 2.4 Consensus size: 141
18236118 GTGAATGTAC
*
18236128 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
18236192 GAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
66 -AATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
18236257 GAATGTGAAAGTGT
128 GAATGTGAAAGTGT
18236271 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGC
* *
18236336 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATG
64 CTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
18236401 AATGTGAAAGTGT
129 AATGTGAAAGTGT
* * * * * *
18236414 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAG
18236475 TCCCGAAGGG
Statistics
Matches: 192, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
141 14 0.07
143 133 0.69
145 43 0.22
146 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
TGTGAAAGTGT
Found at i:18239629 original size:79 final size:81
Alignment explanation
Indices: 18239493--18239675 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
18239483 TCGAATGATG
* *
18239493 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
18239557 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
18239572 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
18239634 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
18239652 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
18239676 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:18239691 original size:40 final size:40
Alignment explanation
Indices: 18239494--18239677 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
18239484 CGAATGATGT
* * * *
18239494 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
18239534 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
18239574 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
18239612 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
18239653 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18239678 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:18239699 original size:79 final size:79
Alignment explanation
Indices: 18239546--18239700 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
18239536 GGACTAAGAT
* **
18239546 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
18239611 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
18239625 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
18239688 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
18239701 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:18241736 original size:28 final size:28
Alignment explanation
Indices: 18241696--18241751 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
18241686 GAAGGAATTT
18241696 CTTGAACTTAAACAAGGTTCCATGTCGG
1 CTTGAACTTAAACAAGGTTCCATGTCGG
18241724 CTTGAACTTAAACAAGGTTCCATGTCGG
1 CTTGAACTTAAACAAGGTTCCATGTCGG
18241752 TTACCGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (28 bp):
CTTGAACTTAAACAAGGTTCCATGTCGG
Found at i:18245781 original size:79 final size:79
Alignment explanation
Indices: 18245679--18245902 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
18245669 GCTCCTCGTT
* *
18245679 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
18245744 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* *
18245759 CAAATGCCTTCGGGCTTAGCCCGGATT-TAGTAACTCCCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
18245822 AATTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * * * *
18245837 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGTTATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
18245901 GA
64 GA
18245903 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 37 0.29
79 54 0.43
80 35 0.28
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:18245793 original size:39 final size:40
Alignment explanation
Indices: 18245679--18245902 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
18245669 GCTCCTCGTT
* *
18245679 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
18245719 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
18245759 CAAATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCCCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
18245798 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
18245837 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
18245878 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18245903 CATCATTCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 71 0.43
40 79 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:18249445 original size:85 final size:85
Alignment explanation
Indices: 18249299--18249477 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
18249289 GGCCGGCCAT
18249299 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
18249364 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
18249384 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
18249449 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
18249469 GAGCATGGG
1 GAGCATGGG
18249478 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:18255119 original size:26 final size:26
Alignment explanation
Indices: 18255090--18255197 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
18255080 TGGTAAAAAT
18255090 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
18255116 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
18255142 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
18255168 TGATAATGGCTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
18255194 TGAT
1 TGAT
18255198 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:18258425 original size:12 final size:12
Alignment explanation
Indices: 18258408--18258438 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
18258398 ACTCGGGGAA
18258408 GAGGCCGTGGTC
1 GAGGCCGTGGTC
18258420 GAGGCCGTGGTC
1 GAGGCCGTGGTC
18258432 GAGGCCG
1 GAGGCCG
18258439 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:18262858 original size:27 final size:27
Alignment explanation
Indices: 18262828--18262921 Score: 104
Period size: 26 Copynumber: 3.6 Consensus size: 27
18262818 TAAGAGGCTC
*
18262828 AAAAT-AATAATATGTAAAAAGAAATTT
1 AAAATAAATAATATATAAAAA-AAATTT
18262855 AAAATAAATAATATATAAAAAAAATTT
1 AAAATAAATAATATATAAAAAAAATTT
* * *
18262882 -AAGTAAATAACATAT-AAAACAATTT
1 AAAATAAATAATATATAAAAAAAATTT
* *
18262907 AAATTAAATATTATA
1 AAAATAAATAATATA
18262922 CATGAAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.16
26 24 0.41
27 11 0.19
28 14 0.24
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATAAATAATATATAAAAAAAATTT
Found at i:18265185 original size:189 final size:188
Alignment explanation
Indices: 18264857--18265263 Score: 679
Period size: 189 Copynumber: 2.2 Consensus size: 188
18264847 GACTTGTTAT
* * * * *
18264857 TTCAACCTGTTTCACTGCAACTTTAGGGAGGCAAAGGTTTGTGATCTATAGCTTCGATTTACTCC
1 TTCAATCTGTTCCACTGCAACTTCAGAGAGGCAAAGGTTTGTGATCTATAGCTTCGATGTACTCC
* * * * *
18264922 ACTGCAACTTCAGGGGGGTAAGATTTTTAACTTCAACCTGCTCTGCTGCAACTTCAGGGAGACAA
66 ACTACAACTTCAGGGGGGTAAGATTTGTAACTTCAACATGCTCCGCTGCAACTTCAGGAAGACAA
18264987 GGTTTGTTTTGATTTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGC
131 GGTTTGTTTTGATTTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGC
* *
18265045 TTCAATCTGTTCCACTACAACATCAGAGAGGCAAAGGTTTGTGATCTATAGCTTCGATGTACTCC
1 TTCAATCTGTTCCACTGCAACTTCAGAGAGGCAAAGGTTTGTGATCTATAGCTTCGATGTACTCC
18265110 ACTACAACTTCAGGGGGGGTAAGATTTGTAACTTCAACATGCTCCGCTGCAACTTCAGGAAGACA
66 ACTACAACTTCA-GGGGGGTAAGATTTGTAACTTCAACATGCTCCGCTGCAACTTCAGGAAGACA
*
18265175 AGGTTTGTTTTGATTTGTTCTACTGCAATTTCAGAGAGATAAGATCTGTAATTTATGGC
130 AGGTTTGTTTTGATTTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGC
*
18265234 TTCAATCTGTTCCACTGCAACTTCATAGAG
1 TTCAATCTGTTCCACTGCAACTTCAGAGAG
18265264 ATAAGACTTA
Statistics
Matches: 202, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
188 69 0.34
189 133 0.66
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (188 bp):
TTCAATCTGTTCCACTGCAACTTCAGAGAGGCAAAGGTTTGTGATCTATAGCTTCGATGTACTCC
ACTACAACTTCAGGGGGGTAAGATTTGTAACTTCAACATGCTCCGCTGCAACTTCAGGAAGACAA
GGTTTGTTTTGATTTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGC
Found at i:18269215 original size:40 final size:40
Alignment explanation
Indices: 18269160--18269241 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
18269150 GTTGGCTTTG
18269160 CTCAGATCTCGATAGTCCACGCACATCCGTACTTTTCTAT
1 CTCAGATCTCGATAGTCCACGCACATCCGTACTTTTCTAT
*
18269200 CTCAGATCTCGATAGTCCACGCACATCTGTACTTTTCTAT
1 CTCAGATCTCGATAGTCCACGCACATCCGTACTTTTCTAT
18269240 CT
1 CT
18269242 TCCTTAGGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (40 bp):
CTCAGATCTCGATAGTCCACGCACATCCGTACTTTTCTAT
Found at i:18273666 original size:19 final size:20
Alignment explanation
Indices: 18273644--18273687 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
18273634 AGGTCTTTTC
* *
18273644 ATGAAATTTAATGCATATG-
1 ATGAAATGTAATGCAAATGA
18273663 ATGAAATGTAATGCAAATGA
1 ATGAAATGTAATGCAAATGA
18273683 ATGAA
1 ATGAA
18273688 TGCAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGAAATGTAATGCAAATGA
Found at i:18277375 original size:16 final size:17
Alignment explanation
Indices: 18277354--18277387 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
18277344 AAAATAGGTA
18277354 ATATATATATAA-AAAT
1 ATATATATATAATAAAT
18277370 ATATATATATAATAAAT
1 ATATATATATAATAAAT
18277387 A
1 A
18277388 CTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATATAATAAAT
Found at i:18277479 original size:21 final size:21
Alignment explanation
Indices: 18277453--18277525 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 21
18277443 AAATAAGTTG
*
18277453 TATAAGACAATTTTAAATAAA
1 TATAAGACAATTTAAAATAAA
18277474 TATAAGACAAGTTTAAAATAATA
1 TATAAGACAA-TTTAAAATAA-A
*
18277497 TATAAAGA-GATTTAAAATAAA
1 TAT-AAGACAATTTAAAATAAA
18277518 TATTAAGA
1 TA-TAAGA
18277526 GAATCAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 17 0.37
22 20 0.43
23 5 0.11
24 4 0.09
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (21 bp):
TATAAGACAATTTAAAATAAA
Found at i:18277510 original size:22 final size:22
Alignment explanation
Indices: 18277485--18277539 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
18277475 ATAAGACAAG
18277485 TTTAAAATAATATATAAAGAGA
1 TTTAAAATAATATATAAAGAGA
*
18277507 TTTAAAATAA-ATATTAAGAGA
1 TTTAAAATAATATATAAAGAGA
* *
18277528 ATCAAAATAATA
1 TTTAAAATAATA
18277540 ATATGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (22 bp):
TTTAAAATAATATATAAAGAGA
Found at i:18277526 original size:21 final size:21
Alignment explanation
Indices: 18277462--18277537 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
18277452 GTATAAGACA
* *
18277462 ATTTTAAATAAATA-TAAGACA
1 ATTTAAAATAAATATTAAGA-G
*
18277483 AGTTTAAAATAATATATAAAGAG
1 A-TTTAAAATAA-ATATTAAGAG
18277506 ATTTAAAATAAATATTAAGAG
1 ATTTAAAATAAATATTAAGAG
* *
18277527 AATCAAAATAA
1 ATTTAAAATAA
18277538 TAATATGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 19 0.41
22 19 0.41
23 4 0.09
24 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (21 bp):
ATTTAAAATAAATATTAAGAG
Found at i:18277599 original size:26 final size:26
Alignment explanation
Indices: 18277532--18277624 Score: 100
Period size: 26 Copynumber: 3.5 Consensus size: 26
18277522 AAGAGAATCA
*
18277532 AAAT-AATAATATGTAAAAAGAAATTT
1 AAATAAATAATATATAAAAA-AAATTT
18277558 AAAATAAATAATATATAAAAAAAATTT
1 -AAATAAATAATATATAAAAAAAATTT
* * *
18277585 AAGTAAATAACATAT-AAAACAATTT
1 AAATAAATAATATATAAAAAAAATTT
*
18277610 AAATTAAATATTATA
1 AAA-TAAATAATATA
18277625 CATGAAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.19
26 22 0.39
27 10 0.18
28 14 0.25
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
AAATAAATAATATATAAAAAAAATTT
Found at i:18280472 original size:26 final size:26
Alignment explanation
Indices: 18280428--18280477 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18280418 AACTTCTATT
*
18280428 TTGAGTTTTTTTTTCAAGAATTTTTC
1 TTGAGTTTTTTTTACAAGAATTTTTC
* *
18280454 TTGAGTTTTTTTTAGAAGAGTTTT
1 TTGAGTTTTTTTTACAAGAATTTT
18280478 AAAAATCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (26 bp):
TTGAGTTTTTTTTACAAGAATTTTTC
Found at i:18284426 original size:3 final size:3
Alignment explanation
Indices: 18284418--18284443 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18284408 TCTCCATTCT
18284418 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
18284444 AGCCAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:18284950 original size:15 final size:16
Alignment explanation
Indices: 18284922--18284951 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18284912 ATTTTATTTT
18284922 AATAATAGATTTTAAC
1 AATAATAGATTTTAAC
18284938 AATAATA-ATTTTAA
1 AATAATAGATTTTAA
18284952 AATTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATAGATTTTAAC
Found at i:18285060 original size:15 final size:15
Alignment explanation
Indices: 18285016--18285091 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 15
18285006 TAACAAAAAT
*
18285016 ATATTATAATTTATAA
1 ATATT-TAATATATAA
18285032 ATATTTAATA-ATAA
1 ATATTTAATATATAA
*
18285046 ATATTTTATATATAA
1 ATATTTAATATATAA
* *
18285061 A-ATATCA-ATAT-A
1 ATATTTAATATATAA
18285073 AT-TTTAATTATATAA
1 ATATTTAA-TATATAA
18285088 ATAT
1 ATAT
18285092 AAGTGCATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.10
13 4 0.08
14 21 0.44
15 12 0.25
16 6 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTAATATATAA
Found at i:18289203 original size:7 final size:7
Alignment explanation
Indices: 18289191--18289236 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
18289181 GAAACAATTA
18289191 TAGTAGT
1 TAGTAGT
18289198 TAGTAGT
1 TAGTAGT
18289205 TAG-AGCT
1 TAGTAG-T
18289212 TAGTAGT
1 TAGTAGT
18289219 TATGTAGT
1 TA-GTAGT
18289227 TA-TAGT
1 TAGTAGT
18289233 TAGT
1 TAGT
18289237 TAACTGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 8 0.23
7 18 0.51
8 9 0.26
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (7 bp):
TAGTAGT
Found at i:18289217 original size:21 final size:21
Alignment explanation
Indices: 18289191--18289236 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
18289181 GAAACAATTA
18289191 TAGTAGTTA-GTAGTTAGAGCT
1 TAGTAGTTATGTAGTTAGAG-T
*
18289212 TAGTAGTTATGTAGTTATAGT
1 TAGTAGTTATGTAGTTAGAGT
18289233 TAGT
1 TAGT
18289237 TAACTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (21 bp):
TAGTAGTTATGTAGTTAGAGT
Found at i:18294515 original size:16 final size:15
Alignment explanation
Indices: 18294494--18294525 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
18294484 CAAAATTAAG
18294494 AAAAGAAAGAAAGAAA
1 AAAAGAAAG-AAGAAA
18294510 AAAAGAAAGAAGAAA
1 AAAAGAAAGAAGAAA
18294525 A
1 A
18294526 GAATGAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGAAA
Found at i:18294516 original size:12 final size:12
Alignment explanation
Indices: 18294491--18294528 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
18294481 AAACAAAATT
18294491 AAGAAAAGAAAGA
1 AAGAAAA-AAAGA
18294504 AAGAAAAAAAGA
1 AAGAAAAAAAGA
*
18294516 AAGAAGAAAAGA
1 AAGAAAAAAAGA
18294528 A
1 A
18294529 TGAGAACTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:18295661 original size:21 final size:22
Alignment explanation
Indices: 18295635--18295719 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 22
18295625 TGATCAGTAT
*
18295635 ACGACACATAAAGTGCCT-AAA
1 ACGACACACAAAGTGCCTGAAA
* *
18295656 ACGACACACAAGGTGCCTGATA
1 ACGACACACAAAGTGCCTGAAA
* *
18295678 A-GACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCTGAAA
* *
18295699 TATGACACATAAAGTGCCTGA
1 -ACGACACACAAAGTGCCTGA
18295720 TCGATAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 34 0.64
22 4 0.08
23 15 0.28
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (22 bp):
ACGACACACAAAGTGCCTGAAA
Found at i:18296115 original size:15 final size:15
Alignment explanation
Indices: 18296090--18296147 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
18296080 TCATGTATAT
18296090 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
18296106 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
18296121 AATAATTTCAATCAA
1 TATAAATTCAATCAA
18296136 TATAAATTCAAT
1 TATAAATTCAAT
18296148 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:18297471 original size:8 final size:8
Alignment explanation
Indices: 18297458--18297486 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18297448 TATCTTTATT
18297458 ATATAATA
1 ATATAATA
18297466 ATATAATA
1 ATATAATA
18297474 ATATAATA
1 ATATAATA
18297482 ATATA
1 ATATA
18297487 CTAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:18309238 original size:39 final size:41
Alignment explanation
Indices: 18309164--18309242 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
18309154 AAATATTATG
*
18309164 CTTAAAAAAAGAAAATCAAGATGAAAACTCGAAAAAGGGCA
1 CTTAAAAAAAGAAAATCAAGATGAAAACTCCAAAAAGGGCA
** *
18309205 CTTAAAAAAA-AGGATCAAGGTGAAAAC-CCAAAAAGGGC
1 CTTAAAAAAAGAAAATCAAGATGAAAACTCCAAAAAGGGC
18309243 GTCTTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 10 0.29
40 14 0.41
41 10 0.29
ACGTcount: A:0.56, C:0.14, G:0.19, T:0.11
Consensus pattern (41 bp):
CTTAAAAAAAGAAAATCAAGATGAAAACTCCAAAAAGGGCA
Found at i:18310196 original size:72 final size:72
Alignment explanation
Indices: 18310073--18310351 Score: 368
Period size: 72 Copynumber: 3.8 Consensus size: 72
18310063 TCTCTATTTT
* * *
18310073 TCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGGTATTCTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT-TCAATT
*
18310138 TCTGCTTG
65 TCTGTTTG
*
18310146 TC-AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATTTTCAAT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTA-TTTCAAT
*
18310209 TTCTGTTTT
64 TTCTGTTTG
*
18310218 TCAAAAAAATCAAC-CTACATTGCGAGAGGTGAGTT-AGGCCTCAGGACACGCTGAGGTAATTTC
1 TC--AAAAATCAACTC-ATATTGCGAGAGGTGAGTTGA-GCCTCAGGACACGCTGAGGT-ATTTC
18310281 AATTTCTGTTTG
61 AATTTCTGTTTG
* * *
18310293 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGATATGCTGAGGTATTT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
18310352 TTAATTTTTG
Statistics
Matches: 183, Mismatches: 12, Indels: 23
0.84 0.06 0.11
Matches are distributed among these distances:
72 64 0.35
73 52 0.28
74 7 0.04
75 59 0.32
76 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (72 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAATTT
CTGTTTG
Found at i:18310373 original size:73 final size:73
Alignment explanation
Indices: 18310069--18310372 Score: 391
Period size: 73 Copynumber: 4.1 Consensus size: 73
18310059 TTTATCTCTA
* * * *
18310069 TTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGGTATTCTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
18310134 AATTTCTG
66 AATTTCTG
* * *
18310142 CTTGTC-AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTT
18310205 CAATTTCTG
65 CAATTTCTG
* *
18310214 TTTTTCAAAAAAATCAAC-CTACATTGCGAGAGGTGAGTT-AGGCCTCAGGACACGCTGAGGTAA
1 TTTTTC--AAAAATCAACTC-ATATTGCGAGAGGTGAGTTGA-GCCTCAGGACACGCTGAGGTAT
18310277 TTTCAATTTCTG
62 TTTCAATTTCTG
* * * * *
18310289 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGATATGCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
*
18310354 AATTTTTG
66 AATTTCTG
18310362 TTTTTTCAAAA
1 -TTTTTCAAAA
18310373 TTTATATTTT
Statistics
Matches: 201, Mismatches: 20, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
72 62 0.31
73 63 0.31
74 16 0.08
75 60 0.30
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (73 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
AATTTCTG
Found at i:18312377 original size:3 final size:3
Alignment explanation
Indices: 18312364--18312393 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
18312354 AGTTTTCTTT
18312364 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
18312394 TTTCTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18312738 original size:12 final size:12
Alignment explanation
Indices: 18312721--18312762 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
18312711 TTGTATATAG
18312721 TATTATCAT-TT
1 TATTATCATATT
18312732 CTATTATCATATT
1 -TATTATCATATT
*
18312745 TATTATTATATT
1 TATTATCATATT
18312757 TATTAT
1 TATTAT
18312763 TTTCACTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 26 0.93
13 2 0.07
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATCATATT
Found at i:18312918 original size:9 final size:8
Alignment explanation
Indices: 18312903--18312964 Score: 58
Period size: 9 Copynumber: 7.5 Consensus size: 8
18312893 TTTAACATTC
18312903 TTATATTA
1 TTATATTA
18312911 TGTATATTA
1 T-TATATTA
18312920 TTATTATTA
1 TTA-TATTA
18312929 TTATTATTA
1 TTA-TATTA
18312938 TTATTATT-
1 TTA-TATTA
18312946 TTATATT-
1 TTATATTA
18312953 TTCATA-TA
1 TT-ATATTA
18312961 TTAT
1 TTAT
18312965 GTATATATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
7 9 0.18
8 11 0.22
9 30 0.60
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TTATATTA
Found at i:18312923 original size:3 final size:3
Alignment explanation
Indices: 18312906--18312949 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
18312896 AACATTCTTA
18312906 TAT TAT GTA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18312950 ATTTTCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18316637 original size:16 final size:15
Alignment explanation
Indices: 18316616--18316647 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
18316606 CAAAATTAAG
18316616 AAAAGAAAGAAAGAAA
1 AAAAGAAAG-AAGAAA
18316632 AAAAGAAAGAAGAAA
1 AAAAGAAAGAAGAAA
18316647 A
1 A
18316648 GAATGAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGAAA
Found at i:18316638 original size:12 final size:12
Alignment explanation
Indices: 18316613--18316650 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
18316603 AAACAAAATT
18316613 AAGAAAAGAAAGA
1 AAGAAAA-AAAGA
18316626 AAGAAAAAAAGA
1 AAGAAAAAAAGA
*
18316638 AAGAAGAAAAGA
1 AAGAAAAAAAGA
18316650 A
1 A
18316651 TGAGAACTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:18317783 original size:21 final size:22
Alignment explanation
Indices: 18317757--18317841 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 22
18317747 TGATCAGTAT
*
18317757 ACGACACATAAAGTGCCT-AAA
1 ACGACACACAAAGTGCCTGAAA
* *
18317778 ACGACACACAAGGTGCCTGATA
1 ACGACACACAAAGTGCCTGAAA
* *
18317800 A-GACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCTGAAA
* *
18317821 TATGACACATAAAGTGCCTGA
1 -ACGACACACAAAGTGCCTGA
18317842 TCGATAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 34 0.64
22 4 0.08
23 15 0.28
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (22 bp):
ACGACACACAAAGTGCCTGAAA
Found at i:18318237 original size:15 final size:15
Alignment explanation
Indices: 18318212--18318269 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
18318202 TCATGTATAT
18318212 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
18318228 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
18318243 AATAATTTCAATCAA
1 TATAAATTCAATCAA
18318258 TATAAATTCAAT
1 TATAAATTCAAT
18318270 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:18323959 original size:26 final size:25
Alignment explanation
Indices: 18323923--18324000 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
18323913 AGAATAAATA
18323923 AAAGAAAGAAAAACAAGAAAAAGAAAC
1 AAAG-AAGAAAAA-AAGAAAAAGAAAC
* * * *
18323950 AAAGAAGAAACGAAATAGAAAGAAAG
1 AAAGAAGAAA-AAAAGAAAAAGAAAC
18323976 AAAGAAGAAAAGAAA-AGAAAAGAAA
1 AAAGAAGAAAA-AAAGA-AAAAGAAA
18324001 AAGGAGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.02
26 36 0.86
27 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.19, T:0.01
Consensus pattern (25 bp):
AAAGAAGAAAAAAAGAAAAAGAAAC
Found at i:18323969 original size:22 final size:22
Alignment explanation
Indices: 18323918--18324002 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
18323908 AATAAAGAAT
18323918 AAATA-AAAGAAAGAAAAACAAG
1 AAATAGAAAGAAAGAAAAAC-AG
* *
18323940 AAAAAGAAACAAAGAAGAAAC-G
1 AAATAGAAAGAAAGAA-AAACAG
*
18323962 AAATAGAAAGAAAGAAAGA-AG
1 AAATAGAAAGAAAGAAAAACAG
18323983 AAA-AGAAAAGAAAAGAAAAA
1 AAATAG-AAAG-AAAGAAAAA
18324003 GGAGAAATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.04
21 10 0.19
22 27 0.52
23 9 0.17
24 4 0.08
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (22 bp):
AAATAGAAAGAAAGAAAAACAG
Found at i:18323990 original size:5 final size:5
Alignment explanation
Indices: 18323922--18324001 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
18323912 AAGAATAAAT
* *
18323922 AAAAG -AAAG AAAA- ACAAG AAAAAG AAACA- AAGAAG AAACG AAATAG
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAA-AG AA-AAG AAAAG AAA-AG
18323968 -AAAG -AAAG AAAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AA-AAG AAAAG AAAAG AAAAG AAAA
18324002 AGGAGAAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
4 13 0.21
5 33 0.54
6 12 0.20
7 3 0.05
ACGTcount: A:0.76, C:0.04, G:0.19, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:18325036 original size:40 final size:37
Alignment explanation
Indices: 18324946--18325036 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 37
18324936 CAAATAGATT
*
18324946 CGATGAGGCGTTGGTCGCCACTTTGCTTCGACTTAGC
1 CGATGAGGCGTTGGTCGCCACTTTGCTTCGACCTAGC
** * *
18324983 CGATGAGAAGTTGGTCGTCACTTATTTGCTTCGACCTATC
1 CGATGAGGCGTTGGTCGCCAC---TTTGCTTCGACCTAGC
18325023 CGATGAGGCGTTGG
1 CGATGAGGCGTTGG
18325037 CCGCAACTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 18 0.41
40 26 0.59
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.31
Consensus pattern (37 bp):
CGATGAGGCGTTGGTCGCCACTTTGCTTCGACCTAGC
Found at i:18326539 original size:25 final size:26
Alignment explanation
Indices: 18326502--18326554 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
18326492 TCAAACATGC
18326502 ATTTAGGTCAATTTAACC-CTAGGGGT
1 ATTTAGGTCAATTT-ACCACTAGGGGT
*
18326528 ATTTCGGT-AATTTACCTACTAGGGGT
1 ATTTAGGTCAATTTACC-ACTAGGGGT
18326554 A
1 A
18326555 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 5 0.21
26 16 0.67
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (26 bp):
ATTTAGGTCAATTTACCACTAGGGGT
Found at i:18328072 original size:26 final size:26
Alignment explanation
Indices: 18328042--18328097 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
18328032 TGAAATTCCC
18328042 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18328068 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18328094 ATCA
1 ATCA
18328098 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:18330645 original size:19 final size:20
Alignment explanation
Indices: 18330618--18330659 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
18330608 TTATTTTTAA
18330618 TTTTATGAAATTTTAA-ATT
1 TTTTATGAAATTTTAATATT
* *
18330637 TTTTTTGAATTTTTAATATT
1 TTTTATGAAATTTTAATATT
18330657 TTT
1 TTT
18330660 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTATGAAATTTTAATATT
Found at i:18331045 original size:29 final size:30
Alignment explanation
Indices: 18331003--18331065 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
18330993 TTTAATGTGC
*
18331003 AATTGTATACATG-AATTTTGATTTTATAT
1 AATTGTATACATGAAATTTTGATTTGATAT
* * *
18331032 AATTTTATATATGAAATTTTGATTTGATTT
1 AATTGTATACATGAAATTTTGATTTGATAT
18331062 AATT
1 AATT
18331066 ATTGTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (30 bp):
AATTGTATACATGAAATTTTGATTTGATAT
Found at i:18333785 original size:26 final size:26
Alignment explanation
Indices: 18333751--18333819 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
18333741 GGGAATACTC
*
18333751 CACAACTCGTGTGAGC-AGACCCATTT
1 CACAGCTCGTGTGAGCAAG-CCCATTT
**
18333777 CGTAGCTCGTGTGAGCAAGCCCATTT
1 CACAGCTCGTGTGAGCAAGCCCATTT
18333803 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
18333820 TATATGTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 35 0.95
27 2 0.05
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAAGCCCATTT
Found at i:18334105 original size:20 final size:20
Alignment explanation
Indices: 18334082--18334122 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18334072 CAAATTTATA
18334082 TGAATCATGTCTAAATGAAC
1 TGAATCATGTCTAAATGAAC
18334102 TGAATCATGTCTAAATGAAC
1 TGAATCATGTCTAAATGAAC
18334122 T
1 T
18334123 AACATGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
TGAATCATGTCTAAATGAAC
Found at i:18337068 original size:31 final size:31
Alignment explanation
Indices: 18337030--18337091 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
18337020 TTAAGAGAAG
*
18337030 GGAAAGACGAGAGACAAAAATTTAGTTTGTA
1 GGAAAGACGAGAGACAAAAATTCAGTTTGTA
18337061 GGAAAGACGAGAGACAAAAATTCAGTTTGTA
1 GGAAAGACGAGAGACAAAAATTCAGTTTGTA
18337092 CTTTTATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.26, T:0.21
Consensus pattern (31 bp):
GGAAAGACGAGAGACAAAAATTCAGTTTGTA
Found at i:18337473 original size:36 final size:36
Alignment explanation
Indices: 18337428--18337521 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
18337418 GGTTCGATTT
* * * *
18337428 TACCTATGAGGTGCAGAGTGCATATTTCCTTCGAATG
1 TACCAATGAGGTGCAGAGTACAT-TTTACTTCGAATA
* **
18337465 T-CCAATGAGGTGCGGAGTACATTTTACTTCGGCTA
1 TACCAATGAGGTGCAGAGTACATTTTACTTCGAATA
18337500 TACCAATGAGGTGC-GAAGTACA
1 TACCAATGAGGTGCAG-AGTACA
18337522 ATTAATACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 11 0.23
36 36 0.75
37 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (36 bp):
TACCAATGAGGTGCAGAGTACATTTTACTTCGAATA
Found at i:18337931 original size:26 final size:26
Alignment explanation
Indices: 18337902--18337957 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
18337892 TGGTACAAAT
18337902 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
18337928 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
18337954 TGAT
1 TGAT
18337958 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:18342115 original size:22 final size:22
Alignment explanation
Indices: 18342084--18342130 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18342074 CAATCGAGTT
* *
18342084 TTTTTAATTTATGTTTTTATTCA
1 TTTTTAATTTAAGATTTTATT-A
18342107 TTTTT-ATTTAAGATTTTATTA
1 TTTTTAATTTAAGATTTTATTA
18342128 TTT
1 TTT
18342131 GTTTTCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTAATTTAAGATTTTATTA
Found at i:18342271 original size:31 final size:31
Alignment explanation
Indices: 18342231--18342334 Score: 122
Period size: 31 Copynumber: 3.3 Consensus size: 31
18342221 ATTATTTAAA
* *
18342231 ATTTCTATTTTAAAATTT-TCTTTATACATGT
1 ATTTTTATTTTAAAATTTATCATTATACAT-T
18342262 ATTTTTATTTTCAAAATTTATACATTATACATT
1 ATTTTTATTTT-AAAATTTAT-CATTATACATT
*
18342295 ATATATTATTTTAAAATTTAT-ATTATACATT
1 AT-TTTTATTTTAAAATTTATCATTATACATT
18342326 ATTATTTAT
1 ATT-TTTAT
18342335 ATATTGTTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
30 1 0.02
31 26 0.41
32 7 0.11
33 13 0.20
34 17 0.27
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.57
Consensus pattern (31 bp):
ATTTTTATTTTAAAATTTATCATTATACATT
Found at i:18345125 original size:37 final size:37
Alignment explanation
Indices: 18345075--18345153 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
18345065 TTATTACGAA
* * *
18345075 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
18345112 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
18345149 GTCTT
1 GTCTT
18345154 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:18345348 original size:49 final size:48
Alignment explanation
Indices: 18345271--18345428 Score: 264
Period size: 49 Copynumber: 3.2 Consensus size: 48
18345261 GCCCTTCGGG
18345271 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATA-AC
18345321 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATA-AC
* *
18345370 ACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATAT-AC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAAC
18345417 ACTTTCACATTC
1 ACTTTCACATTC
18345429 TCAAAGTAAG
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
47 14 0.13
49 87 0.83
50 4 0.04
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (48 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAAC
Found at i:18345747 original size:24 final size:23
Alignment explanation
Indices: 18345699--18345756 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
18345689 TAATCAAACA
18345699 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
18345723 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
18345747 TTATT-TTATA
1 TTATTATTATA
18345757 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:18348958 original size:40 final size:40
Alignment explanation
Indices: 18348926--18349254 Score: 333
Period size: 40 Copynumber: 8.2 Consensus size: 40
18348916 CTTCGAGACC
* * * * ***
18348926 TAGCCCGGATATAACACCAGCACGAATGCTCTTTGGGGTT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
* *
18348966 TAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
18349006 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
* *
18349046 TAGCTCGGATACATCACTAGCACGAATGCTCTTTGGAACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
* * *
18349086 TAGCCCGGGTACATCACTAGCATGAATGCTCTTCGGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
** * *
18349126 TAGCCCGGATACATTGCTAGCATGAATGCTCTTCGGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
* ** * * * *
18349166 TAGTCCGGATTTAGTAACTCGCACCAATGC-CTTCGGATCT
1 TAGCCCGGATACA-TCACTAGCACGAATGCTCTTCGGAACT
* ** *
18349206 TAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTCAGG-ACT
1 TAGCCCGGATA-CATCAC-TAGCACGAATGCTCTTC-GGAACT
18349246 TAGCCCGGA
1 TAGCCCGGA
18349255 CATCGTTCGA
Statistics
Matches: 248, Mismatches: 37, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
40 230 0.93
41 18 0.07
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACT
Found at i:18349601 original size:29 final size:29
Alignment explanation
Indices: 18349562--18349640 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
18349552 CTTAATAATC
* *
18349562 AACCACGCACACTTAGTGTCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
18349592 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
18349621 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
18349641 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:18349683 original size:43 final size:43
Alignment explanation
Indices: 18349622--18349724 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
18349612 TGCATTTCAA
18349622 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
18349665 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
18349708 GCCCGTACACTTAGTGC
1 GCCCGCACACTTAGTGC
18349725 TGAAAACCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:18351626 original size:37 final size:37
Alignment explanation
Indices: 18351567--18351668 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
18351557 TTGAATATAT
18351567 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
18351604 TAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
18351641 AAATCCCCACACGTAGTCATCGGGTCTT
1 TAATCTCCACACGTAGTCATCGGGTCTT
18351669 TAGAGCTCGG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (37 bp):
TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:18352164 original size:24 final size:23
Alignment explanation
Indices: 18352116--18352173 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
18352106 TAATCAAACA
18352116 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
18352140 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
18352164 TTATT-TTATA
1 TTATTATTATA
18352174 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:18355812 original size:69 final size:69
Alignment explanation
Indices: 18355691--18355827 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
18355681 AGAAGGGCTA
* * * *
18355691 ATAGGGTGTGATTCCTCTCATATGTATTATGATGAGGATTCGGGTCTCTCATTGTATTGGGCACA
1 ATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTAGGCACA
18355756 ATTG
66 ATTG
* * * *
18355760 ATAGAGTGTGCTTCCCCTTATATGTATTATGATG-GAGATTTGGGCCTTTCATTGTATTAGGCAC
1 ATAGAGTGTGATTCCCCTCATATGTATTATGATGAG-GATTCGGGCCTCTCATTGTATTAGGCAC
18355824 AATT
65 AATT
18355828 ATATGTGCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.39
Consensus pattern (69 bp):
ATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTAGGCACA
ATTG
Found at i:18359748 original size:46 final size:46
Alignment explanation
Indices: 18359694--18360271 Score: 838
Period size: 46 Copynumber: 12.6 Consensus size: 46
18359684 GCTTTCTGAA
18359694 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
18359740 AAGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
18359786 ATGAAATGTGTAAGACCATGGTTGAAGGACACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
18359832 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
18359878 ATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
18359924 ATAAAATGTGTAAGACCATGGTTAAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
18359970 ATCAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
18360016 ATCAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
18360062 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
18360108 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * ** * *
18360153 CGGGAAT-TAATAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGT-GTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * *
18360199 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
18360245 A-GAAAATGAGTAAGACCATAGTTGAAA
1 ATG-AAATGTGTAAGACCATGGTTGAAA
18360272 AACACTATGG
Statistics
Matches: 485, Mismatches: 43, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
44 1 0.00
45 36 0.07
46 448 0.92
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:18360588 original size:16 final size:17
Alignment explanation
Indices: 18360567--18360599 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18360557 ATGATGGAGC
18360567 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
18360583 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
18360600 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:18364671 original size:38 final size:38
Alignment explanation
Indices: 18364606--18364722 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 38
18364596 CTTTGAGATT
*
18364606 TAGTGGCATTAGCAGCG-TTTTTCAAAAAGCGCCGCTAA
1 TAGTGGCATTAGCGGCGCTTTTTCAAAAA-CGCCGCTAA
* * *
18364644 TAGTGGCATTAGCGGCGCTTTGTAAAAAAAGCCG-TAA
1 TAGTGGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
* * *
18364681 TAGATTGAGTATTAGCGGCGCTTTTTGATAAACGCCGCTAA
1 TAG--TG-GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
18364722 T
1 T
18364723 GCTCGATAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 6 0.09
38 20 0.31
39 11 0.17
40 24 0.37
41 4 0.06
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (38 bp):
TAGTGGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
Found at i:18365421 original size:22 final size:22
Alignment explanation
Indices: 18365384--18365437 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
18365374 CTTAAATCTC
18365384 AAAC-CTTAAACTATAAACCCT
1 AAACTCTTAAACTATAAACCCT
18365405 AAACTCTTAAA-TCATAAACCCT
1 AAACTCTTAAACT-ATAAACCCT
*
18365427 AAAATCTTAAA
1 AAACTCTTAAA
18365438 AATAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACTCTTAAACTATAAACCCT
Found at i:18365927 original size:14 final size:14
Alignment explanation
Indices: 18365910--18366022 Score: 79
Period size: 14 Copynumber: 8.1 Consensus size: 14
18365900 TAGTTTATAA
18365910 GGTTTAGGGTATTG
1 GGTTTAGGGTATTG
18365924 GGTTTAGGGT-TTAG
1 GGTTTAGGGTATT-G
*** *
18365938 GGTTTAATCTATAG
1 GGTTTAGGGTATTG
*
18365952 GGTTTAAGGTATTG
1 GGTTTAGGGTATTG
**
18365966 GGTATT-TTGT-TTAG
1 GGT-TTAGGGTATT-G
** *
18365980 GGTTTAGTCTATAG
1 GGTTTAGGGTATTG
18365994 GGTTTAGGGTATTG
1 GGTTTAGGGTATTG
*
18366008 GGTTTAGTGTATTG
1 GGTTTAGGGTATTG
18366022 G
1 G
18366023 TTTTGGGCTT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
13 6 0.08
14 67 0.87
15 4 0.05
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (14 bp):
GGTTTAGGGTATTG
Found at i:18365935 original size:42 final size:42
Alignment explanation
Indices: 18365888--18366014 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
18365878 TTAGGGTATT
** * *
18365888 GGGTTTAGAATTTAGTTTATAAGGTTTAGGGTATTGGGTTTA
1 GGGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGTTTA
* *
18365930 GGGTTTAGGGTTTAATCTATAGGGTTTAAGGTATTGGGTATT-
1 GGGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGT-TTA
**
18365972 TTGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGTTTA
1 GGGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGTTTA
18366014 G
1 G
18366015 TGTATTGGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 68 0.94
43 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (42 bp):
GGGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGTTTA
Found at i:18365937 original size:35 final size:35
Alignment explanation
Indices: 18365873--18366014 Score: 113
Period size: 35 Copynumber: 3.7 Consensus size: 35
18365863 ATTTAAGTTC
**
18365873 AAGGTTTAGGGTATTGGGTTTAGAATTTAGTTTAT
1 AAGGTTTAGGGTATTGGGTTTAGGGTTTAGTTTAT
18365908 AAGGTTTAGGGTATTGGGTTTAGGGTTTAGGGTTTAATCT
1 AAGGTTTAGGGTATTGGGTTTAGGGTTTA--GTTT-A--T
* *
18365948 ATAGGGTTTAAGGTATTGGGTATTTTGTTTAGGGTTTAGTCTAT
1 A-A-GGTTTAGGGTATT-GG------GTTTAGGGTTTAGTTTAT
*
18365992 AGGGTTTAGGGTATTGGGTTTAG
1 AAGGTTTAGGGTATTGGGTTTAG
18366015 TGTATTGGTT
Statistics
Matches: 87, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
35 33 0.38
37 4 0.05
38 1 0.01
40 2 0.02
41 3 0.03
42 24 0.28
43 2 0.02
44 2 0.02
46 1 0.01
47 3 0.03
49 12 0.14
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.44
Consensus pattern (35 bp):
AAGGTTTAGGGTATTGGGTTTAGGGTTTAGTTTAT
Found at i:18366332 original size:84 final size:83
Alignment explanation
Indices: 18366242--18366395 Score: 184
Period size: 83 Copynumber: 1.8 Consensus size: 83
18366232 ATGAAAATGG
* * * *
18366242 CGTCGTTCTACTT-GGAGGGACAGTGGAGTTAGTGGCGCTAGGTCATAAACGCCGCTAAAAGTAT
1 CGTCGTTCTA-TTCCGAGGG-CAGTGGAGTTAGTGGCGCTAGCTCATAAACGCCACTAAAAATAT
18366306 GAGAAATTGTATTGAAACGT
64 GAGAAATTGTATTGAAACGT
* * * * * * *
18366326 CGTCGTTTTATTCCGCGGGTAGTGGATTTAGTGGTGCTATCTTATAAACGCCACTAAAAATATGA
1 CGTCGTTCTATTCCGAGGGCAGTGGAGTTAGTGGCGCTAGCTCATAAACGCCACTAAAAATATGA
18366391 GAAAT
66 GAAAT
18366396 CGAATGAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
83 45 0.78
84 13 0.22
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (83 bp):
CGTCGTTCTATTCCGAGGGCAGTGGAGTTAGTGGCGCTAGCTCATAAACGCCACTAAAAATATGA
GAAATTGTATTGAAACGT
Done.