Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 47 of 93
Found at i:18061354 original size:20 final size:20
Alignment explanation
Indices: 18061326--18061369 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18061316 AAGGAAGAAG
**
18061326 AAGACAGCTGTTGGAAATTTC
1 AAGACAGCTGCAGG-AATTTC
18061347 AAGA-AGCTGCAGGAATTTC
1 AAGACAGCTGCAGGAATTTC
18061366 AAGA
1 AAGA
18061370 TATTTATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (20 bp):
AAGACAGCTGCAGGAATTTC
Found at i:18065673 original size:18 final size:18
Alignment explanation
Indices: 18065652--18065686 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18065642 CCCCCTGGTT
18065652 TTGA-CATGTATGATAAAA
1 TTGATCATGTAT-ATAAAA
18065670 TTGATCATGTATATAAA
1 TTGATCATGTATATAAA
18065687 TTGCATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (18 bp):
TTGATCATGTATATAAAA
Found at i:18072869 original size:43 final size:43
Alignment explanation
Indices: 18072806--18072913 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
18072796 TATTGACTCG
* *
18072806 GCTATGTGTGAGTAGGGAGTGCGCATAACCCGGTGATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA
* *
18072848 GATTATGTGCGAGTAGGGAGTGCGCATAACTCGATGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA
*
18072892 GCCATGTGCGAGTAGGGAGTGC
1 GCTATGTGCGAGTAGGGAGTGC
18072914 ACATGAGCTG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 56 0.97
44 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA
Found at i:18072952 original size:23 final size:23
Alignment explanation
Indices: 18072922--18072980 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
18072912 GCACATGAGC
18072922 TGATGATGATGGGATAGTGTGCA
1 TGATGATGATGGGATAGTGTGCA
*
18072945 TGATGATGATGGGATGGTGTGCA
1 TGATGATGATGGGATAGTGTGCA
18072968 TGATGATGATGGG
1 TGATGATGATGGG
18072981 TACATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.03, G:0.42, T:0.31
Consensus pattern (23 bp):
TGATGATGATGGGATAGTGTGCA
Found at i:18074250 original size:35 final size:35
Alignment explanation
Indices: 18074201--18074273 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
18074191 CTTACTCAGC
*
18074201 TCATGTGCATTCCCTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
***
18074236 TCATGTGCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
18074271 TCA
1 TCA
18074274 CACGCACTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCA
Found at i:18074281 original size:35 final size:35
Alignment explanation
Indices: 18074211--18074284 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
18074201 TCATGTGCAT
***
18074211 TCCCTACACGCACAAGGCAATATCATCATGTGCAC
1 TCCCTACACGCACAAGGCAATATCATCACACGCAC
***
18074246 TCCCTACACGCACATTTCAATATCATCACACGCAC
1 TCCCTACACGCACAAGGCAATATCATCACACGCAC
18074281 TCCC
1 TCCC
18074285 GCCCACATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.22
Consensus pattern (35 bp):
TCCCTACACGCACAAGGCAATATCATCACACGCAC
Found at i:18075135 original size:12 final size:10
Alignment explanation
Indices: 18075109--18075139 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
18075099 TTTCGTAACA
18075109 ACACATATCC
1 ACACATATCC
18075119 ACACATATCC
1 ACACATATCC
*
18075129 ACACACATCC
1 ACACATATCC
18075139 A
1 A
18075140 AACTCCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (10 bp):
ACACATATCC
Found at i:18075581 original size:19 final size:19
Alignment explanation
Indices: 18075554--18075590 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18075544 GGTAAGGTGA
18075554 AAATAGCATCGGAGCATGG
1 AAATAGCATCGGAGCATGG
* *
18075573 AAATGGCATGGGAGCATG
1 AAATAGCATCGGAGCATG
18075591 AAGAAGACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.16
Consensus pattern (19 bp):
AAATAGCATCGGAGCATGG
Found at i:18081768 original size:34 final size:33
Alignment explanation
Indices: 18081728--18081849 Score: 127
Period size: 34 Copynumber: 3.6 Consensus size: 33
18081718 AAACGATTTC
18081728 GCTTGATCTCATGAAAAAGCTTTGCAAGGGTTTT
1 GCTTGATCTCAT-AAAAAGCTTTGCAAGGGTTTT
** * *
18081762 GCTTGATCTTGTGAAAAATCTTTGCAAGGGTTTC
1 GCTTGATCTCAT-AAAAAGCTTTGCAAGGGTTTT
* *** *
18081796 GCTTGATCTTATAAAAAGCTATTATGAGTGTTTT
1 GCTTGATCTCATAAAAAGCT-TTGCAAGGGTTTT
*
18081830 GCTTGATCCCATAAAAAGCT
1 GCTTGATCTCATAAAAAGCT
18081850 CATTTCCCTT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
33 7 0.09
34 67 0.91
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (33 bp):
GCTTGATCTCATAAAAAGCTTTGCAAGGGTTTT
Found at i:18082283 original size:21 final size:21
Alignment explanation
Indices: 18082259--18082300 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18082249 AACAAAGTAG
18082259 TTGAC-TATGACTTTGTGAATT
1 TTGACTTATGACTTT-TGAATT
*
18082280 TTGACTTTTGACTTTTGAATT
1 TTGACTTATGACTTTTGAATT
18082301 CAATGGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (21 bp):
TTGACTTATGACTTTTGAATT
Found at i:18087593 original size:131 final size:134
Alignment explanation
Indices: 18087279--18087599 Score: 339
Period size: 136 Copynumber: 2.4 Consensus size: 134
18087269 TCACACACAC
* * ** * * *
18087279 ACCAACACAACAACTGGTCATCAATATAAAAAAACAATCATAACAGAATGAGAATAACAACTGGT
1 ACCAACACAACAAC---TAATCAATATATACCAACAATCATAACACAATGACAATAACAACTGAT
* * * * *
18087344 CTCTACATTGTAACTCATCACACATGATAATCTATACAATACAATCACAACACAAACATGTTATA
63 CTCTACATCGCAACACATCACACATGACAATCTATACAACACAATCACAACACAAACATG-T-TA
18087409 TATATATAT
126 TATATATAT
* *
18087418 ATCAACACAACAACTAATCAATATATACCAACAATCACAACACAATGACAATAACAACCT-ATCT
1 ACCAACACAACAACTAATCAATATATACCAACAATCATAACACAATGACAATAACAA-CTGATCT
* *
18087482 TTACATCGCAACACATCACAACATGACAATCTATATAACACAATCACAACACAAACA-G-T-T-T
65 CTACATCGCAACACATCAC-ACATGACAATCTATACAACACAATCACAACACAAACATGTTATAT
18087543 ATATAT
129 ATATAT
* * * * *
18087549 ACCAATACAGCAACTGAA-GAATATATCCCAACAATCTTAACACAATGACAA
1 ACCAACACAACAACT-AATCAATATATACCAACAATCATAACACAATGACAA
18087600 CACAATCATA
Statistics
Matches: 156, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
131 48 0.31
132 3 0.02
133 1 0.01
136 55 0.35
137 36 0.23
139 13 0.08
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (134 bp):
ACCAACACAACAACTAATCAATATATACCAACAATCATAACACAATGACAATAACAACTGATCTC
TACATCGCAACACATCACACATGACAATCTATACAACACAATCACAACACAAACATGTTATATAT
ATAT
Found at i:18090712 original size:51 final size:50
Alignment explanation
Indices: 18090657--18090812 Score: 117
Period size: 51 Copynumber: 3.1 Consensus size: 50
18090647 AGGATTGTTA
18090657 GTTAAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTGGGGT
1 GTTAAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTT-GGGT
* * * ** * * * * *
18090708 GTTAAGTTTG-GATTTTTGGAAGT-TGAAATGAAGAA-AAGGTGCAATCT-GG-
1 GTTAAGATAGTCA-TTTT-GAAGTATGACTTAAACAATAA-ATG-ATTTTGGGT
*
18090757 G-CAAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTAGGGT
1 GTTAAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTT-GGGT
18090807 GTTAAG
1 GTTAAG
18090813 TTTGGATTTT
Statistics
Matches: 72, Mismatches: 22, Indels: 22
0.62 0.19 0.19
Matches are distributed among these distances:
47 8 0.11
48 19 0.26
49 6 0.08
50 6 0.08
51 25 0.35
52 8 0.11
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (50 bp):
GTTAAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTGGGT
Found at i:18090767 original size:99 final size:99
Alignment explanation
Indices: 18090660--18090862 Score: 388
Period size: 99 Copynumber: 2.1 Consensus size: 99
18090650 ATTGTTAGTT
*
18090660 AAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTGGGGTGTTAAGTTTGGATTTTT
1 AAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTAGGGTGTTAAGTTTGGATTTTT
18090725 GGAAGTTGAAATGAAGAAAAGGTGCAATCTGGGC
66 GGAAGTTGAAATGAAGAAAAGGTGCAATCTGGGC
18090759 AAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTAGGGTGTTAAGTTTGGATTTTT
1 AAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTAGGGTGTTAAGTTTGGATTTTT
*
18090824 GGAAGTTGAAATGCAGAAAAGGTGCAATCTGGGC
66 GGAAGTTGAAATGAAGAAAAGGTGCAATCTGGGC
18090858 AAGAT
1 AAGAT
18090863 GTACTAATAC
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 102 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (99 bp):
AAGATAGTCATTTTGAAGTATGACTTAAACAATAAATGATTTTAGGGTGTTAAGTTTGGATTTTT
GGAAGTTGAAATGAAGAAAAGGTGCAATCTGGGC
Found at i:18091695 original size:14 final size:14
Alignment explanation
Indices: 18091672--18091712 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18091662 AGAATTGATA
*
18091672 TGTGTCTATGTGTG
1 TGTGTATATGTGTG
18091686 TGTGTATATGTGTG
1 TGTGTATATGTGTG
* *
18091700 AGTGTGTATGTGT
1 TGTGTATATGTGT
18091713 ATATATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.02, G:0.37, T:0.49
Consensus pattern (14 bp):
TGTGTATATGTGTG
Found at i:18095184 original size:34 final size:32
Alignment explanation
Indices: 18095124--18095186 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
18095114 TTTTGTGAAA
* * *
18095124 TTTTTTTTCTTTATTTTAGAATTTTAAAAACT
1 TTTTTTTTCTTTATTTAAAAAATTTAAAAACT
18095156 TTTTATTTTCTCTTATTTAAAAAATTTAAAA
1 TTTT-TTTTCT-TTATTTAAAAAATTTAAAA
18095187 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 4 0.15
33 6 0.23
34 16 0.62
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTTTTTTCTTTATTTAAAAAATTTAAAAACT
Found at i:18095417 original size:25 final size:25
Alignment explanation
Indices: 18095384--18095433 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
18095374 TACGCGGCAT
*
18095384 ATTCTTATTAATTACTTTTAGACAC
1 ATTCATATTAATTACTTTTAGACAC
*
18095409 ATTCATATTAATTCCTTTTAGACAC
1 ATTCATATTAATTACTTTTAGACAC
18095434 GTTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTCATATTAATTACTTTTAGACAC
Found at i:18095442 original size:25 final size:26
Alignment explanation
Indices: 18095384--18095442 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
18095374 TACGCGGCAT
18095384 ATTC-TTATTAATTACTTTTAGACAC
1 ATTCATTATTAATTACTTTTAGACAC
*
18095409 ATTCA-TATTAATTCCTTTTAGACAC
1 ATTCATTATTAATTACTTTTAGACAC
*
18095434 GTT-ATTATT
1 ATTCATTATT
18095443 TTAGTGACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTCATTATTAATTACTTTTAGACAC
Found at i:18096139 original size:2 final size:2
Alignment explanation
Indices: 18096132--18096160 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18096122 TACTAGTAGC
18096132 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18096161 TTGTAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18098942 original size:3 final size:3
Alignment explanation
Indices: 18098931--18098978 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
18098921 GTGGTGGTGG
* *
18098931 TGA TTA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGG TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
18098979 CCATGGCCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:18102039 original size:39 final size:39
Alignment explanation
Indices: 18101982--18102075 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
18101972 AACGAGATTC
* * *
18101982 TTTCTCGCTGTAGTGAAATTG-TAACCCAGAAACAGAAGG
1 TTTCTCGCTGCAGCGAAATTGCT-ACCCAGAAACAGAAAG
18102021 TTTCTCGCTGCAGCGAAATTGCTACCCAGAAACAGAAAG
1 TTTCTCGCTGCAGCGAAATTGCTACCCAGAAACAGAAAG
*
18102060 TTTCTCGCTACAGCGA
1 TTTCTCGCTGCAGCGA
18102076 GAATGTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 49 0.98
40 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (39 bp):
TTTCTCGCTGCAGCGAAATTGCTACCCAGAAACAGAAAG
Found at i:18102521 original size:43 final size:43
Alignment explanation
Indices: 18102474--18102586 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
18102464 GCTCATGTGA
* ** *
18102474 ACTCCCTACTCGCACGTGGCCGGTTCATCAC-CGGATTATGCGC
1 ACTCCCTACTCGCACATAACCGGGTCATC-CTCGGATTATGCGC
*
18102517 ACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTTATGCGC
1 ACTCCCTACTCGCACATAACCGGGTCATCCTCGGATTATGCGC
* * *
18102560 ACTCCCTACTCTCACATAGCCGAGTCA
1 ACTCCCTACTCGCACATAACCGGGTCA
18102587 ATATAATTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.23
Consensus pattern (43 bp):
ACTCCCTACTCGCACATAACCGGGTCATCCTCGGATTATGCGC
Found at i:18105238 original size:23 final size:23
Alignment explanation
Indices: 18105139--18105475 Score: 138
Period size: 23 Copynumber: 14.9 Consensus size: 23
18105129 TTTGGCACAG
* *
18105139 CATGGATG-GAATATGTGACATGG
1 CATGG-TGAGAATATGTGACACGT
* *
18105162 CA-GGATGAGAATATGTGCCACGA
1 CATGG-TGAGAATATGTGACACGT
* * * * *
18105185 CTTGGAGAGAATATGTGAGATGA
1 CATGGTGAGAATATGTGACACGT
18105208 CATGGTGAGAATATGTGACACGT
1 CATGGTGAGAATATGTGACACGT
* *
18105231 TA-GTGTGAG-A-ATGTGACGCGT
1 CATG-GTGAGAATATGTGACACGT
* * *
18105252 CATGGTGAGAATATGTGAGATGG
1 CATGGTGAGAATATGTGACACGT
* * *
18105275 CATGGTGAGCATACGTGACACGG
1 CATGGTGAGAATATGTGACACGT
* * * * *
18105298 CAAGGTTTAGAGTTTGTGACACGC
1 CATGG-TGAGAATATGTGACACGT
* * * * *
18105322 CATGG-AAGGAATTTATGACCCGA
1 CATGGTGA-GAATATGTGACACGT
* **
18105345 CAAGGTGAGAATATGTGACACAA
1 CATGGTGAGAATATGTGACACGT
* * * *
18105368 CTTGGAGGGAATATGTG--A-GA
1 CATGGTGAGAATATGTGACACGT
* *
18105388 CATGGTGAGAATATGTAACATG-
1 CATGGTGAGAATATGTGACACGT
* * ** *
18105410 C-TAGTGTGAGCATGTGACACGC
1 CATGGTGAGAATATGTGACACGT
* * *
18105432 CATGGTGTGAATATGTGACATGC
1 CATGGTGAGAATATGTGACACGT
* *
18105455 CATGGTGACAACATGTGACAC
1 CATGGTGAGAATATGTGACAC
18105476 AATTGTGACA
Statistics
Matches: 234, Mismatches: 66, Indels: 28
0.71 0.20 0.09
Matches are distributed among these distances:
20 14 0.06
21 31 0.13
22 13 0.06
23 157 0.67
24 19 0.08
ACGTcount: A:0.31, C:0.13, G:0.32, T:0.24
Consensus pattern (23 bp):
CATGGTGAGAATATGTGACACGT
Found at i:18105259 original size:21 final size:21
Alignment explanation
Indices: 18105208--18105263 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
18105198 TGTGAGATGA
18105208 CATGGTGAGAATATGTGACACGT
1 CATGGTGAG-A-ATGTGACACGT
* *
18105231 TA-GTGTGAGAATGTGACGCGT
1 CATG-GTGAGAATGTGACACGT
18105252 CATGGTGAGAAT
1 CATGGTGAGAAT
18105264 ATGTGAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 19 0.68
22 3 0.11
23 6 0.21
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.27
Consensus pattern (21 bp):
CATGGTGAGAATGTGACACGT
Found at i:18105563 original size:81 final size:81
Alignment explanation
Indices: 18105478--18105634 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 81
18105468 TGTGACACAA
* * * *
18105478 TTGTGACACGG-AGGGGTTTAGAGTTTGTGACATGCCATGGAGGGAATTTGTAACACGAAAGGGT
1 TTGTGACACGGCA-AGGTTCAGAGTTTGTGACACGCCATGGAGGGAATGTGTAACACGAAAGGGT
*
18105542 GAGAATATGTGATACGG
65 GAAAATATGTGATACGG
* * * * *
18105559 TTGTGACACGGCAAGGTTCAGAGTTTGTGACACGCTATGGTGGGAATGTGTGACACGACATGGTG
1 TTGTGACACGGCAAGGTTCAGAGTTTGTGACACGCCATGGAGGGAATGTGTAACACGAAAGGGTG
18105624 AAAATATGTGA
66 AAAATATGTGA
18105635 CACGACATGT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 64 0.98
82 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.34, T:0.26
Consensus pattern (81 bp):
TTGTGACACGGCAAGGTTCAGAGTTTGTGACACGCCATGGAGGGAATGTGTAACACGAAAGGGTG
AAAATATGTGATACGG
Found at i:18105614 original size:23 final size:23
Alignment explanation
Indices: 18105584--18105688 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 23
18105574 GTTCAGAGTT
** *
18105584 TGTGACACG-CTATGGTGGGAATG
1 TGTGACACGAC-ATGGTGAAAATA
18105607 TGTGACACGACATGGTGAAAATA
1 TGTGACACGACATGGTGAAAATA
* *
18105630 TGTGACACGACATGTTG-AAATCG
1 TGTGACACGACATGGTGAAAAT-A
* * * * *
18105653 TGTAAGATGACATGGTGAGAATC
1 TGTGACACGACATGGTGAAAATA
18105676 TGTGACACGACAT
1 TGTGACACGACAT
18105689 CATTTGAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
22 4 0.06
23 57 0.88
24 4 0.06
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (23 bp):
TGTGACACGACATGGTGAAAATA
Found at i:18106404 original size:87 final size:87
Alignment explanation
Indices: 18106224--18106397 Score: 213
Period size: 87 Copynumber: 2.0 Consensus size: 87
18106214 GGGTTTTTAA
* * *
18106224 CATGTCACTACATTGGGTATTTTAAGGCAGTCCATGTAACGAGTCAGTAATTATAGTGATTAGCG
1 CATGTCACCACATTGGGTATTTTAAGGCAGTCCATGTAACGAGTAAGTAATTATAGCGATTAGCG
* *
18106289 TATCACAACATGGCATGGTTGG
66 TATCACAACACGACATGGTTGG
* * * * * * *
18106311 CATGTCACCACATTGGGTATTTTATGGTAGTTCGTGTAGCGAGTAAGTTATTATAGCGATTGGCG
1 CATGTCACCACATTGGGTATTTTAAGGCAGTCCATGTAACGAGTAAGTAATTATAGCGATTAGCG
* * *
18106376 TGTCACGACACGACGTGGTTGG
66 TATCACAACACGACATGGTTGG
18106398 TGTGTCATGA
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (87 bp):
CATGTCACCACATTGGGTATTTTAAGGCAGTCCATGTAACGAGTAAGTAATTATAGCGATTAGCG
TATCACAACACGACATGGTTGG
Found at i:18106463 original size:31 final size:31
Alignment explanation
Indices: 18106425--18106531 Score: 160
Period size: 31 Copynumber: 3.5 Consensus size: 31
18106415 TAGCATTGGT
*
18106425 GTGTAACAACATTTGACTTGGTATGCTTAGT
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
*
18106456 GTCTAACAACATTTGACTTGGTATGCTTAGC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
* * * *
18106487 ATGTAACAACATTTAACTTGGTATGCATAAC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
18106518 GTGTAACAACATTT
1 GTGTAACAACATTT
18106532 ATTTCTTTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (31 bp):
GTGTAACAACATTTGACTTGGTATGCTTAGC
Found at i:18108315 original size:151 final size:151
Alignment explanation
Indices: 18108036--18108318 Score: 379
Period size: 151 Copynumber: 1.9 Consensus size: 151
18108026 GGTAAGAACA
* *
18108036 GTTCTAACAGTTTGTGTTCAACATTTCCATATATGTTTATCAAATAACATAGTAATTTCTGTTAT
1 GTTCTAACAGTTTGTGTTCAACATTTCCACATATGTTTATCAAATAACATAGTAATTTCTATTAT
* * ** * * *
18108101 TGCAGTTGACAAAGGCGACGATAGCTTTTCAACCACCGATCGATCTTACTTAACGACACGGTGCT
66 TGCAATTGACAAAGGCGACAATAGCTCCTCAACCACCAACCGATCTTACTCAACGACACGGTGCT
18108166 AATGAGCCATTAATAAGAATG
131 AATGAGCCATTAATAAGAATG
** *
18108187 GTTCTAACAGTTTGTGTTCAACATTTCCACATATGTTTATTGAATAACATAGTAATTTCTATTGT
1 GTTCTAACAGTTTGTGTTCAACATTTCCACATATGTTTATCAAATAACATAGTAATTTCTATTAT
*** * * * *
18108252 TGCAATTGATGGAGGCGACAATAGCTCCTCAACCACTAACC-AGTCTTGCTCAACTACATGGTGC
66 TGCAATTGACAAAGGCGACAATAGCTCCTCAACCACCAACCGA-TCTTACTCAACGACACGGTGC
18108316 TAA
130 TAA
18108319 CAAGCCGTTC
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
150 1 0.01
151 111 0.99
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (151 bp):
GTTCTAACAGTTTGTGTTCAACATTTCCACATATGTTTATCAAATAACATAGTAATTTCTATTAT
TGCAATTGACAAAGGCGACAATAGCTCCTCAACCACCAACCGATCTTACTCAACGACACGGTGCT
AATGAGCCATTAATAAGAATG
Found at i:18109015 original size:81 final size:79
Alignment explanation
Indices: 18108878--18109147 Score: 222
Period size: 81 Copynumber: 3.4 Consensus size: 79
18108868 TGACCCTTCA
* * * * * * *
18108878 ATCAGTTGATGCTGAAGAAAACCATGTTCTTGAGGCTAATGCAGTTA-TCAATGCAGTTGTGGGA
1 ATCAGTTGAGGCTGAAGGAGACCATGTT-TTTAGGCCAATG-AG-TAGTCAAGGCAGTTGCGGGA
18108942 GGGGAAAGGGACCTT-C
63 GGGGAAAGGGACCTTGC
* * **
18108958 ACTCAGTTGAGGTTGAAGGAGACCATGTTTTTAAGGCCAATGTAGTAGTCGAGGCAGTTGCAAGA
1 A-TCAGTTGAGGCTGAAGGAGACCATGTTTTT-AGGCCAATG-AGTAGTCAAGGCAGTTGCGGGA
* *
18109023 GGGGATAGGAACCTTGC
63 GGGGAAAGGGACCTTGC
* * * * * **
18109040 ATTAGTTGAGGCTAAAAGAGACCATGTTTCTTAGGCCGATGGGTAGTCAAGGCAACTGCGGGAGG
1 ATCAGTTGAGGCTGAAGGAGACCATGTTT-TTAGGCCAATGAGTAGTCAAGGCAGTTGCGGGAGG
* *
18109105 GG-ATGGGCATCTTGC
65 GGAAAGGG-ACCTTGC
* * *
18109120 ATCAGTTCAGGTTGAAGGGGACCATGTT
1 ATCAGTTGAGGCTGAAGGAGACCATGTT
18109148 CCTCAATGCA
Statistics
Matches: 149, Mismatches: 35, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
79 2 0.01
80 53 0.36
81 90 0.60
82 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (79 bp):
ATCAGTTGAGGCTGAAGGAGACCATGTTTTTAGGCCAATGAGTAGTCAAGGCAGTTGCGGGAGGG
GAAAGGGACCTTGC
Found at i:18109143 original size:80 final size:81
Alignment explanation
Indices: 18108940--18109147 Score: 215
Period size: 80 Copynumber: 2.6 Consensus size: 81
18108930 GCAGTTGTGG
* *
18108940 GAGGGGAAAGGGACCTT-CACTCAGTTGAGGTTGAAGGAGACCATGTTTTTAAGGCCAATGTAGT
1 GAGGGGATAGGAACCTTGCA-TCAGTTGAGGTTGAAGGAGACCATGTTTTTAAGGCCAATGTAGT
* **
18109004 AGTCGAGGCAGTTGCAA
65 AGTCAAGGCAACTGCAA
* * * * * *
18109021 GAGGGGATAGGAACCTTGCATTAGTTGAGGCTAAAAGAGACCATGTTTCTT-AGGCCGATG-GGT
1 GAGGGGATAGGAACCTTGCATCAGTTGAGGTTGAAGGAGACCATGTTT-TTAAGGCCAATGTAGT
**
18109084 AGTCAAGGCAACTGCGG
65 AGTCAAGGCAACTGCAA
* * * * *
18109101 GAGGGGATGGGCATCTTGCATCAGTTCAGGTTGAAGGGGACCATGTT
1 GAGGGGATAGGAACCTTGCATCAGTTGAGGTTGAAGGAGACCATGTT
18109148 CCTCAATGCA
Statistics
Matches: 103, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
80 52 0.50
81 47 0.46
82 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (81 bp):
GAGGGGATAGGAACCTTGCATCAGTTGAGGTTGAAGGAGACCATGTTTTTAAGGCCAATGTAGTA
GTCAAGGCAACTGCAA
Found at i:18110582 original size:76 final size:76
Alignment explanation
Indices: 18110473--18110806 Score: 400
Period size: 76 Copynumber: 4.4 Consensus size: 76
18110463 ATAAGCCCTA
* * * * * *
18110473 AACGACTTCTAACAATTGGAGCGTTACGTGTCACCCCATAATACTACAACCACGCAACGTGTCAC
1 AACGACATCTAACAATTGGAGCGTGACATGTCACCCCATAATACTGCAACCACTCAGCGTGTCAC
*
18110538 CATAAGATGTC
66 CACAAGATGTC
* * * *
18110549 AATGACATCTAAAAATTGGAGCGTGGCATGTCACCCCAAAATACTGCAACCACTCAGCGTGTCAC
1 AACGACATCTAACAATTGGAGCGTGACATGTCACCCCATAATACTGCAACCACTCAGCGTGTCAC
* *
18110614 CGCAAGATTTC
66 CACAAGATGTC
* * * * * * * *
18110625 AATGACATCTAACAATTGAAGCATGACGTGTCACCCTATAATGCTGTAACCACTCAGTGTGTCAC
1 AACGACATCTAACAATTGGAGCGTGACATGTCACCCCATAATACTGCAACCACTCAGCGTGTCAC
18110690 CACAAGATGTC
66 CACAAGATGTC
* * * * *
18110701 AACGATATCTAACAATTGGAGTGTGACATGTCATCCCATAATGCTGCAACGACTCAGCGTGTCAC
1 AACGACATCTAACAATTGGAGCGTGACATGTCACCCCATAATACTGCAACCACTCAGCGTGTCAC
*
18110766 CACAAGATGTT
66 CACAAGATGTC
* *
18110777 AACGACATCTAACAATTAGAGC-TGGCATGT
1 AACGACATCTAACAATTGGAGCGTGACATGT
18110807 AACAATATAA
Statistics
Matches: 217, Mismatches: 41, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
75 7 0.03
76 210 0.97
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (76 bp):
AACGACATCTAACAATTGGAGCGTGACATGTCACCCCATAATACTGCAACCACTCAGCGTGTCAC
CACAAGATGTC
Found at i:18116598 original size:21 final size:23
Alignment explanation
Indices: 18116565--18116607 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
18116555 TACCTTTTTT
*
18116565 CACTTGTTTCCTTGAA-TTTTCA
1 CACTTGTTCCCTTGAAGTTTTCA
18116587 CACTT-TTCCCTTGAAGTTTTC
1 CACTTGTTCCCTTGAAGTTTTC
18116608 CACCTAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.16, C:0.26, G:0.09, T:0.49
Consensus pattern (23 bp):
CACTTGTTCCCTTGAAGTTTTCA
Found at i:18123642 original size:21 final size:23
Alignment explanation
Indices: 18123609--18123651 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
18123599 TACCTTTTTT
*
18123609 CACTTGTTTCCTTGAAT-TTTCA
1 CACTTGTTCCCTTGAATATTTCA
18123631 CACTT-TTCCCTTGAATATTTC
1 CACTTGTTCCCTTGAATATTTC
18123652 CACCTAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (23 bp):
CACTTGTTCCCTTGAATATTTCA
Found at i:18124441 original size:25 final size:25
Alignment explanation
Indices: 18124387--18124474 Score: 126
Period size: 25 Copynumber: 3.6 Consensus size: 25
18124377 TTAGTCATGT
*
18124387 TGTTACACGCCATGATCAAT--AAA
1 TGTTACACGCCATGTTCAATAAAAA
* *
18124410 TATTACATGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTCAATAAAAA
18124435 TGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTCAATAAAAA
*
18124460 CGTTACACGCCATGT
1 TGTTACACGCCATGT
18124475 GCTAACACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 17 0.30
25 40 0.70
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (25 bp):
TGTTACACGCCATGTTCAATAAAAA
Found at i:18128187 original size:77 final size:78
Alignment explanation
Indices: 18128057--18128221 Score: 242
Period size: 77 Copynumber: 2.1 Consensus size: 78
18128047 AATGCCATCT
* * *
18128057 ATTTTAATTTTTAGTGATTCATAAAAAAATAGGAAATTATTTTCTACTTTAAAAGCAATTCCTAA
1 ATTTTAATTTTGAGTGATTCATAAAAAAATAGGAAATTATTTGCTACTTTAAAAGAAATTCCTAA
18128122 AATTAAAGATAGA
66 AATTAAAGATAGA
* * * * *
18128135 ATTTTAATTTTGGGTGATTTAT-AAATAATAGGAAATTGTTTGCTACTTTAAAAGAAATTCCTCA
1 ATTTTAATTTTGAGTGATTCATAAAAAAATAGGAAATTATTTGCTACTTTAAAAGAAATTCCTAA
*
18128199 AATTAAAGATAGC
66 AATTAAAGATAGA
18128212 ATTTTAATTT
1 ATTTTAATTT
18128222 GAAAAATTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
77 59 0.76
78 19 0.24
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (78 bp):
ATTTTAATTTTGAGTGATTCATAAAAAAATAGGAAATTATTTGCTACTTTAAAAGAAATTCCTAA
AATTAAAGATAGA
Found at i:18131346 original size:15 final size:15
Alignment explanation
Indices: 18131326--18131374 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
18131316 TTTAAAGATC
18131326 AAAGATTTTGGTTTT
1 AAAGATTTTGGTTTT
*
18131341 AAAGA-TATGGATTTT
1 AAAGATTTTGG-TTTT
*
18131356 AAAGTTTTTGGTTTT
1 AAAGATTTTGGTTTT
18131371 AAAG
1 AAAG
18131375 TTGTTTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
AAAGATTTTGGTTTT
Found at i:18134693 original size:13 final size:13
Alignment explanation
Indices: 18134675--18134699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18134665 GGAAAATGAG
18134675 ATTTTATAAAATA
1 ATTTTATAAAATA
18134688 ATTTTATAAAAT
1 ATTTTATAAAAT
18134700 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:18136025 original size:39 final size:39
Alignment explanation
Indices: 18135971--18136057 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
18135961 TTATGTGGTT
18135971 GATCTCGATTAAGCCACATGTATGATGTTGGCTAGTATG
1 GATCTCGATTAAGCCACATGTATGATGTTGGCTAGTATG
*
18136010 GATCTCGATTAAGCCACATGTGTGATGTTGGCTAGTATG
1 GATCTCGATTAAGCCACATGTATGATGTTGGCTAGTATG
*
18136049 GCTCTCGAT
1 GATCTCGAT
18136058 CTTCAAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (39 bp):
GATCTCGATTAAGCCACATGTATGATGTTGGCTAGTATG
Found at i:18141443 original size:29 final size:28
Alignment explanation
Indices: 18141411--18141472 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
18141401 TTGTCAATAA
*
18141411 TTTAGAAAAA-AAAACTTATGTGTTGATTT
1 TTTA-AAAAATAAAAATTAT-TGTTGATTT
* *
18141440 TTTAAAAAATAAAAATTATTTTTTATTT
1 TTTAAAAAATAAAAATTATTGTTGATTT
18141468 TTTAA
1 TTTAA
18141473 TCTACATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTAAAAAATAAAAATTATTGTTGATTT
Found at i:18143424 original size:73 final size:74
Alignment explanation
Indices: 18143291--18143505 Score: 224
Period size: 73 Copynumber: 2.9 Consensus size: 74
18143281 AAGATAACCG
* * * * *
18143291 GTTCAAAAACAGAGACAACTTAATCGACTAAGAAACATT-GCTAGTCGACTAAAAGCTTACTGTC
1 GTTCAGAAACAGAGACAACTTAATCGACTAAG-AAGATTAGTTAGTCGACTAAGAGTTTACTGTC
*
18143355 AGAAAT-TGG
65 AGAAATCTGA
* * ** * *
18143364 GTTTAGAGACAGAGATGACTTAATCGACTAAGAAGTTTAGTTAGTCGACTAAGAGTTTACTGCCA
1 GTTCAGAAACAGAGACAACTTAATCGACTAAGAAGATTAGTTAGTCGACTAAGAGTTTACTGTCA
18143429 G-AATCTGA
66 GAAATCTGA
* * * *
18143437 GTTCAGAAACAGAGACAACTTAATTGACGAAGGAGCA-TAGTTAGTCGACTAAGAGTATT-CTAT
1 GTTCAGAAACAGAGACAACTTAATCGACTAAGAAG-ATTAGTTAGTCGACTAAGAGT-TTACTGT
18143500 CAGAAA
64 CAGAAA
18143506 ATTTGAATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
72 7 0.06
73 104 0.90
74 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (74 bp):
GTTCAGAAACAGAGACAACTTAATCGACTAAGAAGATTAGTTAGTCGACTAAGAGTTTACTGTCA
GAAATCTGA
Found at i:18149325 original size:22 final size:21
Alignment explanation
Indices: 18149286--18149326 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18149276 CCTAGGTGGA
* *
18149286 AAAATTCAGGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGTG
18149307 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAA-AAGTG
18149327 AAAAAAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.17
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGTG
Found at i:18149332 original size:22 final size:21
Alignment explanation
Indices: 18149285--18149332 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
18149275 CCCTAGGTGG
* * *
18149285 AAAAATTCAGGGGAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
18149306 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
18149328 AAAAA
1 AAAAA
18149333 AGTAAGATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:18158078 original size:28 final size:28
Alignment explanation
Indices: 18158038--18158095 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
18158028 ACTCTCGAAA
18158038 TAGTGAGTAACCTTATCATTATTTTAAT
1 TAGTGAGTAACCTTATCATTATTTTAAT
18158066 TAGTGAGTAACCTTATCATTATTTTAAT
1 TAGTGAGTAACCTTATCATTATTTTAAT
18158094 TA
1 TA
18158096 TGTAAAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (28 bp):
TAGTGAGTAACCTTATCATTATTTTAAT
Found at i:18164555 original size:23 final size:22
Alignment explanation
Indices: 18164511--18164555 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
18164501 TAAGGGAGAT
*
18164511 AGAAAGTAGAGGAATTTTAGGG
1 AGAAAGTAGAGGAATTTAAGGG
18164533 AGAAAGTAGAAGTG-ATTTAAGGG
1 AGAAAGTAG-AG-GAATTTAAGGG
18164556 TAATTTAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (22 bp):
AGAAAGTAGAGGAATTTAAGGG
Found at i:18165524 original size:73 final size:73
Alignment explanation
Indices: 18165307--18165509 Score: 189
Period size: 73 Copynumber: 2.8 Consensus size: 73
18165297 GAAGATGGCC
* * * * * * * * * **
18165307 GGTTCAGATAT-AGAGACAACTTAATTGACTAAGAAACATTGCTAATCGACTAAGAGTTTACTGG
1 GGTTCAGAGATAAGA-ACGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTAC
*
18165371 TAGAAATTG
65 CAGAAATTG
* ** *
18165380 GGTTCAGAGATAAGAATGACTTAATCGACTAAGAAGTTTAGTTAGTCAATTAAGAGCTTACTACC
1 GGTTCAGAGATAAGAACGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTACC
18165445 AGAAATTG
66 AGAAATTG
*
18165453 GGTTCAGA-A-ACAGAAACGACTTAATCGACTAA-AGAGCATAGTTAGTCGACTAAGAGC
1 GGTTCAGAGATA-AG-AACGACTTAATCGACTAAGA-AGCATAGTTAGTCAACTAAGAGC
18165510 ATTTTATCAG
Statistics
Matches: 105, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
71 1 0.01
72 4 0.04
73 97 0.92
74 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (73 bp):
GGTTCAGAGATAAGAACGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTACC
AGAAATTG
Found at i:18165965 original size:35 final size:35
Alignment explanation
Indices: 18165937--18166026 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
18165927 GGTTGATCAC
*
18165937 AAGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
1 AAGAAAATCCATTGTTAAAGGTTGTGGTTGAGCCT
*
18165972 ATGAAAATCCATTGTTAAAGGTTGTGGTTGAGCCT
1 AAGAAAATCCATTGTTAAAGGTTGTGGTTGAGCCT
*
18166007 ACGAAAATCCATTGTTAAAG
1 AAGAAAATCCATTGTTAAAG
18166027 CTTGGTGGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (35 bp):
AAGAAAATCCATTGTTAAAGGTTGTGGTTGAGCCT
Found at i:18169396 original size:42 final size:41
Alignment explanation
Indices: 18169339--18169449 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 41
18169329 TTATGTGATA
** * *
18169339 ATGATGACCCAGCTATGTGCGTGTGGGAGTGTACATGAGTTG
1 ATGATGACCCAGCTATGTGCG-GTGGGAGTACACATAAGCTG
*
18169381 ATGATGACCCAGCTATGTGAGGTGTGGAGTACACATAAGCTG
1 ATGATGACCCAGCTATGTGCGGTG-GGAGTACACATAAGCTG
*
18169423 ATGATGACCTAGCTATGTGCGAGTGGG
1 ATGATGACCCAGCTATGTGCG-GTGGG
18169450 GAGCATAGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 3 0.05
42 54 0.90
43 3 0.05
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.26
Consensus pattern (41 bp):
ATGATGACCCAGCTATGTGCGGTGGGAGTACACATAAGCTG
Found at i:18169992 original size:19 final size:19
Alignment explanation
Indices: 18169968--18170004 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18169958 GTTTTAGAGA
18169968 GAAACCCTCGGCCAGTTGT
1 GAAACCCTCGGCCAGTTGT
*
18169987 GAAACCCTCGTCCAGTTG
1 GAAACCCTCGGCCAGTTG
18170005 ATAATTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
GAAACCCTCGGCCAGTTGT
Found at i:18171700 original size:20 final size:20
Alignment explanation
Indices: 18171658--18171700 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18171648 TTAGGTTGAT
*
18171658 TTAATTTAATTTATTTTATG
1 TTAATTTAATTTAGTTTATG
*
18171678 TTAATTTACTTTTAGTTTA-G
1 TTAATTTA-ATTTAGTTTATG
18171698 TTA
1 TTA
18171701 TTATTGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
TTAATTTAATTTAGTTTATG
Found at i:18173946 original size:29 final size:28
Alignment explanation
Indices: 18173815--18173988 Score: 159
Period size: 28 Copynumber: 5.9 Consensus size: 28
18173805 TGAAGACAAC
* * *
18173815 TCTTGTCTCTAATTAAGATAAAAATATTTT
1 TCTTGTCT-AAATTAAGACAAACATA-TTT
* * *
18173845 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
18173874 TCTTGTCTAGATTAAGACAAAAAATATATTTT
1 TCTTGTCTAAATTAAGAC---AAACATA-TTT
* *
18173906 TTTTGTTTTAAAATTAAGACAAACATATTT
1 TCTTG-TCT-AAATTAAGACAAACATATTT
*
18173936 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
18173965 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
18173989 GTTAAAGCTA
Statistics
Matches: 121, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
28 32 0.26
29 32 0.26
30 19 0.16
31 20 0.17
32 7 0.06
33 2 0.02
34 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:18175639 original size:17 final size:18
Alignment explanation
Indices: 18175617--18175654 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18175607 CATAAATTTC
18175617 CAATTC-CAAACAAACTT
1 CAATTCACAAACAAACTT
18175634 CAATTCACAAACAAACTT
1 CAATTCACAAACAAACTT
18175652 CAA
1 CAA
18175655 AATTATGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (18 bp):
CAATTCACAAACAAACTT
Found at i:18176231 original size:40 final size:40
Alignment explanation
Indices: 18176181--18176336 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
18176171 CCTTTTTGAT
* *
18176181 AAGAGAAAGCACAACCTCACGATGTCACTGCCTTTTCAAG
1 AAGAGCAAGCACAACCTCACAATGTCACTGCCTTTTCAAG
* ** * * *
18176221 AGGAGCAAGCACAACCTCACAACATCACTGTCTTTCCAAA
1 AAGAGCAAGCACAACCTCACAATGTCACTGCCTTTTCAAG
* *
18176261 AAGAGCAAGCATAACCTCACAGTGTCACTGCCTTTTCAAG
1 AAGAGCAAGCACAACCTCACAATGTCACTGCCTTTTCAAG
* * * *
18176301 AAGAGTAAGCACAACTTCACAATGTCATTGCATTTT
1 AAGAGCAAGCACAACCTCACAATGTCACTGCCTTTT
18176337 TAAGGTTAAA
Statistics
Matches: 94, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.22
Consensus pattern (40 bp):
AAGAGCAAGCACAACCTCACAATGTCACTGCCTTTTCAAG
Found at i:18176360 original size:40 final size:40
Alignment explanation
Indices: 18176307--18176398 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
18176297 CAAGAAGAGT
* *
18176307 AAGCACAA-C-TTCACAATGTCAT-TGCATTTTTAAGGTTA
1 AAGCACAATCTTTCACAAAGTC-TCTACATTTTTAAGGTTA
*
18176345 AAGCACAATCTTTCACAAAGTCTCTACCTTTTTAAGGTTA
1 AAGCACAATCTTTCACAAAGTCTCTACATTTTTAAGGTTA
*
18176385 AAGCATAACTCTTT
1 AAGCACAA-TCTTT
18176399 TACCTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 8 0.17
39 2 0.04
40 31 0.67
41 5 0.11
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (40 bp):
AAGCACAATCTTTCACAAAGTCTCTACATTTTTAAGGTTA
Found at i:18181491 original size:22 final size:22
Alignment explanation
Indices: 18181466--18181507 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18181456 AAACATAAAG
18181466 AAAAGTAAATAATAAACAACTA
1 AAAAGTAAATAATAAACAACTA
*
18181488 AAAAGTAAATAATAATCAAC
1 AAAAGTAAATAATAAACAAC
18181508 CAAATAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAGTAAATAATAAACAACTA
Found at i:18187778 original size:71 final size:72
Alignment explanation
Indices: 18187663--18187809 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 72
18187653 TGACAATACC
* *
18187663 TCCTTTATAGTTGACTATGGCTATTCTCCAACTTGATTTTCTTGATATTTCTAGAACATGG-TCA
1 TCCTCTATAGTTGACTATGGCTATTCTCAAACTTGATTTTCTTGATATTTCTAGAACA-GGTTCA
18187727 ACTATGCT
65 ACTATGCT
* * * *
18187735 TCCTCTATAGTTGATTATGGCTGTTCT-AAACTTGATTTTCTTGATCTTTCTGGAACAGGTTCAA
1 TCCTCTATAGTTGACTATGGCTATTCTCAAACTTGATTTTCTTGATATTTCTAGAACAGGTTCAA
*
18187799 CTGTGCT
66 CTATGCT
18187806 TCCT
1 TCCT
18187810 TTCTAGTCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 2 0.03
71 41 0.61
72 24 0.36
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.44
Consensus pattern (72 bp):
TCCTCTATAGTTGACTATGGCTATTCTCAAACTTGATTTTCTTGATATTTCTAGAACAGGTTCAA
CTATGCT
Found at i:18189330 original size:35 final size:34
Alignment explanation
Indices: 18189291--18189440 Score: 153
Period size: 35 Copynumber: 4.3 Consensus size: 34
18189281 TTAATTGTTT
*
18189291 AATTTAATCAATTAGGTCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGG-CCAACAACTTAATTAAAC
* *
18189326 AATTTAATTAATTAAGCCCAACAACTTAATTAAAC
1 AATTTAATCAATT-AGGCCAACAACTTAATTAAAC
* **
18189361 AATTTCAACCAATTAGGCCTAATGA-TATAATTAAAC
1 AATTT-AATCAATTAGGCC-AACAACT-TAATTAAAC
* *
18189397 AGTTTAATTAATTAGG-C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCAACAACTTAATTAAAC
18189429 AATTTTAATCAA
1 AA-TTTAATCAA
18189441 GTACTTGAGA
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
32 12 0.13
33 9 0.10
34 1 0.01
35 48 0.51
36 24 0.26
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (34 bp):
AATTTAATCAATTAGGCCAACAACTTAATTAAAC
Found at i:18191633 original size:43 final size:43
Alignment explanation
Indices: 18191572--18191668 Score: 158
Period size: 43 Copynumber: 2.3 Consensus size: 43
18191562 ACTCTCATTC
* *
18191572 AGCTGGGTTATCATCAGCTCATGTGCACTCCTACACCGCACAT
1 AGCTGGGTCATCATCAGCTCATATGCACTCCTACACCGCACAT
*
18191615 AGCTGGATCATCATCAGCTCATATGCACTCCTACACCGCACAT
1 AGCTGGGTCATCATCAGCTCATATGCACTCCTACACCGCACAT
*
18191658 AGTTGGGTCAT
1 AGCTGGGTCAT
18191669 AATTATCACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
AGCTGGGTCATCATCAGCTCATATGCACTCCTACACCGCACAT
Found at i:18194908 original size:39 final size:40
Alignment explanation
Indices: 18194864--18194958 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
18194854 TTTCGCTGAA
* *
18194864 TCTCGCTGCAGTGAAATTTCTACCCAG-AAACA-AAATGTT
1 TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAA-GTT
*
18194903 TCTCGCTGCAATGAAATTGCAACCCAGAAAACAGAAAGTT
1 TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTT
*
18194943 TCTCGCTGCAGCGAAA
1 TCTCGCTGCAGTGAAA
18194959 AGCTGGAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 24 0.49
40 22 0.45
41 3 0.06
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (40 bp):
TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTT
Found at i:18195245 original size:55 final size:54
Alignment explanation
Indices: 18195180--18195288 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 54
18195170 AAGTTTCACA
*
18195180 TGCATTACAACCATAACCCATTATCCATCAATTTCCTATAACACACATATTTAC
1 TGCATTACAACCATAACCCATTATCCATCAATTACCTATAACACACATATTTAC
18195234 NTGCATTACAACCATAACCCATTATCCATCAATTACCTATAACACACATATTTAC
1 -TGCATTACAACCATAACCCATTATCCATCAATTACCTATAACACACATATTTAC
18195289 ATATATATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.30
Consensus pattern (54 bp):
TGCATTACAACCATAACCCATTATCCATCAATTACCTATAACACACATATTTAC
Found at i:18195269 original size:27 final size:27
Alignment explanation
Indices: 18195183--18195269 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
18195173 TTTCACATGC
18195183 ATTACAACCATAACCCATTATCCATCA
1 ATTACAACCATAACCCATTATCCATCA
* * * * *
18195210 ATTTC--CTATAACACACATATTTACNTGC-
1 ATTACAACCATAAC-C-CAT-TATCCAT-CA
18195238 ATTACAACCATAACCCATTATCCATCA
1 ATTACAACCATAACCCATTATCCATCA
18195265 ATTAC
1 ATTAC
18195270 CTATAACACA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 6 0.14
26 2 0.05
27 16 0.37
28 11 0.26
29 2 0.05
30 6 0.14
ACGTcount: A:0.38, C:0.30, G:0.01, T:0.30
Consensus pattern (27 bp):
ATTACAACCATAACCCATTATCCATCA
Found at i:18195464 original size:43 final size:43
Alignment explanation
Indices: 18195340--18195471 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
18195330 CCCATCATCA
* ***
18195340 TCATTACCGA-TTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCGACTT-ATGCGCACTCCCTACTCGCACATAATTGGG
** *
18195383 TCATCACCGGGTTATGCGCACTCCTTACTCGCACATAATTGGG
1 TCATCACCGACTTATGCGCACTCCCTACTCGCACATAATTGGG
* *
18195426 TCATC-CTCGACTTATGTGCACTCCCTACTCGCACATAATTGAG
1 TCATCAC-CGACTTATGCGCACTCCCTACTCGCACATAATTGGG
18195469 TCA
1 TCA
18195472 ATATAATTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 73 0.96
44 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (43 bp):
TCATCACCGACTTATGCGCACTCCCTACTCGCACATAATTGGG
Found at i:18213598 original size:35 final size:35
Alignment explanation
Indices: 18213560--18213679 Score: 159
Period size: 35 Copynumber: 3.4 Consensus size: 35
18213550 TTAATTGTTT
* * *
18213560 AATTTAATCAATTAGGCCCAATAACTTAATTAAAT
1 AATTTAATTAATTAGGCCCAACAACTTAATTAAAC
* * *
18213595 AATTTAATTAATTAAGCCTAACAACTTAGTTAAAC
1 AATTTAATTAATTAGGCCCAACAACTTAATTAAAC
* * *
18213630 AATTTAATTAATTAGGCCCAACGACTTATTTAGAC
1 AATTTAATTAATTAGGCCCAACAACTTAATTAAAC
18213665 AATTTAATTAATTAG
1 AATTTAATTAATTAG
18213680 AAACAACTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (35 bp):
AATTTAATTAATTAGGCCCAACAACTTAATTAAAC
Found at i:18216987 original size:42 final size:42
Alignment explanation
Indices: 18216941--18217028 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
18216931 TTCATATGTT
* *
18216941 GATGATGACCCGACTATGTGCGAGTAGGAGTGTGCATAAGCC
1 GATGATGACCAGACTATGTGCGAGTAGGAGTGCGCATAAGCC
*
18216983 GATGATGACCAGGCTATGTGCGAGTAGGAGTGCGCATAAGCC
1 GATGATGACCAGACTATGTGCGAGTAGGAGTGCGCATAAGCC
18217025 GATG
1 GATG
18217029 CNNNNNNNNN
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.20
Consensus pattern (42 bp):
GATGATGACCAGACTATGTGCGAGTAGGAGTGCGCATAAGCC
Found at i:18217163 original size:2 final size:2
Alignment explanation
Indices: 18217156--18217211 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
18217146 NNNNNNNNNN
18217156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18217198 AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT
18217212 GTTTGCACAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18225603 original size:12 final size:12
Alignment explanation
Indices: 18225586--18225610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18225576 AAGAAAATTG
18225586 AATATTTTATTT
1 AATATTTTATTT
18225598 AATATTTTATTT
1 AATATTTTATTT
18225610 A
1 A
18225611 GTTTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:18226171 original size:34 final size:35
Alignment explanation
Indices: 18226132--18226203 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
18226122 TTTATTCCTA
18226132 AATCTTCA-CTAAGT-ACTAAAATTTAT-GACAAATT
1 AATCTT-ATCTAAGTAACTAAAATTTATAGA-AAATT
* *
18226166 AATCTTATTTAAGTAACTAAAATTTTTAGAAAATT
1 AATCTTATCTAAGTAACTAAAATTTATAGAAAATT
18226201 AAT
1 AAT
18226204 TAAAACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 1 0.03
34 11 0.33
35 19 0.58
36 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (35 bp):
AATCTTATCTAAGTAACTAAAATTTATAGAAAATT
Found at i:18230263 original size:36 final size:36
Alignment explanation
Indices: 18230223--18230323 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
18230213 TAGCCGGAGT
* * *
18230223 CATCATGTGCACCCCTACATTGCGCACAGCTAATGC
1 CATCATGTGCACCCCCACATCGCACACAGCTAATGC
* *
18230259 CATCATGTGCTCCCCCACATCGCACACAGTTAATGC
1 CATCATGTGCACCCCCACATCGCACACAGCTAATGC
** ** *
18230295 CATTGTGTGTTCCCCCACATCGCGCACAG
1 CATCATGTGCACCCCCACATCGCACACAG
18230324 GCAATATCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (36 bp):
CATCATGTGCACCCCCACATCGCACACAGCTAATGC
Found at i:18232909 original size:40 final size:38
Alignment explanation
Indices: 18232852--18232954 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
18232842 ACCCGACTCA
* *
18232852 TGTGCAGCCCCCCACATCGTGCACATAGCTGGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACA-AGC-AGTGCCATCG
* * *
18232892 TGTGCATCCCCCTACATCATGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAAGCAGTGCCATCG
*
18232930 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
18232955 CGGGTACTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 31 0.56
39 2 0.04
40 22 0.40
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.21
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAAGCAGTGCCATCG
Found at i:18240052 original size:38 final size:38
Alignment explanation
Indices: 18239954--18240057 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
18239944 CACACCCGAC
* ** *
18239954 TCATGTGCATCCCCCCACATCGTGCACATAGTCGGCGTCA
1 TCATGTGCATCCCCCCACATCGTG--CATAATCAACGCCA
* *
18239994 TCGTGTGCATCCCCCCACATCGTGCATAATCAATGCCA
1 TCATGTGCATCCCCCCACATCGTGCATAATCAACGCCA
* *
18240032 TCATGTACATCCCCCCACATCATGCA
1 TCATGTGCATCCCCCCACATCGTGCA
18240058 CACGGGCACT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 32 0.58
40 23 0.42
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCATAATCAACGCCA
Found at i:18249013 original size:22 final size:21
Alignment explanation
Indices: 18248988--18249028 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18248978 ACCTTTTTTT
* *
18248988 CACTTGTTTCCTTGGATTTTCA
1 CACTT-TTCCCTTGAATTTTCA
18249010 CACTTTTCCCTTGAATTTT
1 CACTTTTCCCTTGAATTTT
18249029 TTCACCTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.15, C:0.24, G:0.10, T:0.51
Consensus pattern (21 bp):
CACTTTTCCCTTGAATTTTCA
Found at i:18258782 original size:39 final size:39
Alignment explanation
Indices: 18258728--18258803 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
18258718 TCGCTACAGG
*
18258728 GAAATTGTAACCCAGAAACAGAATGTTTCTCACTGCAGT
1 GAAATTGTAACCCAGAAACAGAAAGTTTCTCACTGCAGT
* *
18258767 GAAATTGTAACCCAGAAACAGAAAGTTTTTCGCTGCA
1 GAAATTGTAACCCAGAAACAGAAAGTTTCTCACTGCA
18258804 ACGAGAATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (39 bp):
GAAATTGTAACCCAGAAACAGAAAGTTTCTCACTGCAGT
Found at i:18259276 original size:43 final size:43
Alignment explanation
Indices: 18259203--18259318 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
18259193 CCAGCTCATG
* * * **
18259203 CGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTTATGA
1 CGCACTCCCTACTCGCACATAGCCGAGTCATC-CTCGACTTAT-A
*
18259247 -GCACTCCCTACTCGCACATAACCGAGTCATCCTCGACTTATA
1 CGCACTCCCTACTCGCACATAGCCGAGTCATCCTCGACTTATA
*
18259289 CGCACTCCCTACTCACACATAGCCGAGTCA
1 CGCACTCCCTACTCGCACATAGCCGAGTCA
18259319 ATATAATTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
42 2 0.03
43 60 0.97
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.22
Consensus pattern (43 bp):
CGCACTCCCTACTCGCACATAGCCGAGTCATCCTCGACTTATA
Found at i:18264241 original size:33 final size:33
Alignment explanation
Indices: 18264184--18264273 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
18264174 AAAAATACCA
*
18264184 TATGATCATGTTAGCATGCCACATCATCA-TCAAT
1 TATGAT-ATGTTAGCATGTCACATCATCACT-AAT
* * *
18264218 TATGATATATTAACATGTCACATCATTACTAAT
1 TATGATATGTTAGCATGTCACATCATCACTAAT
*
18264251 TGTGATATGTTAGCATGTCACAT
1 TATGATATGTTAGCATGTCACAT
18264274 TAGCTTCACC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 41 0.85
34 7 0.15
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (33 bp):
TATGATATGTTAGCATGTCACATCATCACTAAT
Found at i:18264404 original size:27 final size:27
Alignment explanation
Indices: 18264336--18264428 Score: 109
Period size: 27 Copynumber: 3.4 Consensus size: 27
18264326 AGTCATAAGG
18264336 ACTTATTTGACTCAAAATAAAAGTAA-AA
1 ACTTATTTGACTCAAAATAAAA--AATAA
* *
18264364 AGCTTATTTAACTCAAACTAAAAAATAA
1 A-CTTATTTGACTCAAAATAAAAAATAA
18264392 ACTTATTTGACTCAAAAT-AAAAATATA
1 ACTTATTTGACTCAAAATAAAAAATA-A
*
18264419 ACTTAATTGA
1 ACTTATTTGA
18264429 ATGTAATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.12
27 27 0.47
28 4 0.07
29 19 0.33
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (27 bp):
ACTTATTTGACTCAAAATAAAAAATAA
Found at i:18264613 original size:23 final size:23
Alignment explanation
Indices: 18264569--18264615 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
18264559 TTATGAAAAT
* *
18264569 ATAATTTAAAAGACCAAATAAAG
1 ATAACTTAAAAGACAAAATAAAG
18264592 ATAACTTAAAAGA-AAAATTAAAG
1 ATAACTTAAAAGACAAAA-TAAAG
18264615 A
1 A
18264616 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGACAAAATAAAG
Found at i:18267369 original size:13 final size:13
Alignment explanation
Indices: 18267351--18267375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18267341 TTTTAGAAAA
18267351 TTTATAAAATCAT
1 TTTATAAAATCAT
18267364 TTTATAAAATCA
1 TTTATAAAATCA
18267376 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18277220 original size:13 final size:13
Alignment explanation
Indices: 18277202--18277228 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18277192 AAGAAAATGG
18277202 AATATTTTTATTT
1 AATATTTTTATTT
18277215 AATATTTTTATTT
1 AATATTTTTATTT
18277228 A
1 A
18277229 GTTTGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATATTTTTATTT
Found at i:18279477 original size:26 final size:26
Alignment explanation
Indices: 18279429--18279482 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
18279419 GGGTTAAGAC
* *
18279429 ATCCATCCACTTCTGATGATAAAATT
1 ATCCATCCACCTCCGATGATAAAATT
* *
18279455 ATCCATCCACCTCCGCTGGTAAAATT
1 ATCCATCCACCTCCGATGATAAAATT
18279481 AT
1 AT
18279483 TCTTAGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (26 bp):
ATCCATCCACCTCCGATGATAAAATT
Found at i:18279978 original size:23 final size:23
Alignment explanation
Indices: 18279946--18279997 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
18279936 TCTTGTTATA
18279946 AAAGTATAACTTAAAAGAACAAAT
1 AAAG-ATAACTTAAAAGAACAAAT
* *
18279970 AAAGATAACTTGAAAGAACAATT
1 AAAGATAACTTAAAAGAACAAAT
18279993 AAAGA
1 AAAGA
18279998 GAAGAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.19
Consensus pattern (23 bp):
AAAGATAACTTAAAAGAACAAAT
Found at i:18285689 original size:32 final size:32
Alignment explanation
Indices: 18285653--18285715 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
18285643 ATCATCACTG
*
18285653 GATGCAGCTCACACGAGTGCTACAATATCCAT
1 GATGCAGCTCACACGAGTGCTACAACATCCAT
18285685 GATGCAGCTCACACGAGTGCTACAACATCCA
1 GATGCAGCTCACACGAGTGCTACAACATCCA
18285716 AGTCTACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (32 bp):
GATGCAGCTCACACGAGTGCTACAACATCCAT
Found at i:18289782 original size:43 final size:43
Alignment explanation
Indices: 18289728--18289855 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
18289718 AAAATCATTA
*
18289728 GCTCATATGCACTCCCTACTCGCACATAACTGGGTCATCATCG
1 GCTCATGTGCACTCCCTACTCGCACATAACTGGGTCATCATCG
* * *
18289771 GCTCATGTGCACTCCCTACTCGCACATAGCCGGGTCATCATTG
1 GCTCATGTGCACTCCCTACTCGCACATAACTGGGTCATCATCG
* * * *
18289814 GCTCATGTACACTCCTTACTCTCACAT-AGTCGGGTCATCATC
1 GCTCATGTGCACTCCCTACTCGCACATAACT-GGGTCATCATC
18289856 ATCACATAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.27
Consensus pattern (43 bp):
GCTCATGTGCACTCCCTACTCGCACATAACTGGGTCATCATCG
Found at i:18305995 original size:17 final size:17
Alignment explanation
Indices: 18305973--18306005 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18305963 CTTTTGTAGG
*
18305973 TTTAATGAAGGAAGAAT
1 TTTAATGAAAGAAGAAT
18305990 TTTAATGAAAGAAGAA
1 TTTAATGAAAGAAGAA
18306006 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
TTTAATGAAAGAAGAAT
Found at i:18306615 original size:23 final size:23
Alignment explanation
Indices: 18306589--18306634 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18306579 TTGTAGCGTC
*
18306589 AAGGA-AGCCAAGGCCGCAGTGCT
1 AAGGAGAG-CAAGGCCACAGTGCT
*
18306612 AAGGAGAGCAAGGCTACAGTGCT
1 AAGGAGAGCAAGGCCACAGTGCT
18306635 GGTGAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.33, C:0.22, G:0.35, T:0.11
Consensus pattern (23 bp):
AAGGAGAGCAAGGCCACAGTGCT
Found at i:18313882 original size:63 final size:63
Alignment explanation
Indices: 18313804--18313946 Score: 169
Period size: 63 Copynumber: 2.3 Consensus size: 63
18313794 CCACATTGTG
* * * * * * **
18313804 GAAGAATAGAGATCTCAAGAAAGAAAAATCAATTCTCTAAAGGCAGAAAGTTCCAGTCTTTAT
1 GAAGAATTGACATCTCAAAAAAGAAAAATAAATTCTCTAAAGACAGAAAGCTCCAAACTTTAT
* * * *
18313867 GAAGAATTGACATCTCAAAAAAGAAGAATAAATTCTTTAGAGACAGAAAGCTCCAAAGTTTAT
1 GAAGAATTGACATCTCAAAAAAGAAAAATAAATTCTCTAAAGACAGAAAGCTCCAAACTTTAT
*
18313930 GAAGAATTGACAACTCA
1 GAAGAATTGACATCTCA
18313947 TGATTAAAGA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (63 bp):
GAAGAATTGACATCTCAAAAAAGAAAAATAAATTCTCTAAAGACAGAAAGCTCCAAACTTTAT
Found at i:18314524 original size:36 final size:37
Alignment explanation
Indices: 18314484--18314572 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
18314474 GATCTTGTGG
*
18314484 AAAGGCATGTTATGAAGGTTACACTTAATCC-TATT-A
1 AAAGGCATGTTATAAAGGTTACACTTAA-CCATATTGA
* * * *
18314520 AAAGGCCTTTTGTAAAGGTTACACTTGACCATATTGA
1 AAAGGCATGTTATAAAGGTTACACTTAACCATATTGA
*
18314557 AAAGGCAAGTTGATAA
1 AAAGGCATGTT-ATAA
18314573 TGGATTCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
35 2 0.05
36 27 0.66
37 9 0.22
38 3 0.07
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (37 bp):
AAAGGCATGTTATAAAGGTTACACTTAACCATATTGA
Found at i:18330957 original size:21 final size:21
Alignment explanation
Indices: 18330928--18330968 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18330918 CTAAAGTAAG
* *
18330928 GATTTAGCTCATATGTTGAAT
1 GATTGAGCTCATATATTGAAT
*
18330949 GATTGAGCTTATATATTGAA
1 GATTGAGCTCATATATTGAA
18330969 GTTAGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (21 bp):
GATTGAGCTCATATATTGAAT
Found at i:18331250 original size:2 final size:2
Alignment explanation
Indices: 18331243--18331267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18331233 GTATATGTAT
18331243 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
18331268 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18348752 original size:21 final size:20
Alignment explanation
Indices: 18348726--18348774 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
18348716 GGTTTTAACA
18348726 AGAAACCTTCATGCAGTTGAG
1 AGAAACCTT-ATGCAGTTGAG
*
18348747 AGAAACCCTTGTGCAGTTGAG
1 AGAAA-CCTTATGCAGTTGAG
*
18348768 AGGAACC
1 AGAAACC
18348775 CTCGTACAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (20 bp):
AGAAACCTTATGCAGTTGAG
Found at i:18348775 original size:21 final size:21
Alignment explanation
Indices: 18348737--18348776 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18348727 GAAACCTTCA
18348737 TGCAGTTGAGAGAAACCCTTG
1 TGCAGTTGAGAGAAACCCTTG
*
18348758 TGCAGTTGAGAGGAACCCT
1 TGCAGTTGAGAGAAACCCT
18348777 CGTACAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (21 bp):
TGCAGTTGAGAGAAACCCTTG
Found at i:18351294 original size:42 final size:42
Alignment explanation
Indices: 18351229--18351310 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
18351219 AATGATATTA
* *
18351229 ACCCGGCTATGTGCGAGTCGGAGTGCACATAAGCCATTGCTG
1 ACCCAGCTATGTGAGAGTCGGAGTGCACATAAGCCATTGCTG
* * *
18351271 ACCCAGCTATGTGAGAGTGGGAGTGCGCATAAGCCGTTGC
1 ACCCAGCTATGTGAGAGTCGGAGTGCACATAAGCCATTGC
18351311 ATATGAGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.21
Consensus pattern (42 bp):
ACCCAGCTATGTGAGAGTCGGAGTGCACATAAGCCATTGCTG
Found at i:18355641 original size:42 final size:42
Alignment explanation
Indices: 18355582--18355673 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
18355572 CGATGCGAGG
* * *
18355582 AGGAGTGAGCATAAGCCGATGCTGACCCGGCTATGTGCAAGT
1 AGGAGTGCGCATAAGCCGATGCTGACCCAGCCATGTGCAAGT
*
18355624 AGGAGTGCGCATAAGCCGATGCTGACCCAGCCATGTGCTAGT
1 AGGAGTGCGCATAAGCCGATGCTGACCCAGCCATGTGCAAGT
*
18355666 GGGAGTGC
1 AGGAGTGC
18355674 ATATTAGCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.35, T:0.18
Consensus pattern (42 bp):
AGGAGTGCGCATAAGCCGATGCTGACCCAGCCATGTGCAAGT
Found at i:18361903 original size:2 final size:2
Alignment explanation
Indices: 18361896--18361939 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
18361886 GAACCAAGTG
18361896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18361938 TA
1 TA
18361940 ACATCCCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18362563 original size:35 final size:35
Alignment explanation
Indices: 18362532--18362623 Score: 148
Period size: 35 Copynumber: 2.6 Consensus size: 35
18362522 ATGCACAAGG
18362532 CAATATCATCATGCGCACTCCCTACACGCACATTT
1 CAATATCATCATGCGCACTCCCTACACGCACATTT
* *
18362567 CAATATCATCATGTGCATTCCCTACACGCACATTT
1 CAATATCATCATGCGCACTCCCTACACGCACATTT
**
18362602 CAATATCATCACACGCACTCCC
1 CAATATCATCATGCGCACTCCC
18362624 GCCCACATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.29, C:0.37, G:0.08, T:0.26
Consensus pattern (35 bp):
CAATATCATCATGCGCACTCCCTACACGCACATTT
Found at i:18364293 original size:43 final size:42
Alignment explanation
Indices: 18364202--18364294 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
18364192 TTTTGTGTCA
* *
18364202 TGATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGC
1 TGATGATGACCCAGCTATGTGCGAGTGGGAGTGCACATGAAC
*
18364244 TAATGATGACCCAGCTATGTGCGAGTGGGGAGTGCACATGAAC
1 TGATGATGACCCAGCTATGTGCGAGT-GGGAGTGCACATGAAC
18364287 TGATGATG
1 TGATGATG
18364295 GTGGGATGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 24 0.52
43 22 0.48
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
TGATGATGACCCAGCTATGTGCGAGTGGGAGTGCACATGAAC
Found at i:18372096 original size:21 final size:21
Alignment explanation
Indices: 18372067--18372109 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18372057 GTGAAGACTA
18372067 TATTCGACAAAAAATTGCTTC
1 TATTCGACAAAAAATTGCTTC
* *
18372088 TATTGGACAAAAAATTGTTTC
1 TATTCGACAAAAAATTGCTTC
18372109 T
1 T
18372110 TACTCTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
TATTCGACAAAAAATTGCTTC
Found at i:18373840 original size:20 final size:20
Alignment explanation
Indices: 18373815--18373853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18373805 AAATACATGT
18373815 AAATGTATCAAGACATTCCC
1 AAATGTATCAAGACATTCCC
* *
18373835 AAATGTATCGATACATTCC
1 AAATGTATCAAGACATTCC
18373854 TAGGTTAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (20 bp):
AAATGTATCAAGACATTCCC
Found at i:18378422 original size:134 final size:136
Alignment explanation
Indices: 18378279--18378549 Score: 388
Period size: 134 Copynumber: 2.0 Consensus size: 136
18378269 TTATTAAGAG
* * *
18378279 TAATCATATAAATAAAATTTATTAGAAGTTATAGTAATGCTTATGTATAAATTAAATATATGTAT
1 TAATAATATAAATAAAATCTATTAGAAGTTATAGCAATGCTTATGTATAAATTAAATATATGTAT
* *
18378344 ATAT-ATAATAT-A-TTGCATTAT-TATATATATAAAATTAATGATACAAATTATATTTTAAAAT
66 ATATAAT-ATATGACTT-CATTATATATATATATAAAATTAATGACACAAATTATATGTTAAAAT
18378405 GTTTTATA
129 GTTTTATA
* * *
18378413 TAATAATATAAATAAAGTCTATTATAAGTTATAGCAATGCTTATGTCTAAATTAAATATATGTAT
1 TAATAATATAAATAAAATCTATTAGAAGTTATAGCAATGCTTATGTATAAATTAAATATATGTAT
* * * *
18378478 ATATAATATATGACTTTATTATATATATATATAAAATTAATGACATAACTTATATGTTATAATGT
66 ATATAATATATGACTTCATTATATATATATATAAAATTAATGACACAAATTATATGTTAAAATGT
18378543 TTTATA
131 TTTATA
18378549 T
1 T
18378550 CAAAGTTTGT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
134 67 0.55
135 8 0.07
136 46 0.38
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (136 bp):
TAATAATATAAATAAAATCTATTAGAAGTTATAGCAATGCTTATGTATAAATTAAATATATGTAT
ATATAATATATGACTTCATTATATATATATATAAAATTAATGACACAAATTATATGTTAAAATGT
TTTATA
Found at i:18385554 original size:2 final size:2
Alignment explanation
Indices: 18385547--18385571 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18385537 TATAATGTGG
18385547 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18385572 CTATGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18392540 original size:55 final size:54
Alignment explanation
Indices: 18392427--18392576 Score: 176
Period size: 55 Copynumber: 2.8 Consensus size: 54
18392417 TATACCACTA
** ** * * ** *
18392427 CATCTCATTCAGCTCATGTGCATCGGCCCACGTCATGCACATGGCCTGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAACCGGACATCC
18392481 CATCTCACCCAGCTCATGTGCATCCCCCCCACATCGTGCACATAACCGGACA-CC
1 CATCTCACCCAGCTCATGTGCAT-CCCCCCACATCGTGCACATAACCGGACATCC
* *
18392535 TCATCTCACCTAGCTCGTGTGCATCCCCCCACATCGTGCACA
1 -CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACA
18392577 GTTAATGCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
54 41 0.49
55 42 0.51
ACGTcount: A:0.21, C:0.42, G:0.15, T:0.21
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAACCGGACATCC
Found at i:18397232 original size:38 final size:40
Alignment explanation
Indices: 18397181--18397283 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
18397171 ATAGTGCCCG
* *
18397181 TGTGCACGATGTGGGGGGATGTACCCAAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACAATGGTGC-CGGATA
* * *
18397219 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACAATGGTGCCGGATA
18397259 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
18397284 TGAGCCGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 26 0.46
39 4 0.07
40 26 0.46
ACGTcount: A:0.19, C:0.17, G:0.41, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACAATGGTGCCGGATA
Found at i:18397713 original size:39 final size:40
Alignment explanation
Indices: 18397647--18397744 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 40
18397637 GTAAAAAAGG
* *
18397647 AATTTCGCTGCAGCGA-AAAACTCTCTGTTTCATCAG-CGA
1 AATTTCACTGCAGTGAGAAAACTCTCTGTTTC-TCAGTCGA
* ** * *
18397686 AATTTCACTGCAGTGAGAAACCT-TCTGTTTCTGGGTTGC
1 AATTTCACTGCAGTGAGAAAACTCTCTGTTTCTCAGTCGA
18397725 AATTTCACTGCAGTGAGAAA
1 AATTTCACTGCAGTGAGAAA
18397745 TAATCTCGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.04
39 43 0.86
40 5 0.10
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (40 bp):
AATTTCACTGCAGTGAGAAAACTCTCTGTTTCTCAGTCGA
Found at i:18404740 original size:20 final size:20
Alignment explanation
Indices: 18404711--18404759 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
18404701 TTAGGAGAGA
*
18404711 GAAAGGAAGAAA-GAAGAAAG
1 GAAAGAAAGAAAGGAA-AAAG
18404731 GAAAGAAAGAAAGGAAAAAG
1 GAAAGAAAGAAAGGAAAAAG
18404751 GAAGAGAAA
1 GAA-AGAAA
18404760 AGCTCGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAGGAAAAAG
Found at i:18408557 original size:20 final size:20
Alignment explanation
Indices: 18408515--18408557 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18408505 AAATGGATGA
* *
18408515 TTTAGATACTTAAATTTATT
1 TTTAGATACTGAAATGTATT
18408535 TTTAGATA-TGAAATGTATAT
1 TTTAGATACTGAAATGTAT-T
18408555 TTT
1 TTT
18408558 TCATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTAGATACTGAAATGTATT
Found at i:18417288 original size:39 final size:39
Alignment explanation
Indices: 18417238--18417453 Score: 233
Period size: 39 Copynumber: 5.6 Consensus size: 39
18417228 GTGCTGGTAG
* *
18417238 TGTGCGGTGTGGGAGAGCACACG-TCAATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGAT-GATGATATATGCCA
*
18417277 TGTGCGGTGTGGGAGAGCACATGATGTTGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
**
18417316 TGTATGGTGTGGGAGAGCACATGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* ** *
18417355 TGCGCTATGTGGGAGAGCACATGACGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* ** * * *
18417394 TGTGCAGTGTACGAGTGCACATGAGGAT-AT-TA-GCTA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * *
18417430 TGTCCGGTATGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
18417454 GCTGAGTTGA
Statistics
Matches: 151, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
36 22 0.15
37 2 0.01
38 2 0.01
39 124 0.82
40 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:18418854 original size:2 final size:2
Alignment explanation
Indices: 18418849--18418875 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18418839 TGTGAATACG
18418849 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18418876 GTGTGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18420564 original size:61 final size:61
Alignment explanation
Indices: 18420478--18420766 Score: 398
Period size: 61 Copynumber: 4.7 Consensus size: 61
18420468 AACTCATGTA
* * * * * *
18420478 CATCATCACCGACATGAGCACTACCCACTCCGCACATGCATGGTTGTAATTATCACGATAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAG
* * * * * *
18420539 CATCATTACCGGCATGTGCACTACCCACCCCGCACATGCATGATTGTAATTATCACAACAT
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAG
* * ** *
18420600 CATCATTATCGGCATGTGCATTGCCCACTCTACACATGCACGGCTGTAATTATCACGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAG
* *
18420661 CATCATTACCAGCATGTGCACTGCCCACTCTGCACATGCACGGTTGTAATTATCACGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAG
*
18420722 CATCATTACCGGCATGTGCATTGCCCACTCCGCACATGCACGGTT
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTT
18420767 ACATTTGTCA
Statistics
Matches: 201, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 201 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (61 bp):
CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAG
Found at i:18421395 original size:23 final size:23
Alignment explanation
Indices: 18421349--18421396 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18421339 TTTCTAAATA
* *
18421349 ATTTCCACCCAAATCCATCTTAT
1 ATTTCCACACAAATCCATCATAT
18421372 ATTTCCACACATAATCCA-CATAT
1 ATTTCCACACA-AATCCATCATAT
18421395 AT
1 AT
18421397 GGCAGCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTTCCACACAAATCCATCATAT
Found at i:18428412 original size:13 final size:13
Alignment explanation
Indices: 18428394--18428418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18428384 TTGCACCAAA
18428394 TAATTAAATCATT
1 TAATTAAATCATT
18428407 TAATTAAATCAT
1 TAATTAAATCAT
18428419 CCACATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAAATCATT
Found at i:18432632 original size:27 final size:27
Alignment explanation
Indices: 18432594--18432648 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
18432584 TTGAGAGTTG
18432594 GTTCTAGCCATTAATCTATCTTCTAGT
1 GTTCTAGCCATTAATCTATCTTCTAGT
18432621 GTTCTAGCCATTAATCTATCTTCTAGT
1 GTTCTAGCCATTAATCTATCTTCTAGT
18432648 G
1 G
18432649 CTCTGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (27 bp):
GTTCTAGCCATTAATCTATCTTCTAGT
Found at i:18435254 original size:20 final size:20
Alignment explanation
Indices: 18435214--18435259 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18435204 ATCAATGATG
* *
18435214 TATCAATACATTTGGCAATA
1 TATCGATACATTTGCCAATA
*
18435234 TATCGATACATTTGCCCATA
1 TATCGATACATTTGCCAATA
*
18435254 TTTCGA
1 TATCGA
18435260 CTAAATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (20 bp):
TATCGATACATTTGCCAATA
Found at i:18461156 original size:13 final size:13
Alignment explanation
Indices: 18461138--18461164 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18461128 GGCAGAGGGC
18461138 ACTTAGTTGACTA
1 ACTTAGTTGACTA
18461151 ACTTAGTTGACTA
1 ACTTAGTTGACTA
18461164 A
1 A
18461165 GTTGGTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACTTAGTTGACTA
Found at i:18462936 original size:20 final size:21
Alignment explanation
Indices: 18462892--18462936 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
18462882 GTCCATTGCT
*
18462892 GAAATATGAAACTCCCAAGAA
1 GAAATAAGAAACTCCCAAGAA
18462913 -AAATAAGAAA-T-CCAAGAAA
1 GAAATAAGAAACTCCCAAG-AA
18462932 GAAAT
1 GAAAT
18462937 GGTGGCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (21 bp):
GAAATAAGAAACTCCCAAGAA
Found at i:18480460 original size:65 final size:64
Alignment explanation
Indices: 18480356--18480485 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 64
18480346 GTTATGAACA
18480356 AAAACACAAAAGAAATATTCAATTTCTCTAGGGTTCCTTGTTGGTCGAACCATGAGGGCTGAAT
1 AAAACACAAAAGAAATATTCAATTTCTCTAGGGTTCCTTGTTGGTCGAACCATGAGGGCTGAAT
* *
18480420 NAAAACACAAAAGAATTATTCAATTTCTCTAGGGTTCCTTGTTGGTTGAACCATGAGGGCTGAAT
1 -AAAACACAAAAGAAATATTCAATTTCTCTAGGGTTCCTTGTTGGTCGAACCATGAGGGCTGAAT
18480485 A
1 A
18480486 TCAATGGGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 1 0.02
65 62 0.98
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (64 bp):
AAAACACAAAAGAAATATTCAATTTCTCTAGGGTTCCTTGTTGGTCGAACCATGAGGGCTGAAT
Found at i:18481416 original size:25 final size:25
Alignment explanation
Indices: 18481388--18481439 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18481378 GCCAGGAGTG
18481388 ATTATGATGATATTGATGTTTGTCT
1 ATTATGATGATATTGATGTTTGTCT
18481413 ATTATGATGATATTGATGTTTGTCT
1 ATTATGATGATATTGATGTTTGTCT
18481438 AT
1 AT
18481440 GTAATTATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (25 bp):
ATTATGATGATATTGATGTTTGTCT
Found at i:18483581 original size:19 final size:18
Alignment explanation
Indices: 18483546--18483581 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18483536 CTACTGATGC
*
18483546 CATGCTGATATTGATTTA
1 CATGCTGATAATGATTTA
18483564 CATGCTGATAAATGATTT
1 CATGCTGAT-AATGATTT
18483582 TTGTTACGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (18 bp):
CATGCTGATAATGATTTA
Found at i:18486417 original size:21 final size:21
Alignment explanation
Indices: 18486393--18486432 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18486383 AACATCACTG
*
18486393 TTCTTCTTCTCTCTTTAGAAT
1 TTCTTCCTCTCTCTTTAGAAT
*
18486414 TTCTTCCTCTTTCTTTAGA
1 TTCTTCCTCTCTCTTTAGA
18486433 TTTTAATTGT
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:0.12, C:0.25, G:0.05, T:0.57
Consensus pattern (21 bp):
TTCTTCCTCTCTCTTTAGAAT
Found at i:18486695 original size:26 final size:23
Alignment explanation
Indices: 18486646--18486696 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
18486636 TTTTGCTAAA
*
18486646 TTCTCTTGTGTAATTTTTCTTTT
1 TTCTCTTGTGTAATTTTTCATTT
*
18486669 TTCTCTTTGTGTCTATTTTTACATTT
1 TTCTC-TTGTGT-AATTTTT-CATTT
18486695 TT
1 TT
18486697 TTGGGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 6 0.26
26 6 0.26
ACGTcount: A:0.10, C:0.14, G:0.08, T:0.69
Consensus pattern (23 bp):
TTCTCTTGTGTAATTTTTCATTT
Found at i:18486861 original size:17 final size:17
Alignment explanation
Indices: 18486829--18486862 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18486819 AGATATGGTC
* *
18486829 TTGGGTTATGAGCCCAT
1 TTGGGTTATAAACCCAT
18486846 TTGGGTTATAAACCCAT
1 TTGGGTTATAAACCCAT
18486863 CATTTCTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (17 bp):
TTGGGTTATAAACCCAT
Found at i:18487343 original size:31 final size:30
Alignment explanation
Indices: 18487306--18487413 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 30
18487296 AAATATAAAC
18487306 TCCTCCATCGAGGCTTCAATATCTTAAGAAT
1 TCCTCCATCGAGG-TTCAATATCTTAAGAAT
* * *
18487337 TTCTCCACCAAGGTTCCAATATCTTAAGAAT
1 TCCTCCATCGAGGTT-CAATATCTTAAGAAT
*
18487368 TCCTCCATCGAGGATAT-AATATCGTAAGAAT
1 TCCTCCATCGAGG-T-TCAATATCTTAAGAAT
*
18487399 TCCTCCATCAAGGTT
1 TCCTCCATCGAGGTT
18487414 AAGAATTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 60 0.91
32 1 0.02
33 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (30 bp):
TCCTCCATCGAGGTTCAATATCTTAAGAAT
Found at i:18490798 original size:31 final size:31
Alignment explanation
Indices: 18490760--18491090 Score: 233
Period size: 31 Copynumber: 10.7 Consensus size: 31
18490750 AAAAAAATCT
* *
18490760 AATATCTTAAGAATTCTTCCATTAAGGTTCC
1 AATATCTTAAGAATTCCTCCATCAAGGTTCC
** *
18490791 AATATCTTAAGAATTCCTCC-TCCAAGAATCT
1 AATATCTTAAGAATTCCTCCAT-CAAGGTTCC
* * * * *
18490822 TATATCTTAAAAATTCCTCGATCGAGGTTAC
1 AATATCTTAAGAATTCCTCCATCAAGGTTCC
* *
18490853 AATATCTTAAGAATTCCTCGA-CTGAGGTTCC
1 AATATCTTAAGAATTCCTCCATC-AAGGTTCC
* * * *
18490884 AATATTTTAAGAATTCTTCCACCAAGATTCC
1 AATATCTTAAGAATTCCTCCATCAAGGTTCC
* * * * * *
18490915 AATATCATAAGATTTCCTTCATCGAGAATT-T
1 AATATCTTAAGAATTCCTCCATCAAG-GTTCC
* * * * * *
18490946 AATATCATAAAAATCCCTCGACCAAAGTTCC
1 AATATCTTAAGAATTCCTCCATCAAGGTTCC
* *
18490977 AATATCTTAAGTA-TCCTTCCA-CAAAGGATCC
1 AATATCTTAAGAATTCC-TCCATC-AAGGTTCC
* * * *
18491008 AATGTCTTAAGAATTCCTCCCTTCAA-GATCT
1 AATATCTTAAGAATTCCT-CCATCAAGGTTCC
* *
18491039 AATATCTTAAGAATTCCTCCATCAAGCTTTC
1 AATATCTTAAGAATTCCTCCATCAAGGTTCC
*
18491070 AATATCTTAAGAATTCTTCCA
1 AATATCTTAAGAATTCCTCCA
18491091 CCGATGTTCT
Statistics
Matches: 231, Mismatches: 57, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
30 13 0.06
31 205 0.89
32 12 0.05
33 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (31 bp):
AATATCTTAAGAATTCCTCCATCAAGGTTCC
Done.