Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 158 of 322
Found at i:51937142 original size:23 final size:23
Alignment explanation
Indices: 51937103--51937146 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
51937093 ATAAAAAAAA
*
51937103 TTTTAAAAAGTTTTAAAATATTT
1 TTTTAAAAAGTTATAAAATATTT
51937126 TTTTATAAAA-TTATAAAATAT
1 TTTTA-AAAAGTTATAAAATAT
51937147 ATAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTAAAAAGTTATAAAATATTT
Found at i:51937154 original size:23 final size:21
Alignment explanation
Indices: 51937128--51937188 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
51937118 AAATATTTTT
51937128 TTATAAAATTATAAAATATATAA
1 TTATAAAATTA-AAAAT-TATAA
*
51937151 TTATAAATTTAAAAATTATAA
1 TTATAAAATTAAAAATTATAA
*
51937172 --ATAATATATAAAAATTA
1 TTATAAAAT-TAAAAATTA
51937189 GAAAAGGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 5 0.15
20 9 0.26
21 5 0.15
22 5 0.15
23 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTATAAAATTAAAAATTATAA
Found at i:51937173 original size:15 final size:16
Alignment explanation
Indices: 51937127--51937173 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
51937117 AAAATATTTT
51937127 TTTATAAAATTATAAA
1 TTTATAAAATTATAAA
* *
51937143 -ATATATAATTATAAA
1 TTTATAAAATTATAAA
51937158 TTTA-AAAATTATAAA
1 TTTATAAAATTATAAA
51937173 T
1 T
51937174 AATATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 24 0.92
16 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTATAAAATTATAAA
Found at i:51938211 original size:43 final size:43
Alignment explanation
Indices: 51938163--51938249 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
51938153 TAAAAATACT
51938163 AAAAATTTAAAATAAAATTGATTTGTCATTTTTCCTCCTCTAC
1 AAAAATTTAAAATAAAATTGATTTGTCATTTTTCCTCCTCTAC
51938206 AAAAATTTAAAATAAAATTGATTTGTCATTTTTCCTCCTCTAC
1 AAAAATTTAAAATAAAATTGATTTGTCATTTTTCCTCCTCTAC
51938249 A
1 A
51938250 TATACCTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (43 bp):
AAAAATTTAAAATAAAATTGATTTGTCATTTTTCCTCCTCTAC
Found at i:51945859 original size:35 final size:36
Alignment explanation
Indices: 51945796--51945866 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
51945786 CAATGATATG
51945796 CAATCTTAGATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
51945832 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
51945867 TGCAAACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:51945885 original size:17 final size:19
Alignment explanation
Indices: 51945788--51945878 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
51945778 ATAATCTTCA
51945788 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
51945807 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
51945826 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
51945843 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
51945861 ATGATATGCAAACTTAGA
1 ATGATATGCAATCTTAGA
51945879 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:51946192 original size:17 final size:17
Alignment explanation
Indices: 51946168--51946202 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
51946158 TGTTTCCCTG
*
51946168 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
51946186 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
51946203 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:51955738 original size:89 final size:87
Alignment explanation
Indices: 51955610--51955770 Score: 198
Period size: 89 Copynumber: 1.8 Consensus size: 87
51955600 TTCGACAGAG
* * *
51955610 AGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTCACATCAAAGTAGATCCAAGATGA
1 AGCAGATCGAAGACATAGCAGATCTAACCTTCCGATGTTTACAC-T-AAAGCAGATCCAAGATGA
51955675 TTTGGCATCCTTGCATTTACAAGA
64 TTTGGCATCCTTGCATTTACAAGA
* ** * * * *
51955699 AGCAGATCGAAGACATAGCAGATTTGGCTTTCACG-TGTTTACGCTGAAGCAGATCTAAGATGAT
1 AGCAGATCGAAGACATAGCAGATCTAACCTTC-CGATGTTTACACTAAAGCAGATCCAAGATGAT
51955763 TTGGCATC
65 TTGGCATC
51955771 TCTGTACTGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
87 24 0.39
88 1 0.02
89 35 0.57
90 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (87 bp):
AGCAGATCGAAGACATAGCAGATCTAACCTTCCGATGTTTACACTAAAGCAGATCCAAGATGATT
TGGCATCCTTGCATTTACAAGA
Found at i:51955911 original size:78 final size:78
Alignment explanation
Indices: 51955803--51956190 Score: 587
Period size: 78 Copynumber: 4.8 Consensus size: 78
51955793 CGAAGAAACA
** * *
51955803 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
51955868 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
51955881 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGATCGGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
51955946 GCAGATCCAAGAT
66 GCAGATCCAAGAT
51955959 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA-----
51956024 TTACATCGAAGCAGATCCAAGAT
61 -T---T-GAAGCAGATCCAAGAT
*
51956047 GACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCAT
1 ----GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
51956112 TGAAGCAGATCCAAGAT
62 TGAAGCAGATCCAAGAT
51956129 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATT
51956191 TGTTTACATC
Statistics
Matches: 286, Mismatches: 10, Indels: 28
0.88 0.03 0.09
Matches are distributed among these distances:
78 191 0.67
82 16 0.06
83 1 0.00
84 1 0.00
86 1 0.00
87 1 0.00
88 16 0.06
92 59 0.21
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:51956068 original size:92 final size:88
Alignment explanation
Indices: 51955943--51956256 Score: 450
Period size: 92 Copynumber: 3.6 Consensus size: 88
51955933 GACCTTCATT
*
51955943 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
51956008 TCTGACCTTCATGTGTTTACATC
66 TCTGACCTTCATGTGTTTACATC
51956031 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAG
1 GAAGCAGATCCAAGAT----GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAG
51956096 CAGATCTGACCTTCA------T---T-
62 CAGATCTGACCTTCATGTGTTTACATC
*
51956113 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
*
51956178 TCTGACCTTCATTTGTTTACATC
66 TCTGACCTTCATGTGTTTACATC
*
51956201 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG
1 GAAGCAGATCCAAGAT----GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCG
51956257 GAGATAACAG
Statistics
Matches: 205, Mismatches: 3, Indels: 32
0.85 0.01 0.13
Matches are distributed among these distances:
78 59 0.29
82 16 0.08
83 1 0.00
84 1 0.00
86 1 0.00
87 1 0.00
88 32 0.16
92 94 0.46
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (88 bp):
GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
TCTGACCTTCATGTGTTTACATC
Found at i:51956070 original size:170 final size:170
Alignment explanation
Indices: 51955865--51956268 Score: 712
Period size: 170 Copynumber: 2.4 Consensus size: 170
51955855 GACCTTCATT
51955865 GAAGCAGATCCAAGAT----GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAA
1 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAA
51955926 CAGATCGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
66 CAGATCGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
51955991 ATCGAAGACATAGCAGATCTGACCTTCATGTGTTTACATC
131 ATCGAAGACATAGCAGATCTGACCTTCATGTGTTTACATC
* *
51956031 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAG
1 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAA
*
51956096 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
66 CAGATCGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
*
51956161 ATCGAAGACATAGCAGATCTGACCTTCATTTGTTTACATC
131 ATCGAAGACATAGCAGATCTGACCTTCATGTGTTTACATC
* *
51956201 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG--GAGATAA
1 GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAA
51956264 CAGAT
66 CAGAT
51956269 TTGGCATCTC
Statistics
Matches: 226, Mismatches: 8, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
166 16 0.07
168 9 0.04
170 201 0.89
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (170 bp):
GAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAA
CAGATCGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
ATCGAAGACATAGCAGATCTGACCTTCATGTGTTTACATC
Found at i:51956082 original size:45 final size:44
Alignment explanation
Indices: 51955959--51956402 Score: 318
Period size: 45 Copynumber: 10.1 Consensus size: 44
51955949 GATCCAAGAT
51955959 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATA-CA
* * * * * * *
51956006 GATCTGACCT-TCATGTGTTTACATC--GAAGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGAT-ACA
*
51956051 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATA-CA
* *
51956098 GATCT-G-A-C-CT-TCATT-GA-----AGCAGATCCAAGAT---
1 GATTTGGCATCTCTGT-ATTAGACGGGGAGCAGATCGAAGATACA
51956129 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATA-CA
* * * * * * *
51956176 GATCTGACCTTCATTTGT-TTACATC--GAAGCAGATCCAAGATGACA
1 GATTTG-GCATC-TCTGTATTAGA-CGGGGAGCAGATCGAAGAT-ACA
* *
51956221 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAT-ACA
*
51956266 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATA-CA
*
51956310 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAT-ACA
* * * *
51956355 GATTTGGCGTCTCTGTATTAGACGGTGAGTAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATA-CA
51956400 GAT
1 GAT
51956403 ATCGCTTTCC
Statistics
Matches: 313, Mismatches: 45, Indels: 80
0.71 0.10 0.18
Matches are distributed among these distances:
31 4 0.01
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.02
36 3 0.01
37 11 0.04
41 11 0.04
42 3 0.01
43 14 0.04
44 53 0.17
45 133 0.42
46 9 0.03
47 46 0.15
48 11 0.04
49 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATACA
Found at i:51956329 original size:89 final size:90
Alignment explanation
Indices: 51956129--51956402 Score: 306
Period size: 89 Copynumber: 3.0 Consensus size: 90
51956119 GATCCAAGAT
* * * * * *
51956129 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAG--ATAACAGATTTG-GCATC-TCTGT
* * *
51956194 -TTACATC--GAAGCAGATCCAAGAT-GACA
62 ATTAGA-CGGGGAGCAGATCAAAGATAG-CA
*
51956221 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
**
51956286 GACGGGGAGCAGATTGAAGA-AGCA
66 GACGGGGAGCAGATCAAAGATAGCA
* * *
51956310 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
* *
51956375 GACGGTGAGTAGATCAAAGATAGCA
66 GACGGGGAGCAGATCAAAGATAGCA
51956400 GAT
1 GAT
51956403 ATCGCTTTCC
Statistics
Matches: 158, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
88 5 0.03
89 86 0.54
90 30 0.19
92 37 0.23
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (90 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
GACGGGGAGCAGATCAAAGATAGCA
Found at i:51956372 original size:134 final size:136
Alignment explanation
Indices: 51956129--51956379 Score: 341
Period size: 134 Copynumber: 1.9 Consensus size: 136
51956119 GATCCAAGAT
* *
51956129 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA-ATAGCAGATCTGACCGTCATCTGT
*
51956194 TTACATCGAAGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGA
65 TTACATCGAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGA
51956259 GATAACA
130 GATAACA
* * *
51956266 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAG-A-AGCAGATTTG-GCGTC-TCTGTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAGATCTGACCGTCATCTGT-
* * * *
51956327 TTAGA-CGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGACGG
65 TTACATC--GAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGG
51956380 TGAGTAGATC
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
132 5 0.05
133 7 0.07
134 50 0.50
135 1 0.01
137 38 0.38
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (136 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAGATCTGACCGTCATCTGTT
TACATCGAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAG
ATAACA
Found at i:51958231 original size:15 final size:15
Alignment explanation
Indices: 51958211--51958241 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51958201 ACTTGAAAAG
51958211 AAAATATATACATAA
1 AAAATATATACATAA
*
51958226 AAAATATTTACATAA
1 AAAATATATACATAA
51958241 A
1 A
51958242 GTTATATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATATACATAA
Found at i:51960426 original size:176 final size:177
Alignment explanation
Indices: 51960121--51960743 Score: 823
Period size: 176 Copynumber: 3.5 Consensus size: 177
51960111 TTACTTGAGA
* *
51960121 AAATAAGATCTTC-AGTCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCCA-TCTTT
1 AAATAAGATCTTCAAATC-TCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-CATTCTTC
* * * * * *
51960184 AACCTGCTCTTTTGCTACCTCAGAGAAATAAGGCTAGTGGTAAAATCTACTCCATCACCGATACA
64 AACCTGCTCTATTGCTACCTCAGAGAGATAAGGCTGGTGATAAAATCTGCTCCATTACCGATACA
* * *
51960249 TGGAGAT-AGAATTCACCATT-TTAGATCTGCTCCACTGCAATCTTAGGG
129 TGAAGATAAG-ATTCACCATTCTTAGATCTGCTCCACTGCAATCTCAGAG
* * * * *
51960297 AGATAAAATCTTCAAAACTCAATCTGCTTCCTTGCTACCTCAGGAAGATAAGATTCATTCTTCAA
1 AAATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAA
* * * *
51960362 CCTGGTCTATTGCTATCTCAGAGAGATAAGGCTGGTGATAAAATCTGCTCCATTGCCAATACATG
66 CCTGCTCTATTGCTACCTCAGAGAGATAAGGCTGGTGATAAAATCTGCTCCATTACCGATACATG
*
51960427 AAGATAAGATTCACCATTCTT-GATCTGCTCCACTGCAATCTCAGTG
131 AAGATAAGATTCACCATTCTTAGATCTGCTCCACTGCAATCTCAGAG
51960473 AAATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAA
1 AAATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAA
* * *
51960538 CCTGCTCTCTTGCTACCTTAGAGAGATGAGGCTGGTGATAAAATCTGCTCCATTACCGATACATG
66 CCTGCTCTATTGCTACCTCAGAGAGATAAGGCTGGTGATAAAATCTGCTCCATTACCGATACATG
* ** * **
51960603 AAGATAAGATTCACTATCTGCAAAAATCTGCTCTGCTGCAA-CTCAGAG
131 AAGATAAGATTCACCAT-T-CTTAGATCTGCTCCACTGCAATCTCAGAG
* *
51960651 ATATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGAAAGATAAGACTCATTCTTCAA
1 AAATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAA
* *
51960716 CCT-TTC-CTTGCTACCTCA-AGAAGATAAG
66 CCTGCTCTATTGCTACCTCAGAG-AGATAAG
51960744 ACTCATTCTT
Statistics
Matches: 395, Mismatches: 44, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
175 4 0.01
176 295 0.75
177 9 0.02
178 73 0.18
179 14 0.04
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (177 bp):
AAATAAGATCTTCAAATCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAA
CCTGCTCTATTGCTACCTCAGAGAGATAAGGCTGGTGATAAAATCTGCTCCATTACCGATACATG
AAGATAAGATTCACCATTCTTAGATCTGCTCCACTGCAATCTCAGAG
Found at i:51960432 original size:86 final size:86
Alignment explanation
Indices: 51960340--51960615 Score: 234
Period size: 88 Copynumber: 3.2 Consensus size: 86
51960330 GCTACCTCAG
*
51960340 GAAGATAAGATTCATTCTTCAACCTGGTCTATTGCTATCTCAGAGAGATAAGGCTGGTGATAAAA
1 GAAGATAAGATTCATTCTTCAACCTGCTCTATTGCTATCTCAGAGAGATAAGGCTGGTGATAAAA
51960405 TCTGCTCCATTGCCAATACAT
66 TCTGCTCCATTGCCAATACAT
* * * * * * * * ****
51960426 GAAGATAAGATTCACCATTCTT-GATCTGCTCCACTGCAATCTCAGTGAAATAAGATCTTCAAAT
1 GAAGATAAGATT---CATTCTTCAACCTGCTCTATTGCTATCTCAGAGAGATAAG-GCTGGTGAT
** * * * *
51960490 CTCAGTCTGCTTCC-TTGCTACCT-CAG
62 -AAAATCTGC-TCCATTGCCA-ATACAT
* * * * *
51960516 GAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTTAGAGAGATGAGGCTGGTGATAAAA
1 GAAGATAAGATTCATTCTTCAACCTGCTCTATTGCTATCTCAGAGAGATAAGGCTGGTGATAAAA
* *
51960581 TCTGCTCCATTACCGATACAT
66 TCTGCTCCATTGCCAATACAT
51960602 GAAGATAAGATTCA
1 GAAGATAAGATTCA
51960616 CTATCTGCAA
Statistics
Matches: 135, Mismatches: 45, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
85 4 0.03
86 36 0.27
87 11 0.08
88 45 0.33
89 11 0.08
90 24 0.18
91 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (86 bp):
GAAGATAAGATTCATTCTTCAACCTGCTCTATTGCTATCTCAGAGAGATAAGGCTGGTGATAAAA
TCTGCTCCATTGCCAATACAT
Found at i:51960730 original size:41 final size:40
Alignment explanation
Indices: 51960678--51960783 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 40
51960668 CTCAGTCTGC
51960678 TTCCTTGCTACCTCAGAAAGATAAGACTCATTCTTCAACCT
1 TTCCTTGCTACCTCAGAAAGATAAGACTCATTCTTCAA-CT
51960719 TTCCTTGCTACCTCA-AGAAGATAAGACTCATTCTTCAACT
1 TTCCTTGCTACCTCAGA-AAGATAAGACTCATTCTTCAACT
*
51960759 TGCTCTCTTGCTACCTCAGAGAGAT
1 T--TC-CTTGCTACCTCAGAAAGAT
51960784 GAGGCTGGTG
Statistics
Matches: 59, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
40 4 0.07
41 36 0.61
42 2 0.03
43 16 0.27
44 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.32
Consensus pattern (40 bp):
TTCCTTGCTACCTCAGAAAGATAAGACTCATTCTTCAACT
Found at i:51961157 original size:64 final size:63
Alignment explanation
Indices: 51961055--51961181 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 63
51961045 TTCATGTATC
* *
51961055 ATGCTTATGCCAAATAATTAGGATATTATAATCAAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATACTATAATCAAAATGAAT-AAATGCTCCTAACTAAATGTG
** * * * *
51961119 ATGCTTATGTTAAATAATTAGGATGCTATGATCGAAATGAATAAATGTTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATACTATAATCAAAATGAATAAATGCTCCTAACTAAATGTG
51961182 TTATGAATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (63 bp):
ATGCTTATGCCAAATAATTAGGATACTATAATCAAAATGAATAAATGCTCCTAACTAAATGTG
Found at i:51967462 original size:33 final size:33
Alignment explanation
Indices: 51967420--51967486 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
51967410 ATAATTCTCT
51967420 ATCCCACTATCACTTTCTTTTGTGCTCGAAATA
1 ATCCCACTATCACTTTCTTTTGTGCTCGAAATA
51967453 ATCCCACTATCACTTTCTTTTGTGCTCGAAATA
1 ATCCCACTATCACTTTCTTTTGTGCTCGAAATA
51967486 A
1 A
51967487 CTAACCCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (33 bp):
ATCCCACTATCACTTTCTTTTGTGCTCGAAATA
Found at i:51968995 original size:21 final size:21
Alignment explanation
Indices: 51968966--51969005 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
51968956 TGGGACAACT
51968966 GACTCATCATCT-TTCTTTGG
1 GACTCATCATCTGTTCTTTGG
51968986 GACTCCATCATCTGTTCTTT
1 GACT-CATCATCTGTTCTTT
51969006 CATCTCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.15, C:0.28, G:0.12, T:0.45
Consensus pattern (21 bp):
GACTCATCATCTGTTCTTTGG
Found at i:51973492 original size:16 final size:16
Alignment explanation
Indices: 51973473--51973504 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51973463 ACTTGAAAAG
51973473 AAAATATATACATAAA
1 AAAATATATACATAAA
*
51973489 AAAATATTTACATAAA
1 AAAATATATACATAAA
51973505 GTTATATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATATATACATAAA
Found at i:51977294 original size:5 final size:5
Alignment explanation
Indices: 51977267--51977314 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
51977257 TTGTGTGTTC
* * *
51977267 TTTAT TTCAT TTTAT TCTAT TTTCT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
51977315 TCACAAATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:51980835 original size:28 final size:28
Alignment explanation
Indices: 51980785--51980844 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
51980775 AACTTATTTA
51980785 AATTTTTTAATAATATAAAAACTAAATT
1 AATTTTTTAATAATATAAAAACTAAATT
* *
51980813 AATTTATTTAATAATA-AATAACTAATTT
1 AATTT-TTTAATAATATAAAAACTAAATT
51980841 AATT
1 AATT
51980845 CATTCCTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTTTTTAATAATATAAAAACTAAATT
Found at i:51983553 original size:5 final size:5
Alignment explanation
Indices: 51983543--51983572 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
51983533 TATATTGTTC
*
51983543 CTTTT CTTTT CTTTT CTTTT TTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
51983573 TTATCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:51984438 original size:22 final size:23
Alignment explanation
Indices: 51984412--51984454 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
51984402 CTTTTAATGG
*
51984412 TTTAAGGA-AAAAAATTAATTCA
1 TTTAAGAATAAAAAATTAATTCA
*
51984434 TTTAATAATAAAAAATTAATT
1 TTTAAGAATAAAAAATTAATT
51984455 TGACTCAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (23 bp):
TTTAAGAATAAAAAATTAATTCA
Found at i:51987013 original size:25 final size:25
Alignment explanation
Indices: 51986985--51987068 Score: 64
Period size: 31 Copynumber: 3.1 Consensus size: 25
51986975 CAAATCGAAC
51986985 AAAAAAATTTAAATACAAAATTAAAA
1 AAAAAAATTTAAATACAAAATT-AAA
*
51987011 AAAAATGTCAAGTTTAAATACTAAATTTAAA
1 AAAAA----AA-TTTAAATAC-AAAATTAAA
*
51987042 AAAATAAA--TAAATACCAAATTAAA
1 AAAA-AAATTTAAATACAAAATTAAA
51987066 AAA
1 AAA
51987069 TTATCAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
24 10 0.21
25 7 0.15
26 5 0.10
28 2 0.04
30 2 0.04
31 16 0.33
32 6 0.12
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAAAATTTAAATACAAAATTAAA
Found at i:52000105 original size:20 final size:20
Alignment explanation
Indices: 52000080--52000126 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
52000070 AGGGGCACAC
52000080 GCCCGTGTGGCCT-GAGACAT
1 GCCCGTGTGGCCTGGA-ACAT
52000100 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
52000120 GCCCGTG
1 GCCCGTG
52000127 GGCAAATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.13, C:0.32, G:0.36, T:0.19
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:52002164 original size:54 final size:54
Alignment explanation
Indices: 52002092--52002229 Score: 267
Period size: 54 Copynumber: 2.6 Consensus size: 54
52002082 ATTGTCGTTG
52002092 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
*
52002146 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTG
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
52002200 CAGGGGATTTAGCCTGGACTGGTAATCCCG
1 CAGGGGATTTAGCCTGGACTGGTAATCCCG
52002230 CTGCAAGGTT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (54 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
Found at i:52004655 original size:14 final size:13
Alignment explanation
Indices: 52004612--52004677 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
52004602 TATCATATAT
*
52004612 ATTATATTATTTTA
1 ATTATA-TATTTTC
*
52004626 ATATATATTTTATTC
1 AT-TATATATT-TTC
52004641 ATTATATCATTTTC
1 ATTATAT-ATTTTC
*
52004655 ATTATATATTAT-
1 ATTATATATTTTC
52004667 ATTATAT-TTTT
1 ATTATATATTTT
52004678 ATTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
11 3 0.07
12 7 0.16
13 4 0.09
14 20 0.45
15 10 0.23
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATATTTTC
Found at i:52004663 original size:30 final size:29
Alignment explanation
Indices: 52004612--52004669 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
52004602 TATCATATAT
* *
52004612 ATTATATTATTTTAATATATATTTTATTC
1 ATTATATCATTTTAATATATATTATATTC
*
52004641 ATTATATCATTTTCATTATATATTATATT
1 ATTATATCATTTT-AATATATATTATATT
52004670 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTATATCATTTTAATATATATTATATTC
Found at i:52019409 original size:18 final size:18
Alignment explanation
Indices: 52019386--52019420 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52019376 GGTTTGGCGT
52019386 CTCTATATTGACAGAGAG
1 CTCTATATTGACAGAGAG
52019404 CTCTATATTGACAGAGA
1 CTCTATATTGACAGAGA
52019421 ACAGATCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (18 bp):
CTCTATATTGACAGAGAG
Found at i:52019429 original size:62 final size:62
Alignment explanation
Indices: 52019342--52019462 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 62
52019332 TATTTGGCGT
* * *
52019342 CTCTGTATTGTCAGAGAGCAAATCGAAGATAACAGGTTTGGCGTCTCTATATTGACAGAGAG
1 CTCTATATTGACAGAGAACAAATCGAAGATAACAGGTTTGGCGTCTCTATATTGACAGAGAG
* * * *
52019404 CTCTATATTGACAGAGAACAGATCGAAGATAACAGGTTTGGTGTCTCTGTATTGGCAGA
1 CTCTATATTGACAGAGAACAAATCGAAGATAACAGGTTTGGCGTCTCTATATTGACAGA
52019463 AAATAGATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (62 bp):
CTCTATATTGACAGAGAACAAATCGAAGATAACAGGTTTGGCGTCTCTATATTGACAGAGAG
Found at i:52019597 original size:44 final size:44
Alignment explanation
Indices: 52019404--52019616 Score: 241
Period size: 44 Copynumber: 4.8 Consensus size: 44
52019394 TGACAGAGAG
* * * * *
52019404 CTCTATATTGACAGAGAACAGATCGAAGATAACAGGTTTGGTGT
1 CTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGT
* * **
52019448 CTCTGTATTGGCAGAAAATAGATCGAAGAT-GACAGATTTGGCGT
1 CTCTGTATTGACAGAGAGCAGATCGAAGATAG-CAGATTTGGCGT
*
52019492 ATCTGTATTGACAGAGAGCAGATCGAAGAT-GACAGATTTGGCGT
1 CTCTGTATTGACAGAGAGCAGATCGAAGATAG-CAGATTTGGCGT
* * * *
52019536 CTCTGTATTGTCGGAGAGCAGATAGAAGATAGTAGATTTGGCGT
1 CTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGT
* * *
52019580 CTCTGTACTGACAGAGAGTAGATTGAAGATAGCAGAT
1 CTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGAT
52019617 CTGATATTTG
Statistics
Matches: 144, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
44 143 0.99
45 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (44 bp):
CTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGT
Found at i:52021329 original size:16 final size:15
Alignment explanation
Indices: 52021294--52021372 Score: 58
Period size: 17 Copynumber: 5.1 Consensus size: 15
52021284 ATCATATATA
52021294 TATTATATTATTTTA-
1 TATTATA-TATTTTAT
52021309 -A-TATATATTTTAT
1 TATTATATATTTTAT
52021322 TCATTATATCATTTTCAT
1 T-ATTATAT-ATTTT-AT
*
52021340 TATATATTATATTATAT
1 TAT-TA-TATATTTTAT
*
52021357 TATTATTTA-TTTAT
1 TATTATATATTTTAT
52021371 TA
1 TA
52021373 CTATGTACAA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
12 7 0.13
13 4 0.08
14 7 0.13
15 4 0.08
16 7 0.13
17 12 0.23
18 9 0.17
19 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAT
Found at i:52021346 original size:30 final size:29
Alignment explanation
Indices: 52021295--52021352 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
52021285 TCATATATAT
* *
52021295 ATTATATTATTTTAATATATATTTTATTC
1 ATTATATCATTTTAATATATATTATATTC
*
52021324 ATTATATCATTTTCATTATATATTATATT
1 ATTATATCATTTT-AATATATATTATATT
52021353 ATATTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTATATCATTTTAATATATATTATATTC
Found at i:52023131 original size:40 final size:38
Alignment explanation
Indices: 52023087--52023178 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 38
52023077 CAGAATGGCA
*
52023087 ACCAACGCCTCATCGGA-T-AGTTCGAAGCAAATAAGTGACG
1 ACCAACGCCTCATCGGACTAAG-CCGAAGC--A-AAGTGACG
** *
52023127 ACCAACATCTCATC-GACTAAGCCGAAGCAAAGTGGCG
1 ACCAACGCCTCATCGGACTAAGCCGAAGCAAAGTGACG
52023164 ACCAACGCCTCATCG
1 ACCAACGCCTCATCG
52023179 AATCTATCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
37 19 0.44
38 1 0.02
39 2 0.05
40 19 0.44
41 2 0.05
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (38 bp):
ACCAACGCCTCATCGGACTAAGCCGAAGCAAAGTGACG
Found at i:52025203 original size:135 final size:132
Alignment explanation
Indices: 52024926--52025225 Score: 315
Period size: 135 Copynumber: 2.3 Consensus size: 132
52024916 CGGGAGATTG
* **
52024926 CAACCCAGCACGATAGGGCACTATTCCTCGAATTTCCAAACAGCGAACATTTCTTTCGTTTTAAA
1 CAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACAGCGAACATGCCTTTCGTTTTAAA
* ** * * * * *
52024991 GAGTTTTTAAAAAACGTGAATGAAATTCTGAAGGGATCTTCGATCGTTTTAGACAAATGGAAATG
66 GAGTTTTTAAAAAACATGAATGAAAACCTAAAAGAATATTCGATCGTTTTAGACAAACGGAAATG
*
52025056 CG
131 CA
* *
52025058 CAACCCAGCACGATAGGGTACGATT-CTCGAATTGT-CAAACATCGAACATCGCCTTT-GTTTTA
1 CAACCCAGCACGATAGGGCACGATTCCTCGAATT-TCCAAACAGCGAACAT-GCCTTTCGTTTTA
* * *
52025120 AAGGGTTTTCTTAAAAAAAACATGAGTGAAAACCTAAAAGAATATTCGATTGTTTT-GAACAAAC
64 AAGAG-TTT-TT--AAAAAACATGAATGAAAACCTAAAAGAATATTCGATCGTTTTAG-ACAAAC
52025184 GAGAAAT-CA
124 G-GAAATGCA
* *
52025193 CAATCCAGCACGATAGGGCATGATTCCT-GAATT
1 CAACCCAGCACGATAGGGCACGATTCCTCGAATT
52025226 GACAAATACT
Statistics
Matches: 139, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
131 31 0.22
132 31 0.22
133 2 0.01
134 1 0.01
135 67 0.48
136 7 0.05
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (132 bp):
CAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACAGCGAACATGCCTTTCGTTTTAAA
GAGTTTTTAAAAAACATGAATGAAAACCTAAAAGAATATTCGATCGTTTTAGACAAACGGAAATG
CA
Found at i:52026030 original size:238 final size:238
Alignment explanation
Indices: 52025612--52026064 Score: 870
Period size: 238 Copynumber: 1.9 Consensus size: 238
52025602 TTGGATTTTG
*
52025612 TAAAACCACGTTTCAAAACTCAAGTGGAAAACGATGATATGGGATAATTGACATATATGAGGTGC
1 TAAAACCACGTTTCAAAACTCAAGTGGAAAACGATGACATGGGATAATTGACATATATGAGGTGC
*
52025677 AATCAACTAACGAACTAATAATTAAATATAGATAACCTAAAAATGTAATCCGATTACAATAATGC
66 AATCAACTAACAAACTAATAATTAAATATAGATAACCTAAAAATGTAATCCGATTACAATAATGC
52025742 ATGGAGAATAATTAACATGACAACATAGGACAATGAACAAATAATATGCTACAACAACATGCATG
131 ATGGAGAATAATTAACATGACAACATAGGACAATGAACAAATAATATGCTACAACAACATGCATG
52025807 ACATAACATAAAATGACTACAACATGGAATAATTAACATAACA
196 ACATAACATAAAATGACTACAACATGGAATAATTAACATAACA
52025850 TAAAACCACGTTTCAAAACTCAAGTGGAAAACGATGACATGGGATAATTGACATATATGAGGTGC
1 TAAAACCACGTTTCAAAACTCAAGTGGAAAACGATGACATGGGATAATTGACATATATGAGGTGC
* *
52025915 GATCAACTAACAAACTAATAATTAAATATAGCTAACCTAAAAATGTAATCCGATTACAATAATGC
66 AATCAACTAACAAACTAATAATTAAATATAGATAACCTAAAAATGTAATCCGATTACAATAATGC
52025980 ATGGAGAATAATTAACATGACAACATAGGACAATGAACAAATAATATGCTACAACAACATGCATG
131 ATGGAGAATAATTAACATGACAACATAGGACAATGAACAAATAATATGCTACAACAACATGCATG
52026045 ACATAACATAAAATGACTAC
196 ACATAACATAAAATGACTAC
52026065 TACTAGATGC
Statistics
Matches: 211, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 211 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (238 bp):
TAAAACCACGTTTCAAAACTCAAGTGGAAAACGATGACATGGGATAATTGACATATATGAGGTGC
AATCAACTAACAAACTAATAATTAAATATAGATAACCTAAAAATGTAATCCGATTACAATAATGC
ATGGAGAATAATTAACATGACAACATAGGACAATGAACAAATAATATGCTACAACAACATGCATG
ACATAACATAAAATGACTACAACATGGAATAATTAACATAACA
Found at i:52028386 original size:3 final size:3
Alignment explanation
Indices: 52028378--52028403 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52028368 GGTCATTACA
52028378 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52028404 GTAAATATCT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52046631 original size:31 final size:30
Alignment explanation
Indices: 52046595--52046658 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
52046585 ATTTGAATAA
*
52046595 AAATATTATATCTGAACAATTAACTTAGGAT
1 AAATATTATATCTGAAAAATTAACTTAGG-T
* *
52046626 AAATATTATATTTGAAAAATTAGCTTAGGT
1 AAATATTATATCTGAAAAATTAACTTAGGT
52046656 AAA
1 AAA
52046659 AAATGTCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (30 bp):
AAATATTATATCTGAAAAATTAACTTAGGT
Found at i:52053318 original size:50 final size:50
Alignment explanation
Indices: 52053259--52053420 Score: 154
Period size: 50 Copynumber: 3.2 Consensus size: 50
52053249 TTTATATTGA
*
52053259 TTAGGATAAGGTGTTTCAATCTTACTAAAATATGGCTTTACAAGTTTATT
1 TTAGAATAAGGTGTTTCAATCTTACTAAAATATGGCTTTACAAGTTTATT
* * * * * ** *
52053309 TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCAT--CTATTTTATA-TTGA--
1 TTAGAATAAGG-TGTTTCAATCTTACTAAAAT--ATGGCT-TTACA-AGTTTATT
*
52053359 TTAGGATAAGGTGTTTCAATCTTACTAAAATATGGCTTTACAAGTTTATT
1 TTAGAATAAGGTGTTTCAATCTTACTAAAATATGGCTTTACAAGTTTATT
52053409 TTAGAATAAGGT
1 TTAGAATAAGGT
52053421 TTTTTAAACC
Statistics
Matches: 83, Mismatches: 19, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
47 3 0.04
48 6 0.07
49 17 0.20
50 31 0.37
51 17 0.20
52 6 0.07
53 3 0.04
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (50 bp):
TTAGAATAAGGTGTTTCAATCTTACTAAAATATGGCTTTACAAGTTTATT
Found at i:52053376 original size:100 final size:100
Alignment explanation
Indices: 52053203--52053502 Score: 591
Period size: 100 Copynumber: 3.0 Consensus size: 100
52053193 CTTCTTTTAT
52053203 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
1 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
52053268 GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
66 GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
52053303 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
1 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
52053368 GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
66 GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
52053403 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
1 TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
*
52053468 GGTGTTTCAATCTTACTAGAATATGGCTTTACAAG
66 GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
52053503 CCTATAAATA
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 199 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (100 bp):
TTTATTTTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGATTAGGATAA
GGTGTTTCAATCTTACTAAAATATGGCTTTACAAG
Found at i:52054171 original size:22 final size:20
Alignment explanation
Indices: 52054132--52054171 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
52054122 ATCTTATATC
*
52054132 ATAAAAAATTAAAATTAATT
1 ATAAAAAAATAAAATTAATT
52054152 ATAAAACAAATAAAAGTTAA
1 ATAAAA-AAATAAAA-TTAA
52054172 AAAATTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAAAAAAATAAAATTAATT
Found at i:52055643 original size:33 final size:33
Alignment explanation
Indices: 52055601--52055667 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
52055591 ATTTTTATCT
52055601 TAAGTATGAAATTGATCTATTCCATTAATGTAC
1 TAAGTATGAAATTGATCTATTCCATTAATGTAC
52055634 TAAGTATGAAATTGATCTATTCCATTAATGTAC
1 TAAGTATGAAATTGATCTATTCCATTAATGTAC
52055667 T
1 T
52055668 TAGAGTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TAAGTATGAAATTGATCTATTCCATTAATGTAC
Found at i:52056827 original size:29 final size:30
Alignment explanation
Indices: 52056760--52056836 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 30
52056750 GTAACAAAAT
* **
52056760 AATAACATAAGTGACTAAAATGTAATATTTC
1 AATAA-ATAAGTGACTAAAATGTAATACTGA
* *
52056791 AA-ACATAAGTGACTAAAATGTAA-CCTGA
1 AATAAATAAGTGACTAAAATGTAATACTGA
52056819 AATAAATAAAAGTGACTA
1 AATAAAT--AAGTGACTA
52056837 TTTTTGTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.08
29 22 0.59
30 1 0.03
31 11 0.30
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (30 bp):
AATAAATAAGTGACTAAAATGTAATACTGA
Found at i:52060072 original size:20 final size:20
Alignment explanation
Indices: 52060044--52060082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52060034 CAGGTTAATA
52060044 TTCCATATGATCATATATTC
1 TTCCATATGATCATATATTC
* * *
52060064 TTCCGTATGTTCATGTATT
1 TTCCATATGATCATATATT
52060083 GGACGCACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TTCCATATGATCATATATTC
Found at i:52062310 original size:43 final size:43
Alignment explanation
Indices: 52062249--52062334 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
52062239 AAAAATTACA
52062249 ACTGAAACGTTAGTTAAACGCAAGGCTGTTTGGAAAGCTTTCT
1 ACTGAAACGTTAGTTAAACGCAAGGCTGTTTGGAAAGCTTTCT
52062292 ACTGAAACGTTAGTTAAACGCAAGGCTGTTTGGAAAGCTTTCT
1 ACTGAAACGTTAGTTAAACGCAAGGCTGTTTGGAAAGCTTTCT
52062335 TCAGTGCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (43 bp):
ACTGAAACGTTAGTTAAACGCAAGGCTGTTTGGAAAGCTTTCT
Found at i:52062605 original size:25 final size:25
Alignment explanation
Indices: 52062577--52062625 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
52062567 AGGTAAGGCC
52062577 CCTTCTCCTTCTTCCGTTCTTCATT
1 CCTTCTCCTTCTTCCGTTCTTCATT
* *
52062602 CCTTTTTCTTCTTCCGTTCTTCAT
1 CCTTCTCCTTCTTCCGTTCTTCAT
52062626 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.37, G:0.04, T:0.55
Consensus pattern (25 bp):
CCTTCTCCTTCTTCCGTTCTTCATT
Found at i:52062858 original size:8 final size:8
Alignment explanation
Indices: 52062845--52062872 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
52062835 GTCATTAACT
52062845 TGGAATTG
1 TGGAATTG
52062853 TGGAATTG
1 TGGAATTG
52062861 TGGAATTG
1 TGGAATTG
52062869 TGGA
1 TGGA
52062873 TTATGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (8 bp):
TGGAATTG
Found at i:52065565 original size:30 final size:30
Alignment explanation
Indices: 52065529--52065585 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
52065519 TTATATTCAA
* *
52065529 TATTTTTGTAAGCGCAATACACATAAAAGG
1 TATTTTTGTAAGAGCAATACAAATAAAAGG
52065559 TATTTTTGTAAGAGCAATACAAATAAA
1 TATTTTTGTAAGAGCAATACAAATAAA
52065586 TATAATTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (30 bp):
TATTTTTGTAAGAGCAATACAAATAAAAGG
Found at i:52065637 original size:19 final size:18
Alignment explanation
Indices: 52065595--52065640 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
52065585 ATATAATTGT
*
52065595 AATAATTTTTAATTCTTT
1 AATAATTTTTAATTCTTA
* *
52065613 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTCTTA
52065632 AATAATTTT
1 AATAATTTT
52065641 AAAAACATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTCTTA
Found at i:52065800 original size:21 final size:21
Alignment explanation
Indices: 52065752--52065803 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
52065742 CACCGCTATT
*
52065752 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
52065773 TCCAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
52065794 -CTTAATCTCA
1 TC-TAATCTCA
52065804 TCGCCACCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.31
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:52081290 original size:15 final size:14
Alignment explanation
Indices: 52081267--52081323 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
52081257 TAAATATATT
52081267 TATAA-AAAAGTTAA
1 TATAATAAAAGTT-A
52081281 TATAATAAAAGTTGA
1 TATAATAAAAGTT-A
*
52081296 GATAATAAATA-TTA
1 TATAATAAA-AGTTA
52081310 TGATAATAAAAGTT
1 T-ATAATAAAAGTT
52081324 CAAATCTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.19
15 28 0.78
16 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (14 bp):
TATAATAAAAGTTA
Found at i:52086404 original size:54 final size:54
Alignment explanation
Indices: 52086342--52086456 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
52086332 AGAAAAAATC
*
52086342 TCATATTCCACATGTCAAAAAGAACCATCAGTCTAAATTTTTTCTCAATCAAGT
1 TCATATTCCACATGTCAAAAAGAACCATCAGCCTAAATTTTTTCTCAATCAAGT
52086396 TCATATTCCACATGTCAAAAAGAACCATCAGCCTAAATTTTTTCTCAATCAAGT
1 TCATATTCCACATGTCAAAAAGAACCATCAGCCTAAATTTTTTCTCAATCAAGT
*
52086450 ACATATT
1 TCATATT
52086457 GTTTATAGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (54 bp):
TCATATTCCACATGTCAAAAAGAACCATCAGCCTAAATTTTTTCTCAATCAAGT
Found at i:52089874 original size:10 final size:10
Alignment explanation
Indices: 52089861--52089891 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
52089851 TTATAGTTTC
*
52089861 ATATATATAT
1 ATATGTATAT
52089871 ATATGTATAT
1 ATATGTATAT
52089881 ATATGTATAT
1 ATATGTATAT
52089891 A
1 A
52089892 CGGATAGAAT
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:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
ATATGTATAT
Found at i:52090831 original size:14 final size:16
Alignment explanation
Indices: 52090812--52090848 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
52090802 CTTTTTATGT
*
52090812 ATTTTTTAT-TTTA-A
1 ATTTTTTATAATTATA
52090826 ATTTTTTATAATTATA
1 ATTTTTTATAATTATA
52090842 ATTTTTT
1 ATTTTTT
52090849 GAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTTATAATTATA
Found at i:52091158 original size:13 final size:13
Alignment explanation
Indices: 52091140--52091167 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52091130 CCACTAGCTC
52091140 TAGTTTACCCAAT
1 TAGTTTACCCAAT
52091153 TAGTTTACCCAAT
1 TAGTTTACCCAAT
52091166 TA
1 TA
52091168 ATATCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (13 bp):
TAGTTTACCCAAT
Found at i:52093199 original size:28 final size:28
Alignment explanation
Indices: 52093159--52093215 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
52093149 TTCAAAGGTT
52093159 AGTTTAGCAGAATTGATGAATGCTTTAC
1 AGTTTAGCAGAATTGATGAATGCTTTAC
52093187 AGTTTAGCAGAATTGATGAATGCTTTAC
1 AGTTTAGCAGAATTGATGAATGCTTTAC
52093215 A
1 A
52093216 TGCACAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (28 bp):
AGTTTAGCAGAATTGATGAATGCTTTAC
Found at i:52099241 original size:3 final size:3
Alignment explanation
Indices: 52099233--52099257 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52099223 TTTCAAACAA
52099233 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
52099258 TACTTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52099361 original size:9 final size:9
Alignment explanation
Indices: 52099322--52099438 Score: 74
Period size: 9 Copynumber: 12.4 Consensus size: 9
52099312 AAAAATTAAA
52099322 TTTTAAATT
1 TTTTAAATT
52099331 TTTCTATATATT
1 TTT-TA-A-ATT
52099343 TTTTAGAATT
1 TTTTA-AATT
52099353 TTTTAAATT
1 TTTTAAATT
**
52099362 TTTTAAAAA
1 TTTTAAATT
**
52099371 AATTAAA-T
1 TTTTAAATT
*
52099379 TTTGAAATT
1 TTTTAAATT
52099388 TTTATAAATAT
1 TTT-TAAAT-T
*
52099399 TTTTGAATT
1 TTTTAAATT
**
52099408 TTAAAAATT
1 TTTTAAATT
* *
52099417 GTTTAAAAT
1 TTTTAAATT
*
52099426 TTTTGAATT
1 TTTTAAATT
52099435 TTTT
1 TTTT
52099439 TTATTTTTTT
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
8 4 0.05
9 45 0.56
10 18 0.22
11 8 0.10
12 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (9 bp):
TTTTAAATT
Found at i:52099435 original size:27 final size:29
Alignment explanation
Indices: 52099383--52099436 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
52099373 TTAAATTTTG
*
52099383 AAATTTTTATAAATATTTTTGAATTTTAA
1 AAATTGTTATAAATATTTTTGAATTTTAA
52099412 AAATTGTT-TAAA-ATTTTTGAATTTT
1 AAATTGTTATAAATATTTTTGAATTTT
52099437 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 4 0.17
29 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (29 bp):
AAATTGTTATAAATATTTTTGAATTTTAA
Found at i:52099436 original size:55 final size:56
Alignment explanation
Indices: 52099307--52099424 Score: 168
Period size: 56 Copynumber: 2.1 Consensus size: 56
52099297 AAAATTATTA
* * ** *
52099307 TTTAAAAAAATTAAATTTTAAATTTTTCTATATATTTTTTAGAATTTTTTAAATTT
1 TTTAAAAAAATTAAATTTTAAATTTTTATAAATATTTTTTAGAATTTTAAAAATTG
52099363 TTTAAAAAAATTAAATTTTGAAATTTTTATAAATA-TTTTT-GAATTTTAAAAATTG
1 TTTAAAAAAATTAAATTTT-AAATTTTTATAAATATTTTTTAGAATTTTAAAAATTG
52099418 TTTAAAA
1 TTTAAAA
52099425 TTTTTGAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
55 19 0.34
56 24 0.43
57 13 0.23
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (56 bp):
TTTAAAAAAATTAAATTTTAAATTTTTATAAATATTTTTTAGAATTTTAAAAATTG
Found at i:52099608 original size:24 final size:24
Alignment explanation
Indices: 52099581--52099732 Score: 304
Period size: 24 Copynumber: 6.3 Consensus size: 24
52099571 CGAACTCGAA
52099581 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099605 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099629 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099653 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099677 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099701 ACTCGAATCCAGTTATTCGAGTTG
1 ACTCGAATCCAGTTATTCGAGTTG
52099725 ACTCGAAT
1 ACTCGAAT
52099733 AATTCAAATA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 128 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (24 bp):
ACTCGAATCCAGTTATTCGAGTTG
Found at i:52099894 original size:29 final size:30
Alignment explanation
Indices: 52099861--52099920 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
52099851 GTATATTTAG
52099861 AATTTAATTGTTCTA-TTTT-GATTTTCAAA
1 AATTTAATTGTTCTACTTTTAGA-TTTCAAA
* *
52099890 AATTTAGTTTTTCTACTTTTAGATTTCAAA
1 AATTTAATTGTTCTACTTTTAGATTTCAAA
52099920 A
1 A
52099921 TTTTGATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 12 0.44
31 2 0.07
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (30 bp):
AATTTAATTGTTCTACTTTTAGATTTCAAA
Found at i:52121748 original size:3 final size:3
Alignment explanation
Indices: 52121740--52121785 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
52121730 AATGCTTTTG
* *
52121740 CTT CTT CTT CTT CTG CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
52121786 ATGATAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:52122178 original size:3 final size:3
Alignment explanation
Indices: 52122170--52122199 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52122160 AAAGCCTCAA
52122170 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
52122200 GAGGAGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52123814 original size:41 final size:41
Alignment explanation
Indices: 52123747--52123992 Score: 318
Period size: 41 Copynumber: 6.0 Consensus size: 41
52123737 TTGTAAAACA
** *
52123747 CAGAGCAATAGCGGCG-TTTTACTAAAAACGCCGCTAAAAAT
1 CAGAGCAATAGCGGCGCTTTTGGT-AAAACGCCGCTAAAAGT
52123788 -AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
* * *
52123828 CGGAGCAATAGCGGCGTTTTTTGTAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
* * *
52123869 CGGAGCACTAGCGGCGCTTTTTGTAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
* * * *
52123910 CGGAGCATTAGTGGCGCTTTTGGTAAAACGCCAC-AAAAGT
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
* * *
52123950 CAGAGCATTAGCGGTGCTTTTGATAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
52123991 CA
1 CA
52123993 TATAACCCCT
Statistics
Matches: 185, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 66 0.36
41 119 0.64
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (41 bp):
CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT
Found at i:52123979 original size:81 final size:81
Alignment explanation
Indices: 52123749--52123991 Score: 321
Period size: 81 Copynumber: 3.0 Consensus size: 81
52123739 GTAAAACACA
** *
52123749 GAGCAATAGCGGCG-TTTTACTAAAAACGCCGCTAAAAAT-AGAGCAATAGCGGCGCTTTTGGTA
1 GAGCAATAGCGGCGCTTTTGGT-AAAACGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTTT-GTA
52123812 AAACGCCGCTAAAAGTCG
64 AAACGCCGCTAAAAGTCG
* * * *
52123830 GAGCAATAGCGGCGTTTTTTGTAAAACGCCGCTAAAAGTCGGAGCACTAGCGGCGCTTTTTGTAA
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAATAGCGGCGC-TTTTGTAA
52123895 AACGCCGCTAAAAGTCG
65 AACGCCGCTAAAAGTCG
* * * * *
52123912 GAGCATTAGTGGCGCTTTTGGTAAAACGCCAC-AAAAGTCAGAGCATTAGCGGTGCTTTTGATAA
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTTTG-TAA
52123976 AACGCCGCTAAAAGTC
65 AACGCCGCTAAAAGTC
52123992 ATATAACCCC
Statistics
Matches: 145, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
80 5 0.03
81 69 0.48
82 67 0.46
83 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (81 bp):
GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTTTGTAAA
ACGCCGCTAAAAGTCG
Found at i:52124060 original size:8 final size:7
Alignment explanation
Indices: 52124039--52124100 Score: 52
Period size: 7 Copynumber: 8.1 Consensus size: 7
52124029 AATCTATAAC
52124039 CCCTAAAA
1 CCCT-AAA
*
52124047 CACTAAA
1 CCCTAAA
52124054 CCTCTAAA
1 CC-CTAAA
*
52124062 CCTTAAAA
1 CCCT-AAA
52124070 CCCTAAA
1 CCCTAAA
*
52124077 CCTTTAAAA
1 CC-CT-AAA
52124086 CCCTAAA
1 CCCTAAA
52124093 CCCTAAA
1 CCCTAAA
52124100 C
1 C
52124101 TATAACTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 21 0.48
8 18 0.41
9 5 0.11
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:52124060 original size:16 final size:15
Alignment explanation
Indices: 52124051--52124099 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
52124041 CTAAAACACT
52124051 AAACCTCTAAACCTTA
1 AAACC-CTAAACCTTA
52124067 AAACCCTAAACCTTTA
1 AAACCCTAAACC-TTA
*
52124083 AAACCCTAAACCCTA
1 AAACCCTAAACCTTA
52124098 AA
1 AA
52124100 CTATAACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTAAACCTTA
Found at i:52124075 original size:23 final size:23
Alignment explanation
Indices: 52124042--52124129 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
52124032 CTATAACCCC
*
52124042 TAAAACACTAAACCTCTAAACCT
1 TAAAACCCTAAACCTCTAAACCT
* *
52124065 TAAAACCCTAAACCTTTAAAACCC
1 TAAAACCCTAAACCTCT-AAACCT
* *
52124089 T-AAACCCTAAA-CTAT-AACTTT
1 TAAAACCCTAAACCTCTAAAC-CT
*
52124110 TAAAACCCTAAACCCCTAAA
1 TAAAACCCTAAACCTCTAAA
52124130 AACATCACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 3 0.06
21 1 0.02
22 13 0.25
23 27 0.52
24 8 0.15
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAAACCCTAAACCTCTAAACCT
Found at i:52124291 original size:15 final size:15
Alignment explanation
Indices: 52124252--52124302 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
52124242 CGGTTTAATA
*
52124252 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* * *
52124266 TCTATGATTTAGGGT
1 TTTATGGTTTAAGGT
52124281 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
52124296 TTAATGG
1 TTTATGG
52124303 CCATGGGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:52131029 original size:14 final size:15
Alignment explanation
Indices: 52131001--52131034 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
52130991 GATTTTGATC
*
52131001 ATTAATTTAATATTA
1 ATTAATTTAAGATTA
52131016 ATTAA-TTAAGATTA
1 ATTAATTTAAGATTA
52131030 ATTAA
1 ATTAA
52131035 ATTGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTAATTTAAGATTA
Found at i:52144907 original size:43 final size:43
Alignment explanation
Indices: 52144843--52145072 Score: 334
Period size: 43 Copynumber: 5.3 Consensus size: 43
52144833 TTTGATGTAA
* *
52144843 TGGCACTAAGTGTGCGATATAATTATAGCTTAGGCTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
* * * *
52144886 TAGCACTAAGTGTGCGTTATAATTATAGCTTTGGCTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
*
52144929 TGGCACTAAGTGTGCAATACAATTATAGCTTCGGCTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
* *
52144972 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGTTAATTGAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
* * * *
52145015 TGGCACTAAGTGTGCGAAACCATTATAACTTCGGTTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
*
52145058 TAGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
52145073 AAGTTTGTTG
Statistics
Matches: 171, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 171 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (43 bp):
TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
Found at i:52145304 original size:45 final size:45
Alignment explanation
Indices: 52145240--52145353 Score: 148
Period size: 45 Copynumber: 2.6 Consensus size: 45
52145230 GAGGAAATAT
*
52145240 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATG-TCGGTGAGAT-A
1 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAATGCT-GGTGAAATGA
52145284 CTATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCTGGTGAAATGA
1 -TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCTGGTGAAATGA
*
52145330 TA-TCGGGC-CTCGAGCCTAGCAGGC
1 TATTCGGGCTTTCGAGCCTAGCAGGC
52145354 GAAATACCGG
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
43 15 0.23
44 10 0.16
45 37 0.58
46 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (45 bp):
TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCTGGTGAAATGA
Found at i:52146600 original size:15 final size:16
Alignment explanation
Indices: 52146582--52146630 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
52146572 TAGGGTTTTT
52146582 AAATAAATAA-TACAA
1 AAATAAATAATTACAA
*
52146597 AAAT-AATAATTACTA
1 AAATAAATAATTACAA
52146612 AAATAAGATACATTACAA
1 AAATAA-ATA-ATTACAA
52146630 A
1 A
52146631 TTATTTACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 12 0.43
16 1 0.04
17 3 0.11
18 7 0.25
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATAAATAATTACAA
Found at i:52148886 original size:5 final size:5
Alignment explanation
Indices: 52148876--52148908 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
52148866 ATAACCCACA
52148876 CATAT CATAT CATAT CATAT CATAT -ATAT -ATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
52148909 AACCGTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (5 bp):
CATAT
Found at i:52155518 original size:14 final size:14
Alignment explanation
Indices: 52155490--52155523 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52155480 AAAAAATAAC
52155490 ATATATTTATTAAA
1 ATATATTTATTAAA
52155504 ATAT-TTTATTAAAA
1 ATATATTTATT-AAA
52155518 ATATAT
1 ATATAT
52155524 GAAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 11 0.61
15 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTTATTAAA
Found at i:52156203 original size:17 final size:17
Alignment explanation
Indices: 52156183--52156229 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
52156173 TCGAACTTAA
*
52156183 TTAATATTTTAAATAAT
1 TTAATATTTTAAATAAC
*
52156200 TTAATTTTTTATAA-AAC
1 TTAATATTTTA-AATAAC
52156217 TT-ATATTTTAAAT
1 TTAATATTTTAAAT
52156230 GTACAACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 7 0.28
17 14 0.56
18 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATATTTTAAATAAC
Found at i:52158950 original size:14 final size:14
Alignment explanation
Indices: 52158931--52158959 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52158921 TGATGGCTCA
52158931 ATCATAATGTAAAT
1 ATCATAATGTAAAT
52158945 ATCATAATGTAAAT
1 ATCATAATGTAAAT
52158959 A
1 A
52158960 GTAGTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATCATAATGTAAAT
Found at i:52159591 original size:31 final size:32
Alignment explanation
Indices: 52159539--52159605 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
52159529 TTTGAGGTGC
* *
52159539 ATTTTTATTTTTATCATGTTTTAATTGTTTTT
1 ATTTTTATTGTTATCACGTTTTAATTGTTTTT
52159571 ATTTTTA-TGTTATCACGTTTTAATTGTTTTT
1 ATTTTTATTGTTATCACGTTTTAATTGTTTTT
52159602 ATTT
1 ATTT
52159606 ATTCTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.69
Consensus pattern (32 bp):
ATTTTTATTGTTATCACGTTTTAATTGTTTTT
Found at i:52182673 original size:2 final size:2
Alignment explanation
Indices: 52182662--52182702 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
52182652 CCATACAACT
52182662 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52182703 ACTCAAGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52201351 original size:12 final size:12
Alignment explanation
Indices: 52201330--52201359 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52201320 ATTTAATTAA
52201330 ATAAAAATAAAC
1 ATAAAAATAAAC
*
52201342 ATAAACATAAAC
1 ATAAAAATAAAC
52201354 ATAAAA
1 ATAAAA
52201360 GACTTTACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAAATAAAC
Found at i:52202943 original size:25 final size:25
Alignment explanation
Indices: 52202915--52202966 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
52202905 CTATTAATAT
52202915 TTATATTAATATCAAA-TAAATAAAA
1 TTATATTAATATCAAATTAAA-AAAA
* *
52202940 TTATATTCATATTAAATTAAAAAAA
1 TTATATTAATATCAAATTAAAAAAA
52202965 TT
1 TT
52202967 CCCTCCATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TTATATTAATATCAAATTAAAAAAA
Found at i:52204040 original size:8 final size:8
Alignment explanation
Indices: 52204027--52204066 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
52204017 AGTTGTTCCC
52204027 TTTTTCTT
1 TTTTTCTT
52204035 TTTTTCTT
1 TTTTTCTT
52204043 TTTTTC-T
1 TTTTTCTT
52204050 TTTTTCTT
1 TTTTTCTT
*
52204058 TCTTTCTT
1 TTTTTCTT
52204066 T
1 T
52204067 CTTCATTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:52204052 original size:15 final size:15
Alignment explanation
Indices: 52204027--52204066 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
52204017 AGTTGTTCCC
52204027 TTTTTCTTTTTTTCTT
1 TTTTTC-TTTTTTCTT
52204043 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
*
52204058 TCTTTCTTT
1 TTTTTCTTT
52204067 CTTCATTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:52204061 original size:4 final size:4
Alignment explanation
Indices: 52204029--52204069 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
52204019 TTGTTCCCTT
* *
52204029 TTTC TTTT TTTC TTTT TTTC TTT- TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
52204070 CATTCCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:52204215 original size:13 final size:13
Alignment explanation
Indices: 52204197--52204229 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52204187 TATTATATTG
*
52204197 TTTGTTTGAATTA
1 TTTGTTTCAATTA
52204210 TTTG-TTCAATTA
1 TTTGTTTCAATTA
52204222 TTTGTTTC
1 TTTGTTTC
52204230 TATTTTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTGTTTCAATTA
Found at i:52206830 original size:43 final size:43
Alignment explanation
Indices: 52206782--52206894 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
52206772 TGACAATTTT
* * *
52206782 AATATTTCGTAAGATGGTAAGCAAATAGCATACGAATAAAACA
1 AATATTTCGTAACATGGTAAACAAATAGCATACAAATAAAACA
** * **
52206825 AATATTTTTTAACATGGTAAATAAATATTATACAAATAAAACA
1 AATATTTCGTAACATGGTAAACAAATAGCATACAAATAAAACA
* *
52206868 AATA-TTCTTTAACACGGTAAACAAATA
1 AATATTTC-GTAACATGGTAAACAAATA
52206895 TTATATCAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 2 0.03
43 56 0.97
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (43 bp):
AATATTTCGTAACATGGTAAACAAATAGCATACAAATAAAACA
Found at i:52206895 original size:43 final size:43
Alignment explanation
Indices: 52206797--52206918 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
52206787 TTCGTAAGAT
* ** * * *
52206797 GGTAAGCAAATAGCATACGAATAAAACAAATATTTTTTAACAT
1 GGTAAACAAATATTATACAAATAAAACAAATATTCTTTAACAC
*
52206840 GGTAAATAAATATTATACAAATAAAACAAATATTCTTTAACAC
1 GGTAAACAAATATTATACAAATAAAACAAATATTCTTTAACAC
* *
52206883 GGTAAACAAATATTATATCAATATTATACAAATATT
1 GGTAAACAAATATTATA-CAA-ATAAAACAAATATT
52206919 GAAGCAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 52 0.78
44 3 0.04
45 12 0.18
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (43 bp):
GGTAAACAAATATTATACAAATAAAACAAATATTCTTTAACAC
Found at i:52206926 original size:22 final size:22
Alignment explanation
Indices: 52206888--52206929 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52206878 AACACGGTAA
*
52206888 ACAAATATTATATCAATATTAT
1 ACAAATATTATAGCAATATTAT
52206910 ACAAATATTGA-AGCAATATT
1 ACAAATATT-ATAGCAATATT
52206930 TTATCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (22 bp):
ACAAATATTATAGCAATATTAT
Found at i:52208559 original size:23 final size:23
Alignment explanation
Indices: 52208454--52208563 Score: 104
Period size: 23 Copynumber: 5.0 Consensus size: 23
52208444 CCTGATCAAT
* *
52208454 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAGGTGCCTGAA
* *
52208476 A-AAGACACACGAGGTGCCTG--
1 ATACGACACACAAGGTGCCTGAA
*
52208496 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAGGTGCCTGAA
*
52208519 ATACGACACA-AGTGGTGCCTGAA
1 ATACGACACACA-AGGTGCCTGAA
* *
52208542 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAGGTGCCTGA
52208564 TCAATAAAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.01
21 32 0.44
22 1 0.01
23 38 0.52
24 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAGGTGCCTGAA
Found at i:52208961 original size:15 final size:15
Alignment explanation
Indices: 52208935--52208991 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
52208925 CATATATATT
52208935 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
52208949 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
52208964 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
52208979 ATATAAATTCAAT
1 ATATAATTTCAAT
52208992 AAATTCATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.15
15 33 0.85
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:52210183 original size:42 final size:42
Alignment explanation
Indices: 52210120--52210246 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
52210110 CTTCGTTTTC
** * **
52210120 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATAATCACAT-A
*
52210163 T-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATAATCACATA
*
52210204 TCGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATAATCACATA
52210245 TC
1 TC
52210247 TCACTGATGC
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 13 0.17
42 62 0.82
43 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATAATCACATA
Found at i:52210308 original size:47 final size:46
Alignment explanation
Indices: 52210164--52210328 Score: 169
Period size: 47 Copynumber: 3.7 Consensus size: 46
52210154 TTCACATAAT
* * * *
52210164 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAT-----C
1 GATGCCATATCCCAGATATGGTCTTATACG-AAGCACATATCACACC
* * * * * *
52210206 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACT
1 GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACC
* *
52210252 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
1 GATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACACC
52210299 GATGCCATATCCCAGATATGGTCTTATACG
1 GATGCCATATCCCAGATATGGTCTTATACG
52210329 GAAATCACTT
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
41 10 0.09
42 30 0.28
46 27 0.25
47 41 0.38
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACC
Found at i:52210448 original size:31 final size:31
Alignment explanation
Indices: 52210353--52210450 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
52210343 CTTGTCACTT
*
52210353 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
52210384 ATAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
52210415 GTAGCCGGAGCTACCACTTTTCGCTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
52210446 GTAGC
1 GTAGC
52210451 TGTCAGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:52219931 original size:10 final size:11
Alignment explanation
Indices: 52219906--52219930 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52219896 TGTTTGATAA
52219906 TTTTAATTATT
1 TTTTAATTATT
52219917 TTTTAATTATT
1 TTTTAATTATT
52219928 TTT
1 TTT
52219931 ATCCTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAATTATT
Found at i:52220391 original size:3 final size:3
Alignment explanation
Indices: 52220383--52220407 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52220373 TCCCACCATA
52220383 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
52220408 TGTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52229574 original size:31 final size:31
Alignment explanation
Indices: 52229512--52229575 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
52229502 AAAAACCAAC
* * * **
52229512 AAATTGACTCTTTTTTAAAGGTAGATGGTCA
1 AAATCGACTCTTTTTAAAAGATAGAAAGTCA
52229543 AAATCGACTCTTTTTAAAAGATAGAAAGTCA
1 AAATCGACTCTTTTTAAAAGATAGAAAGTCA
52229574 AA
1 AA
52229576 TTTAGCTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (31 bp):
AAATCGACTCTTTTTAAAAGATAGAAAGTCA
Found at i:52234180 original size:23 final size:22
Alignment explanation
Indices: 52234142--52234192 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
52234132 ATTCAAGTAA
*
52234142 TTAATTTATTAAATTGAGTTAT
1 TTAATTAATTAAATTGAGTTAT
52234164 TTAATTAATTTAAATTGAGTTAT
1 TTAATTAA-TTAAATTGAGTTAT
*
52234187 TCAATT
1 TTAATT
52234193 CAGTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (22 bp):
TTAATTAATTAAATTGAGTTAT
Found at i:52239311 original size:16 final size:17
Alignment explanation
Indices: 52239292--52239324 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52239282 AAGTCTTACA
52239292 AAAAAAAAAAGA-AAAG
1 AAAAAAAAAAGAGAAAG
*
52239308 AAAAGAAAAAGAGAAAG
1 AAAAAAAAAAGAGAAAG
52239325 TGTTTGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAGAAAG
Found at i:52244534 original size:30 final size:30
Alignment explanation
Indices: 52244500--52244561 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
52244490 TTCGAGCTTC
*
52244500 TTCCAACCGCCCTGCTTTTCTCGGTAAGTT
1 TTCCAACAGCCCTGCTTTTCTCGGTAAGTT
* *
52244530 TTCCAACAGCTCTGCTTTTCTCGTTAAGTT
1 TTCCAACAGCCCTGCTTTTCTCGGTAAGTT
52244560 TT
1 TT
52244562 TCCCTTCGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.42
Consensus pattern (30 bp):
TTCCAACAGCCCTGCTTTTCTCGGTAAGTT
Found at i:52246912 original size:33 final size:34
Alignment explanation
Indices: 52246862--52246925 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
52246852 TGTACTTTAT
*
52246862 TTTATTTTTTTATATATTCTTTA-AAATTTTGAG
1 TTTATTTTTTGATATATTCTTTATAAATTTTGAG
*
52246895 TTTATTTATTTGA-ATATTTTTTATAAATTTT
1 TTTATTT-TTTGATATATTCTTTATAAATTTT
52246926 AAATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (34 bp):
TTTATTTTTTGATATATTCTTTATAAATTTTGAG
Found at i:52247605 original size:25 final size:25
Alignment explanation
Indices: 52247573--52247623 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52247563 TCTTTAATTA
52247573 TTTATGCTTTATTTGTTTTACTCAT
1 TTTATGCTTTATTTGTTTTACTCAT
52247598 TTTATGCTTTATTTGTTTTACTCAT
1 TTTATGCTTTATTTGTTTTACTCAT
52247623 T
1 T
52247624 CTAAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTATGCTTTATTTGTTTTACTCAT
Found at i:52249550 original size:17 final size:18
Alignment explanation
Indices: 52249515--52249553 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52249505 AAACATAAAC
52249515 TTAAAATTTTATAAATAT
1 TTAAAATTTTATAAATAT
*
52249533 TTAAAATTTTA-CAATAT
1 TTAAAATTTTATAAATAT
52249550 TTAA
1 TTAA
52249554 TATAACTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATTTTATAAATAT
Found at i:52251103 original size:41 final size:42
Alignment explanation
Indices: 52251039--52251124 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 42
52251029 TTTAAAGTTA
52251039 AGTGACTTAAATCGTAAACCTATTAATAGTTTAGTGATCTTT
1 AGTGACTTAAATCGTAAACCTATTAATAGTTTAGTGATCTTT
*
52251081 AGTGACTT-AATCGTAAATCTATTAATAGTTTAGTGATCTTT
1 AGTGACTTAAATCGTAAACCTATTAATAGTTTAGTGATCTTT
52251122 AGT
1 AGT
52251125 TAGTTTGCCC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 35 0.81
42 8 0.19
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (42 bp):
AGTGACTTAAATCGTAAACCTATTAATAGTTTAGTGATCTTT
Found at i:52259679 original size:90 final size:90
Alignment explanation
Indices: 52259210--52259667 Score: 718
Period size: 90 Copynumber: 5.1 Consensus size: 90
52259200 AATGTTTGAA
* * *
52259210 CGTCGCCGTCTTCTCCAAGATGAAGATGGACTTCCGGTTATTGGCCATTCTGATTGGACTTCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
52259275 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
* * *
52259300 CGTCGCCGTCTTCTTCAAGACGAAGATGGACTTCCGATTATTGGCCATTCCGACTGGACATCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
52259365 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
* * * *
52259390 CGTCGTCGTCTTCTTCAAGACGAAGATAGACTTTCGGTTATTGGCCATTCCGATTGGACATCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
52259455 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
* * *
52259480 CGTCACCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACATCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
* *
52259545 TTTAGAATGAAACAAAGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
* * * *
52259570 CGTCGTCGTCTTCTCCAAGACGAAGATAGACTTCCGGTTATCGGCCATTCCGATTGGACATCATT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
* *
52259635 TTTAGAACGGAACAAGGAATGGAAC
66 TTTAGAACGAAACAAGGAATGGAAT
*
52259660 CGCCGCCG
1 CGTCGCCG
52259668 GATGCTCCAA
Statistics
Matches: 337, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 337 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (90 bp):
CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
TTTAGAACGAAACAAGGAATGGAAT
Found at i:52262838 original size:21 final size:21
Alignment explanation
Indices: 52262812--52262855 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52262802 AGACGAGCAA
* *
52262812 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
52262833 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
52262854 TA
1 TA
52262856 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:52265442 original size:51 final size:51
Alignment explanation
Indices: 52265382--52265782 Score: 523
Period size: 51 Copynumber: 7.9 Consensus size: 51
52265372 AAAACTGAAG
* * * *
52265382 ACAAAGGGTTGATCCCTACGTCCCTAGATGTTCCCGCTAGTAAACCCGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
*
52265433 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCTGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
52265484 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
* * * *
52265535 ACAGTGGGCTCATCCCTACCTCTCCAGATGTTTCCGCTAGTAAACCCGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
* * * * *
52265586 ACAGTGGGGTGATCCCTACCTCCCCAAATGTTCCCGTTAGTAAACCCGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
* *
52265637 ACAATGGGTTCATCCCTACCTCCCCAGATGTTTCCGTTAGTAAACCCGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
* * * * * * *
52265688 ACAGTGGGTTGATCCCTATCTCTCCAGATCTTTCCGCTAGTAAACCTGAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
* ** * * * * *
52265739 ACAATGGGGTGGTCTCTATCTCCCCAAATCTTTCCGCTAGTAAA
1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAA
52265783 GCCGCACACA
Statistics
Matches: 316, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 316 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (51 bp):
ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
Found at i:52265621 original size:153 final size:153
Alignment explanation
Indices: 52265393--52265782 Score: 584
Period size: 153 Copynumber: 2.5 Consensus size: 153
52265383 CAAAGGGTTG
* * * *
52265393 ATCCCTACGTC-CCTAGATGTTCCCGCTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTCCC
1 ATCCCTACCTCTCC-AGATGTTTCCGCTAGTAAACCCGAAAACAATGGGGTGATCCCTACCTCCC
* *
52265457 CAGATGTTCCCGCTAGTAAACCTGAAAACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCT
65 CAAATGTTCCCGCTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCT
52265522 AGTAAACCCGAAAACAGTGGGCTC
130 AGTAAACCCGAAAACAGTGGGCTC
*
52265546 ATCCCTACCTCTCCAGATGTTTCCGCTAGTAAACCCGAAAACAGTGGGGTGATCCCTACCTCCCC
1 ATCCCTACCTCTCCAGATGTTTCCGCTAGTAAACCCGAAAACAATGGGGTGATCCCTACCTCCCC
* * *
52265611 AAATGTTCCCGTTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTCCCCAGATGTTTCCGTTA
66 AAATGTTCCCGCTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTA
* *
52265676 GTAAACCCGAAAACAGTGGGTTG
131 GTAAACCCGAAAACAGTGGGCTC
* * * * * *
52265699 ATCCCTATCTCTCCAGATCTTTCCGCTAGTAAACCTGAAAACAATGGGGTGGTCTCTATCTCCCC
1 ATCCCTACCTCTCCAGATGTTTCCGCTAGTAAACCCGAAAACAATGGGGTGATCCCTACCTCCCC
* *
52265764 AAATCTTTCCGCTAGTAAA
66 AAATGTTCCCGCTAGTAAA
52265783 GCCGCACACA
Statistics
Matches: 214, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
153 212 0.99
154 2 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (153 bp):
ATCCCTACCTCTCCAGATGTTTCCGCTAGTAAACCCGAAAACAATGGGGTGATCCCTACCTCCCC
AAATGTTCCCGCTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTA
GTAAACCCGAAAACAGTGGGCTC
Found at i:52265855 original size:21 final size:21
Alignment explanation
Indices: 52265831--52265878 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
52265821 ACACAAGAAA
52265831 AAGAAGCACCATGGAAAAGGG
1 AAGAAGCACCATGGAAAAGGG
*
52265852 AAGAAGCACCATGGGAAAGGG
1 AAGAAGCACCATGGAAAAGGG
52265873 AAGAAG
1 AAGAAG
52265879 AAAGGGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.35, T:0.04
Consensus pattern (21 bp):
AAGAAGCACCATGGAAAAGGG
Found at i:52272252 original size:17 final size:18
Alignment explanation
Indices: 52272212--52272253 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
52272202 GTTCTTTTAA
* *
52272212 TTAATTATAATTACGTAT
1 TTAAATATAATAACGTAT
52272230 TT-AATATAATAACGT-T
1 TTAAATATAATAACGTAT
52272246 TTAAATAT
1 TTAAATAT
52272254 TTGTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 16 0.76
18 2 0.10
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (18 bp):
TTAAATATAATAACGTAT
Found at i:52272714 original size:21 final size:22
Alignment explanation
Indices: 52272675--52272715 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52272665 AAAAAAATAT
*
52272675 AAAATTGATTGATGAATTAAAA
1 AAAATTGATTAATGAATTAAAA
*
52272697 AAAATTG-TTAATGGATTAA
1 AAAATTGATTAATGAATTAA
52272716 TTTTCCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (22 bp):
AAAATTGATTAATGAATTAAAA
Found at i:52282123 original size:14 final size:14
Alignment explanation
Indices: 52282104--52282131 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52282094 AAAATATGAC
52282104 CAATATGGTCATTA
1 CAATATGGTCATTA
52282118 CAATATGGTCATTA
1 CAATATGGTCATTA
52282132 TTAGTTATGT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
CAATATGGTCATTA
Found at i:52286262 original size:12 final size:12
Alignment explanation
Indices: 52286245--52286269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52286235 AGAGAAAAAA
52286245 TAATATATTGTC
1 TAATATATTGTC
52286257 TAATATATTGTC
1 TAATATATTGTC
52286269 T
1 T
52286270 TTTGTGTCGA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TAATATATTGTC
Found at i:52289168 original size:83 final size:81
Alignment explanation
Indices: 52289006--52289377 Score: 274
Period size: 82 Copynumber: 4.5 Consensus size: 81
52288996 AAGCTCGAAT
* * * * * *
52289006 TTAGCAAGTAGTACCCATAAAAGGTGTGTGCTCAAATAATTAGCCAAGTGTCTTAAAAGGTTAGC
1 TTAGCAAGCAGTA-CC-TCAAAGGTGTGTGCTCAAATAATTGGCTAAGTGTCTTAAGAGGCTAG-
* * *
52289071 AATG-G-TTCTACTATTAAC
63 AA-GCGATTTTGCTATTAGC
* * *
52289089 TTAGGAAGCAGTACACTCAAAGCGAGTGTGCTCAAATAATTGGTTAAGT-TCCTTAAGAGGCTAG
1 TTAGCAAGCAGTAC-CTCAAAG-GTGTGTGCTCAAATAATTGGCTAAGTGT-CTTAAGAGGCTAG
52289153 AAGC-AGTTTTGCTATTAGC
63 AAGCGA-TTTTGCTATTAGC
* * * * *
52289172 TTCA-CAAGCAG-ATCTTCAAAGGGTGCGTGCCCAACTAATTGGCTAAGTGTCTTAAGAGGCTTG
1 TT-AGCAAGCAGTA-CCTCAAA-GGTGTGTGCTCAAATAATTGGCTAAGTGTCTTAAGAGGCTAG
*
52289235 CAGCGATTTTGCTATTAGC
63 AAGCGATTTTGCTATTAGC
* * * *
52289254 TTAGCAAGCAGTACCCTCAAA-GTGTGTTCTCAAATAATTAGCTAAGTGTCTT-AGAAGACTAGC
1 TTAGCAAGCAGTA-CCTCAAAGGTGTGTGCTCAAATAATTGGCTAAGTGTCTTAAG-AGGCTAGA
* * * *
52289317 AGTGATTCTACTATTAAC
64 AGCGATTTTGCTATTAGC
* * **
52289335 TTTAGCAAGTAGGACGCTCAAACAATGTGTGCTCAAATAATTG
1 -TTAGCAAGCAGTAC-CTCAAA-GGTGTGTGCTCAAATAATTG
52289378 TTTCAATGCC
Statistics
Matches: 232, Mismatches: 39, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
80 2 0.01
81 49 0.21
82 90 0.39
83 74 0.32
84 17 0.07
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (81 bp):
TTAGCAAGCAGTACCTCAAAGGTGTGTGCTCAAATAATTGGCTAAGTGTCTTAAGAGGCTAGAAG
CGATTTTGCTATTAGC
Found at i:52289482 original size:84 final size:84
Alignment explanation
Indices: 52289312--52289498 Score: 214
Period size: 84 Copynumber: 2.2 Consensus size: 84
52289302 TCTTAGAAGA
* * * **
52289312 CTAGCAGTGATTCTACTATTAACTTTAGCAAGTAGGACGCTCAAACAATGTGTGCTCAAATAATT
1 CTAGCAGTGGTTCTACTATTAACTTTAGCAAGTACGACCCTCAAACAATGTGAACTCAAATAATT
*
52289377 GTTTCAATGCCTTCAAAGG
66 GATTCAATGCCTTCAAAGG
* * *
52289396 CTAGCAGTGGTTCTGCTATTAACTTTGGCAAGTACTACCCTCAAAC-ATCGTGAACTCAAATAAT
1 CTAGCAGTGGTTCTACTATTAACTTTAGCAAGTACGACCCTCAAACAAT-GTGAACTCAAATAAT
* * ** *
52289460 TGATTCATTGTCTTGGATGG
65 TGATTCAATGCCTTCAAAGG
* *
52289480 CTAGCAATGGTTTTACTAT
1 CTAGCAGTGGTTCTACTAT
52289499 AACGTAGTGA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 2 0.02
84 83 0.98
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (84 bp):
CTAGCAGTGGTTCTACTATTAACTTTAGCAAGTACGACCCTCAAACAATGTGAACTCAAATAATT
GATTCAATGCCTTCAAAGG
Found at i:52299584 original size:21 final size:21
Alignment explanation
Indices: 52299559--52299598 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52299549 GTATTAAGTC
52299559 AATAAAAATGCA-AAAAATAAT
1 AATAAAAAT-CATAAAAATAAT
*
52299580 AATAAATATCATAAAAATA
1 AATAAAAATCATAAAAATA
52299599 TGTGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (21 bp):
AATAAAAATCATAAAAATAAT
Found at i:52306756 original size:43 final size:44
Alignment explanation
Indices: 52306708--52306916 Score: 216
Period size: 43 Copynumber: 4.9 Consensus size: 44
52306698 GTTACCGAGA
* *
52306708 TGTGATTACATGTAAGACCAAGTCTGGGACATTGGCATTGTT-T
1 TGTGATTACGTGTAAGACCAAGTCTGGGACATTGGCATCGTTAT
* * * *
52306751 TGTGATTACGTGTAAGACCATGTCTGGGGCATTGACATCATTAT
1 TGTGATTACGTGTAAGACCAAGTCTGGGACATTGGCATCGTTAT
*
52306795 T-CGATTACGTGTAAGACCATA-TCTGGGACATTGGCATCGTTAT
1 TGTGATTACGTGTAAGACCA-AGTCTGGGACATTGGCATCGTTAT
* ** * *
52306838 T-TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATA-
1 TGTGATTACGTGTAAGACCAAGTCTGGGACATTGGCATCGTTAT
* * *
52306880 TGTGATAACATGTAAGACCATA-TCTGGGATA-TGGCAT
1 TGTGATTACGTGTAAGACCA-AGTCTGGGACATTGGCAT
52306917 TGTACGAGCT
Statistics
Matches: 138, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
42 7 0.05
43 129 0.93
44 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (44 bp):
TGTGATTACGTGTAAGACCAAGTCTGGGACATTGGCATCGTTAT
Done.