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 91 of 279
Found at i:29895129 original size:21 final size:22
Alignment explanation
Indices: 29895105--29895153 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
29895095 AAGGTTTTAG
*
29895105 GGTTTTAAATAAATTAAGTT-A
1 GGTTTTAAATAAATTAAATTAA
*
29895126 GGTTTAAAATAAATTAAATTAA
1 GGTTTTAAATAAATTAAATTAA
29895148 GGTTTT
1 GGTTTT
29895154 GGGTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (22 bp):
GGTTTTAAATAAATTAAATTAA
Found at i:29895164 original size:107 final size:108
Alignment explanation
Indices: 29894898--29895238 Score: 531
Period size: 107 Copynumber: 3.1 Consensus size: 108
29894888 AAACGTGCCC
*
29894898 TAAGTTAGGGTTTAAAATAAATTAAATTAGGGTTTGGGTTTGGGTTTATTAAATTAAGGTTTGGG
1 TAAGTTAGGGTTTAAAATAAATTAAATTAGGG--T---TTTGGGTTTATTAAATTAAGGTTTGTG
* *
29894963 TTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGGATTTTAAATAAAT
61 TTTTTTAAATAGATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAAT
*
29895011 TAAGTTAGGGTTTAAAATAAATTAAATTAGGGTTTTTGGTTTATTAAATTAAGGTTTGTGTTTTT
1 TAAGTTAGGGTTTAAAATAAATTAAATTAGGGTTTTGGGTTTATTAAATTAAGGTTTGTGTTTTT
*
29895076 TAAATAGATTAAGTAAATTAAGGTTTTAGGGTTTTAAATAAAT
66 TAAATAGATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAAT
* * *
29895119 TAAGTTA-GGTTTAAAATAAATTAAATTAAGGTTTTGGGTTTATTAAATTAGGGTTTATGTTTTT
1 TAAGTTAGGGTTTAAAATAAATTAAATTAGGGTTTTGGGTTTATTAAATTAAGGTTTGTGTTTTT
*
29895183 TAAATTGATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAAT
66 TAAATAGATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAAT
* *
29895226 TAAATTAAGGTTT
1 TAAGTTAGGGTTT
29895239 TGGGTTTATT
Statistics
Matches: 215, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
107 100 0.47
108 82 0.38
111 1 0.00
113 32 0.15
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (108 bp):
TAAGTTAGGGTTTAAAATAAATTAAATTAGGGTTTTGGGTTTATTAAATTAAGGTTTGTGTTTTT
TAAATAGATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAAT
Found at i:29895185 original size:21 final size:21
Alignment explanation
Indices: 29895138--29895188 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
29895128 TTTAAAATAA
29895138 ATTAAATTAAGGTTTTGGGTTT
1 ATTAAATTAAGGTTTT-GGTTT
*
29895160 ATTAAATTAGGGTTTAT-GTTT
1 ATTAAATTAAGGTTT-TGGTTT
*
29895181 TTTAAATT
1 ATTAAATT
29895189 GATTAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 14 0.54
23 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (21 bp):
ATTAAATTAAGGTTTTGGTTT
Found at i:29895228 original size:34 final size:34
Alignment explanation
Indices: 29895162--29895228 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
29895152 TTGGGTTTAT
** **
29895162 TAAATTAGGGTTTATGTTTTTTAAATTGATTAAG
1 TAAATTAGGGTTTATGGGTTTTAAATAAATTAAG
29895196 TAAATTAGGGTTT-TAGGGTTTTAAATAAATTAA
1 TAAATTAGGGTTTAT-GGGTTTTAAATAAATTAA
29895229 ATTAAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 1 0.04
34 27 0.96
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (34 bp):
TAAATTAGGGTTTATGGGTTTTAAATAAATTAAG
Found at i:29895249 original size:22 final size:24
Alignment explanation
Indices: 29895223--29895279 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
29895213 GTTTTAAATA
29895223 AATTAAATTAAGGTTT-TGGGTTT
1 AATTAAATTAAGGTTTATGGGTTT
* *
29895246 -ATTAAATTAGGGTTTATGGTTTT
1 AATTAAATTAAGGTTTATGGGTTT
*
29895269 AAATAAATTAA
1 AATTAAATTAA
29895280 ATTAGGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 14 0.50
23 6 0.21
24 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.46
Consensus pattern (24 bp):
AATTAAATTAAGGTTTATGGGTTT
Found at i:29895653 original size:126 final size:124
Alignment explanation
Indices: 29895347--29895719 Score: 516
Period size: 126 Copynumber: 3.0 Consensus size: 124
29895337 TTTTACCCTG
* * * * *
29895347 AAAAAATAATTTTGACAAGACATTTTTAAACAAATAGTGTCAAAAACGCTTCAAGTAGGATGCAC
1 AAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGATGCAC
* * * * *
29895412 TGTCAGTAAAAATACAAAAAAAAGCTACCACGTGGA-CTTTTTTCGCTATAGTAGTTCCT
66 TGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGAGCTCTTTT-GCTACAGTAGTTCCT
*
29895471 GAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGATGCAC
1 AAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGATGCAC
29895536 TGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
66 TGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGA-GCTCTTTTGCTACAGTAGTTCCT
** * *
29895596 AAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACACTTTAAGCAGGATCCA
1 -AAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGATGCA
* * * *
29895661 CTGTCAGCAAAATTTCTGAAAAAAGCTCTCACGTGGATGCTCTCTTT-CTACAGTAGTTC
65 CTGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGA-GCTCT-TTTGCTACAGTAGTTC
29895720 ATGCTTGGCC
Statistics
Matches: 224, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
124 92 0.41
125 14 0.06
126 115 0.51
127 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (124 bp):
AAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGATGCAC
TGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGAGCTCTTTTGCTACAGTAGTTCCT
Found at i:29896153 original size:12 final size:12
Alignment explanation
Indices: 29896138--29896168 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29896128 TTCTCTTTTA
29896138 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
29896150 TTTTTCTTTCTC
1 TTTTTCTTTCCC
29896162 TTTTTCT
1 TTTTTCT
29896169 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:29900758 original size:21 final size:21
Alignment explanation
Indices: 29900734--29900773 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29900724 TAGTATATGT
*
29900734 TTTATTATATATGCATATATC
1 TTTAATATATATGCATATATC
*
29900755 TTTAATATATATGTATATA
1 TTTAATATATATGCATATA
29900774 ATTGTGTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTAATATATATGCATATATC
Found at i:29900888 original size:26 final size:25
Alignment explanation
Indices: 29900817--29900900 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 25
29900807 TTCTAATATG
*
29900817 TATATATTATGTAA-ATA-TTTTAA
1 TATATATTATGTAATATATTTTTTA
29900840 TAGTATATTATGT-ATATATTTTTTA
1 TA-TATATTATGTAATATATTTTTTA
*
29900865 TATATGTTATGTACATATATTTTTTAA
1 TATATATTATGTA-ATATATTTTTT-A
29900892 TATTATATT
1 TA-TATATT
29900901 TTTATATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.06
24 22 0.43
25 7 0.14
26 11 0.22
27 3 0.06
28 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (25 bp):
TATATATTATGTAATATATTTTTTA
Found at i:29900907 original size:13 final size:15
Alignment explanation
Indices: 29900880--29900912 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29900870 GTTATGTACA
29900880 TATATTTTTTAATAT
1 TATATTTTTTAATAT
29900895 TATA-TTTTTATATAT
1 TATATTTTTTA-ATAT
29900910 TAT
1 TAT
29900913 TATGTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTTTAATAT
Found at i:29900972 original size:25 final size:23
Alignment explanation
Indices: 29900817--29900972 Score: 91
Period size: 24 Copynumber: 6.9 Consensus size: 23
29900807 TTCTAATATG
* * *
29900817 TATATATTATGTAAATATTTTAA
1 TATATTTTATGTATATATTTTTA
*
29900840 TAGTATATTATGTATATATTTTTTA
1 TA-TATTTTATGTATATA-TTTTTA
*
29900865 TATATGTTATGTACATATATTTTT-
1 TATATTTTATGT--ATATATTTTTA
29900889 TA-A---TAT-TATAT-TTTTATA
1 TATATTTTATGTATATATTTT-TA
*
29900907 TAT-TATTATGTATATATT-TTA
1 TATATTTTATGTATATATTTTTA
*
29900928 -ATATCATTA-GTTATATATTTTTTA
1 TATAT-TTTATG-TATATA-TTTTTA
29900952 TACTATTTTATGTATATATTT
1 TA-TATTTTATGTATATATTT
29900973 CTAATACTAT
Statistics
Matches: 109, Mismatches: 4, Indels: 39
0.72 0.03 0.26
Matches are distributed among these distances:
16 4 0.04
17 5 0.05
18 2 0.02
19 1 0.01
20 5 0.05
21 7 0.06
22 16 0.15
23 7 0.06
24 31 0.28
25 22 0.20
26 9 0.08
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TATATTTTATGTATATATTTTTA
Found at i:29901167 original size:25 final size:24
Alignment explanation
Indices: 29901093--29901167 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 24
29901083 ATATATCATG
29901093 TATATATGATTTTTTTTACATATAT
1 TATATAT-ATTTTTTTTACATATAT
* **
29901118 TATGTATATATCTTTAATACTATATAAT
1 TA--TATATATTTTTTTTAC-ATAT-AT
29901146 T-TATATATTTTTTCTTACATAT
1 TATATATATTTTTT-TTACATAT
29901168 TATCTTACGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
25 16 0.41
26 11 0.28
27 9 0.23
28 3 0.08
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (24 bp):
TATATATATTTTTTTTACATATAT
Found at i:29901316 original size:27 final size:26
Alignment explanation
Indices: 29901286--29901346 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
29901276 TAATATATAA
*
29901286 ATTATGTATACATTTTTTAAATACTAT
1 ATTATGTATACATTTTTT-AATACCAT
* *
29901313 ATTATATATATATTTTTTAATACCAT
1 ATTATGTATACATTTTTTAATACCAT
29901339 ATTATGTA
1 ATTATGTA
29901347 CATATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATGTATACATTTTTTAATACCAT
Found at i:29901335 original size:26 final size:27
Alignment explanation
Indices: 29901286--29901352 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
29901276 TAATATATAA
* *
29901286 ATTATGTATACATTTTTTAAATACTAT
1 ATTATGTATATATTTTTTAAATACCAT
*
29901313 ATTATATATATATTTTTT-AATACCAT
1 ATTATGTATATATTTTTTAAATACCAT
*
29901339 ATTATGTACATATT
1 ATTATGTATATATT
29901353 ATTATATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTATGTATATATTTTTTAAATACCAT
Found at i:29901445 original size:24 final size:22
Alignment explanation
Indices: 29901376--29901458 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 22
29901366 TTACCCCTAT
29901376 TATAT-TTATTATTAATATTAGTA
1 TATATATT-TTATT-ATATTAGTA
29901399 TATATATTTTATTATACGTGTA-TA
1 TATATATTTTATTATA--T-TAGTA
*
29901423 TATATACTTT-TTATATATAGTA
1 TATATATTTTATTATAT-TAGTA
29901445 T-TAT-TTTTA-TATAT
1 TATATATTTTATTATAT
29901459 CATTATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 8 0.16
21 6 0.12
22 6 0.12
23 15 0.29
24 14 0.27
25 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATATTTTATTATATTAGTA
Found at i:29901457 original size:16 final size:16
Alignment explanation
Indices: 29901430--29901470 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
29901420 ATATATATAC
*
29901430 TTTTTATATATAGTATTA
1 TTTTTATATAT--CATTA
29901448 TTTTTATATATCATTA
1 TTTTTATATATCATTA
29901464 TTTTTAT
1 TTTTTAT
29901471 TATTATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
18 11 0.50
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTTATATATCATTA
Found at i:29901475 original size:3 final size:3
Alignment explanation
Indices: 29901443--29901526 Score: 50
Period size: 3 Copynumber: 28.0 Consensus size: 3
29901433 TTATATATAG
* * *
29901443 TAT TAT TTT TAT ATAT CAT TAT TTT TAT TAT TA- TACT TAT TAT T-T
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * *
29901488 TCAC TAT TGT TACT TAT TAT T-T TAT T-T TAA TAT TAT TAT
1 T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
29901527 GCATTATTTG
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
2 8 0.13
3 44 0.72
4 9 0.15
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29903094 original size:26 final size:26
Alignment explanation
Indices: 29903065--29903149 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 26
29903055 AAAAAAAATT
29903065 ATAAAATAAAAATTAATTAAAATTAC
1 ATAAAATAAAAATTAATTAAAATTAC
* * *
29903091 ATAAATGAAAAAAATATTAAATAATATT-C
1 AT-AA--AATAAAA-ATTAATTAAAATTAC
*
29903120 A-AAAATTAAAATTAATTAAAATTAC
1 ATAAAATAAAAATTAATTAAAATTAC
29903145 ATAAA
1 ATAAA
29903150 TGAAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
24 11 0.24
25 7 0.15
26 5 0.11
27 4 0.09
29 8 0.17
30 11 0.24
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.31
Consensus pattern (26 bp):
ATAAAATAAAAATTAATTAAAATTAC
Found at i:29903135 original size:54 final size:54
Alignment explanation
Indices: 29903067--29903185 Score: 211
Period size: 54 Copynumber: 2.2 Consensus size: 54
29903057 AAAAAATTAT
*
29903067 AAAATAAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
1 AAAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
29903121 AAAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
1 AAAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
**
29903175 AATTTTAAAAT
1 AAAATTAAAAT
29903186 AAACCATTAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (54 bp):
AAAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
Found at i:29903177 original size:18 final size:19
Alignment explanation
Indices: 29903102--29903183 Score: 50
Period size: 18 Copynumber: 4.5 Consensus size: 19
29903092 TAAATGAAAA
29903102 AAATATTAAATAAT-ATTC
1 AAATATTAAATAATAATTC
* *
29903120 AAAAATTAAA-ATTAATT-
1 AAATATTAAATAATAATTC
* **
29903137 AAA-ATTACATAAATGAA-AA
1 AAATATTAAAT-AAT-AATTC
29903156 AAATATTAAATAAT-ATTC
1 AAATATTAAATAATAATTC
*
29903174 AAATTTTAAA
1 AAATATTAAA
29903184 ATAAACCATT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
16 5 0.10
17 6 0.12
18 23 0.48
19 8 0.17
20 6 0.12
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
AAATATTAAATAATAATTC
Found at i:29905056 original size:21 final size:21
Alignment explanation
Indices: 29905026--29905070 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
29905016 ACAATACATA
29905026 AAACAATATAAACTTATGCAC
1 AAACAATATAAACTTATGCAC
*
29905047 AAACATTATAAACTTATGCAC
1 AAACAATATAAACTTATGCAC
29905068 AAA
1 AAA
29905071 TGTCACCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.24
Consensus pattern (21 bp):
AAACAATATAAACTTATGCAC
Found at i:29906378 original size:30 final size:30
Alignment explanation
Indices: 29906332--29906393 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
29906322 ACTTACTTTA
29906332 TTGTCAATTTTCTTATTATTTTAAAGACAT
1 TTGTCAATTTTCTTATTATTTTAAAGACAT
* * *
29906362 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTCAATTTTCTTATTATTTTAAAGACAT
29906392 TT
1 TT
29906394 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (30 bp):
TTGTCAATTTTCTTATTATTTTAAAGACAT
Found at i:29908226 original size:33 final size:35
Alignment explanation
Indices: 29908183--29908249 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
29908173 CTACATACTT
* *
29908183 CATTTCTTTTAACGT-A-GTTTTTTTTATGTTTTC
1 CATTTATTTTAACATAACGTTTTTTTTATGTTTTC
*
29908216 CATTTATTTTAACATAACTTTTTTTTTATGTTTT
1 CATTTATTTTAACATAACGTTTTTTTTATGTTTT
29908250 TGAAACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 13 0.45
34 1 0.03
35 15 0.52
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.64
Consensus pattern (35 bp):
CATTTATTTTAACATAACGTTTTTTTTATGTTTTC
Found at i:29913950 original size:69 final size:69
Alignment explanation
Indices: 29913854--29914049 Score: 320
Period size: 69 Copynumber: 2.8 Consensus size: 69
29913844 TCTCGAATGC
* * * *
29913854 ACAAATGAGAAAGAGAGGGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTACAG
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACAATTACAG
29913919 ATAG
66 ATAG
*
29913923 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACAATTCCAG
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACAATTACAG
29913988 ATAG
66 ATAG
* * *
29913992 ACAAATAAGAAAGAGAGTGTGGAAGCATGATTGGGGGCATGGATTGGAGGTTGGGACA
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACA
29914050 GTCAAGGATA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 119 1.00
ACGTcount: A:0.34, C:0.09, G:0.37, T:0.19
Consensus pattern (69 bp):
ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACAATTACAG
ATAG
Found at i:29915466 original size:30 final size:30
Alignment explanation
Indices: 29915427--29915486 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
29915417 CCCTATCATG
29915427 CCTTCAATCACCATCAATATCATCATCTTT
1 CCTTCAATCACCATCAATATCATCATCTTT
*
29915457 CCTTGAATCACCATCAATATCATCATCTTT
1 CCTTCAATCACCATCAATATCATCATCTTT
29915487 ACCCCATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.37
Consensus pattern (30 bp):
CCTTCAATCACCATCAATATCATCATCTTT
Found at i:29917973 original size:21 final size:21
Alignment explanation
Indices: 29917949--29917988 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29917939 CTTCATCATT
29917949 GCTAACGGGACTTGTAAAACA
1 GCTAACGGGACTTGTAAAACA
29917970 GCTAACGGGACTTGTAAAA
1 GCTAACGGGACTTGTAAAA
29917989 TCACCTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (21 bp):
GCTAACGGGACTTGTAAAACA
Found at i:29918910 original size:32 final size:34
Alignment explanation
Indices: 29918874--29918941 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 34
29918864 GGTTACATAC
*
29918874 TTCATTTCTTTTAACAT-A-GTTTTTCTATGTTT
1 TTCATTTATTTTAACATAACGTTTTTCTATGTTT
* *
29918906 TTCATTTATTTTAACATAACTTTTTTTTATGTTT
1 TTCATTTATTTTAACATAACGTTTTTCTATGTTT
29918940 TT
1 TT
29918942 GAAACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.52
33 1 0.03
34 14 0.45
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (34 bp):
TTCATTTATTTTAACATAACGTTTTTCTATGTTT
Found at i:29920883 original size:36 final size:33
Alignment explanation
Indices: 29920842--29920929 Score: 86
Period size: 39 Copynumber: 2.5 Consensus size: 33
29920832 AAAATTAGAA
29920842 AAAATTATAAAAAAATAAAAATAGATAAAATTT
1 AAAATTATAAAAAAATAAAAATAGATAAAATTT
** *
29920875 AGATAAATTATTAAATTTTAATAAAAATATATAAAATTT
1 --A-AAATTA-TAAA--AAAATAAAAATAGATAAAATTT
*
29920914 AAAATTATTAAAAAAT
1 AAAATTATAAAAAAAT
29920930 TAGAAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
33 3 0.07
35 4 0.09
36 12 0.28
37 5 0.12
39 19 0.44
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAATTATAAAAAAATAAAAATAGATAAAATTT
Found at i:29920909 original size:20 final size:20
Alignment explanation
Indices: 29920855--29920915 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
29920845 ATTATAAAAA
*
29920855 AATAAAAATAGATAAAATTT
1 AATAAAAATATATAAAATTT
* *
29920875 AGAT-AAATTAT-TAAATTTT
1 A-ATAAAAATATATAAAATTT
29920894 AATAAAAATATATAAAATTT
1 AATAAAAATATATAAAATTT
29920914 AA
1 AA
29920916 AATTATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 15 0.45
21 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AATAAAAATATATAAAATTT
Found at i:29920930 original size:47 final size:44
Alignment explanation
Indices: 29920879--29921004 Score: 112
Period size: 47 Copynumber: 2.8 Consensus size: 44
29920869 AAATTTAGAT
* *
29920879 AAATTATTAAATTTTAATAAAAATATATAAAATTTAAAATTATTAAA
1 AAATTATAAAATTTTAATAAAAATATATAAAATTT--AA-CATTAAA
* * * * *
29920926 AAATTAGAAATTTTTTTATAAAAAT-TGTAAAATTTTACATTAAA
1 AAATTATAAA-ATTTTAATAAAAATATATAAAATTTAACATTAAA
29920970 AAATTATAAAATTTTACATTAAAAA-ATTATAAAAT
1 AAATTATAAAATTTTA-A-TAAAAATA-TATAAAAT
29921005 GCATCAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 4 0.06
44 16 0.25
45 7 0.11
46 7 0.11
47 17 0.27
48 12 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (44 bp):
AAATTATAAAATTTTAATAAAAATATATAAAATTTAACATTAAA
Found at i:29920971 original size:23 final size:23
Alignment explanation
Indices: 29920920--29921004 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
29920910 ATTTAAAATT
*
29920920 ATTAAAAAATTA-GAAATTTT--
1 ATTAAAAAATTATAAAATTTTAC
* *
29920940 TTTATAAAAATTGTAAAATTTTAC
1 ATTA-AAAAATTATAAAATTTTAC
29920964 ATTAAAAAATTATAAAATTTTAC
1 ATTAAAAAATTATAAAATTTTAC
29920987 ATTAAAAAATTATAAAAT
1 ATTAAAAAATTATAAAAT
29921005 GCATCAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.05
21 7 0.12
22 7 0.12
23 36 0.64
24 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTAAAAAATTATAAAATTTTAC
Found at i:29921724 original size:11 final size:12
Alignment explanation
Indices: 29921708--29921736 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
29921698 TACAACACAA
29921708 AAAAAATAT-AT
1 AAAAAATATAAT
29921719 AAAAAATATAAT
1 AAAAAATATAAT
29921731 AAAAAA
1 AAAAAA
29921737 GAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATATAAT
Found at i:29922388 original size:75 final size:75
Alignment explanation
Indices: 29922300--29922451 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
29922290 TAATATAGTA
29922300 TATGTTTTATTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATCATTTTTA
1 TATGTTTTATTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATCATTTTTA
29922365 CTATACATAT
66 CTATACATAT
* *
29922375 TATGTTTTGTTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATTATTTTTA
1 TATGTTTTATTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATCATTTTTA
29922440 CTATACATAT
66 CTATACATAT
29922450 TA
1 TA
29922452 CGTATATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (75 bp):
TATGTTTTATTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATCATTTTTA
CTATACATAT
Found at i:29922418 original size:20 final size:21
Alignment explanation
Indices: 29922393--29922434 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
29922383 GTTATATACG
*
29922393 TATATAGTATGTGTATT-TTA
1 TATATAGTATGTATATTATTA
*
29922413 TATATATTATGTATATTATTA
1 TATATAGTATGTATATTATTA
29922434 T
1 T
29922435 TTTTACTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATAGTATGTATATTATTA
Found at i:29922483 original size:75 final size:75
Alignment explanation
Indices: 29922307--29922501 Score: 238
Period size: 75 Copynumber: 2.6 Consensus size: 75
29922297 GTATATGTTT
* * *
29922307 TATTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATCATTTTTACTATACA
1 TATTAAATACATATATAGTATATGTATTTTATATATATTATGTATATTATCATTTTTACTATACA
* *
29922372 TATTATGTTT
66 TATTACGTTA
* * * * *
29922382 TGTTATATACGTATATAGTATGTGTATTTTATATATATTATGTATATTATTATTTTTACTATACA
1 TATTAAATACATATATAGTATATGTATTTTATATATATTATGTATATTATCATTTTTACTATACA
29922447 TATTACGTATA
66 TATTACGT-TA
29922458 TATTAAATATCATAT-TA-T-TCATGTATTTTAT-TATA-TATGTATAT
1 TATTAAATA-CATATATAGTAT-ATGTATTTTATATATATTATGTATAT
29922502 ATCTTTAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
73 9 0.08
74 5 0.05
75 81 0.74
76 10 0.09
77 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (75 bp):
TATTAAATACATATATAGTATATGTATTTTATATATATTATGTATATTATCATTTTTACTATACA
TATTACGTTA
Found at i:29922508 original size:21 final size:21
Alignment explanation
Indices: 29922484--29922523 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29922474 ATTCATGTAT
*
29922484 TTTATTATATATGTATATATC
1 TTTAATATATATGTATATATC
*
29922505 TTTAATATATATTTATATA
1 TTTAATATATATGTATATA
29922524 AGTATATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAATATATATGTATATATC
Found at i:29922623 original size:24 final size:25
Alignment explanation
Indices: 29922596--29922646 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
29922586 ATGTGTGTGC
29922596 ATATTATGTAAATGTTTTA-ATATT
1 ATATTATGTAAATGTTTTATATATT
**
29922620 ATATTATGTGTATGTTTTATATATT
1 ATATTATGTAAATGTTTTATATATT
29922645 AT
1 AT
29922647 GAACATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (25 bp):
ATATTATGTAAATGTTTTATATATT
Found at i:29928027 original size:15 final size:15
Alignment explanation
Indices: 29928007--29928046 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
29927997 GAGGCCTCCA
29928007 TACCCGAAATGGTAC
1 TACCCGAAATGGTAC
29928022 TACCCGAAATGGTAC
1 TACCCGAAATGGTAC
29928037 TACCC-AAATG
1 TACCCGAAATG
29928047 CTGGTTGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (15 bp):
TACCCGAAATGGTAC
Found at i:29934851 original size:75 final size:74
Alignment explanation
Indices: 29934746--29935259 Score: 485
Period size: 75 Copynumber: 7.0 Consensus size: 74
29934736 CTGTTTTAAA
*
29934746 AAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTC-GAGGTATTTTCAAAT
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTCTGAGGTATTTTCAATT
*
29934810 TCTACTT-TC
65 TCTATTTGTC
* * *** * *
29934819 AAAAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTTGGCTTACGTGTTGA-GTCACTTTC
1 ---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGT-CTGAGGT-ATTTTC
*
29934883 AATTTCTGTTT-T-
61 AATTTCTATTTGTC
* * * * * *
29934895 ---TATCAACTCATATTGCGGGAAGTGAGTTAAGCCTCAGGGCACG-CTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTCTGAGGTATTTTCAATTT
29934956 CTATTTGTC
66 CTATTTGTC
* * ** * *
29934965 AAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGT-CTGAGGTATTTTCAATT
29935030 TCTATTTGTC
65 TCTATTTGTC
* * *
29935040 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCCGGGCACG-CTGAGGTATTTTCGATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTCTGAGGTATTTTCAATTT
* *
29935104 CTGCTCT-TC
66 CT-ATTTGTC
* * * * * *
29935113 AAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACAC-ACTAAGGTAATTTCAAT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTCTGAGGTATTTTCAAT
*
29935177 TTCTGTTTGTC
64 TTCTATTTGTC
* * ** * *
29935188 AGAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGT-CTGAGGTATTTTCAATT
29935253 TCTATTT
65 TCTATTT
29935260 TTAATTTCTG
Statistics
Matches: 358, Mismatches: 62, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
68 18 0.05
69 3 0.01
70 33 0.09
73 94 0.26
74 4 0.01
75 174 0.49
76 16 0.04
77 16 0.04
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (74 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGTCTGAGGTATTTTCAATTT
CTATTTGTC
Found at i:29935378 original size:89 final size:87
Alignment explanation
Indices: 29935170--29936082 Score: 774
Period size: 89 Copynumber: 10.6 Consensus size: 87
29935160 ACTAAGGTAA
* * *
29935170 TTTCAATTTCTGTTTGTCAGAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* ** *
29935234 TGCTGAGGTCTTTTCAATTTCTATT
63 CGCTGAGGTAATTTCAATTTCTGTT
* *
29935259 TTT-AATTTCTGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
1 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
29935323 TGAGGTAATTTCAATTTTTGTT
66 TGAGGTAATTTCAATTTCTGTT
* * *
29935345 TTCTCCAATTTATGTTTTTCAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TT-T-CAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * *
29935410 ACTGAGGTATTTTCAATTTCTGCT
64 GCTGAGGTAATTTCAATTTCTGTT
** * * *
29935434 TTTCAATTTCTACTTTCCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTAGGACAC
1 TTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * *
29935499 GCTGA-GTGATTTCGATTTATGTT
64 GCTGAGGTAATTTCAATTTCTGTT
* * *
29935522 TGTCAA------------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAC
1 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * *
29935575 TGAGGTATTTTCGATTTCTGCT
66 TGAGGTAATTTCAATTTCTGTT
* * *
29935597 TTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
29935662 GCTGAGGTAATTTCAATTTATGTT
64 GCTGAGGTAATTTCAATTTCTGTT
* ** *** * * * * * * * * *
29935686 TGTCAAAAATC---AACTC--ATATC-GC-GAGA--G-GTGAGTTGAGCCTCAG-CTC---ACAT
1 TTTC-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG-TTGAGCCTCAGGACAC
** *
29935737 GCTGAGGTCTTTTCAATTTCTATT
64 GCTGAGGTAATTTCAATTTCTGTT
* * *
29935761 TTT-AATTTCTGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCTGGACATGC
1 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
29935825 TGAGGTAATTTCAATTTCTGTT
66 TGAGGTAATTTCAATTTCTGTT
* * * * *
29935847 TTCTCCAATTTATGTTTTTCAAAAATCAGCTCATATTGCGAGATGTGAGTTGAGCCTCAGGGCAA
1 TT-T-CAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
29935912 GCTGAGGTATTTTCAATTTCTGTT
64 GCTGAGGTAATTTCAATTTCTGTT
** * *
29935936 TTTCAATTTCTGCTTTTAAAAAAAAAACCAACTCATATTACGAGAGGTGAGTTGAGCCTC-GGCT
1 TTTCAATTTCTG-TTTT---TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--
* * *
29936000 CACATGCTGAGGTATTTTCAATTTATGTTT
60 -ACACGCTGAGGTAATTTCAATTTCTG-TT
* * *
29936030 TTTCAATTTATATTTTTCAAAGATCAACTCATATTGCGAG-GGTGAGTTGAGCC
1 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
29936083 GTGGGTTCAC
Statistics
Matches: 666, Mismatches: 110, Indels: 96
0.76 0.13 0.11
Matches are distributed among these distances:
73 4 0.01
74 46 0.07
75 43 0.06
76 2 0.00
78 15 0.02
79 5 0.01
80 2 0.00
81 2 0.00
82 5 0.01
83 15 0.02
86 53 0.08
87 23 0.03
88 72 0.11
89 281 0.42
90 25 0.04
91 34 0.05
93 27 0.04
94 12 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (87 bp):
TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGTT
Found at i:29935438 original size:14 final size:14
Alignment explanation
Indices: 29935419--29935449 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29935409 CACTGAGGTA
*
29935419 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
29935433 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
29935447 TTT
1 TTT
29935450 CCAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:29935548 original size:163 final size:164
Alignment explanation
Indices: 29935350--29936029 Score: 783
Period size: 163 Copynumber: 4.1 Consensus size: 164
29935340 TTGTTTTCTC
* *
29935350 CAATTTATGTTTTTC--AGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACA-C
1 CAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAGC
* *
29935412 TGAGGTATTTTCAATTTCTGCTTTTCAATTTCTACTTTCCAAAAAAATCAACTCATATTGTGAGA
66 TGAGGTATTTTCAATTTCTGCTTTTCAATTTCTGCTTT-CAAAAAAATCAACTCATATTGCGAGA
*
29935477 GGTGAGTTGAGCCTTAGGACACGCTGA-GTGATTT
130 GGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTT
*
29935511 CGATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACA-C
1 CAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAGC
* *
29935575 TGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGA
66 TGAGGTATTTTCAATTTCTGCTTTTCAATTTCTGCT-TTCAAAAAAATCAACTCATATTGCGAGA
*
29935640 GGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
130 GGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTT
* **
29935675 CAATTTATGTTTGTC--AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCTCACATG
1 CAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACA-G
* * * * *
29935738 CTGAGGTCTTTTCAATTTCT-ATTTTTAATTTCTGTTTTTC--AAAAATCAACTCATACTGCGAG
65 CTGAGGTATTTTCAATTTCTGCTTTTCAATTTCTG-CTTTCAAAAAAATCAACTCATATTGCGAG
*
29935800 AGGTGAGTTGAGCCTCT-GGACATGCTGAGGTAATTT
129 AGGTGAGTTGAGCCT-TAGGACACGCTGAGGTAATTT
* * * *
29935836 CAATTTCTGTTTTCTCCAATTTATGTTTTTCAAAAATCAGCTCATATTGCGAGATGTGAGTTGAG
1 CAATTTATG-TTTGT-C-A---A--------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * *
29935901 CCTCAGGGCA-AGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTTTTAAAAAAAAAACC
52 CCTCAGGGCACAGCTGAGGTATTTTCAATTTCTGCTTTTCAATTTCTGC-TTT--CAAAAAAATC
* * * *
29935965 AACTCATATTACGAGAGGTGAGTTGAGCC-TCGGCTCACATGCTGAGGTATTTT
114 AACTCATATTGCGAGAGGTGAGTTGAGCCTTAGG---ACACGCTGAGGTAATTT
29936018 CAATTTATGTTT
1 CAATTTATGTTT
29936030 TTTCAATTTA
Statistics
Matches: 446, Mismatches: 39, Indels: 48
0.84 0.07 0.09
Matches are distributed among these distances:
161 75 0.17
162 47 0.11
163 145 0.33
164 41 0.09
175 20 0.04
176 16 0.04
177 39 0.09
178 1 0.00
179 2 0.00
180 33 0.07
181 3 0.01
182 24 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (164 bp):
CAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAGC
TGAGGTATTTTCAATTTCTGCTTTTCAATTTCTGCTTTCAAAAAAATCAACTCATATTGCGAGAG
GTGAGTTGAGCCTTAGGACACGCTGAGGTAATTT
Found at i:29935578 original size:74 final size:75
Alignment explanation
Indices: 29935451--29935591 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 75
29935441 TTCTACTTTC
* * *
29935451 CAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTAGGACACGCTGA-GTGA-TTTCGA
1 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGT-ATTTTCGA
29935514 TTTATGTTTGT
65 TTTATGTTTGT
*
29935525 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTATTTTCGAT
1 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCGAT
29935590 TT
66 TT
29935592 CTGCTTTCCA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 50 0.82
75 11 0.18
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (75 bp):
CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCGAT
TTATGTTTGT
Found at i:29935751 original size:75 final size:73
Alignment explanation
Indices: 29935617--29935755 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 73
29935607 TGCTCTTCAA
* *
29935617 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTA
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCACACGCTGAGGTAATTTCAATTTA
29935682 TGTTTGTC
66 TGTTTGTC
* **
29935690 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAG--CACACGCTGAGGTAATTTCAATT
29935755 T
64 T
29935756 CTATTTTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 39 0.66
75 20 0.34
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (73 bp):
AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCACACGCTGAGGTAATTTCAATTTA
TGTTTGTC
Found at i:29935940 original size:14 final size:15
Alignment explanation
Indices: 29935921--29935952 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
29935911 AGCTGAGGTA
29935921 TTTTCAATTTCTG-T
1 TTTTCAATTTCTGCT
29935935 TTTTCAATTTCTGCT
1 TTTTCAATTTCTGCT
29935950 TTT
1 TTT
29935953 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTTCAATTTCTGCT
Found at i:29936034 original size:15 final size:15
Alignment explanation
Indices: 29936014--29936046 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29936004 TGCTGAGGTA
*
29936014 TTTTCAATTTATGTT
1 TTTTCAATTTATATT
29936029 TTTTCAATTTATATT
1 TTTTCAATTTATATT
29936044 TTT
1 TTT
29936047 CAAAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:29938042 original size:20 final size:21
Alignment explanation
Indices: 29938019--29938060 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
29938009 GTTATATACG
*
29938019 TATATAGTATGTGTATT-TTA
1 TATATAGTATGTATATTATTA
*
29938039 TATATATTATGTATATTATTA
1 TATATAGTATGTATATTATTA
29938060 T
1 T
29938061 TTTTACTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATAGTATGTATATTATTA
Found at i:29938134 original size:21 final size:21
Alignment explanation
Indices: 29938110--29938149 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29938100 ATTCATGTAT
*
29938110 TTTATTATATATGTATATATC
1 TTTAATATATATGTATATATC
*
29938131 TTTAATATATATTTATATA
1 TTTAATATATATGTATATA
29938150 AGTATATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAATATATATGTATATATC
Found at i:29938249 original size:24 final size:25
Alignment explanation
Indices: 29938222--29938272 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
29938212 ATGTGTGTAC
29938222 ATATTATGTAAATGTTTTA-ATATT
1 ATATTATGTAAATGTTTTATATATT
**
29938246 ATATTATGTGTATGTTTTATATATT
1 ATATTATGTAAATGTTTTATATATT
29938271 AT
1 AT
29938273 GAACATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (25 bp):
ATATTATGTAAATGTTTTATATATT
Found at i:29939350 original size:10 final size:10
Alignment explanation
Indices: 29939335--29939485 Score: 72
Period size: 10 Copynumber: 15.7 Consensus size: 10
29939325 TTGGTATGAT
29939335 AATTTTTATA
1 AATTTTTATA
29939345 AATTTTTTATGA
1 AA-TTTTTAT-A
29939357 AA--TTTAT-
1 AATTTTTATA
29939364 -ATTTCTT-TA
1 AATTT-TTATA
*
29939373 CATTTTGTATA
1 AATTTT-TATA
* *
29939384 ATTTTCTTATG
1 AATTT-TTATA
* *
29939395 ACTTTATA-A
1 AATTTTTATA
29939404 AA-TTTTATA
1 AATTTTTATA
*
29939413 TATTTTTAT-
1 AATTTTTATA
*
29939422 -ATTTCTATA
1 AATTTTTATA
*
29939431 TA-TTTTAT-
1 AATTTTTATA
29939439 AATTTTTATA
1 AATTTTTATA
29939449 AATTTTTATA
1 AATTTTTATA
* *
29939459 AAATTTTACA
1 AATTTTTATA
*
29939469 ATTTTTTATA
1 AATTTTTATA
*
29939479 TATTTTT
1 AATTTTT
29939486 TTTACGATTT
Statistics
Matches: 106, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
6 1 0.01
8 14 0.13
9 22 0.21
10 46 0.43
11 19 0.18
12 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
AATTTTTATA
Found at i:29939430 original size:18 final size:17
Alignment explanation
Indices: 29939405--29939458 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
29939395 ACTTTATAAA
29939405 ATTTTATATATTTTTAT
1 ATTTTATATATTTTTAT
29939422 ATTTCTATATA-TTTTAT
1 ATTT-TATATATTTTTAT
*
29939439 AATTTTTATAAATTTTTAT
1 -A-TTTTATATATTTTTAT
29939458 A
1 A
29939459 AAATTTTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 10 0.31
18 13 0.41
19 9 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATATTTTTAT
Found at i:29939445 original size:9 final size:9
Alignment explanation
Indices: 29939333--29939527 Score: 69
Period size: 10 Copynumber: 20.1 Consensus size: 9
29939323 TTTTGGTATG
29939333 ATAATTTTT
1 ATAATTTTT
29939342 ATAAATTTTTT
1 AT-AA-TTTTT
*
29939353 ATGAA-ATTT
1 AT-AATTTTT
29939362 AT-ATTTCTT
1 ATAATTT-TT
29939371 -TACATTTTGT
1 ATA-ATTTT-T
29939381 ATAATTTTCTT
1 ATAA-TTT-TT
* *
29939392 ATGA-CTTT
1 ATAATTTTT
*
29939400 ATAAAATTTT
1 AT-AATTTTT
29939410 ATATATTTTT
1 ATA-ATTTTT
*
29939420 AT-ATTTCT
1 ATAATTTTT
29939428 AT-ATATTTT
1 ATAAT-TTTT
29939437 ATAATTTTT
1 ATAATTTTT
29939446 ATAAATTTTT
1 AT-AATTTTT
*
29939456 ATAAAATTTT
1 AT-AATTTTT
*
29939466 ACAATTTTTT
1 ATAA-TTTTT
29939476 ATATATTTTTT
1 ATA-A-TTTTT
*
29939487 TTACGATTTTT
1 ATA--ATTTTT
*
29939498 ATATTTTTT
1 ATAATTTTT
* *
29939507 CTAATATTTA
1 ATAAT-TTTT
29939517 ATAAATTTTT
1 AT-AATTTTT
29939527 A
1 A
29939528 AGATTTGATT
Statistics
Matches: 142, Mismatches: 23, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 15 0.11
9 34 0.24
10 53 0.37
11 37 0.26
12 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:29939462 original size:11 final size:10
Alignment explanation
Indices: 29939397--29939485 Score: 78
Period size: 10 Copynumber: 9.3 Consensus size: 10
29939387 TTCTTATGAC
*
29939397 TTTATAAAAT
1 TTTATAAATT
*
29939407 TTTATATATT
1 TTTATAAATT
29939417 TTTAT--ATT
1 TTTATAAATT
* *
29939425 TCTATATA-T
1 TTTATAAATT
29939434 TTTAT-AATT
1 TTTATAAATT
29939443 TTTATAAATT
1 TTTATAAATT
*
29939453 TTTATAAAAT
1 TTTATAAATT
* *
29939463 TTTACAATTT
1 TTTATAAATT
*
29939473 TTTATATATT
1 TTTATAAATT
29939483 TTT
1 TTT
29939486 TTTACGATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
8 8 0.13
9 11 0.17
10 44 0.70
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTATAAATT
Found at i:29939487 original size:22 final size:21
Alignment explanation
Indices: 29939462--29939506 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
29939452 TTTTATAAAA
29939462 TTTTACAATTTTTTATATATTTT
1 TTTTACAA-TTTTTATAT-TTTT
*
29939485 TTTTACGATTTTTATATTTTT
1 TTTTACAATTTTTATATTTTT
29939506 T
1 T
29939507 CTAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTACAATTTTTATATTTTT
Found at i:29941585 original size:9 final size:9
Alignment explanation
Indices: 29941557--29941641 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 9
29941547 ATTTTTTTTT
29941557 AAATT-TAA
1 AAATTATAA
*
29941565 AAATTCAAAA
1 AAATT-ATAA
29941575 AAATTATAA
1 AAATTATAA
29941584 AAATTATTTTTAA
1 AAATTA----TAA
29941597 AAA-TA-AA
1 AAATTATAA
* *
29941604 AAATCATTA
1 AAATTATAA
*
29941613 AAATGATTAA
1 AAATTA-TAA
29941623 AAATTATAA
1 AAATTATAA
29941632 AAA-TATAA
1 AAATTATAA
29941640 AA
1 AA
29941642 GAAATATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 5 0.08
8 13 0.21
9 21 0.34
10 14 0.23
12 2 0.03
13 6 0.10
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:29941604 original size:38 final size:39
Alignment explanation
Indices: 29941552--29941629 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
29941542 CATTTATTTT
** * *
29941552 TTTTTAAATTTAAAAATTCAAAAAAATTA-TAAAAATTA
1 TTTTTAAAAATAAAAAATCAAAAAAATGATTAAAAATTA
**
29941590 TTTTTAAAAATAAAAAATCATTAAAATGATTAAAAATTA
1 TTTTTAAAAATAAAAAATCAAAAAAATGATTAAAAATTA
29941629 T
1 T
29941630 AAAAATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
38 23 0.70
39 10 0.30
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (39 bp):
TTTTTAAAAATAAAAAATCAAAAAAATGATTAAAAATTA
Found at i:29941634 original size:19 final size:18
Alignment explanation
Indices: 29941563--29941654 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 18
29941553 TTTTAAATTT
*
29941563 AAAAATTCAAAAAAATTATA
1 AAAAATT-ATAAAAA-TATA
* *
29941583 AAAATTATTTTTAAAA-ATA
1 AAAA--ATTATAAAAATATA
* * *
29941602 AAAAATCATTAAAATGATT
1 AAAAATTATAAAAAT-ATA
29941621 AAAAATTATAAAAATATA
1 AAAAATTATAAAAATATA
*
29941639 AAAGAAATATAAAAAT
1 AAA-AATTATAAAAAT
29941655 CCAATATGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
17 8 0.14
18 5 0.09
19 33 0.58
20 4 0.07
21 4 0.07
22 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAAAATATA
Found at i:29953820 original size:19 final size:16
Alignment explanation
Indices: 29953790--29953837 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
29953780 ACAAGTAGGC
*
29953790 AAGAAAAATAAATAGAT
1 AAGAAAACTAAATA-AT
29953807 AAATGAAAACTAAATAAT
1 -AA-GAAAACTAAATAAT
29953825 AAGAAAAC-AAATA
1 AAGAAAACTAAATA
29953838 TAGGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (16 bp):
AAGAAAACTAAATAAT
Found at i:29953857 original size:3 final size:3
Alignment explanation
Indices: 29953849--29954196 Score: 105
Period size: 3 Copynumber: 115.3 Consensus size: 3
29953839 AGGTGAAAGT
* * * * * ** *
29953849 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ACA ATA ATA AAA AGG GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
29953896 ATA ATA AT- ATA TTAA ATA GTA A-A ATAA ATA ATA GTA ACA GTA ATTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA A-TA
* * *
29953942 A-A A-A ATG ATA ATA ATA ATA ATA ATA ACA ATA ATA GA-A ATTA AGGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA A-TA
** * * *
29953987 ATA ATA ATA AT- ATCA ACC AT- ATT ATAA ATA ATAA ATA AAA ATA AAA
1 ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA
* * * * *
29954033 ATC ATA ATA ATA A-A AT- ATA AGTA ATA GTA ATG ATA ATG GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
** * * *
29954077 ACG ATA ATAA ATA ATA GTA GTA GATA ATGA A-A ATA ATA ATA GTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA
** * *
29954124 ATA ATA ATGA A-A ATA GGGA A-A ATA ATA ATA GTA ATG ATA ATA A-A
1 ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
29954168 TATA AGTA ATA GTA A-A ATA ATA TTA ATA A
1 -ATA A-TA ATA ATA ATA ATA ATA ATA ATA A
29954197 ATAAATTAAT
Statistics
Matches: 246, Mismatches: 69, Indels: 60
0.66 0.18 0.16
Matches are distributed among these distances:
2 27 0.11
3 183 0.74
4 36 0.15
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:29954110 original size:22 final size:21
Alignment explanation
Indices: 29954085--29954125 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29954075 TAACGATAAT
*
29954085 AAATAATAGTAGTAGATAATGA
1 AAATAATAATAGTA-ATAATGA
29954107 AAATAATAATAGTAATAAT
1 AAATAATAATAGTAATAAT
29954126 AATAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAATAATAATAGTAATAATGA
Found at i:29958096 original size:19 final size:16
Alignment explanation
Indices: 29958066--29958113 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
29958056 ACAAGTAGGC
*
29958066 AAGAAAAATAAATAGAT
1 AAGAAAACTAAATA-AT
29958083 AAATGAAAACTAAATAAT
1 -AA-GAAAACTAAATAAT
29958101 AAGAAAAC-AAATA
1 AAGAAAACTAAATA
29958114 TAGGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (16 bp):
AAGAAAACTAAATAAT
Found at i:29958133 original size:3 final size:3
Alignment explanation
Indices: 29958125--29958504 Score: 139
Period size: 3 Copynumber: 127.0 Consensus size: 3
29958115 AGGTGAAAGT
* * * * * ** *
29958125 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ACA ATA ATA AAA AGG GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
29958172 ATA ATA AT- ATA TTAA ATA GTA A-A ATAA ATA ATA GTA ACA GTA ATTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA A-TA
* * *
29958218 A-A A-A ATG ATA ATA ATA ATA ATA ATA ACA ATA ATA GA-A ATTA AGGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA A-TA
** * * *
29958263 ATA ATA ATA AT- ATCA ACC AT- ATT ATAA ATA ATAA ATA AAA ATA AAA
1 ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA
* * * * *
29958309 ATC ATA ATA ATA A-A AT- ATA AGTA ATA GTA ATG ATA ATG GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
** * * *
29958353 ACG ATA ATAA ATA ATA GTA GTA GATA ATGA A-A ATA ATA ATA GTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA
* * *
29958400 ATA ATA ATGA A-A ATA GTGA A-A ATA ATA ATA GTA AT- ATA ATA GTA
1 ATA ATA AT-A ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
29958444 ATA ATA GTA ATG ATA ATA A-A TATA AGTA ACA GTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA
29958489 ATA A-A A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
29958505 TATTAAATTA
Statistics
Matches: 273, Mismatches: 72, Indels: 64
0.67 0.18 0.16
Matches are distributed among these distances:
2 33 0.12
3 204 0.75
4 36 0.13
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:29958386 original size:22 final size:21
Alignment explanation
Indices: 29958361--29958454 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 21
29958351 TAACGATAAT
*
29958361 AAATAATAGTAGTAGATAATGA
1 AAATAATAATAGTA-ATAATGA
29958383 AAATAATAATAGTAATAAT--
1 AAATAATAATAGTAATAATGA
* *
29958402 -AATAATGA-A--AATAGTGA
1 AAATAATAATAGTAATAATGA
29958419 AAATAATAATAGTAAT-AT-A
1 AAATAATAATAGTAATAATGA
*
29958438 ATAGTAATAATAGTAAT
1 A-AATAATAATAGTAAT
29958455 GATAATAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
15 5 0.08
17 1 0.02
18 14 0.24
19 3 0.05
20 15 0.25
21 8 0.14
22 13 0.22
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATAATAATAGTAATAATGA
Found at i:29959361 original size:11 final size:11
Alignment explanation
Indices: 29959334--29959380 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
29959324 GGGCTAATAG
*
29959334 TTGGGTTTAGGT
1 TTGGGTTT-GTT
*
29959346 TTGGGTTGGTT
1 TTGGGTTTGTT
*
29959357 TTGGGTTTGTA
1 TTGGGTTTGTT
29959368 TTGGGTTTGTT
1 TTGGGTTTGTT
29959379 TT
1 TT
29959381 AGCCCGGGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 23 0.77
12 7 0.23
ACGTcount: A:0.04, C:0.00, G:0.38, T:0.57
Consensus pattern (11 bp):
TTGGGTTTGTT
Found at i:29959376 original size:17 final size:17
Alignment explanation
Indices: 29959334--29959376 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29959324 GGGCTAATAG
* *
29959334 TTGGGTTTAGGTTTGGG
1 TTGGGTTTGGGTTTGGA
* *
29959351 TTGGTTTTGGGTTTGTA
1 TTGGGTTTGGGTTTGGA
29959368 TTGGGTTTG
1 TTGGGTTTG
29959377 TTTTAGCCCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.00, G:0.42, T:0.53
Consensus pattern (17 bp):
TTGGGTTTGGGTTTGGA
Found at i:29959919 original size:41 final size:42
Alignment explanation
Indices: 29959600--29960209 Score: 320
Period size: 45 Copynumber: 13.8 Consensus size: 42
29959590 TGTTGCTTTA
* *
29959600 ATCTGCTCCACTGCAACTTCAGGAAAATAAGATTTGCTATCTTT-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--AT-TTTG
* * * * **
29959644 AGTCTGCTACACTGCAACTTTAGGGAGATAAGACTAGTGACTTCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TTGATTTTG
* * * * *
29959689 ACCTACTCCACTGCAACTTAATGGAGATAAGGTTTG-TTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATTTTG
* * **
29959730 ATCTGCTCTACTGCAACTTCA--GAGA-GAGATTT-ATAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGAT---TTTG
* * * ** *
29959771 ATCTGTTCCACTACAACTTCAGGGAAATAAGATTTGCTACCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--ATTTTG
* **
29959815 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTGATTTCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TTGATTTTG
* *
29959860 ACCTGCTCCACTGCAACTTCAGGGAGATAAAATTTG-TTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATTTTG
* * * *
29959901 ATCTGCTCTACTGCAACTTCAGAGACATAAGATCCGTGATTTATAG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT--TTGATTT-T-G
* * * * *
29959947 CTTCAATCTGTTTCACTGCAACTTCAGGGAAATAAGATTTGCTATATTC
1 -----ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--ATTTTG
* * * **
29959996 AGTCTGCTCCACTGCAACTTAAGGAAGATAAGACTAGTGATTTCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TTGATTTTG
* * *
29960041 ACCTCCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATTTTG
* * *
29960082 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATGATTTATAG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TGATTT-T-G
* * *
29960128 CTTCAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTT-
1 -----ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--AT-TTTG
*
29960177 AGTCTGCTCCACTACAACTTCAGGGAGATAAGA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA
29960210 CTCATAATTT
Statistics
Matches: 426, Mismatches: 94, Indels: 91
0.70 0.15 0.15
Matches are distributed among these distances:
38 6 0.01
39 4 0.01
41 100 0.23
42 7 0.02
43 10 0.02
44 99 0.23
45 119 0.28
46 5 0.01
47 7 0.02
49 4 0.01
50 2 0.00
51 61 0.14
52 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATTTTG
Found at i:29960253 original size:181 final size:181
Alignment explanation
Indices: 29959594--29960234 Score: 935
Period size: 181 Copynumber: 3.6 Consensus size: 181
29959584 AGGACTTGTT
* * * * *
29959594 GCTTTAATCTGCTCCACTGCAACTTCAGGAAAATAAGATTTGCTATCTTTAGTCTGCTACACTGC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* * * *
29959659 AACTTTAGGGAGATAAGACTAGTGACTTCAACCTACTCCACTGCAACTTAATGGAGATAAGGTTT
66 AACTTCAGGGAGATAAGACTAGTGATTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTT
29959724 GTTTTGATCTGCTCTACTGCAACTTCAGAG-----AG----A-GATTTATA
131 GTTTTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCCATGATTTATA
* *
29959765 GCTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTGCTACCTTCAGTCTGCTCCACTGC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* **
29959830 AACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAATTT
66 AACTTCAGGGAGATAAGACTAGTGATTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTT
*
29959895 GTTTTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCCGTGATTTATA
131 GTTTTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCCATGATTTATA
* *
29959946 GCTTCAATCTGTTTCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTCCACTGC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* * *
29960011 AACTTAAGGAAGATAAGACTAGTGATTTCAACCTCCTCCACTGCAACTTCAGGGAGATAAGGTTT
66 AACTTCAGGGAGATAAGACTAGTGATTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTT
* * *
29960076 GTTTTGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATGATTTATA
131 GTTTTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCCATGATTTATA
* * *
29960127 GCTTCAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTAC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* *
29960192 AACTTCAGGGAGATAAGACTCA-TAATTTTCAGCCTACTCCACT
66 AACTTCAGGGAGATAAGACT-AGTGA-TTTCAACCTACTCCACT
29960235 ATTGCTTAGG
Statistics
Matches: 420, Mismatches: 38, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
171 146 0.35
176 2 0.00
181 256 0.61
182 16 0.04
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (181 bp):
GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
AACTTCAGGGAGATAAGACTAGTGATTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTT
GTTTTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCCATGATTTATA
Found at i:29960307 original size:88 final size:88
Alignment explanation
Indices: 29960179--29960627 Score: 557
Period size: 88 Copynumber: 5.1 Consensus size: 88
29960169 CTATCTTTAG
** * * ** *
29960179 TCTGCTCCACTACAACTTCAGGGAGATAAGA-CTCATAATTTTCAGCCTACT-CCACTATTGCTT
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCT-GTAATCTTCAGCCTGTTACC-CTACTGCTT
* * * *
29960242 AGGGAGATAAGGCTTACCGTCTGCGA
63 AGGGGGTTAAGGCTTACTGTCTTCGA
* * * * * * *
29960268 TCTGCTCCACTATTGTTTAGGGAGATAAAATCTATAATTTTTAGTCTGTTACCCTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
* *
29960333 GGGTTAAGGCTCACCGTCTTCGA
66 GGGTTAAGGCTTACTGTCTTCGA
* * *
29960356 TTTGCTCCACTACTGCTTAAGGAGATAAGAACTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
29960421 GGGTTAAGGCTCT-CTGTATTCGA
66 GGGTTAAGGCT-TACTGTCTTCGA
*
29960444 TCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
29960509 GGGTTAAAGCTCT-CTGTCTTCGA
66 GGGTTAAGGCT-TACTGTCTTCGA
*
29960532 TCT-CTCCGCTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
* *
29960596 GAGTTAAGGCTCACTGTCTTCGA
66 GGGTTAAGGCTTACTGTCTTCGA
29960619 TCTGCTCCA
1 TCTGCTCCA
29960628 TTGCTATCTC
Statistics
Matches: 316, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
87 82 0.26
88 216 0.68
89 18 0.06
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (88 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGG
GGGTTAAGGCTTACTGTCTTCGA
Found at i:29960413 original size:44 final size:44
Alignment explanation
Indices: 29960365--29960603 Score: 195
Period size: 44 Copynumber: 5.5 Consensus size: 44
29960355 ATTTGCTCCA
* *
29960365 CTACTGCTTAAGGAGATAAGAACTGTAATCTTCAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGAGCTGTAATCTTCAGCCTGTTACC
* * * ** * * *
29960409 CTACTGCTTAGGGGGTTAAG-GCTCTCTGTATTCGATCC-GCT-CC
1 CTACTGCTTAGGGAGATAAGAGCTGT-AATCTTC-AGCCTGTTACC
*
29960452 ACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGAGCTGTAATCTTCAGCCTGTTACC
* * * ** * *
29960497 CTACTGCTTAGGGGGTTAA-AGCTCTCTGTCTTC-GATCT-CT-CC
1 CTACTGCTTAGGGAGATAAGAGCTGT-AATCTTCAG-CCTGTTACC
*
29960539 GCTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGAGCTGTAATCTTCAGCCTGTTACC
*
29960584 CTACTGCTTAGGGAGTTAAG
1 CTACTGCTTAGGGAGATAAG
29960604 GCTCACTGTC
Statistics
Matches: 146, Mismatches: 36, Indels: 26
0.70 0.17 0.12
Matches are distributed among these distances:
42 2 0.01
43 38 0.26
44 96 0.66
45 10 0.07
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGAGCTGTAATCTTCAGCCTGTTACC
Found at i:29960616 original size:44 final size:43
Alignment explanation
Indices: 29960313--29960616 Score: 190
Period size: 44 Copynumber: 6.9 Consensus size: 43
29960303 AATTTTTAGT
* * * *
29960313 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGAGTTAA-GCTCTCTGTCTTCAG-C
* * * * ** * *
29960357 TTGCT-CCACTACTGCTTAAGGAGATAAGAACTGTAATCTTCAGC
1 CTGTTACC-CTACTGCTTAGGGAGTTAAGCTCTCT-GTCTTCAGC
* * *
29960401 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCTCTGTATTCGATC
1 CTGTTACCCTACTGCTTAGGGAGTTAA-GCTCTCTGTCTTC-AGC
* * * * *
29960446 C-GCT-CCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGC
1 CTGTTACC-CTACTGCTTAGGGAGTTAAGCTCTCT-GTCTTCAGC
* *
29960489 CTGTTACCCTACTGCTTAGGGGGTTAAAGCTCTCTGTCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGAGTT-AAGCTCTCTGTCTTCAG-C
* * * * *
29960533 CT-CT-CCGCTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGC
1 CTGTTACC-CTACTGCTTAGGGAGTTAAGCTCTCT-GTCTTCAGC
*
29960576 CTGTTACCCTACTGCTTAGGGAGTTAAGGCTCACTGTCTTC
1 CTGTTACCCTACTGCTTAGGGAGTTAA-GCTCTCTGTCTTC
29960617 GATCTGCTCC
Statistics
Matches: 191, Mismatches: 51, Indels: 36
0.69 0.18 0.13
Matches are distributed among these distances:
42 9 0.05
43 38 0.20
44 119 0.62
45 25 0.13
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGAGTTAAGCTCTCTGTCTTCAGC
Found at i:29962448 original size:20 final size:20
Alignment explanation
Indices: 29962425--29962470 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
29962415 TTTTGTTGTC
29962425 TTTTTTACTTTTTTCTTCTT
1 TTTTTTACTTTTTTCTTCTT
* *
29962445 TTTTGTATTTTTTTCTTCTT
1 TTTTTTACTTTTTTCTTCTT
29962465 TTTTTT
1 TTTTTT
29962471 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTACTTTTTTCTTCTT
Found at i:29963226 original size:16 final size:16
Alignment explanation
Indices: 29963205--29963235 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29963195 ATGGCATGAT
29963205 CATGAAAAAAAGAATA
1 CATGAAAAAAAGAATA
*
29963221 CATGAAAAAGAGAAT
1 CATGAAAAAAAGAAT
29963236 CTAAGAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13
Consensus pattern (16 bp):
CATGAAAAAAAGAATA
Found at i:29964620 original size:29 final size:29
Alignment explanation
Indices: 29964573--29964641 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
29964563 ACAAGGACGA
*
29964573 ATGAAAATGCAACGAAAGGATCTCTTATT
1 ATGAAAATGCAACGAAAGGATCTCTTATG
* *
29964602 ATGAAAATGCAATGTAAGGATCTCTTATG
1 ATGAAAATGCAACGAAAGGATCTCTTATG
29964631 ATGAAAATGCA
1 ATGAAAATGCA
29964642 GTGTGATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (29 bp):
ATGAAAATGCAACGAAAGGATCTCTTATG
Found at i:29966430 original size:19 final size:16
Alignment explanation
Indices: 29966400--29966447 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
29966390 ACAAGTAGGC
*
29966400 AAGAAAAATAAATAGAT
1 AAGAAAACTAAATA-AT
29966417 AAATGAAAACTAAATAAT
1 -AA-GAAAACTAAATAAT
29966435 AAGAAAAC-AAATA
1 AAGAAAACTAAATA
29966448 TAGGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (16 bp):
AAGAAAACTAAATAAT
Found at i:29966467 original size:3 final size:3
Alignment explanation
Indices: 29966459--29966931 Score: 145
Period size: 3 Copynumber: 155.3 Consensus size: 3
29966449 AGGTGAAAGT
* * * * * ** *
29966459 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ACA ATA ATA AAA AGG GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
29966506 ATA ATA AT- ATA TTAA ATA ATA A-A ATAA ATA ATA GTA ACA GTA ATTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA A-TA
* *
29966552 AAA ATA ATA ATA ATA ATA ATA ATA GA-A ATTA AGGA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA A-TA ATA ATA ATA ATA
** * * * * *
29966598 ATCA ACC AT- ATT ATAA ATA ATAA ATA AAA ACA AAA ATC ATA ATA ATA
1 AT-A ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * **
29966645 A-A AT- ATA AGTA ATA GTA ATG ATA ATG GTA ATA ACG ATA ATAA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * *
29966690 ATA GTA GTA GATA ATGA A-A ATA ATA ATA GTA ATA ATA ATA ATGA A-A
1 ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
** * * *
29966736 ATA GGGA A-A ATA ATA ATA GTA ATG ATA ATA A-A TATA AGTA ATA GTA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA
* * * **
29966782 A-A ATA ATA TTA ATAA ATA ATA ATG GTA ATA ACG ATA ATAA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* * * *
29966828 GTA GTA GATA ATGA A-A ATA ATA ATA GTC ATA ATA ATA ATGA A-A ATA
1 ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
** * * *
29966874 GGGA A-A ATA ATA ATA GTA ATG ATA ATA A-A TATA AGTA ATA GTA A-A
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA ATA
*
29966919 ATA ATA TTA ATA A
1 ATA ATA ATA ATA A
29966932 ATTAATTAAT
Statistics
Matches: 338, Mismatches: 90, Indels: 84
0.66 0.18 0.16
Matches are distributed among these distances:
2 32 0.09
3 253 0.75
4 53 0.16
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:29966710 original size:22 final size:21
Alignment explanation
Indices: 29966685--29966725 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29966675 TAACGATAAT
*
29966685 AAATAATAGTAGTAGATAATGA
1 AAATAATAATAGTA-ATAATGA
29966707 AAATAATAATAGTAATAAT
1 AAATAATAATAGTAATAAT
29966726 AATAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAATAATAATAGTAATAATGA
Found at i:29966832 original size:135 final size:135
Alignment explanation
Indices: 29966665--29966933 Score: 529
Period size: 135 Copynumber: 2.0 Consensus size: 135
29966655 AATAGTAATG
29966665 ATAATGGTAATAACGATAATAAATAATAGTAGTAGATAATGAAAATAATAATAGTAATAATAATA
1 ATAATGGTAATAACGATAATAAATAATAGTAGTAGATAATGAAAATAATAATAGTAATAATAATA
29966730 ATGAAAATAGGGAAAATAATAATAGTAATGATAATAAATATAAGTAATAGTAAAATAATATTAAT
66 ATGAAAATAGGGAAAATAATAATAGTAATGATAATAAATATAAGTAATAGTAAAATAATATTAAT
29966795 AAATA
131 AAATA
*
29966800 ATAATGGTAATAACGATAATAAATAATAGTAGTAGATAATGAAAATAATAATAGTCATAATAATA
1 ATAATGGTAATAACGATAATAAATAATAGTAGTAGATAATGAAAATAATAATAGTAATAATAATA
29966865 ATGAAAATAGGGAAAATAATAATAGTAATGATAATAAATATAAGTAATAGTAAAATAATATTAAT
66 ATGAAAATAGGGAAAATAATAATAGTAATGATAATAAATATAAGTAATAGTAAAATAATATTAAT
29966930 AAAT
131 AAAT
29966934 TAATTAATTA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (135 bp):
ATAATGGTAATAACGATAATAAATAATAGTAGTAGATAATGAAAATAATAATAGTAATAATAATA
ATGAAAATAGGGAAAATAATAATAGTAATGATAATAAATATAAGTAATAGTAAAATAATATTAAT
AAATA
Found at i:29966937 original size:25 final size:25
Alignment explanation
Indices: 29966745--29966865 Score: 78
Period size: 25 Copynumber: 4.9 Consensus size: 25
29966735 AATAGGGAAA
*
29966745 ATAA-TAATAGTAATGATAATAAAT
1 ATAAGTAATAGTAATAATAATAAAT
29966769 ATAAGTAATAGTAA-AATAATATTAAT
1 ATAAGTAATAGTAATAATAATA--AAT
* **
29966795 AAATAA-TAATGGTAATAACGAT-AAT
1 --ATAAGTAATAGTAATAATAATAAAT
*
29966820 A-AA-TAATAGTAGTAGATAATGAAA-
1 ATAAGTAATAGTAATA-ATAAT-AAAT
*
29966844 ATAA-TAATAGTCATAATAATAA
1 ATAAGTAATAGTAATAATAATAA
29966866 TGAAAATAGG
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
22 11 0.14
23 6 0.08
24 16 0.21
25 25 0.32
26 3 0.04
27 8 0.10
28 8 0.10
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (25 bp):
ATAAGTAATAGTAATAATAATAAAT
Found at i:29968024 original size:11 final size:11
Alignment explanation
Indices: 29967997--29968043 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
29967987 GGGTTGATAA
*
29967997 TTGGGTTTAGGT
1 TTGGGTTT-GTT
*
29968009 TTGGGTTGGTT
1 TTGGGTTTGTT
*
29968020 TTGGGTTTGTA
1 TTGGGTTTGTT
29968031 TTGGGTTTGTT
1 TTGGGTTTGTT
29968042 TT
1 TT
29968044 AGCTCGGGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 23 0.77
12 7 0.23
ACGTcount: A:0.04, C:0.00, G:0.38, T:0.57
Consensus pattern (11 bp):
TTGGGTTTGTT
Found at i:29969363 original size:15 final size:15
Alignment explanation
Indices: 29969343--29969372 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29969333 AATTTTATTT
*
29969343 ATATTAGGATAATTA
1 ATATTAAGATAATTA
29969358 ATATTAAGATAATTA
1 ATATTAAGATAATTA
29969373 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:29969400 original size:27 final size:26
Alignment explanation
Indices: 29969339--29969401 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
29969329 ACTCAATTTT
29969339 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
29969366 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
29969394 ATTTTATT
1 ATTTTATT
29969402 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:29969416 original size:10 final size:10
Alignment explanation
Indices: 29969397--29969428 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
29969387 TTTTAGGATT
29969397 TTAT-TTTAA
1 TTATCTTTAA
29969406 TTATCTTTAA
1 TTATCTTTAA
29969416 TTATCTTTAA
1 TTATCTTTAA
29969426 TTA
1 TTA
29969429 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:29970871 original size:21 final size:22
Alignment explanation
Indices: 29970845--29970898 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 22
29970835 GGTGATGATA
29970845 TTTCTTTAAA-CTCAATTTTCC
1 TTTCTTTAAATCTCAATTTTCC
29970866 TTTCTTTGTAAATTGCTCAATTTTCC
1 TTTC-TT-TAAA-T-CTCAATTTTCC
29970892 TTTCTTT
1 TTTCTTT
29970899 GTAAAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 4 0.14
24 1 0.04
25 2 0.07
26 15 0.54
ACGTcount: A:0.19, C:0.20, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTCTTTAAATCTCAATTTTCC
Found at i:29970885 original size:26 final size:27
Alignment explanation
Indices: 29970855--29970908 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
29970845 TTTCTTTAAA
29970855 CTCAATTTTCCTTTCTTTGT-AAATTG
1 CTCAATTTTCCTTTCTTTGTAAAATTG
29970881 CTCAATTTTCCTTTCTTTGTAAAATTG
1 CTCAATTTTCCTTTCTTTGTAAAATTG
29970908 C
1 C
29970909 ATGATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.52
Consensus pattern (27 bp):
CTCAATTTTCCTTTCTTTGTAAAATTG
Found at i:29972366 original size:63 final size:63
Alignment explanation
Indices: 29972267--29972399 Score: 212
Period size: 63 Copynumber: 2.1 Consensus size: 63
29972257 GAATATTTCG
* * *
29972267 AACATGGTATCTGTTAAGAGTGTGTTAAAAAACATTTAAGAGAAATGACATAAGGTGCGAGTA
1 AACATGGTATCTGTAAAGAGCGTGTTAAAAAACATTTAAGAGAAATAACATAAGGTGCGAGTA
* * *
29972330 AACATGGTATCTGTAAAGAGCGTGTTCAAAAACATTTAAGAGAAATAATATAAGGTGTGAGTA
1 AACATGGTATCTGTAAAGAGCGTGTTAAAAAACATTTAAGAGAAATAACATAAGGTGCGAGTA
29972393 AACATGG
1 AACATGG
29972400 GCAGTAGTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.26
Consensus pattern (63 bp):
AACATGGTATCTGTAAAGAGCGTGTTAAAAAACATTTAAGAGAAATAACATAAGGTGCGAGTA
Found at i:29976575 original size:17 final size:17
Alignment explanation
Indices: 29976555--29976589 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29976545 TTATTGATTG
29976555 TATTATTTTAT-TAAAAT
1 TATTA-TTTATGTAAAAT
29976572 TATTATTTATGTAAAAT
1 TATTATTTATGTAAAAT
29976589 T
1 T
29976590 GTTTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATTTATGTAAAAT
Found at i:29977107 original size:15 final size:15
Alignment explanation
Indices: 29977087--29977116 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29977077 TTTTTAATAC
*
29977087 TTTTGAGTATTTTAT
1 TTTTGAATATTTTAT
29977102 TTTTGAATATTTTAT
1 TTTTGAATATTTTAT
29977117 AATTATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
TTTTGAATATTTTAT
Found at i:29978866 original size:41 final size:42
Alignment explanation
Indices: 29978809--29978894 Score: 138
Period size: 41 Copynumber: 2.0 Consensus size: 42
29978799 AGAAGTGGAA
*
29978809 AAATTGGAAAAAGAATATCTTTTTTACTTA-CAAAAAAAAGG
1 AAATTGGAAAAAGAATATCTTTTTTACTTAGAAAAAAAAAGG
*
29978850 AAATTGGAAAATGAATATCTTTTTTACTTATGAAAAAAAAAGG
1 AAATTGGAAAAAGAATATCTTTTTTACTTA-GAAAAAAAAAGG
29978893 AA
1 AA
29978895 TTTTGGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 29 0.71
43 12 0.29
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (42 bp):
AAATTGGAAAAAGAATATCTTTTTTACTTAGAAAAAAAAAGG
Found at i:29985721 original size:51 final size:50
Alignment explanation
Indices: 29985614--29985723 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 50
29985604 ACATAAATAC
* * *
29985614 ACAT-ATATATGTTAAAAATATATACATAATAAGGATATTAAAAGCATGT
1 ACATAATATATGTTAAAAATACATACATAATAAGGATATTAAAAACATAT
* * * *
29985663 ACGTAATATAGTGTTAAAAATGCATACATAATATA-GTTATTAAAAATATAT
1 ACATAATATA-TGTTAAAAATACATACATAATA-AGGATATTAAAAACATAT
29985714 ACATAATATA
1 ACATAATATA
29985724 ATAAAGTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.06
50 5 0.10
51 41 0.82
52 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (50 bp):
ACATAATATATGTTAAAAATACATACATAATAAGGATATTAAAAACATAT
Found at i:29985733 original size:21 final size:21
Alignment explanation
Indices: 29985705--29985811 Score: 78
Period size: 21 Copynumber: 4.9 Consensus size: 21
29985695 ATAGTTATTA
29985705 AAAATATATACATAATATAAT
1 AAAATATATACATAATATAAT
*
29985726 AAAGTATATGA-ATAATATGATATT
1 AAAATATAT-ACATAATAT-A-A-T
29985750 AAAAAATATATACATAATAT-AT
1 --AAAATATATACATAATATAAT
* * *
29985772 AAAAAATATA-AT-ATTTAAAA
1 AAAATATATACATAATAT-AAT
29985792 AAAATAATATACATAATATA
1 AAAAT-ATATACATAATATA
29985812 TGTAGACACT
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
18 3 0.04
19 2 0.03
20 14 0.21
21 20 0.30
22 6 0.09
23 5 0.07
24 1 0.01
25 1 0.01
26 15 0.22
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATATATACATAATATAAT
Found at i:29985769 original size:26 final size:25
Alignment explanation
Indices: 29985625--29985781 Score: 116
Period size: 26 Copynumber: 6.4 Consensus size: 25
29985615 CATATATATG
*
29985625 TTAAAAATATATACATAATAAGGATA
1 TTAAAAATATATACATAAT-ATGATA
** * * *
29985651 TTAAAAGCATGTACGTAATAT-AGTG
1 TTAAAAATATATACATAATATGA-TA
** *
29985676 TTAAAAATGCATACATAATATAGTTA
1 TTAAAAATATATACATAATAT-GATA
29985702 TTAAAAATATATACATAATAT-A-A
1 TTAAAAATATATACATAATATGATA
*
29985725 -T-AAAGTATATGA-ATAATATGATA
1 TTAAAAATATAT-ACATAATATGATA
29985748 TTAAAAAATATATACATAATAT-ATA
1 TT-AAAAATATATACATAATATGATA
29985773 --AAAAATATA
1 TTAAAAATATA
29985782 ATATTTAAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
21 15 0.15
22 12 0.12
23 2 0.02
24 2 0.02
25 21 0.21
26 50 0.49
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAAAAATATATACATAATATGATA
Found at i:29985780 original size:37 final size:40
Alignment explanation
Indices: 29985716--29985812 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 40
29985706 AAATATATAC
* * *
29985716 ATAATATA-ATAAAGTATATGAATAATATGATA-TT-AAAAA
1 ATAATATACAT-AA-TATATAAAAAATATAATATTTAAAAAA
29985755 AT-ATATACATAATATATAAAAAATATAATATTTAAAAAAA
1 ATAATATACATAATATATAAAAAATATAATATTT-AAAAAA
29985795 ATAATATACATAATATAT
1 ATAATATACATAATATAT
29985813 GTAGACACTC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 15 0.30
38 9 0.18
39 4 0.08
40 7 0.14
41 15 0.30
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (40 bp):
ATAATATACATAATATATAAAAAATATAATATTTAAAAAA
Found at i:29985784 original size:16 final size:16
Alignment explanation
Indices: 29985763--29985802 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29985753 AAATATATAC
*
29985763 ATAATATATAAAAAAT
1 ATAATATATAAAAAAA
*
29985779 ATAATATTTAAAAAAA
1 ATAATATATAAAAAAA
29985795 ATAATATA
1 ATAATATA
29985803 CATAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATATATAAAAAAA
Found at i:29985795 original size:18 final size:18
Alignment explanation
Indices: 29985739--29985797 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
29985729 GTATATGAAT
*
29985739 AATATGATA-TTAAAAAA
1 AATATAATATTTAAAAAA
* * *
29985756 TATATACATAATATATAAAA
1 AATATA-AT-ATTTAAAAAA
29985776 AATATAATATTTAAAAAA
1 AATATAATATTTAAAAAA
29985794 AATA
1 AATA
29985798 ATATACATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 4 0.12
18 14 0.44
19 3 0.09
20 11 0.34
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AATATAATATTTAAAAAA
Found at i:29986021 original size:16 final size:17
Alignment explanation
Indices: 29985971--29986021 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
29985961 ATGGAAATAT
*
29985971 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
29985988 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
29986007 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
29986022 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:29986040 original size:22 final size:21
Alignment explanation
Indices: 29985981--29986023 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
29985971 AATCTTTAAG
29985981 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
29986000 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
29986021 GAT
1 GAT
29986024 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:30001908 original size:1 final size:1
Alignment explanation
Indices: 30001902--30001976 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
30001892 CTTCTATTTC
** * * * * * * * *
30001902 AAAAAAAAAGGAAAAAAAGAAAAGAAAAAGAGAAAAAAATAAAAAGAAAAAAAAGAAAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
30001967 AAATAAAAAA
1 AAAAAAAAAA
30001977 TGGAGAGGCC
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (1 bp):
A
Found at i:30001975 original size:36 final size:36
Alignment explanation
Indices: 30001902--30001977 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
30001892 CTTCTATTTC
* *
30001902 AAAA-AAAAAGGAAAAAAAGAAAAGAAAAAGAGAAA
1 AAAATAAAAAGAAAAAAAAGAAAAGAAAAAGAAAAA
30001937 AAAATAAAAAGAAAAAAAAGAAAA-AATAAA-AAATAA
1 AAAATAAAAAGAAAAAAAAGAAAAGAA-AAAGAAA-AA
30001973 AAAAT
1 AAAAT
30001978 GGAGAGGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (36 bp):
AAAATAAAAAGAAAAAAAAGAAAAGAAAAAGAAAAA
Found at i:30001977 original size:7 final size:7
Alignment explanation
Indices: 30001935--30001977 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
30001925 GAAAAAGAGA
30001935 AAAAAAT
1 AAAAAAT
*
30001942 AAAAAGAA
1 AAAAA-AT
*
30001950 AAAAAAG
1 AAAAAAT
30001957 AAAAAAT
1 AAAAAAT
30001964 AAAAAAT
1 AAAAAAT
30001971 AAAAAAT
1 AAAAAAT
30001978 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:30003022 original size:44 final size:44
Alignment explanation
Indices: 30002972--30003115 Score: 136
Period size: 44 Copynumber: 3.3 Consensus size: 44
30002962 GATCTTATCT
30002972 CCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATC
1 CCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATC
* ** *** * *
30003016 CCCTAAGCAGTAG-GGA-TACAGGTTAAATTTG-C-AGATCTT-ATC
1 CCCTAAGCAGTAGCGGAGTATA--TCGACGATGACTCG-CCTTAATC
30003058 TCCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATC
1 -CCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATC
*
30003103 CCCTGAGCAGTAG
1 CCCTAAGCAGTAG
30003116 GGTAACAGGT
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
42 7 0.09
43 24 0.32
44 36 0.49
45 7 0.09
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (44 bp):
CCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATC
Found at i:30003076 original size:87 final size:86
Alignment explanation
Indices: 30002924--30003629 Score: 861
Period size: 87 Copynumber: 8.4 Consensus size: 86
30002914 CAAAATTCAG
* *
30002924 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* * *
30002984 GCGGAGTATATCGACGATGACT
66 GTGGAGCAGATCGA-GATGACT
30003006 CGCCTTAATCCCCTAAGCAGTAGGG-ATACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 CGCCTTAATCCCCTAAGCAGTAGGGTA-ACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
* * *
30003070 AGCGGAGTATATCGACGATGACT
65 AGTGGAGCAGATCGA-GATGACT
*
30003093 CGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
30003158 GTGGAACAGATCGA-A-GACT
66 GTGGAGCAGATCGAGATGACT
* *
30003177 CGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTT-CA----CAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
30003237 GCGGAGCAGATCAATGATGACT
66 GTGGAGCAGATCGA-GATGACT
*
30003259 CGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
30003324 GTGGAGCAGATCGA-A-GACAT
66 GTGGAGCAGATCGAGATGAC-T
* * *
30003344 -GCCTTAATCCTCTAAGCGGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
30003408 GTGGAGCATATTGA-A-GACT
66 GTGGAGCAGATCGAGATGACT
* * *
30003427 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCTTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* **
30003487 GAGGAGCAGATCGATGGCGACT
66 GTGGAGCAGATCGA-GATGACT
* * *
30003509 CACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATCTCCCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
30003574 GTGGAGTAGATTGA-A-GA-T
66 GTGGAGCAGATCGAGATGACT
* * *
30003592 GCGCCTTAACCCCCTAAGTAGTAGGGTAATAGGTTAAA
1 -CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
30003630 GTATAGCAGA
Statistics
Matches: 552, Mismatches: 46, Indels: 50
0.85 0.07 0.08
Matches are distributed among these distances:
79 72 0.13
81 2 0.00
82 99 0.18
83 4 0.01
84 179 0.32
85 3 0.01
87 192 0.35
88 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (86 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAGATGACT
Found at i:30003207 original size:41 final size:40
Alignment explanation
Indices: 30003089--30003207 Score: 109
Period size: 43 Copynumber: 2.9 Consensus size: 40
30003079 TATCGACGAT
* *
30003089 GACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTTAA
1 GACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAGATGAA
* * *
30003129 -ATTTGCAGATCTT-ATCTCCCTAAGCAGTAGTGG-AACAGATCGAA
1 GA-CT-C-G-CCTTAATC-CCCTGAGCAGTAG-GGTAACAGAT-GAA
30003173 GACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAG
1 GACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAG
30003208 GTTCACAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
39 1 0.02
40 3 0.05
41 21 0.34
42 8 0.13
43 22 0.36
44 5 0.08
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (40 bp):
GACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAGATGAA
Found at i:30003258 original size:166 final size:168
Alignment explanation
Indices: 30002924--30003629 Score: 797
Period size: 166 Copynumber: 4.2 Consensus size: 168
30002914 CAAAATTCAG
*
30002924 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTCGCAGATCTTATCTCCCTAAGCAGTA
* * *
30002984 GCGGAGTATATCGACGATGACTCGCCTTAATCCCCTAAGCAGTAGGG-ATACAGGTTAAATTTGC
66 GTGGAGCAGATCGA-GA-GACTCGCCTTAATCCCCTAAGCAGTAGGGTA-ACAGGTTAAA--T-C
* * * * *
30003048 AGATCTTATCTCCCTAAGCAGTAGCGGAGTATATCGACGATGACT
125 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGAT-AATGAAGACT
* *
30003093 CGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTCGCAGATCTTATCTCCCTAAGCAGTA
* * *
30003158 GTGGAACAGATCGA-AGACTCGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTT-CA-CAGATCT
66 GTGGAGCAGATCGAGAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATCAGATCT
*
30003220 TATCTCCCTAAGCAGTAGCGGAGCAGATCAATGATGACT
131 TATCTCCCTAAGCAGTAGCGGAGCAGAT-AATGAAGACT
* *
30003259 CGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTCGCAGATCTTATCTCCCTAAGCAGTA
* * *
30003324 GTGGAGCAGATCGA-AGACAT-GCCTTAATCCTCTAAGCGGTAGGGTAACAAGTTAAATTTGCAG
66 GTGGAGCAGATCGAGAGAC-TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA--T-CAG
* *
30003387 ATCTTATCTCCCTAAGCAGTAGTGGAGC--ATATTGAAGACT
127 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATAATGAAGACT
* *
30003427 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCTTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTCGCAGATCTTATCTCCCTAAGCAGTA
* * * *
30003487 GAGGAGCAGATCGATGGCGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTA
66 GTGGAGCAGATCGA--GAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA--T-CA
* * *
30003552 GATCTTATCTCCCTAAGTAGTAGTGGAGTAGAT--TGAAGA-T
126 GATCTTATCTCCCTAAGCAGTAGCGGAGCAGATAATGAAGACT
* * *
30003592 GCGCCTTAACCCCCTAAGTAGTAGGGTAATAGGTTAAA
1 -CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
30003630 GTATAGCAGA
Statistics
Matches: 472, Mismatches: 41, Indels: 46
0.84 0.07 0.08
Matches are distributed among these distances:
163 39 0.08
165 2 0.00
166 252 0.53
167 2 0.00
168 40 0.08
169 32 0.07
170 1 0.00
171 65 0.14
172 2 0.00
174 37 0.08
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (168 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTCGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAGAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATCAGATCT
TATCTCCCTAAGCAGTAGCGGAGCAGATAATGAAGACT
Found at i:30003469 original size:250 final size:250
Alignment explanation
Indices: 30002924--30003629 Score: 1058
Period size: 250 Copynumber: 2.8 Consensus size: 250
30002914 CAAAATTCAG
*
30002924 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
* * *
30002989 GTATATCGACGATGACTCGCCTTAATCCCCTAAGCAGTAGGG-ATACAGGTTAAATTTGCAGATC
66 GCAGATCGATGATGACTCGCCTTAATCCCCTAAGCAGTAGGGTA-ACAGGTTAAATTTGCAGATC
* * *
30003053 TTATCTCCCTAAGCAGTAGCGGAGTATATCGACGATGACTCGCCTTAATCCCCTGAGCAGTAGGG
130 TTATCTCCCTAAGCAGTAGTGGAGTAGATCGA--A-GACTCGCCTTAATCCCCTAAGCAGTAGGG
*
30003118 TAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACT
192 TAACAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACT
* *
30003177 CGCCTTAATCCCCTGAGCAGTAGGGTAACAGGTTCACAGATCTTATCTCCCTAAGCAGTAGCGGA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
* *
30003242 GCAGATCAATGATGACTCGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCT
66 GCAGATCGATGATGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCT
* * *
30003307 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAT-GCCTTAATCCTCTAAGCGGTAGGGTAA
131 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAC-TCGCCTTAATCCCCTAAGCAGTAGGGTAA
* * *
30003371 CAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATTGAAGACT
195 CAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACT
* * *
30003427 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCTCCTTAAGCAGTAGAGGA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
** * *
30003492 GCAGATCGATGGCGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAGATCT
66 GCAGATCGATGATGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCT
* * * *
30003557 TATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGA-TGCGCCTTAACCCCCTAAGTAGTAGGGTAA
131 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACT-CGCCTTAATCCCCTAAGCAGTAGGGTAA
* *
30003621 TAGGTTAAA
195 CAAGTTAAA
30003630 GTATAGCAGA
Statistics
Matches: 411, Mismatches: 38, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
248 1 0.00
250 259 0.63
251 2 0.00
253 148 0.36
254 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (250 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
GCAGATCGATGATGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCT
TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAAC
AAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACT
Found at i:30004045 original size:44 final size:44
Alignment explanation
Indices: 30003993--30004213 Score: 205
Period size: 44 Copynumber: 5.0 Consensus size: 44
30003983 GATTTCAGCA
30003993 TGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * *
30004037 TGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGCAGATC
1 TGACATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
* * * * ** *** **
30004081 TGACATTCCTGTGCTTACAGTGAA-ACAGATCAAAGATTTTA-ACA
1 TGACATCCCTGTGTTTATAGGGAACA-AG-TTGAAGATAGCAGATT
* *
30004125 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGGTT
1 TGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * *
30004169 TGACATCCCTATGTTTACAGGGAACAAATTGAAGACATAGCAGAT
1 TGACATCCCTGTGTTTATAGGGAACAAGTTGAAG--ATAGCAGAT
30004214 CTGATTTTTG
Statistics
Matches: 138, Mismatches: 32, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
43 9 0.07
44 109 0.79
45 12 0.09
46 8 0.06
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (44 bp):
TGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
Found at i:30004139 original size:132 final size:132
Alignment explanation
Indices: 30003900--30004217 Score: 465
Period size: 132 Copynumber: 2.4 Consensus size: 132
30003890 ATCCAAGATA
* *
30003900 ATTTGGCATCCCTGTATTTATAGGGAACAGATCGAAGACGTAGCAGATCTAACATTCCTATGCTT
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGA--TAGCAGATCTGACATTCCTATGCTT
* * *
30003965 ACAGCGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
64 ACAGCGAAACAGATCAAAGATTTCAACATGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
30004030 GCAG
129 GCAG
*
30004034 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTAC
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTATGCTTAC
* * *
30004099 AGTGAAACAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
66 AGCGAAACAGATCAAAGATTTCAACATGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
30004164 AG
131 AG
* * * * * *
30004166 GTTTGACATCCCTATGTTTACAGGGAACAAATTGAAGACATAGCAGATCTGA
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAG--ATAGCAGATCTGA
30004218 TTTTTGGATG
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
132 117 0.70
134 50 0.30
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTATGCTTAC
AGCGAAACAGATCAAAGATTTCAACATGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
AG
Found at i:30004370 original size:174 final size:175
Alignment explanation
Indices: 30004180--30004571 Score: 633
Period size: 174 Copynumber: 2.2 Consensus size: 175
30004170 GACATCCCTA
* * * * * *
30004180 TGTTTACAGGGAACAAATTGAAGACATAGCAGATCTGATTTTTGGATGTTCTCACACCAAAGCAG
1 TGTTTACAAGGAACAAATCGAAGACATAGCAGATCTGACTTTCGGATGTTATCACACCAAAGCAA
30004245 ATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
66 ATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
* * *
30004310 CAGATG-TTATACTGAAGTAGATCCAAGATGATTTGGCATTCTTG
131 CAGATGATTATACTGAAGCAGATCCAAAATGATTTGGCATCCTTG
* *
30004354 TGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTATTACACCAAAGCAA
1 TGTTTACAAGGAACAAATCGAAGACATAGCAGATCTGACTTTCGGATGTTATCACACCAAAGCAA
30004419 ATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
66 ATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
* *
30004484 CAGATGATTTTATTGAAGCAGATCCAAAATGATTTGGCATCCTTG
131 CAGATGATTATACTGAAGCAGATCCAAAATGATTTGGCATCCTTG
* * *
30004529 TGTTCACAAGGAGCAAATCGAAGACATAGCAGATTTGACTTTC
1 TGTTTACAAGGAACAAATCGAAGACATAGCAGATCTGACTTTC
30004572 ACGTGTTTAC
Statistics
Matches: 202, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
174 128 0.63
175 74 0.37
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (175 bp):
TGTTTACAAGGAACAAATCGAAGACATAGCAGATCTGACTTTCGGATGTTATCACACCAAAGCAA
ATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
CAGATGATTATACTGAAGCAGATCCAAAATGATTTGGCATCCTTG
Found at i:30004510 original size:86 final size:85
Alignment explanation
Indices: 30004239--30004510 Score: 234
Period size: 86 Copynumber: 3.1 Consensus size: 85
30004229 TCTCACACCA
30004239 AAGCAGATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCT
1 AAGCAGATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCT
*
30004304 AACCTTCAGATGTTATACTG
66 AACCTTCAGATGTTTTACTG
* * * *** * *
30004324 AAGTAGATCCAAGAT----GATTTGGCATTCTTGTGTTTAC-AAGGA-A-CAAATCGAAGACATA
1 AAGCAGATCCAAGATAACAGATCTAGCA-TC-TCCATTT-CGACGGAGAGC--A--G-ATACATA
* * * * **
30004382 GCAGATTTGACTTTCGGATGTTATTACACCA
58 GCAGATCTAACCTTCAGATGTT-TT--ACTG
*
30004413 AAGCAAATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCT
1 AAGCAGATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCT
*
30004478 AACCTTCAGATGATTTTATTG
66 AACCTTCAGATG-TTTTACTG
30004499 AAGCAGATCCAA
1 AAGCAGATCCAA
30004511 AATGATTTGG
Statistics
Matches: 136, Mismatches: 32, Indels: 37
0.66 0.16 0.18
Matches are distributed among these distances:
81 8 0.06
82 3 0.02
83 9 0.07
84 1 0.01
85 15 0.11
86 36 0.26
87 1 0.01
88 24 0.18
89 18 0.13
90 1 0.01
91 9 0.07
92 3 0.02
93 8 0.06
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (85 bp):
AAGCAGATCCAAGATAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCT
AACCTTCAGATGTTTTACTG
Found at i:30006325 original size:18 final size:18
Alignment explanation
Indices: 30006302--30006340 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
30006292 ACTAGTACTA
*
30006302 ATAATATTAATAATAAAT
1 ATAATAATAATAATAAAT
30006320 ATAATAATAATAATAAAT
1 ATAATAATAATAATAAAT
30006338 ATA
1 ATA
30006341 TGTACATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATAATAATAAAT
Found at i:30006426 original size:26 final size:25
Alignment explanation
Indices: 30006386--30006438 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
30006376 AAAATATAAC
* * *
30006386 TAAATATAATATGATGATAATAATA
1 TAAAAATAATATGATAACAATAATA
30006411 TAAAAATAATAGTGATAACAATAATA
1 TAAAAATAATA-TGATAACAATAATA
30006437 TA
1 TA
30006439 TATAACATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (25 bp):
TAAAAATAATATGATAACAATAATA
Found at i:30007079 original size:2 final size:2
Alignment explanation
Indices: 30007074--30007120 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
30007064 TATATATATA
30007074 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
30007116 TG TG T
1 TG TG T
30007121 ATAGATTAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:30008943 original size:30 final size:29
Alignment explanation
Indices: 30008874--30008944 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
30008864 TTTTTATAGT
* *
30008874 TATATTTTTATAATTTTTAAAGGATTAAA
1 TATAATTTTATAATTTTTAAAGGATAAAA
30008903 TCA-AATTTTTATAA-TTTTAAAGGGACTAAAA
1 T-ATAA-TTTTATAATTTTTAAA-GGA-TAAAA
30008934 TATAATTTTAT
1 TATAATTTTAT
30008945 TTTTACTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
29 9 0.26
30 19 0.54
31 7 0.20
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAAGGATAAAA
Found at i:30012188 original size:60 final size:60
Alignment explanation
Indices: 30012095--30012213 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
30012085 ACATTACTAG
* * *
30012095 GTCAAAATTGAATATCCCCGATATATAACTTATTCCCTTATATTATTCGAATTTAAGTAA
1 GTCAAAATTGAATATCCCCAATATATAACTTATTACCTTATATTATTCGAATTCAAGTAA
* * * * *
30012155 GTCAAGATTGAATATCTCTAATTTATAACTTATTATCTTATATTATTCGAATTCAAGTA
1 GTCAAAATTGAATATCCCCAATATATAACTTATTACCTTATATTATTCGAATTCAAGTA
30012214 TAGATATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.41
Consensus pattern (60 bp):
GTCAAAATTGAATATCCCCAATATATAACTTATTACCTTATATTATTCGAATTCAAGTAA
Found at i:30016867 original size:23 final size:23
Alignment explanation
Indices: 30016837--30016883 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30016827 TACTTTGATA
30016837 TTTTTTTCAATAAGAAAATTTAT
1 TTTTTTTCAATAAGAAAATTTAT
30016860 TTTTTTTCAATAAGAAAATTTAT
1 TTTTTTTCAATAAGAAAATTTAT
30016883 T
1 T
30016884 CACACACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTTTTCAATAAGAAAATTTAT
Found at i:30017844 original size:26 final size:27
Alignment explanation
Indices: 30017807--30017876 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 27
30017797 ATACATATTT
30017807 AATTATCT-ATATTTAATCA-TATAATA
1 AATTAT-TAATATTTAATCATTATAATA
* *
30017833 AATTATTAATATAGTTGATCATTTTAATA
1 AATTATTAATAT--TTAATCATTATAATA
30017862 AATTACTTAATATTT
1 AATTA-TTAATATTT
30017877 TAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 1 0.03
26 10 0.27
28 8 0.22
29 11 0.30
30 7 0.19
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTATTAATATTTAATCATTATAATA
Found at i:30017959 original size:15 final size:15
Alignment explanation
Indices: 30017941--30017997 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
30017931 ATTCAATATT
30017941 AATATTTTAATAATA
1 AATATTTTAATAATA
*
30017956 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
30017975 AATATATTAATAATA
1 AATATTTTAATAATA
30017990 AATATTTT
1 AATATTTT
30017998 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:30018866 original size:93 final size:93
Alignment explanation
Indices: 30018754--30018947 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 93
30018744 TATGATTCTC
* *
30018754 TAAT-AAAATATCAAGAAAAAATTTATCATTATTTACTAATTTATGAGTAAATTTTTATTAAATC
1 TAATAAAAATATCAAGAAAAAATTTATCATTATTCACTAATTTATGAATAAATTTTTATTAAATC
*
30018818 ACTTGACTTCTTTTTACAAGTTAATTAA
66 ACTTGACTTCTTTTGACAAGTTAATTAA
* * *
30018846 TAATAAAAATATCGAGAAAAAATTTATCATTATTCACTAATTTATGAATAATTTTTTGTTAAATC
1 TAATAAAAATATCAAGAAAAAATTTATCATTATTCACTAATTTATGAATAAATTTTTATTAAATC
30018911 ACTTGACTTCTTTTGACAAGTTAATTAA
66 ACTTGACTTCTTTTGACAAGTTAATTAA
30018939 TAATAAAAA
1 TAATAAAAA
30018948 AAGGGGCCGG
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 4 0.04
93 91 0.96
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (93 bp):
TAATAAAAATATCAAGAAAAAATTTATCATTATTCACTAATTTATGAATAAATTTTTATTAAATC
ACTTGACTTCTTTTGACAAGTTAATTAA
Found at i:30023093 original size:18 final size:19
Alignment explanation
Indices: 30023058--30023094 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
30023048 TGAATAAAAG
*
30023058 TGAAAATAGTGTAAATTGA
1 TGAAAATAGTGAAAATTGA
30023077 TGAAAAT-GTGAAAATTGA
1 TGAAAATAGTGAAAATTGA
30023095 ATTGGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (19 bp):
TGAAAATAGTGAAAATTGA
Found at i:30025203 original size:17 final size:17
Alignment explanation
Indices: 30025181--30025213 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30025171 ATCCGTAAAT
30025181 ATTTATTTATTTACTTG
1 ATTTATTTATTTACTTG
30025198 ATTTATTTATTTACTT
1 ATTTATTTATTTACTT
30025214 TTTACTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTATTTATTTACTTG
Found at i:30041175 original size:14 final size:15
Alignment explanation
Indices: 30041148--30041176 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30041138 ATGTTAAGTT
30041148 CTTAGGTGTAATAAA
1 CTTAGGTGTAATAAA
30041163 CTTAGGT-TAATAAA
1 CTTAGGTGTAATAAA
30041177 AATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
CTTAGGTGTAATAAA
Done.