Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 104 of 325
Found at i:33478987 original size:43 final size:43
Alignment explanation
Indices: 33478939--33479351 Score: 263
Period size: 44 Copynumber: 9.6 Consensus size: 43
33478929 ATCTACTCTG
* ** *
33478939 CTGTAACCTCAGAGAGATAAGATCCTTTATTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTGGATTTAATCTGCTCCA
* * ** ** ** *
33478982 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTGGATTTAATCTGCTCCA
* * *
33479025 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTGGATTTAATCTGCTCCA
* ** *
33479069 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTG-GATT-TAATCTGCTCCA
* * * * *
33479113 CTGTAACCTCAGGGAAATAAGA-CCT-GATGTGATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCCTGGATTTAATCTGCTCCA
* * *
33479154 CTGTAACTTCAGAGAGATAAGATCC----TTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTGGATTTAATCTGCTCCA
* * * * * * *
33479193 TTGTAATCTCAAGGAGATAGGATTACT--ATCTTGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGA-TCCTGGAT-TTAATCTGCTCCA
* * * *
33479236 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATC-CTGGATTTAATCTGCTCCA
* ** *
33479280 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTG-GA---TTTAATCTGCTCCA
*
33479326 CTGTAATCTCAGGGAGATAAGA-CCTG
1 CTGTAACCTCAGGGAGATAAGATCCTG
33479352 TATAATAAAC
Statistics
Matches: 287, Mismatches: 66, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
39 25 0.09
40 2 0.01
41 28 0.10
42 12 0.04
43 85 0.30
44 101 0.35
45 1 0.00
46 33 0.11
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCCTGGATTTAATCTGCTCCA
Found at i:33479042 original size:86 final size:87
Alignment explanation
Indices: 33478927--33479087 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 87
33478917 AGACTTGATG
* ** * *
33478927 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGGATTCAATCCGCTCCACTGTAACCT
33478991 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
* * * * *
33479013 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGGATTCAATCCGCTCCACTGTAACCT
33479078 CAGGGAGATA
66 CAGGGAGATA
33479088 AGATCTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
86 32 0.50
87 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGGATTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:33479256 original size:211 final size:213
Alignment explanation
Indices: 33478888--33479351 Score: 693
Period size: 211 Copynumber: 2.2 Consensus size: 213
33478878 GTTGTTTTTA
* * * * *
33478888 GTCTATTCCACTGCATCTTCAGGGAAATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* * *
33478953 AGATAAGATCCTTTATTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATC
66 AGATAAGATCC--T-TTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATC
33479018 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
128 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
33479083 AGATAAGATCTGAAATTC-TG
193 AGATAAGATCTGAAATTCTTG
* * * *
33479103 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
*
33479168 AGATAAGATCC-TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTT-GATCT
66 AGATAAGATCCTTTTAATCCGCTCCACTGTAACT-TCAAGGAGATAGGA-TACTATCTTCGATCT
*
33479230 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCTCAGGGA
129 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
33479295 GATAAGATCTGAAATTCTTTG
194 GATAAGATCTGAAATTC-TTG
* * *
33479316 GTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTG
33479352 TATAATAAAC
Statistics
Matches: 227, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
210 1 0.00
211 118 0.52
212 7 0.03
213 34 0.15
215 67 0.30
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (213 bp):
GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGATCTGAAATTCTTG
Found at i:33492143 original size:33 final size:32
Alignment explanation
Indices: 33492106--33492178 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
33492096 ACATACATAG
33492106 ATTATAAA-A-TAGATAATATAGTCATGTATATAT
1 ATTATAAATATTAGA-AATATA-T-ATGTATATAT
*
33492139 ATTATTAAATATTAGACATATATATGTATATAT
1 ATTA-TAAATATTAGAAATATATATGTATATAT
33492172 ATATATA
1 AT-TATA
33492179 GTAAGATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
33 18 0.51
34 7 0.20
35 6 0.17
36 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (32 bp):
ATTATAAATATTAGAAATATATATGTATATAT
Found at i:33507926 original size:18 final size:19
Alignment explanation
Indices: 33507900--33507935 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33507890 ATTTCTTTTC
33507900 CTTTCCTTTCCTT-TCTTT
1 CTTTCCTTTCCTTCTCTTT
*
33507918 CTTTGCTTTCCTTCTCTT
1 CTTTCCTTTCCTTCTCTT
33507936 CTTATTCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (19 bp):
CTTTCCTTTCCTTCTCTTT
Found at i:33508403 original size:43 final size:43
Alignment explanation
Indices: 33508356--33508441 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
33508346 AAAAAAAAGA
*
33508356 GTGAAGGATAAAAAAATTGTAATGGTTTGAAAAACCTCAAAAC
1 GTGAACGATAAAAAAATTGTAATGGTTTGAAAAACCTCAAAAC
*
33508399 GTGAACGATAAAAAATTTGTAATGGTTTGAAAAACCTCAAAAC
1 GTGAACGATAAAAAAATTGTAATGGTTTGAAAAACCTCAAAAC
33508442 TAAGTATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.24
Consensus pattern (43 bp):
GTGAACGATAAAAAAATTGTAATGGTTTGAAAAACCTCAAAAC
Found at i:33509891 original size:17 final size:18
Alignment explanation
Indices: 33509869--33509910 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
33509859 GATATTATTT
33509869 ATTAAATTAATTTTC-CA
1 ATTAAATTAATTTTCTCA
33509886 ATTAAA-TAATTTTCTCA
1 ATTAAATTAATTTTCTCA
*
33509903 AGTAAATT
1 ATTAAATT
33509911 TTAATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATTTTCTCA
Found at i:33511025 original size:172 final size:172
Alignment explanation
Indices: 33510727--33511071 Score: 627
Period size: 172 Copynumber: 2.0 Consensus size: 172
33510717 CCTTAAAGGT
33510727 AGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAATT
1 AGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAATT
* * *
33510792 CATGCGTCAATAGCTACTGCTATTTCATTTCCTTGTTCTTGCAAAATTTATTTAATTGCTTTTCA
66 CATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTCA
*
33510857 AGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTTAAACTC
131 AGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACTC
33510899 AGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAATT
1 AGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAATT
* * *
33510964 CATGCGTGAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTGTTTATTTGCTTTTCA
66 CATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTCA
33511029 AGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACTC
131 AGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACTC
33511071 A
1 A
33511072 TTCCATAGCC
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
172 166 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (172 bp):
AGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAATT
CATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTCA
AGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACTC
Found at i:33513206 original size:30 final size:30
Alignment explanation
Indices: 33513170--33513227 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
33513160 AAAACGAATT
* *
33513170 CCACACGGGCTGAG-CACATGCCCGTGTGAG
1 CCACACGGGCT-AGCCACACGCCCATGTGAG
33513200 CCACACGGGCTAGCCACACGCCCATGTG
1 CCACACGGGCTAGCCACACGCCCATGTG
33513228 GCAGCCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTAGCCACACGCCCATGTGAG
Found at i:33521072 original size:16 final size:16
Alignment explanation
Indices: 33521053--33521083 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33521043 AACTGAGAAA
33521053 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
33521069 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
33521084 GAACACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:33525524 original size:16 final size:16
Alignment explanation
Indices: 33525503--33525533 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33525493 AATTTGAGAA
33525503 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
33525519 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
33525534 GAACACACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:33531787 original size:23 final size:24
Alignment explanation
Indices: 33531737--33531788 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
33531727 TTGTTTTATT
* * *
33531737 TTTATTTTTATTTTTTTGCCCTTA
1 TTTATTGTTATTTTATTGCCATTA
33531761 -TTATTGTTATTTTATT-CCATTA
1 TTTATTGTTATTTTATTGCCATTA
33531783 TTTATT
1 TTTATT
33531789 TGTTTATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTATTGTTATTTTATTGCCATTA
Found at i:33531885 original size:18 final size:18
Alignment explanation
Indices: 33531837--33531877 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
33531827 TTCATCATTA
*
33531837 TTATTATTATTATTATTG
1 TTATTGTTATTATTATTG
33531855 TTATTGTTATTATTATTG
1 TTATTGTTATTATTATTG
33531873 TTATT
1 TTATT
33531878 TATATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (18 bp):
TTATTGTTATTATTATTG
Found at i:33531905 original size:3 final size:3
Alignment explanation
Indices: 33531823--33531877 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
33531813 TAAAATTTAG
* * *
33531823 ATT ATT CATC ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
33531869 ATT GTT ATT
1 ATT ATT ATT
33531878 TATATTATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:33531927 original size:28 final size:29
Alignment explanation
Indices: 33531882--33531937 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
33531872 GTTATTTATA
* *
33531882 TTATCATGTTCATCATTATTATT-ACTAT
1 TTATCATGTTCAACATTATGATTCACTAT
33531910 TTATGCATGTT-AACATTATGATTCACTA
1 TTAT-CATGTTCAACATTATGATTCACTA
33531938 ATATCATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (29 bp):
TTATCATGTTCAACATTATGATTCACTAT
Found at i:33543830 original size:44 final size:44
Alignment explanation
Indices: 33543767--33543876 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
33543757 CATGGAAAAT
* * *
33543767 CTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCGTTAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAATAGATTAAAACCATTAAC
* *
33543811 CTTATCTCCTTAAAGTTGCAGTGGAATAGATTAAAACCATTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAATAGATTAAAACCATTAAC
* * *
33543855 CTTATCTCTCTGAAGCTGCAGT
1 CTTATCTCCCTAAAGTTGCAGT
33543877 AGAGCAGGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAATAGATTAAAACCATTAAC
Found at i:33544301 original size:89 final size:88
Alignment explanation
Indices: 33544118--33544381 Score: 287
Period size: 89 Copynumber: 3.0 Consensus size: 88
33544108 AATGGAGAAT
**
33544118 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGCCA-CGAATCTTATCTCCTTGAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGAAAGCGAATCTTATCTCC-TGAAGTTACA
* * * ***
33544182 ATGGAACAGATTAAAGCCACACGT
65 ATGGAGCAGATTAAAGCTATAAAC
* * *
33544206 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATCTCTCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGAAAGCGAATCTTATCTC-CTGAAGTTACA
*
33544271 ATAGAGCAGATTAAAGCTATAAAC
65 ATGGAGCAGATTAAAGCTATAAAC
* * * * * * * * *
33544295 CTTATCTCCATGAAATTGCAATGGAGTAGATTGAAGATAGCGAATCTCATTTCCCTAAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGAAAGCGAATCTTATCT-CCTGAAGTTACA
* *
33544360 GTGGGGCAGATTAAAGCTATAA
65 ATGGAGCAGATTAAAGCTATAA
33544382 GTCACAAATC
Statistics
Matches: 146, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
88 36 0.25
89 108 0.74
90 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (88 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGAAAGCGAATCTTATCTCCTGAAGTTACAA
TGGAGCAGATTAAAGCTATAAAC
Found at i:33544326 original size:44 final size:44
Alignment explanation
Indices: 33544115--33544376 Score: 227
Period size: 44 Copynumber: 5.9 Consensus size: 44
33544105 GAAAATGGAG
* * * *
33544115 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGCCACG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCACA
* * *
33544159 AATCTTATCTCCTTGAAGTTACAATGGAACAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCACA
** * * **
33544203 CGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCA-CA
* * * *
33544248 AATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCACA
* * * * * ** *
33544292 AACCTTATCTCCATGAAATTGCAATGGAGTAGATTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCA-CA
* * * * * *
33544337 AATCTCATTTCCCTAAAGTTACAGTGGGGCAGATTAAAGC
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGC
33544377 TATAAGTCAC
Statistics
Matches: 169, Mismatches: 47, Indels: 3
0.77 0.21 0.01
Matches are distributed among these distances:
44 105 0.62
45 64 0.38
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCACA
Found at i:33545930 original size:12 final size:12
Alignment explanation
Indices: 33545915--33545962 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
33545905 TTTTAAAAAA
33545915 ATTTTATTTAAT
1 ATTTTATTTAAT
**
33545927 ATTTCCTTTAAT
1 ATTTTATTTAAT
*
33545939 ATTTTATTTATTT
1 ATTTTATTTA-AT
33545952 ATTTT-TTTAAT
1 ATTTTATTTAAT
33545963 CAAACTTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 1 0.03
12 22 0.76
13 6 0.21
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTATTTAAT
Found at i:33546021 original size:6 final size:6
Alignment explanation
Indices: 33546010--33546037 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33546000 TTTTAACTTG
33546010 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
33546038 TTGCGCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:33546151 original size:12 final size:12
Alignment explanation
Indices: 33546117--33546145 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33546107 AGATTATTCA
33546117 TTATTATTATTG
1 TTATTATTATTG
33546129 TTATTATTATTG
1 TTATTATTATTG
33546141 TTATT
1 TTATT
33546146 TATATTATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:33547979 original size:3 final size:3
Alignment explanation
Indices: 33547971--33547996 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33547961 TAAATCCTTT
33547971 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
33547997 GTTATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33551166 original size:16 final size:17
Alignment explanation
Indices: 33551147--33551178 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33551137 TTTTAAAAAT
33551147 TAATATAAT-TAACTTG
1 TAATATAATATAACTTG
33551163 TAATATAATATAACTT
1 TAATATAATATAACTT
33551179 TTATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATATAATATAACTTG
Found at i:33552671 original size:17 final size:17
Alignment explanation
Indices: 33552650--33552694 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
33552640 AGTTTTTCAC
33552650 ATATTATATATTTTAAA
1 ATATTATATATTTTAAA
* **
33552667 CTATTATCCATTTTAAA
1 ATATTATATATTTTAAA
*
33552684 ATTTTATATAT
1 ATATTATATAT
33552695 ATTATTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATATTTTAAA
Found at i:33552707 original size:26 final size:26
Alignment explanation
Indices: 33552678--33552742 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
33552668 TATTATCCAT
* *
33552678 TTTAAAATTTTATATATATTATTTAC
1 TTTAAAATATTATATATAATATTTAC
* *
33552704 TTTAAACTATTATATATAATATTTAT
1 TTTAAAATATTATATATAATATTTAC
* *
33552730 TTTGAATTATTAT
1 TTTAAAATATTAT
33552743 TTTTTATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAAAATATTATATATAATATTTAC
Found at i:33552804 original size:27 final size:27
Alignment explanation
Indices: 33552774--33552841 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
33552764 AAAAAAATTG
* *
33552774 TTTTGTATATTTTTTAT-TTAAATTTCT
1 TTTTATATATTATTTATCTTAAA-TTCT
33552801 TTTTATATATTATTTATCTTAAATTC-
1 TTTTATATATTATTTATCTTAAATTCT
*
33552827 TTTTATATTTTATTT
1 TTTTATATATTATTT
33552842 TAAGGTGTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.38
27 18 0.49
28 5 0.14
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTTATATATTATTTATCTTAAATTCT
Found at i:33552843 original size:27 final size:26
Alignment explanation
Indices: 33552768--33552843 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
33552758 TTTTTAAAAA
* *
33552768 AAATTGTTTTGTATATT-TTTTATTT
1 AAATTCTTTTATATATTATTTTATTT
33552793 AAATTTCTTTTTATATATTA-TTTATCTT
1 AAA-TTC-TTTTATATATTATTTTAT-TT
*
33552821 AAATTCTTTTATATTTTATTTTA
1 AAATTCTTTTATATATTATTTTA
33552844 AGGTGTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 22 0.51
28 5 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (26 bp):
AAATTCTTTTATATATTATTTTATTT
Found at i:33552910 original size:26 final size:26
Alignment explanation
Indices: 33552768--33552961 Score: 159
Period size: 26 Copynumber: 7.7 Consensus size: 26
33552758 TTTTTAAAAA
* *
33552768 AAATTGTTTTGTATATTTTTTA-TTT
1 AAATTGTTTTATATATTATTTATTTT
* *
33552793 AAATTTCTTTTTATATATTATTTATCTT
1 AAA-TT-GTTTTATATATTATTTATTTT
*
33552821 AAATT-CTTT-TATA-T-TTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
** *
33552843 AAGGTGTCTTATATATTATTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * *
33552869 AAGTTGCTTTGTATATTATTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * **
33552895 AATTTGTTTTACATATTACGTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * *
33552921 AAATTG-TTT-TATACTATTTACTTC
1 AAATTGTTTTATATATTATTTATTTT
33552945 AAATTGTTTTATATATT
1 AAATTGTTTTATATATT
33552962 TTTTTGTTTC
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
22 10 0.08
23 3 0.02
24 23 0.17
25 13 0.10
26 62 0.47
27 16 0.12
28 5 0.04
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.61
Consensus pattern (26 bp):
AAATTGTTTTATATATTATTTATTTT
Found at i:33552955 original size:50 final size:52
Alignment explanation
Indices: 33552863--33552961 Score: 130
Period size: 50 Copynumber: 1.9 Consensus size: 52
33552853 ATATATTATT
* * * * *
33552863 TATTTTAAGTTGCTTTGTATATTATTTATTTTAATTTGTTTTACATATTACG
1 TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATTACG
*
33552915 TATTTTAAATTG-TTT-TATACTATTTACTTCAAATTGTTTTATATATT
1 TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATT
33552962 TTTTTGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 27 0.66
51 3 0.07
52 11 0.27
ACGTcount: A:0.27, C:0.06, G:0.07, T:0.60
Consensus pattern (52 bp):
TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATTACG
Found at i:33556478 original size:22 final size:22
Alignment explanation
Indices: 33556456--33556502 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
33556446 ATGCTTTTTA
33556456 TATTTCAATATTATTACAATTAT
1 TATTT-AATATTATTACAATTAT
*
33556479 TATTTATTATTATTACTAA-TAT
1 TATTTAATATTATTAC-AATTAT
33556501 TA
1 TA
33556503 GGGTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTAATATTATTACAATTAT
Found at i:33557820 original size:17 final size:19
Alignment explanation
Indices: 33557798--33557832 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
33557788 CTAAAATAGT
33557798 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
33557815 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
33557833 TCTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:33559952 original size:16 final size:15
Alignment explanation
Indices: 33559908--33559958 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
33559898 AGAAATATCT
33559908 TTTTATATTTTTTCAA
1 TTTTATATTTTTT-AA
* **
33559924 TTTTAAAGATTTTATA
1 TTTTATATTTTTTA-A
33559940 TTTTATATTTTTTAA
1 TTTTATATTTTTTAA
33559955 TTTT
1 TTTT
33559959 TTTGTATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTATATTTTTTAA
Found at i:33560190 original size:14 final size:15
Alignment explanation
Indices: 33560171--33560201 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
33560161 ATTTTTATAA
33560171 TTTTTAAT-ATTTAT
1 TTTTTAATAATTTAT
33560185 TTTTTAATAATTTAT
1 TTTTTAATAATTTAT
33560200 TT
1 TT
33560202 ACTTTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATAATTTAT
Found at i:33562744 original size:24 final size:25
Alignment explanation
Indices: 33562717--33562766 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
33562707 ATAATAATAG
*
33562717 TATG-TACATAATATGGTATTAAAA
1 TATGATACATAATATAGTATTAAAA
*
33562741 TATGTATATATAATATAGTATTAAAA
1 TATG-ATACATAATATAGTATTAAAA
33562767 ACGTATACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
26 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (25 bp):
TATGATACATAATATAGTATTAAAA
Found at i:33562856 original size:12 final size:12
Alignment explanation
Indices: 33562835--33562872 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33562825 TACTACATAA
*
33562835 ATATACATATAT
1 ATATAAATATAT
33562847 ATATAAATATAT
1 ATATAAATATAT
*
33562859 AT-TAAAAATAT
1 ATATAAATATAT
33562870 ATA
1 ATA
33562873 CATAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:33562869 original size:13 final size:13
Alignment explanation
Indices: 33562841--33562899 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
33562831 ATAAATATAC
*
33562841 ATATATA-TATAA
1 ATATATATTAAAA
33562853 ATATATATTAAAA
1 ATATATATTAAAA
* *
33562866 ATATATACATAATA
1 ATATATA-TTAAAA
*
33562880 AT-GATATTAAAA
1 ATATATATTAAAA
*
33562892 GTATATAT
1 ATATATAT
33562900 GTGATATAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
12 12 0.33
13 18 0.50
14 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATATATTAAAA
Found at i:33562896 original size:26 final size:24
Alignment explanation
Indices: 33562841--33563073 Score: 112
Period size: 25 Copynumber: 9.6 Consensus size: 24
33562831 ATAAATATAC
*
33562841 ATATATATATAAATAT-ATATTAAAA
1 ATATATACAT-AATATGATATT-AAA
33562866 ATATATACATAATAATGATATTAAA
1 ATATATACATAAT-ATGATATTAAA
** * *
33562891 AGTATATATGTGATAT-AGTGTTAAA
1 A-TATATACATAATATGA-TATTAAA
* *
33562916 ATACT-TGCATAATATAGTTATTAAAAA
1 ATA-TATACATAATAT-GATATT--AAA
33562943 ATATATACATAATAT-A-A-TAAA
1 ATATATACATAATATGATATTAAA
* * * *
33562964 GTATA-AAATATATGAT-AT-TAACA
1 ATATATACATA-AT-ATGATATTAAA
** *
33562987 ATGCATACATAATATAATTATTAAAA
1 ATATATACATAATATGA-TATT-AAA
33563013 ATATATACATAATAT-A-A-TAAA
1 ATATATACATAATATGATATTAAA
*
33563034 ATATATAAATAATATGATATTAACA
1 ATATATACATAATATGATATTAA-A
*
33563059 ATACATACATAATAT
1 ATATATACATAATAT
33563074 AGTTAAAAAA
Statistics
Matches: 157, Mismatches: 28, Indels: 46
0.68 0.12 0.20
Matches are distributed among these distances:
20 4 0.03
21 26 0.17
22 7 0.04
23 10 0.06
24 21 0.13
25 44 0.28
26 30 0.19
27 15 0.10
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (24 bp):
ATATATACATAATATGATATTAAA
Found at i:33563027 original size:70 final size:73
Alignment explanation
Indices: 33562858--33563086 Score: 258
Period size: 70 Copynumber: 3.2 Consensus size: 73
33562848 TATAAATATA
** * *
33562858 TATT-AAAAATATATACATAATAATGATATTAAAAGTATATATGTGATAT-AGTGTTAA-AATAC
1 TATTAAAAAATATATACATAAT-AT-A-A-TAAAA-TATATAAATAATATGA-TATTAACAATAC
* * *
33562920 TTGCATAATATAGT
60 ATACATAATATAAT
* *
33562934 TATTAAAAAATATATACATAATATAATAAAGTATA-AAAT-ATATGATATTAACAATGCATACAT
1 TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
33562997 AATATAAT
66 AATATAAT
33563005 TATT-AAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
1 TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
*
33563069 AATATAGT
66 AATATAAT
33563077 TA--AAAAAATA
1 TATTAAAAAATA
33563087 ATATTAAAAA
Statistics
Matches: 136, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
70 38 0.28
71 33 0.24
72 36 0.26
73 4 0.03
74 1 0.01
75 1 0.01
76 6 0.04
77 17 0.12
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (73 bp):
TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
AATATAAT
Found at i:33563058 original size:72 final size:71
Alignment explanation
Indices: 33562923--33563086 Score: 253
Period size: 72 Copynumber: 2.3 Consensus size: 71
33562913 AAAATACTTG
* *
33562923 CATAATATAGTTATTAAAAAATATATACATAATATAATAAAGTATAAAATATATGATATTAACAA
1 CATAATATAATTATTAAAAAATATATACATAATATAATAAAATATAAAATATATGATATTAACAA
*
33562988 TGCATA
66 TACATA
33562994 CATAATATAATTATT-AAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAAC
1 CATAATATAATTATTAAAAAATATATACATAATATAATAAAATATA-AAAT-ATATGATATTAAC
33563058 AATACATA
64 AATACATA
*
33563066 CATAATATAGTTA--AAAAAATA
1 CATAATATAATTATTAAAAAATA
33563087 ATATTAAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
70 29 0.34
71 25 0.29
72 32 0.37
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (71 bp):
CATAATATAATTATTAAAAAATATATACATAATATAATAAAATATAAAATATATGATATTAACAA
TACATA
Found at i:33563990 original size:11 final size:11
Alignment explanation
Indices: 33563974--33563999 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33563964 GATTTGAAAA
33563974 AAAATAATAAT
1 AAAATAATAAT
33563985 AAAATAATAAT
1 AAAATAATAAT
33563996 AAAA
1 AAAA
33564000 AAACAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:33577752 original size:22 final size:24
Alignment explanation
Indices: 33577714--33577767 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
33577704 TAAATACTTT
33577714 AATTTTTAATATAATTTT-AGTTAA
1 AATTTTTAATATAATTTTGA-TTAA
*
33577738 TATTTTTAAT-T-ATTTTGATTAA
1 AATTTTTAATATAATTTTGATTAA
33577760 AATTTTTA
1 AATTTTTA
33577768 CACTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTTTAATATAATTTTGATTAA
Found at i:33577951 original size:16 final size:13
Alignment explanation
Indices: 33577920--33577945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33577910 CTTCTCCTTT
33577920 TAAAGTTATTATA
1 TAAAGTTATTATA
33577933 TAAAGTTATTATA
1 TAAAGTTATTATA
33577946 AGATAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAAAGTTATTATA
Found at i:33580428 original size:11 final size:10
Alignment explanation
Indices: 33580404--33580467 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 10
33580394 ATCCATGCTT
33580404 TTTTTTATAA
1 TTTTTTATAA
33580414 -TTTTTATGAA
1 TTTTTTAT-AA
33580424 TTTTTTAT-A
1 TTTTTTATAA
33580433 -TTTTTA-AA
1 TTTTTTATAA
*
33580441 TTTAATTTTTAA
1 TTT--TTTATAA
33580453 -TTTTTATAA
1 TTTTTTATAA
33580462 TTTTTT
1 TTTTTT
33580468 GAATTACTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
8 7 0.16
9 16 0.36
10 7 0.16
11 12 0.27
12 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:33580429 original size:20 final size:19
Alignment explanation
Indices: 33580404--33580467 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
33580394 ATCCATGCTT
33580404 TTTTTTATAATTTTTATGAA
1 TTTTTTATAATTTTTAT-AA
33580424 TTTTTTAT-ATTTTTA-AA
1 TTTTTTATAATTTTTATAA
*
33580441 TTTAATTTTTAATTTTTATAA
1 TTT--TTTATAATTTTTATAA
33580462 TTTTTT
1 TTTTTT
33580468 GAATTACTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 5 0.13
19 14 0.36
20 15 0.38
21 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTTTATAA
Found at i:33580447 original size:22 final size:21
Alignment explanation
Indices: 33580425--33580464 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
33580415 TTTTATGAAT
33580425 TTTTTATATTTTTA-AATTTAA
1 TTTTTA-ATTTTTATAATTTAA
33580446 TTTTTAATTTTTATAATTT
1 TTTTTAATTTTTATAATTT
33580465 TTTGAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTAATTTTTATAATTTAA
Found at i:33581034 original size:18 final size:18
Alignment explanation
Indices: 33580997--33581034 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33580987 CAAATTTCTC
*
33580997 TATTTTTTAATATTTTTT
1 TATTTTTTAATATTTATT
33581015 TATTTTATTAAT-TTTATT
1 TATTTT-TTAATATTTATT
33581033 TA
1 TA
33581035 ATAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTAATATTTATT
Found at i:33582026 original size:20 final size:20
Alignment explanation
Indices: 33581989--33582026 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33581979 AGCAATTTAA
*
33581989 TTTTTTTATGTCTTTTCTTT
1 TTTTTTTATGTCTCTTCTTT
33582009 TTTTTTTCAT-TCTCTTCT
1 TTTTTTT-ATGTCTCTTCT
33582027 GAATCTCGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTTATGTCTCTTCTTT
Found at i:33585172 original size:28 final size:28
Alignment explanation
Indices: 33585132--33585188 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
33585122 GTGCCTCTGG
*
33585132 TTAGACTAGAGCCGATGATGAACTTGTC
1 TTAGACTAGAGCCGATGATGAACCTGTC
33585160 TTAGACTAGAGCCGATGATGAACCTGTC
1 TTAGACTAGAGCCGATGATGAACCTGTC
33585188 T
1 T
33585189 CAGGACATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (28 bp):
TTAGACTAGAGCCGATGATGAACCTGTC
Found at i:33588676 original size:48 final size:48
Alignment explanation
Indices: 33588612--33588759 Score: 224
Period size: 48 Copynumber: 3.1 Consensus size: 48
33588602 TTGATGTACA
*
33588612 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
33588660 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** *
33588708 AGCCATGCATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
33588756 AGAT
1 AGAT
33588760 GTGTATATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:33590996 original size:101 final size:100
Alignment explanation
Indices: 33590804--33591059 Score: 293
Period size: 101 Copynumber: 2.5 Consensus size: 100
33590794 CTTATTGTAT
* * * * * ** *
33590804 CATAGTCCAACTATGGTCTTACATAT-GCATTGCCATGGCCCTGCCATGGTCTTATGTTCATAGT
1 CATAGCCCAACTATGATCTTACATATAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
* ** * *
33590868 GCCATAACTCGGTTACGGTCTTATCATCAGAATGC
66 GCCATAACCCAATTACAGTCCTATCATCAGAATGC
*
33590903 CATAGCCCAACCATGATCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACG-TCTATA
1 CATAGCCCAACTATGATCTTACATAT-AACACTGCCATGGTCCAACCATGGTCTTACGTTC-ATA
* *
33590967 GTGCCATAACCCAATTATAGTCCTGTCATCAGAATGC
64 GTGCCATAACCCAATTACAGTCCTATCATCAGAATGC
* *
33591004 CATAGCCCAGCTAT-AGTCTTACATATATACACTGCCACGGTCCAACCATGGTCTTA
1 CATAGCCCAACTATGA-TCTTACATATA-ACACTGCCATGGTCCAACCATGGTCTTA
33591060 TGTTTGAATA
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
99 23 0.17
100 4 0.03
101 106 0.80
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (100 bp):
CATAGCCCAACTATGATCTTACATATAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
GCCATAACCCAATTACAGTCCTATCATCAGAATGC
Found at i:33592617 original size:46 final size:46
Alignment explanation
Indices: 33592556--33592675 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 46
33592546 AAAATCTTTT
* *
33592556 TTGGTTCTGGCCTTCTAATGGCTGGCATCAAACTAGTAAAAAAAAA
1 TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
* *
33592602 TTGGTTCTGGTCTTCTAATGGCCGGCACCAGACTAGTAAAAAAAAA
1 TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
*
33592648 TTGGTGT-TGGCC-TGTAGATGGCCGGCAC
1 TTGGT-TCTGGCCTTCTA-ATGGCCGGCAC
33592676 TAGGTATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
45 3 0.05
46 62 0.94
47 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (46 bp):
TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
Found at i:33592744 original size:153 final size:156
Alignment explanation
Indices: 33592463--33592801 Score: 395
Period size: 155 Copynumber: 2.2 Consensus size: 156
33592453 TTTGGCCTTT
* * * *
33592463 TAATGGTCGGCACCAAACTAG-AAAAAAAATTTAGTGCTAGCCTGTGGATAGCTGGCACCAGGTA
1 TAATGGCCGGCACC-AACTAGTAAAAAAAAATTAGTGCTAGCCTGTAGATAGCCGGCACCAGGTA
* * *
33592527 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTGGCCTTCTAATGGCTGGCATCAAACTAG
65 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAG
* * *
33592592 T-AAAAAAAAA-TTGGTTCTGGTCTTC
130 TAAAAAAAAAATTTGGTGCTGGGCATC
* * * * *
33592617 TAATGGCCGGCACCAGACTAGTAAAAAAAAATTGGTGTTGGCCTGTAGATGGCCGGCACTAGGTA
1 TAATGGCCGGCACCA-ACTAGTAAAAAAAAATTAGTGCTAGCCTGTAGATAGCCGGCACCAGGTA
* * * * * * *
33592682 -TTTTTTCGTGTTCTAAT-ACAATTTTTTTTTGTTCTAGCCTTCTAATGGCCGGCACCAGACTAG
65 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAG
*
33592745 TAAAAAAAAAATTTGGTGCTGGGCATG
130 TAAAAAAAAAATTTGGTGCTGGGCATC
*
33592772 TATTGGCCGGCACCAA--AGTAAAAAAAAATT
1 TAATGGCCGGCACCAACTAGTAAAAAAAAATT
33592802 CAAATTTTTG
Statistics
Matches: 157, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
152 14 0.09
153 41 0.26
154 42 0.27
155 60 0.38
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (156 bp):
TAATGGCCGGCACCAACTAGTAAAAAAAAATTAGTGCTAGCCTGTAGATAGCCGGCACCAGGTAC
TTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAGT
AAAAAAAAAATTTGGTGCTGGGCATC
Found at i:33595938 original size:43 final size:45
Alignment explanation
Indices: 33595865--33596003 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 45
33595855 GAAAAAATTG
* * *
33595865 AAAATT-ACATGGAAAGATAGATAATTTAAATGAAATGAGAAAAA
1 AAAATTGAAATGGAAACAAAGATAATTTAAATGAAATGAGAAAAA
* * *
33595909 AAAATTGAAAT-G-AACAAATATAATATAAATGAATTGAGAAAAAA
1 AAAATTGAAATGGAAACAAAGATAATTTAAATGAAATGAG-AAAAA
* * *
33595953 ATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAAA
1 A--AAATTGAAATGGAAACAAAGAT-AATTTAAATGAAATGAGAAAAA
33596001 AAA
1 AAA
33596004 TTATTTAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
43 21 0.28
44 13 0.17
45 3 0.04
46 10 0.13
47 1 0.01
48 13 0.17
49 15 0.20
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (45 bp):
AAAATTGAAATGGAAACAAAGATAATTTAAATGAAATGAGAAAAA
Found at i:33596087 original size:26 final size:25
Alignment explanation
Indices: 33596051--33596108 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
33596041 AAAAGAAAGA
* *
33596051 TAAATTTAAATGAAACGAGGAAATATT
1 TAAA-TTAAATG-AACGAGGAAAAAAT
*
33596078 TAAATTAAATGAATGAGGAAAAAAT
1 TAAATTAAATGAACGAGGAAAAAAT
33596103 TAAATT
1 TAAATT
33596109 TGCATGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 17 0.61
26 7 0.25
27 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (25 bp):
TAAATTAAATGAACGAGGAAAAAAT
Found at i:33596095 original size:25 final size:26
Alignment explanation
Indices: 33595977--33596108 Score: 73
Period size: 26 Copynumber: 5.2 Consensus size: 26
33595967 GAAAGAAAGA
* *
33595977 TAAATTTAAATGAAATGAGAAAAAAAAT
1 TAAA-TTAAATGAAACGAG-GAAAAAAT
* * * *
33596005 T-ATTTAAAAGATATGA-GAAAAAAT
1 TAAATTAAATGAAACGAGGAAAAAAT
* *
33596029 TAAATTAAAATTAAA--A-G-AAAGA-
1 TAAATT-AAATGAAACGAGGAAAAAAT
* *
33596051 TAAATTTAAATGAAACGAGGAAATATT
1 TAAA-TTAAATGAAACGAGGAAAAAAT
*
33596078 TAAATTAAATG-AATGAGGAAAAAAT
1 TAAATTAAATGAAACGAGGAAAAAAT
33596103 TAAATT
1 TAAATT
33596109 TGCATGGAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 19
0.70 0.14 0.17
Matches are distributed among these distances:
22 11 0.14
23 6 0.08
24 11 0.14
25 21 0.26
26 25 0.31
27 5 0.06
28 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.12, T:0.27
Consensus pattern (26 bp):
TAAATTAAATGAAACGAGGAAAAAAT
Found at i:33596133 original size:47 final size:46
Alignment explanation
Indices: 33596082--33596248 Score: 195
Period size: 47 Copynumber: 3.7 Consensus size: 46
33596072 AATATTTAAA
**
33596082 TTAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAAT
1 TTAAATGAAATGA-GAAAAAATTAAATTTAAATGG-AAGATAGATAAT
33596129 TTAAATGAAATGAGAAAAAATTAAATTTAAAT--AA-A-A-ATAAT
1 TTAAATGAAATGAGAAAAAATTAAATTTAAATGGAAGATAGATAAT
* * *
33596170 ATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGATAAA
1 TTAAATGAAATGAG--AAAAAATTAAATTTAAAT-GGAAGATAGATAAT
33596219 TTAAATGAAATGAGAAAAAA-TAAATTTAAA
1 TTAAATGAAATGAGAAAAAATTAAATTTAAA
33596249 ATAAAAAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
41 18 0.17
42 1 0.01
43 18 0.17
44 2 0.02
46 11 0.11
47 31 0.30
48 6 0.06
49 17 0.16
ACGTcount: A:0.60, C:0.01, G:0.14, T:0.26
Consensus pattern (46 bp):
TTAAATGAAATGAGAAAAAATTAAATTTAAATGGAAGATAGATAAT
Found at i:33596159 original size:73 final size:74
Alignment explanation
Indices: 33595934--33596160 Score: 275
Period size: 74 Copynumber: 3.1 Consensus size: 74
33595924 AAATATAATA
*
33595934 TAAATGAATTGAGAAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAA
1 TAAATGAA-TGAGGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAA
33595999 AAA--AATTATT
65 AAATTAA--ATT
* * * ** *
33596009 TAAAAGATATGA-GAAAAAATTAAATTAAAATTAAAAGAAAGATAAATTTAAATGAAACGAGGAA
1 TAAATGA-ATGAGGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGA-GAA
* *
33596073 ATATTTAAA-T
64 AAAATTAAATT
* *
33596083 TAAATGAATGAGGAAAAAATTAAATTTGCATGGAAAGATAGAT-AATTTAAATGAAATGAGAAAA
1 TAAATGAATGAGGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
33596147 AATTAAATT
66 AATTAAATT
33596156 TAAAT
1 TAAAT
33596161 AAAAATAATA
Statistics
Matches: 127, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
72 10 0.08
73 25 0.20
74 74 0.58
75 15 0.12
76 1 0.01
77 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.14, T:0.27
Consensus pattern (74 bp):
TAAATGAATGAGGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
AATTAAATT
Found at i:33596169 original size:41 final size:41
Alignment explanation
Indices: 33596124--33596272 Score: 158
Period size: 41 Copynumber: 3.4 Consensus size: 41
33596114 GGAAAGATAG
*
33596124 ATAATTTAAATGAAATGAGAAAAAATTAAATTTAAATAAAA
1 ATAATATAAATGAAATGAGAAAAAATTAAATTTAAATAAAA
*
33596165 ATAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATA
1 ATAATATAAATGAAATGAG--AAAAAATTAAATTTAAAT---AA-A-A
33596213 GATAA-ATTAAATGAAATGAGAAAAAA-TAAATTTAAAATAAAA
1 -ATAATA-TAAATGAAATGAGAAAAAATTAAATTT-AAATAAAA
* *
33596255 AAAATATAAATTAAATGA
1 ATAATATAAATGAAATGA
33596273 AATGGAAATA
Statistics
Matches: 92, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
41 32 0.35
42 2 0.02
43 18 0.20
44 2 0.02
46 8 0.09
47 11 0.12
48 2 0.02
49 17 0.18
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (41 bp):
ATAATATAAATGAAATGAGAAAAAATTAAATTTAAATAAAA
Found at i:33596197 original size:90 final size:89
Alignment explanation
Indices: 33596079--33596272 Score: 277
Period size: 90 Copynumber: 2.2 Consensus size: 89
33596069 GGAAATATTT
* *** *
33596079 AAAT-TAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAATTTAAATGAAATGA
1 AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
33596142 GAAAAAATTAAATTT-AAATAAAAA
66 GAAAAAA-TAAATTTAAAATAAAAA
* *
33596166 TAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGATAAATTAAATGAAATG
1 AAATATAAATGAAATGAG-AAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATG
33596231 AGAAAAAATAAATTTAAAATAAAAA
65 AGAAAAAATAAATTTAAAATAAAAA
*
33596256 AAATATAAATTAAATGA
1 AAATATAAATGAAATGA
33596273 AATGGAAATA
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
87 3 0.03
88 6 0.06
89 13 0.14
90 72 0.77
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (89 bp):
AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
GAAAAAATAAATTTAAAATAAAAA
Found at i:33596280 original size:6 final size:5
Alignment explanation
Indices: 33596262--33596345 Score: 69
Period size: 5 Copynumber: 15.6 Consensus size: 5
33596252 AAAAAAATAT
* * *
33596262 AAATT AAATG AAATGG AAATAG GAATGG AAATGG AAATA AAATG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAAT-G AAATG AAATG AAATG
* *
33596311 AAATG AAATGG AAATG AAATTG GAATG ATATG AAA
1 AAATG AAAT-G AAATG AAA-TG AAATG AAATG AAA
33596346 AAAAAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
5 37 0.57
6 28 0.43
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:33596281 original size:11 final size:11
Alignment explanation
Indices: 33596267--33596335 Score: 79
Period size: 12 Copynumber: 6.2 Consensus size: 11
33596257 AATATAAATT
33596267 AAATGAAATGG
1 AAATGAAATGG
*
33596278 AAATAGGAATGG
1 AAAT-GAAATGG
*
33596290 AAATGGAAAT-A
1 AAAT-GAAATGG
33596301 AAATGAAAT-G
1 AAATGAAATGG
33596311 AAATGAAATGG
1 AAATGAAATGG
33596322 AAATGAAATTGG
1 AAATGAAA-TGG
33596334 AA
1 AA
33596336 TGATATGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
10 14 0.28
11 17 0.34
12 19 0.38
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:33596337 original size:11 final size:10
Alignment explanation
Indices: 33596268--33596338 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 10
33596258 ATATAAATTA
33596268 AATGAAATGG
1 AATGAAATGG
*
33596278 AAATAGGAATGG
1 -AAT-GAAATGG
**
33596290 AAATGGAAATAA
1 -AAT-GAAATGG
*
33596302 AATGAAATGA
1 AATGAAATGG
33596312 AATGAAATGG
1 AATGAAATGG
33596322 AAATGAAATTGG
1 -AATGAAA-TGG
33596334 AATGA
1 AATGA
33596339 TATGAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 15 0.30
11 18 0.36
12 17 0.34
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (10 bp):
AATGAAATGG
Found at i:33596343 original size:16 final size:15
Alignment explanation
Indices: 33596262--33596345 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 15
33596252 AAAAAAATAT
*
33596262 AAATTAAATGAAATGG
1 AAATGAAATGAAAT-G
*
33596278 AAATAGGAATGGAAATGG
1 AAAT-GAAAT-GAAAT-G
*
33596296 AAATAAAATGAAATG
1 AAATGAAATGAAATG
33596311 AAATGAAATGGAAATG
1 AAATGAAAT-GAAATG
* *
33596327 AAATTGGAATGATATG
1 AAA-TGAAATGAAATG
33596343 AAA
1 AAA
33596346 AAAAAAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
15 9 0.16
16 26 0.46
17 11 0.19
18 11 0.19
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:33596575 original size:21 final size:22
Alignment explanation
Indices: 33596551--33596597 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
33596541 AAATTGACAA
33596551 AAATAAAATATGAAAAAAATT-
1 AAATAAAATATGAAAAAAATTG
33596572 AAATAAAATATGAAAAAAATTG
1 AAATAAAATATGAAAAAAATTG
33596594 AAAT
1 AAAT
33596598 GACCTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (22 bp):
AAATAAAATATGAAAAAAATTG
Found at i:33596591 original size:16 final size:16
Alignment explanation
Indices: 33596534--33596576 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
33596524 TAACAAATTT
*
33596534 AAAAATTAAAT-TGAC
1 AAAAATTAAATATGAA
*
33596549 AAAAATAAAATATGAA
1 AAAAATTAAATATGAA
33596565 AAAAATTAAATA
1 AAAAATTAAATA
33596577 AAATATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAATTAAATATGAA
Found at i:33596595 original size:10 final size:11
Alignment explanation
Indices: 33596555--33596596 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
33596545 TGACAAAAAT
33596555 AAAATATGAAA
1 AAAATATGAAA
33596566 AAAAT-T-AAA
1 AAAATATGAAA
33596575 TAAAATATGAAA
1 -AAAATATGAAA
33596587 AAAAT-TGAAA
1 AAAATATGAAA
33596597 TGACCTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.11
10 11 0.39
11 11 0.39
12 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (11 bp):
AAAATATGAAA
Found at i:33596678 original size:14 final size:15
Alignment explanation
Indices: 33596622--33596675 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
33596612 GACTACTTCT
33596622 AATTAATATGAAAAA
1 AATTAATATGAAAAA
* *
33596637 ATATGAAATGAATTAAAAA
1 A-AT-TAAT--ATGAAAAA
33596656 AATTAATATGAAAAA
1 AATTAATATGAAAAA
33596671 AATTA
1 AATTA
33596676 TATTAGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 13 0.42
16 2 0.06
17 6 0.19
18 2 0.06
19 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AATTAATATGAAAAA
Found at i:33596723 original size:5 final size:5
Alignment explanation
Indices: 33596713--33596834 Score: 59
Period size: 5 Copynumber: 22.4 Consensus size: 5
33596703 AAAAAAAATT
* * *
33596713 AATGA AATGA AATGTTA AAAGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
* *
33596765 AATGA ATATGA AATTA AATGA AATGTTA AATGA ATATAA AATGA AATG-
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
* *
33596813 -ATGA TTATGA AATGG AATGA AA
1 AATGA -AATGA AATGA AATGA AA
33596835 GTTTAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
5 49 0.54
6 26 0.29
7 13 0.14
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:33596778 original size:28 final size:28
Alignment explanation
Indices: 33596738--33596813 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
33596728 TAAAAGAAAT
* *
33596738 ATGAATATGAAATGAAATGTAAT-TTGTA
1 ATGAATATGAAATGAAATGAAATGTT-AA
*
33596766 ATGAATATGAAATTAAATGAAATGTTAA
1 ATGAATATGAAATGAAATGAAATGTTAA
*
33596794 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
33596814 TGATTATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 40 0.95
29 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (28 bp):
ATGAATATGAAATGAAATGAAATGTTAA
Found at i:33596951 original size:5 final size:5
Alignment explanation
Indices: 33596941--33597008 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
33596931 TAGATAATTT
* *
33596941 AAATG AAATG AAAATG AAAATG TAAATA AAATG AAATG AAATG CACATG
1 AAATG AAATG -AAATG -AAATG -AAATG AAATG AAATG AAATG -AAATG
*
33596990 AAATTG GAATG AAATG AAA
1 AAA-TG AAATG AAATG AAA
33597009 AAAAAACAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 30 0.57
6 23 0.43
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:33596957 original size:6 final size:6
Alignment explanation
Indices: 33596941--33596981 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
33596931 TAGATAATTT
*
33596941 AAATG- AAATGA AAATGA AAATGT AAAT-A AAATG- AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
33596982 TGCACATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 14 0.45
6 17 0.55
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (6 bp):
AAATGA
Found at i:33596957 original size:11 final size:10
Alignment explanation
Indices: 33596941--33597008 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
33596931 TAGATAATTT
33596941 AAATGAAATG
1 AAATGAAATG
33596951 AAAATGAAAATG
1 -AAATG-AAATG
*
33596963 TAAATAAAATG
1 -AAATGAAATG
33596974 AAATGAAATG
1 AAATGAAATG
*
33596984 CACATGAAATTG
1 -AAATGAAA-TG
*
33596996 GAATGAAATG
1 AAATGAAATG
33597006 AAA
1 AAA
33597009 AAAAAACAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 13 0.28
11 23 0.49
12 11 0.23
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (10 bp):
AAATGAAATG
Found at i:33596971 original size:17 final size:17
Alignment explanation
Indices: 33596941--33597009 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
33596931 TAGATAATTT
33596941 AAATGAAATGAAAATGA
1 AAATGAAATGAAAATGA
33596958 AAATGTAAAT-AAAATG-
1 AAATG-AAATGAAAATGA
* *
33596974 AAATGAAATGCACATGA
1 AAATGAAATGAAAATGA
* *
33596991 AATTGGAATG-AAATGA
1 AAATGAAATGAAAATGA
33597007 AAA
1 AAA
33597010 AAAAACAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 4 0.09
16 16 0.37
17 19 0.44
18 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.20
Consensus pattern (17 bp):
AAATGAAATGAAAATGA
Found at i:33600623 original size:52 final size:51
Alignment explanation
Indices: 33600548--33600732 Score: 182
Period size: 51 Copynumber: 3.6 Consensus size: 51
33600538 AGAAAAAATA
* * * *
33600548 CCTGGTGCCGGCCATCTA-CAGGCCAGCACAAACAAATAATTTGTTTTACTAG
1 CCTGGTGCCGACCAT-TAGAAGGCCAG-ACAAACAAATTATTTTTTTTACTAG
* * * *
33600600 TCTGGTGCCGGCCATTAGAAGGCCAG--AACCAAATTTTGTTTTTTTTACTAG
1 CCTGGTGCCGACCATTAGAAGGCCAGACAAACAAA--TTATTTTTTTTACTAG
* *
33600651 CCTGGTGCCGACCATTAGAAGGCCAG--AACCAAATTTTGTTTTTTTACTAG
1 CCTGGTGCCGACCATTAGAAGGCCAGACAAACAAATTAT-TTTTTTTACTAG
*
33600701 CCTGGTGCCGACCATTAGAAGCCCAAGACAAA
1 CCTGGTGCCGACCATTAGAAGGCC-AGACAAA
33600733 AAAAAATTGC
Statistics
Matches: 115, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
49 9 0.08
50 35 0.30
51 48 0.42
52 21 0.18
53 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (51 bp):
CCTGGTGCCGACCATTAGAAGGCCAGACAAACAAATTATTTTTTTTACTAG
Found at i:33600714 original size:50 final size:51
Alignment explanation
Indices: 33600591--33600721 Score: 237
Period size: 51 Copynumber: 2.6 Consensus size: 51
33600581 AAATAATTTG
* *
33600591 TTTTACTAGTCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
1 TTTTACTAGCCTGGTGCCGACCATTAGAAGGCCAGAACCAAATTTTGTTTT
33600642 TTTTACTAGCCTGGTGCCGACCATTAGAAGGCCAGAACCAAATTTTG-TTT
1 TTTTACTAGCCTGGTGCCGACCATTAGAAGGCCAGAACCAAATTTTGTTTT
33600692 TTTTACTAGCCTGGTGCCGACCATTAGAAG
1 TTTTACTAGCCTGGTGCCGACCATTAGAAG
33600722 CCCAAGACAA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
50 33 0.42
51 45 0.58
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (51 bp):
TTTTACTAGCCTGGTGCCGACCATTAGAAGGCCAGAACCAAATTTTGTTTT
Found at i:33616474 original size:21 final size:20
Alignment explanation
Indices: 33616450--33616489 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
33616440 GCCGTGTTGA
33616450 TTTCGTACTTTGGCCCATTTT
1 TTTCGT-CTTTGGCCCATTTT
*
33616471 TTTCGTTTTTGGCCCATTT
1 TTTCGTCTTTGGCCCATTT
33616490 CTCATTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.07, C:0.23, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTCGTCTTTGGCCCATTTT
Found at i:33623063 original size:34 final size:35
Alignment explanation
Indices: 33623017--33623086 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
33623007 CTTTGGTACA
33623017 TAGACTCTGCCCTAAAATAACAGACAATCATCTGG
1 TAGACTCTGCCCTAAAATAACAGACAATCATCTGG
33623052 TAGACT-TGCCCTAAAATAACAGACAATCATCTGG
1 TAGACTCTGCCCTAAAATAACAGACAATCATCTGG
33623086 T
1 T
33623087 CCAGTCTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (35 bp):
TAGACTCTGCCCTAAAATAACAGACAATCATCTGG
Found at i:33629752 original size:22 final size:22
Alignment explanation
Indices: 33629724--33629776 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
33629714 TCAGGGAATT
**
33629724 TTTTTTTTTGCAAAATCTTAAA
1 TTTTTTTCAGCAAAATCTTAAA
33629746 TTTTTTTCAGCAAAATCTTAAA
1 TTTTTTTCAGCAAAATCTTAAA
33629768 TTTTTTTCA
1 TTTTTTTCA
33629777 AGATACAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTTTTCAGCAAAATCTTAAA
Found at i:33631130 original size:24 final size:25
Alignment explanation
Indices: 33631099--33631181 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 25
33631089 TCTGGGCTAT
*
33631099 ATAA-CAGGAATCTCATAAGAGCC-
1 ATAATCAGGAAGCTCATAAGAGCCA
*
33631122 ATAATCAGGAAGCTCATACGAGCCA
1 ATAATCAGGAAGCTCATAAGAGCCA
* *
33631147 ATAAT-AGGTAGCTTC-GAAGAGCCA
1 ATAATCAGGAAGC-TCATAAGAGCCA
* *
33631171 TTAATTAGGAA
1 ATAATCAGGAA
33631182 ACTTCGGATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 4 0.08
24 34 0.69
25 11 0.22
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (25 bp):
ATAATCAGGAAGCTCATAAGAGCCA
Found at i:33631186 original size:25 final size:24
Alignment explanation
Indices: 33631141--33631187 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
33631131 AAGCTCATAC
* *
33631141 GAGCCAATAATAGGTAGCTTCGAA
1 GAGCCAATAATAGGAAACTTCGAA
*
33631165 GAGCCATTAATTAGGAAACTTCG
1 GAGCCAATAA-TAGGAAACTTCG
33631188 GATAGTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (24 bp):
GAGCCAATAATAGGAAACTTCGAA
Found at i:33631282 original size:26 final size:27
Alignment explanation
Indices: 33631194--33631282 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 27
33631184 TTCGGATAGT
33631194 TATATATCGGGAAGCTC-CGGAA-AGCCA
1 TATA-ATCGGGAAGCTCAC-GAAGAGCCA
* *
33631221 T-TAATCAGGAAGCTCACAAAGAGCC-
1 TATAATCGGGAAGCTCACGAAGAGCCA
* *
33631246 TTTAATTGGGAAGCTCACGAAGAGCCA
1 TATAATCGGGAAGCTCACGAAGAGCCA
33631273 TAT-ATCGGGA
1 TATAATCGGGA
33631283 CACTCATAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
25 14 0.27
26 34 0.67
27 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
TATAATCGGGAAGCTCACGAAGAGCCA
Found at i:33631777 original size:26 final size:26
Alignment explanation
Indices: 33631748--33631797 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
33631738 TACGAGTAAG
*
33631748 TTTAACTCAATTTAATACAATTCATA
1 TTTAACTCAATTCAATACAATTCATA
* *
33631774 TTTAATTCAATTCAATTCAATTCA
1 TTTAACTCAATTCAATACAATTCA
33631798 CATCTTAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTAACTCAATTCAATACAATTCATA
Found at i:33631778 original size:16 final size:16
Alignment explanation
Indices: 33631757--33631787 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33631747 GTTTAACTCA
33631757 ATTTAATACAATTCAT
1 ATTTAATACAATTCAT
*
33631773 ATTTAATTCAATTCA
1 ATTTAATACAATTCA
33631788 ATTCAATTCA
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:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAATACAATTCAT
Found at i:33631787 original size:5 final size:5
Alignment explanation
Indices: 33631754--33631797 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
33631744 TAAGTTTAAC
* * *
33631754 TCAAT TTAAT ACAAT TCATAT TTAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCA
33631798 CATCTTAGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (5 bp):
TCAAT
Found at i:33633688 original size:18 final size:18
Alignment explanation
Indices: 33633653--33633702 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
33633643 ATCTAAAAAA
33633653 TAACAACAA-AAT-AATAG
1 TAACAA-AATAATGAATAG
*
33633670 TAACATAATAATGAATAG
1 TAACAAAATAATGAATAG
*
33633688 TAACAAAATAGTGAA
1 TAACAAAATAATGAA
33633703 AAAAATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 18 0.64
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (18 bp):
TAACAAAATAATGAATAG
Found at i:33636151 original size:14 final size:14
Alignment explanation
Indices: 33636132--33636159 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33636122 TACAATACCC
33636132 AAACAATAGCAACA
1 AAACAATAGCAACA
33636146 AAACAATAGCAACA
1 AAACAATAGCAACA
33636160 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACAATAGCAACA
Found at i:33636242 original size:51 final size:51
Alignment explanation
Indices: 33636141--33636241 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
33636131 CAAACAATAG
* * * * *
33636141 CAACAAAACAATAGCAACATAATAGTGAAATAATAGTAAAATAATGAAAAA
1 CAACAAAACAATAGCAACAAAATAGTGAAAAAACAGCAAAACAATGAAAAA
*
33636192 CAACAAGAA-AATAGCAACAAAATAGT-AAAAAACAGCAAAACAGTGAAAAA
1 CAACAA-AACAATAGCAACAAAATAGTGAAAAAACAGCAAAACAATGAAAAA
33636242 AATTGCATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 19 0.44
51 22 0.51
52 2 0.05
ACGTcount: A:0.64, C:0.12, G:0.11, T:0.13
Consensus pattern (51 bp):
CAACAAAACAATAGCAACAAAATAGTGAAAAAACAGCAAAACAATGAAAAA
Found at i:33641063 original size:20 final size:21
Alignment explanation
Indices: 33641029--33641082 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
33641019 TGATGATATT
*
33641029 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
33641050 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
33641070 TTTTATTATTTTA
1 TTATATTATTTTA
33641083 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:33641088 original size:11 final size:11
Alignment explanation
Indices: 33641072--33641099 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
33641062 ATGAGATATT
33641072 TTATTATTTTA
1 TTATTATTTTA
33641083 TTATTATTTTA
1 TTATTATTTTA
33641094 TTATTA
1 TTATTA
33641100 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:33642787 original size:46 final size:46
Alignment explanation
Indices: 33642734--33643166 Score: 629
Period size: 46 Copynumber: 9.4 Consensus size: 46
33642724 GTGGAAAAAA
33642734 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
*
33642780 AAAGATACCATGGCAACATGATATGAAATGTGCAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* *
33642826 AAAGATACCATGGCAACAAGAT-TAGAAATGTGTAAGACCATGATTG
1 AAAGATACCATGGCAACATGATAT-GAAATGTGTAAGACCATGGTTG
33642872 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* *
33642918 AAAGATACCATGGCAACCTTATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* * * * * **
33642964 GAAGATACCATAGTAACGTGACATGAAA-GAATAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
*
33643009 AAAGATACCATAGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* *
33643055 AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGATTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* * * *
33643101 AAAGATATCATGGCAACATGACA-GAAATTGAGTAAGACCATAGTTG
1 AAAGATACCATGGCAACATGATATGAAA-TGTGTAAGACCATGGTTG
* * *
33643147 AAAGACACTATGGCATCATG
1 AAAGATACCATGGCAACATG
33643167 TCAAAGATAA
Statistics
Matches: 348, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
45 44 0.13
46 303 0.87
47 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
Found at i:33644350 original size:24 final size:25
Alignment explanation
Indices: 33644319--33644366 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
33644309 CCCTCCCAAA
33644319 AAAAACCTAA-CCCAAAAAAAAAAG
1 AAAAACCTAACCCCAAAAAAAAAAG
33644343 AAAAACCTAACCCCAAAAAAAAAA
1 AAAAACCTAACCCCAAAAAAAAAA
33644367 CCAAGAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.71, C:0.23, G:0.02, T:0.04
Consensus pattern (25 bp):
AAAAACCTAACCCCAAAAAAAAAAG
Found at i:33664093 original size:24 final size:24
Alignment explanation
Indices: 33664049--33664216 Score: 70
Period size: 24 Copynumber: 6.8 Consensus size: 24
33664039 AAGTTCATGC
* *
33664049 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
33664073 GAGCCATTAACGGGAATCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
* ** * *
33664097 TAGCCATATATTGGGAAG-TTCAAGA
1 GAGCCAT-TAACGGGAAGCTCCGA-A
* * * *
33664122 GAGCCA-TATCAGGTAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
** *
33664145 GAGCCATTAACAAGAAGCTCACAAA
1 GAGCCATTAACGGGAAGCTC-CGAA
* * *
33664170 GATCCTTTAATCAGGAAGCTCACGAA
1 GAGCCATTAA-CGGGAAGCTC-CGAA
* * *
33664196 TAGTCATATAACGGGATGCTC
1 GAGCCAT-TAACGGGAAGCTC
33664217 ATAAGAGCTG
Statistics
Matches: 104, Mismatches: 33, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
23 14 0.13
24 40 0.38
25 23 0.22
26 24 0.23
27 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:33664290 original size:24 final size:24
Alignment explanation
Indices: 33664263--33664317 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
33664253 CACAACCGAT
33664263 CGGGATGCTCCGA-AGAGCTATTAA
1 CGGGATGCT-CGAGAGAGCTATTAA
* *
33664287 CGGGAAGCTCGAGAGGGCTATTAA
1 CGGGATGCTCGAGAGAGCTATTAA
33664311 CGGGATG
1 CGGGATG
33664318 TTTTTTCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (24 bp):
CGGGATGCTCGAGAGAGCTATTAA
Found at i:33664844 original size:20 final size:20
Alignment explanation
Indices: 33664819--33664858 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33664809 CCATGCATTT
*
33664819 CATAAAATTCATAACTTTTC
1 CATAAAATTCACAACTTTTC
* *
33664839 CATAAATTTTACAACTTTTC
1 CATAAAATTCACAACTTTTC
33664859 AATTTAATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (20 bp):
CATAAAATTCACAACTTTTC
Found at i:33666403 original size:24 final size:23
Alignment explanation
Indices: 33666376--33666447 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
33666366 TATATTTAAA
*
33666376 AATTCAAATAATGAATAAAAAATT
1 AATT-AAATAATTAATAAAAAATT
**
33666400 AATTACAATAATTAA-AAATATTTT
1 AATTA-AATAATTAATAAA-AAATT
*
33666424 ATTTAAA-AATTAATAAAAAATT
1 AATTAAATAATTAATAAAAAATT
33666446 AA
1 AA
33666448 ACGCGTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 10 0.26
23 9 0.24
24 19 0.50
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (23 bp):
AATTAAATAATTAATAAAAAATT
Found at i:33669092 original size:24 final size:24
Alignment explanation
Indices: 33669061--33669109 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
33669051 TAAGGGAAAT
33669061 TAAAAGATATTCAACTCCCTTTAC
1 TAAAAGATATTCAACTCCCTTTAC
33669085 TAAAAGATATTCAACTCCCTTTAC
1 TAAAAGATATTCAACTCCCTTTAC
33669109 T
1 T
33669110 TTCCCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (24 bp):
TAAAAGATATTCAACTCCCTTTAC
Found at i:33671020 original size:13 final size:13
Alignment explanation
Indices: 33671002--33671026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33670992 CATGAGCAAA
33671002 ATTTTAAGTTGAT
1 ATTTTAAGTTGAT
33671015 ATTTTAAGTTGA
1 ATTTTAAGTTGA
33671027 ACCAAATTTA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
ATTTTAAGTTGAT
Found at i:33686577 original size:13 final size:14
Alignment explanation
Indices: 33686550--33686580 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
33686540 TTGAGATGAG
33686550 AATATTATCTTAAA
1 AATATTATCTTAAA
33686564 AATATTAT-TTAAA
1 AATATTATCTTAAA
33686577 AATA
1 AATA
33686581 AAATAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATTATCTTAAA
Found at i:33687208 original size:20 final size:21
Alignment explanation
Indices: 33687164--33687209 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
33687154 TAATGATAAC
33687164 AGCTTGTTTAACCAAATTAAA
1 AGCTTGTTTAACCAAATTAAA
33687185 AGCTTGTTTAACCAAATT-AA
1 AGCTTGTTTAACCAAATTAAA
33687205 AGCTT
1 AGCTT
33687210 TCCTAGGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (21 bp):
AGCTTGTTTAACCAAATTAAA
Found at i:33690374 original size:12 final size:12
Alignment explanation
Indices: 33690357--33690381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33690347 CCATAAATAC
33690357 ACAATAATTGAA
1 ACAATAATTGAA
33690369 ACAATAATTGAA
1 ACAATAATTGAA
33690381 A
1 A
33690382 GTTGGAACAT
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
ACAATAATTGAA
Found at i:33694473 original size:21 final size:20
Alignment explanation
Indices: 33694439--33694492 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 20
33694429 TAAGTGATAC
33694439 TTTAA-TTTATTTATGCAAA
1 TTTAATTTTATTTATGCAAA
33694458 TTTAATTTTCATTTATGCAAA
1 TTTAATTTT-ATTTATGCAAA
*
33694479 TTTAATTTTTTTTA
1 TTTAATTTTATTTA
33694493 ATTTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 5 0.16
20 7 0.22
21 20 0.62
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTAATTTTATTTATGCAAA
Found at i:33695508 original size:7 final size:7
Alignment explanation
Indices: 33695496--33695520 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33695486 AGTCGTTTCA
33695496 TATTTAG
1 TATTTAG
33695503 TATTTAG
1 TATTTAG
33695510 TATTTAG
1 TATTTAG
33695517 TATT
1 TATT
33695521 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:33696056 original size:30 final size:30
Alignment explanation
Indices: 33696017--33696115 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
33696007 GGACGACGAT
33696017 GCAGGCCCATCAACAGCGCCCACACAATCA
1 GCAGGCCCATCAACAGCGCCCACACAATCA
* *
33696047 GCTGGCCCATCAACAGCGCCCATACAATCA
1 GCAGGCCCATCAACAGCGCCCACACAATCA
*
33696077 GCAAGCCCATCAACAGCGCCGC-CACAATCA
1 GCAGGCCCATCAACAGCGCC-CACACAATCA
*
33696107 CCAGGCCCA
1 GCAGGCCCA
33696116 ACAATTCAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 60 0.98
31 1 0.02
ACGTcount: A:0.31, C:0.43, G:0.17, T:0.08
Consensus pattern (30 bp):
GCAGGCCCATCAACAGCGCCCACACAATCA
Found at i:33696069 original size:13 final size:13
Alignment explanation
Indices: 33696021--33696096 Score: 71
Period size: 15 Copynumber: 5.2 Consensus size: 13
33696011 GACGATGCAG
33696021 GCCCATCAACAGC
1 GCCCATCAACAGC
*
33696034 GCCCACACAATCAGC
1 GCCCA-TCAA-CAGC
33696049 TGGCCCATCAACAGC
1 --GCCCATCAACAGC
33696064 GCCCATACAATCAGC
1 GCCCAT-CAA-CAGC
33696079 AAGCCCATCAACAGC
1 --GCCCATCAACAGC
33696094 GCC
1 GCC
33696097 GCCACAATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
13 14 0.26
14 6 0.11
15 16 0.30
16 6 0.11
17 11 0.21
ACGTcount: A:0.32, C:0.43, G:0.16, T:0.09
Consensus pattern (13 bp):
GCCCATCAACAGC
Found at i:33696193 original size:18 final size:18
Alignment explanation
Indices: 33696172--33696209 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33696162 TGTCAGGTAC
*
33696172 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
*
33696190 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
33696208 GT
1 GT
33696210 TTCATTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:33700628 original size:126 final size:126
Alignment explanation
Indices: 33700403--33701530 Score: 1887
Period size: 126 Copynumber: 9.0 Consensus size: 126
33700393 ATAGCCTCAG
* *
33700403 TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCAACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
33700468 CAGTGCATCCAGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * *
33700529 TTTTTCTACGAACTATTGTAGCAAAAGCGCGTCCATGTGGGAGATTTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
33700594 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * *
33700655 TTTTTCTATGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGATTTTTTCTGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
33700720 CGGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* *
33700781 TTTTTCTATGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCTGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
33700846 CGGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCATAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* *
33700907 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTAGGAGCTTTTTTCTGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* * * *
33700972 CGGTGCATCCTGCTTGAAGTGTTTTTGACACTATTTGTTCAAAAACGTCTACTCAAAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
*
33701033 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGATCTTTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
33701098 CAGTGCATCCTGCTTGAAACGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * * * * *
33701159 TTTTTCTATGAACTACTGTAGCAAAAGTGCGTCCACATGGTAGCTTTTTTTCAAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
33701224 CAGTGCATCCTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * *
33701285 TTTTTCTACTAACTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTTTTTCCTAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
33701350 CAGTGCATACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGGATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * * * *
33701411 TTTTTCTACGAACTATTATAGCAAAAGGGCGTCCACGTGGGAGCTTTTTTCTGAAATTTTGTTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
33701476 CAGTGCATCTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
33701531 ATTAACCTAA
Statistics
Matches: 945, Mismatches: 57, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 945 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (126 bp):
TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
Found at i:33701676 original size:19 final size:19
Alignment explanation
Indices: 33701652--33701724 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
33701642 ACCATTATGT
33701652 ATCAATTAACCCTAAATTA
1 ATCAATTAACCCTAAATTA
* * *
33701671 ATCAATTAACGCTCATTTA
1 ATCAATTAACCCTAAATTA
*
33701690 ATCGAA-TAACCCTAATTTA
1 ATC-AATTAACCCTAAATTA
* * *
33701709 ATTAACTAACCATAAA
1 ATCAATTAACCCTAAA
33701725 CCTTAAACTC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.05
19 40 0.91
20 2 0.05
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAATTAACCCTAAATTA
Found at i:33701819 original size:21 final size:21
Alignment explanation
Indices: 33701793--33701838 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
33701783 CCTAAAATCA
33701793 TAAACCACTAACCATAAACCC
1 TAAACCACTAACCATAAACCC
*
33701814 TAAACCACTAACTATAAACCC
1 TAAACCACTAACCATAAACCC
33701835 TAAA
1 TAAA
33701839 ACAACTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCACTAACCATAAACCC
Found at i:33702451 original size:15 final size:16
Alignment explanation
Indices: 33702427--33702471 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
33702417 TTTTGAAAGG
33702427 CTTAAAAATATTTTAT
1 CTTAAAAATATTTTAT
*
33702443 -TTAACAATATTTTAT
1 CTTAAAAATATTTTAT
*
33702458 CTCAAAAATATTTT
1 CTTAAAAATATTTT
33702472 TTTGTCCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
CTTAAAAATATTTTAT
Found at i:33704295 original size:19 final size:19
Alignment explanation
Indices: 33704245--33704306 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
33704235 AAATTACAAA
*
33704245 AAAAATTTAAAATAATTT-T
1 AAAATTTTAAAAT-ATTTAT
* *
33704264 CAAATATTCAAAATATTTAT
1 AAAAT-TTTAAAATATTTAT
* *
33704284 AAAATTTTAAAAAAATTAT
1 AAAATTTTAAAATATTTAT
33704303 AAAA
1 AAAA
33704307 ATAAATAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTTAAAATATTTAT
Found at i:33704568 original size:16 final size:17
Alignment explanation
Indices: 33704529--33704572 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
33704519 AACTCGAATA
33704529 ATTTCACTC-AA-TTCG
1 ATTTCACTCGAATTTCG
33704544 ACTTT-ACTCGAATTTC-
1 A-TTTCACTCGAATTTCG
33704560 ATTTCACTCGAAT
1 ATTTCACTCGAAT
33704573 CAATTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.32
16 14 0.56
17 3 0.12
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (17 bp):
ATTTCACTCGAATTTCG
Found at i:33706650 original size:3 final size:3
Alignment explanation
Indices: 33706642--33706707 Score: 64
Period size: 3 Copynumber: 21.3 Consensus size: 3
33706632 TCCATTTCGG
* *
33706642 GAA GAA GAAA GAA GGA GAAA GAGA GAA GAAA GAA GAA -AA GAA GGA GAA
1 GAA GAA G-AA GAA GAA G-AA GA-A GAA G-AA GAA GAA GAA GAA GAA GAA
33706690 GAA GAA -AA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G
33706708 GAGAGGAAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 4 0.08
3 38 0.72
4 11 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33706677 original size:14 final size:13
Alignment explanation
Indices: 33706644--33706711 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 13
33706634 CATTTCGGGA
33706644 AGAAGAAAGAAGG
1 AGAAGAAAGAAGG
* *
33706657 AGAAAGAGAGAAGAA
1 AG-AAGAAAGAAG-G
33706672 AGAAGAAAAGAAGG
1 AGAAG-AAAGAAGG
*
33706686 AGAAG-AAGAA-A
1 AGAAGAAAGAAGG
33706697 AGAAG-AAGAAGG
1 AGAAGAAAGAAGG
33706709 AGA
1 AGA
33706712 GGAAGGAGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 10 0.22
12 8 0.18
13 2 0.04
14 17 0.38
15 8 0.18
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AGAAGAAAGAAGG
Found at i:33706681 original size:8 final size:8
Alignment explanation
Indices: 33706665--33706703 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
33706655 GGAGAAAGAG
33706665 AGAAG-AA
1 AGAAGAAA
33706672 AGAAGAAA
1 AGAAGAAA
*
33706680 AGAAGGAGA
1 AGAA-GAAA
33706689 AGAAGAAA
1 AGAAGAAA
33706697 AGAAGAA
1 AGAAGAA
33706704 GAAGGAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 5 0.18
8 16 0.57
9 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
AGAAGAAA
Found at i:33707264 original size:15 final size:15
Alignment explanation
Indices: 33707218--33707286 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
33707208 AAAATAGTAT
33707218 AAAAAATAAAATACT-
1 AAAAAATAAAATA-TG
***
33707233 AAAAAATATCTTAATG
1 AAAAAATAAAAT-ATG
33707249 AAAAAATAAAATATG
1 AAAAAATAAAATATG
*
33707264 AAAAGAAATAAAAGATG
1 -AAA-AAATAAAATATG
33707281 AAAAAA
1 AAAAAA
33707287 GACTTTTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 16 0.37
16 16 0.37
17 11 0.26
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAATATG
Found at i:33707272 original size:17 final size:17
Alignment explanation
Indices: 33707252--33707284 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33707242 CTTAATGAAA
*
33707252 AAATAAAATATGAAAAG
1 AAATAAAAGATGAAAAG
33707269 AAATAAAAGATGAAAA
1 AAATAAAAGATGAAAA
33707285 AAGACTTTTT
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:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATAAAAGATGAAAAG
Found at i:33707560 original size:118 final size:118
Alignment explanation
Indices: 33707364--33707627 Score: 368
Period size: 119 Copynumber: 2.2 Consensus size: 118
33707354 TAATATATTT
*
33707364 TAAAAAATAAAATCTGAAAATTTTTAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTA
1 TAAAAAATAAAATCCGAAAA----TAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTA
*
33707429 AATTATTAT-AAAAACACTAAAATAATACATTTGAAACATTATATACTAAAATAATA
62 AATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATATACTAAAATAATA
* * * * * *
33707485 TAAAAAATAAAATCCGAAAATAAAAACTACCAATAAAGTGTCAAAATCAGGGTTATTTATTAAAT
1 TAAAAAATAAAATCCGAAAATAAAAA-TACAAACAAAGGGCCAAAATCAGAGTTATTTACTAAAT
* *
33707550 TAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATA
65 TAATATAAAAAACACTAAAATAATACATTTGAAACATTATATACTAAAATAATA
*
33707604 TAAAAAAATAAAATACGAAAATAA
1 T-AAAAAATAAAATCCGAAAATAA
33707628 TATATATTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
117 6 0.05
118 37 0.29
119 46 0.36
120 21 0.16
121 19 0.15
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (118 bp):
TAAAAAATAAAATCCGAAAATAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTAAATT
AATATAAAAAACACTAAAATAATACATTTGAAACATTATATACTAAAATAATA
Found at i:33707613 original size:13 final size:13
Alignment explanation
Indices: 33707595--33707659 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
33707585 ATTATGTACT
*
33707595 AAAATAATATAAA
1 AAAATAAAATAAA
33707608 AAAATAAAATACGAA
1 AAAATAAAATA--AA
* *
33707623 AATAATATATATTAA
1 AA-AATA-AAATAAA
*
33707638 AAAATAAAATAAG
1 AAAATAAAATAAA
33707651 AAAATAAAA
1 AAAATAAAA
33707660 ATTTACCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 23 0.55
14 4 0.10
15 8 0.19
16 4 0.10
17 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:33707642 original size:30 final size:29
Alignment explanation
Indices: 33707597--33707657 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
33707587 TATGTACTAA
*
33707597 AATAATATAAAAAAATAAAATACGAAAAT
1 AATAATATAAAAAAATAAAATAAGAAAAT
*
33707626 AATATATATTAAAAAATAAAATAAGAAAAT
1 AATA-ATATAAAAAAATAAAATAAGAAAAT
33707656 AA
1 AA
33707658 AAATTTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (29 bp):
AATAATATAAAAAAATAAAATAAGAAAAT
Found at i:33710412 original size:26 final size:26
Alignment explanation
Indices: 33710376--33710459 Score: 91
Period size: 26 Copynumber: 3.1 Consensus size: 26
33710366 GGAACAAACT
33710376 TTAAATACATTACAACATTAATCTAA
1 TTAAATACATTACAACATTAATCTAA
*
33710402 TTAAATACATTA-ATCTAATTGGAA-CATTAA
1 TTAAATACATTACAAC--ATT--AATC--TAA
33710432 TTAAATACATTACAACATTAATCTAA
1 TTAAATACATTACAACATTAATCTAA
33710458 TT
1 TT
33710460 GGAACAAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
25 2 0.04
26 17 0.35
27 5 0.10
28 2 0.04
29 5 0.10
30 15 0.31
31 2 0.04
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (26 bp):
TTAAATACATTACAACATTAATCTAA
Done.