Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 71 of 210
Found at i:21242933 original size:18 final size:17
Alignment explanation
Indices: 21242881--21242933 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
21242871 TAAATAGATG
21242881 AGTAAATGATAATAAAAT
1 AGTAAAT-ATAATAAAAT
* * *
21242899 AATAATAGATGATAAAAT
1 AGTAA-ATATAATAAAAT
21242917 AGTAAATATAATGAAAA
1 AGTAAATATAAT-AAAA
21242934 CGTAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 5 0.19
18 21 0.78
19 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AGTAAATATAATAAAAT
Found at i:21244285 original size:24 final size:24
Alignment explanation
Indices: 21244253--21244298 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
21244243 TTTTGGGTCT
21244253 GTTTGGGTTAGGTTT-AGTTTGGTG
1 GTTTGGGTT-GGTTTGAGTTTGGTG
*
21244277 GTTTTGGTTGGTTTGAGTTTGG
1 GTTTGGGTTGGTTTGAGTTTGG
21244299 GTTGGGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.52
Consensus pattern (24 bp):
GTTTGGGTTGGTTTGAGTTTGGTG
Found at i:21244934 original size:239 final size:242
Alignment explanation
Indices: 21244494--21244976 Score: 742
Period size: 239 Copynumber: 2.0 Consensus size: 242
21244484 CCACTTCAGG
*
21244494 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAGATAAGACTCGTAACTTCAACCTGC
1 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTT--ACC-GC
* * *
21244559 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCTACTATAACTTCAGAGAGAT
63 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAA
* * *
21244624 AAGATTCGCTATCTTCCAAGAGATAATATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
128 AAGATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
21244689 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
193 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
* *
21244739 GAAATAATATCGTTAGTCTGCTCCACTTCAACTTCAGGGAAATAAGACTCGTAAC-T-CC-CCCA
1 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
* * * *
21244801 CTACAACTTT-AGGGATATAAGGTTTATAGCTTTAATCTGCCCTACTGCAACTTTAGAGAGAAAA
66 CTACAA-TTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAA
* *
21244865 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTGCAA-TTTCAGGAA
130 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG-A
*
21244929 GTTCAGATTTGTAACTTATAGCCTTAATCTGTTCCACTGTAACTTCAA
194 GTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAA
21244977 GGTTGATGCT
Statistics
Matches: 220, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
238 6 0.03
239 156 0.71
240 3 0.01
241 2 0.01
244 1 0.00
245 52 0.24
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (242 bp):
GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
CTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAAG
ATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGGAGT
TCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
Found at i:21245162 original size:11 final size:10
Alignment explanation
Indices: 21245148--21245213 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
21245138 GGCCTCTCCT
21245148 TTTTCTTTTTC
1 TTTT-TTTTTC
*
21245159 TTTTCTTTTCC
1 TTTT-TTTTTC
* *
21245170 TTATTTTTCC
1 TTTTTTTTTC
21245180 TTATTTTTTTC
1 TT-TTTTTTTC
*
21245191 TTATTTTTTC
1 TTTTTTTTTC
*
21245201 -TTATTTTTC
1 TTTTTTTTTC
21245210 TTTT
1 TTTT
21245214 ATGAAACATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
9 7 0.16
10 17 0.38
11 21 0.47
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:21245186 original size:9 final size:10
Alignment explanation
Indices: 21245164--21245209 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
21245154 TTTTCTTTTC
21245164 TTTTCCTTAT
1 TTTTCCTTAT
21245174 TTTTCCTTATT
1 TTTTCCTTA-T
*
21245185 TTTTTCTTAT
1 TTTTCCTTAT
*
21245195 TTTTTCTTAT
1 TTTTCCTTAT
21245205 TTTTC
1 TTTTC
21245210 TTTTATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCCTTAT
Found at i:21245188 original size:21 final size:21
Alignment explanation
Indices: 21245164--21245208 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
21245154 TTTTCTTTTC
21245164 TTTTCCTTATTTTTCCTTATT
1 TTTTCCTTATTTTTCCTTATT
* *
21245185 TTTTTCTTATTTTTTCTTATT
1 TTTTCCTTATTTTTCCTTATT
21245206 TTT
1 TTT
21245209 CTTTTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCCTTATTTTTCCTTATT
Found at i:21245207 original size:8 final size:9
Alignment explanation
Indices: 21245153--21245211 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 9
21245143 CTCCTTTTTC
*
21245153 TTTTTCTTT
1 TTTTTCTTA
21245162 TCTTTTCCTTA
1 T-TTTT-CTTA
21245173 TTTTTCCTTA
1 TTTTT-CTTA
21245183 TTTTTTTCTTA
1 --TTTTTCTTA
21245194 TTTTTTCTTA
1 -TTTTTCTTA
21245204 TTTTTCTT
1 TTTTTCTT
21245212 TTATGAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 9 0.20
10 23 0.51
11 8 0.18
12 5 0.11
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:21245215 original size:21 final size:21
Alignment explanation
Indices: 21245153--21245215 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
21245143 CTCCTTTTTC
* *
21245153 TTTTTCTTTTCTTTTC-CTTAT
1 TTTTTCTTAT-TTTTCTTTTAT
*
21245174 TTTTCCTTATTTTT-TTCTTAT
1 TTTTTCTTATTTTTCTT-TTAT
21245195 TTTTTCTTATTTTTCTTTTAT
1 TTTTTCTTATTTTTCTTTTAT
21245216 GAAACATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 29 0.83
22 2 0.06
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTATTTTTCTTTTAT
Found at i:21251955 original size:44 final size:44
Alignment explanation
Indices: 21251905--21252834 Score: 660
Period size: 44 Copynumber: 20.6 Consensus size: 44
21251895 TTTGAACCTA
*
21251905 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * * *
21251949 CCCCACTATAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * *
21251993 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
21252037 CTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
21252081 CTCCACTGTAACTTCAGGTAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
21252125 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
21252169 CTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-A----T--CTTCAATCTG
* * * *
21252220 TTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* * * *
21252265 CTCCACTGCAACTTTAGGGAAATAAGATTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * *
21252309 CTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * *
21252353 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
21252398 CTCCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
21252442 CCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTT-AATCTG
1 CTCCACTGCAACTTCAGGGAGAT---A-AG--ATTTGTA-TCTTCAATCTG
* * * * ** * * *
21252492 TTCCACTGCAACTTTAAGGAAATAAGATTCACTATATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * ** * * *
21252537 CTCCATTGCAACTTTAGGGAGATAAAACTCATAACTTAAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * ** * * *
21252581 CCCCACTGCAACTTAAAGGG-GATCCGATTTGTATTTTGTAGCCTTGATATG
1 CTCCACTGCAACTT-CAGGGAGATAAGATTTGTA-TCT-T---C--AATCTG
* * * ** **
21252632 TTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * * *
21252677 CTCCATTGCAACTTTAGGGATATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
21252721 C-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTA
1 CTCC-ACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
21252765 CTCTAATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
21252810 CTCCACTACAACTTTAGGGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
21252835 AATTCGTCAT
Statistics
Matches: 685, Mismatches: 170, Indels: 61
0.75 0.19 0.07
Matches are distributed among these distances:
43 2 0.00
44 414 0.60
45 167 0.24
46 2 0.00
47 4 0.01
48 1 0.00
50 33 0.05
51 59 0.09
52 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
Found at i:21252104 original size:132 final size:133
Alignment explanation
Indices: 21251899--21252834 Score: 789
Period size: 133 Copynumber: 6.9 Consensus size: 133
21251889 ATGTAATTTG
* * * * **
21251899 AACCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCCCCACTATAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
21251964 AGGGAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
21252028 TTC
131 TTC
* * *
21252031 AACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * * *
21252096 AGGTAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
21252160 TTC
131 TTC
* * * * * * *
21252163 AACCCGCTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTGTTCCATTG
1 AACCTGCTCCACTGCAACTTCAGGGAGAT-AAG---GT---TTGTAGCTTTAATCTGCTCCACTG
* * * * *
21252228 CAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGAT
59 CAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
21252293 TTGTAGCTTT
124 TTGTAGCTTC
* ** * *
21252303 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTACTGCAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * * * * *
21252368 AGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTATC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
21252433 TTC
131 TTC
* * * * * * * *
21252436 AATCTGCCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAATCTGTTCCACTGC
1 AACCTGCTCCACTGCAACTTCAGGGAGAT---A-AG--GTTTGTAGCTTTAATCTGCTCCACTGC
* * * ** ** * * * * * *
21252501 AACTTTAAGGAAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAAACT
60 AACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
** * *
21252566 CATAACTTA
125 TGTAGCTTC
* * ** * * * * * *
21252575 AACCTGCCCCACTGCAACTTAAAGGGGATCCGATTTGTATTTTGTAGCCTTGATATGTTCCACCG
1 AACCTGCTCCACTGCAACTT-CA-GGGA---GATAAG--GTTTGTAGCTTTAATCTGCTCCACTG
* ** * ** * * * *
21252640 CAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCATTGCAACTTTAGGGATATAAGAC
59 CAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
21252705 TTGTAACTTC
124 TTGTAGCTTC
* * * * * *
21252715 AACCTGC-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTAATACAACTT
1 AACCTGCTCC-ACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTT
* * * * *
21252779 CAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
65 CAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
21252835 AATTCGTCAT
Statistics
Matches: 672, Mismatches: 112, Indels: 39
0.82 0.14 0.05
Matches are distributed among these distances:
132 151 0.22
133 182 0.27
135 4 0.01
136 4 0.01
137 1 0.00
138 4 0.01
139 143 0.21
140 177 0.26
141 3 0.00
144 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (133 bp):
AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
TTC
Found at i:21252482 original size:272 final size:268
Alignment explanation
Indices: 21251907--21252834 Score: 866
Period size: 272 Copynumber: 3.4 Consensus size: 268
21251897 TGAACCTACT
* * * * *
21251907 CCACTGCAACTTCAGGGAGAT-A-AG--ATTTGTATCTTTAATCTGCCCCACTATAACTTCAGGG
1 CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
* * * * * * *
21251968 AGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
66 AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTAA
* *
21252032 ACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTCA
131 ACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
* * * * * * * *
21252097 GGTAGATAAGATTTTTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT
196 GG-AGATAAGATTTCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTT
* *
21252162 CAACCCGCT
260 CAACCTGCC
* * * * * * *
21252171 CCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTGTTCCATTGCAACTTTA
1 CCACTGTAACTTCAGGGAGATGA---TTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCA
*
21252236 GGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGATTTGTAGCT
63 GGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCT
* * * * ** * *
21252301 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTACTGCAACT
128 TAAACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACT
21252366 TCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTA
193 TCAG-GAGATAAGATTT-CTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTA
* *
21252431 TCTTCAATCTGCC
256 ACTTCAACCTGCC
** * * * * * *
21252444 CCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAATCTGTTCCACTGCAACTTTAA
1 CCACTGTAACTTCAGGGAGAT--GATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAG
** * * * * * * ** *
21252509 GGAAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAAACTCATAACTT
64 GGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTT
* ** * * * * * *
21252574 AAACCTGCCCCACTGCAACTTAAAGGGGATCCGATTTGTATTTTGTAGCCTTGATATGTTCCACC
129 AAACCTGCTCCACTGCAACTT-AA-GGGA---GATAAG--CTTTGTAGCTTTAATCTGCTCCACT
* * * * *
21252639 GCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCATTGCAACTTTAGGGATATAAGA
187 GCAACTTCA-GGAGATAAGATT-TCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGA
21252704 CTTGTAACTTCAACCTGCC
250 CTTGTAACTTCAACCTGCC
* * * * * * *
21252723 CTACTGTAACTTCAGGGAGAT-A-AG--GTTTATAGCTTTAATCTACTCTAATACAACTTCAGGG
1 CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
* * * *
21252784 AGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
66 AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
21252835 AATTCGTCAT
Statistics
Matches: 537, Mismatches: 106, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
264 18 0.03
265 1 0.00
269 1 0.00
271 39 0.07
272 222 0.41
273 137 0.26
274 4 0.01
275 3 0.01
276 1 0.00
277 4 0.01
279 106 0.20
280 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (268 bp):
CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTAA
ACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
GGAGATAAGATTTCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTC
AACCTGCC
Found at i:21252679 original size:412 final size:405
Alignment explanation
Indices: 21251890--21252834 Score: 1061
Period size: 412 Copynumber: 2.3 Consensus size: 405
21251880 GTATAGGAAA
* * * * * * * *
21251890 TGTAATTTGAACCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCCCCAC
1 TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
* * * * * *
21251955 TATAACTTCAGGGAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAG
66 TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
* * * * * *
21252019 ATTTGTAGCTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTC
131 ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTC
* * * ** * * *
21252084 CACTGTAACTTCAGGTAGATAAGATTTTTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATA
196 CACTGCAACTTAAGGTAAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* * ** * * * * * * * * *
21252149 AGATTTGTAGCTTCAACCCGCTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTT
261 AAACTCATAACTTAAACCCGCCCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTT
* ** * **
21252214 AATCTGTTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
326 AATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTT
*
21252279 TAGGGAAATAAGATT
391 TAGGGAAATAAGACT
* * * *
21252294 TGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTAC
1 TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
* * *
21252359 TGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAG
66 TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
* * * *
21252424 ACTTGTATCTTCAATCTGCCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAAT
131 ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGAT---A-AG--ATTTGTAGCCTTAAT
* * * * * *
21252489 CTGTTCCACTGCAACTTTAAGG-AAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTA
190 CTGCTCCACTGCAAC-TTAAGGTAAATAAGATT-ACTAGATTCAATCTGCTCCACTGCAACTTCA
* * **
21252553 GGGAGATAAAACTCATAACTTAAACCTGCCCCACTGCAACTTAAAGGG-GATCCGATTTGTATTT
253 GGGAGATAAAACTCATAACTTAAACCCGCCCCACTGCAACTT-AAGGGAGATCAGATTTGTAACT
* **
21252617 TGTAGCCTTGATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCA
317 TGTAGCCTTAATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCA
* *
21252682 TTGCAACTTTAGGGATATAAGACT
382 CTGCAACTTTAGGGAAATAAGACT
* * *
21252706 TGTAACTTCAACCTGC-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTA
1 TGTAACTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTA
* *
21252770 ATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
65 CTACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAA
21252835 AATTCGTCAT
Statistics
Matches: 445, Mismatches: 85, Indels: 14
0.82 0.16 0.03
Matches are distributed among these distances:
404 75 0.17
405 68 0.15
408 1 0.00
409 1 0.00
411 37 0.08
412 259 0.58
413 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (405 bp):
TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTC
CACTGCAACTTAAGGTAAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AAACTCATAACTTAAACCCGCCCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTT
AATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTT
TAGGGAAATAAGACT
Found at i:21255814 original size:21 final size:23
Alignment explanation
Indices: 21255790--21255832 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21255780 CAACACAACT
21255790 TCTCA-ATT-AGTGAATATCTTG
1 TCTCATATTAAGTGAATATCTTG
*
21255811 TCTCATATTAAGTGAATTTCTT
1 TCTCATATTAAGTGAATATCTT
21255833 ACTGAGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (23 bp):
TCTCATATTAAGTGAATATCTTG
Found at i:21256366 original size:41 final size:42
Alignment explanation
Indices: 21256249--21256375 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 42
21256239 GCCCCAAAAG
*
21256249 TACATTTTGCTAGATTGAGCTTCAGTTGGAATTTTCTCAATC
1 TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
* * * *
21256291 TACATTTTTGTTGGATTAAGCTTCAGCTAGAATTTTCTCAATC
1 TACA-TTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
* *
21256334 TACATTTTACT-GAATGAGCTTCAGCTGGAATTTTCTCAATC
1 TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
21256375 T
1 T
21256376 CAAGAACAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 28 0.38
42 9 0.12
43 37 0.50
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (42 bp):
TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
Found at i:21261059 original size:19 final size:20
Alignment explanation
Indices: 21261028--21261081 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
21261018 GGTCTTTTTC
* *
21261028 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGCA
*
21261047 TGCAATGTAATGCAAATGCA
1 TGAAATGTAATGCAAATGCA
21261067 TGAAATG-AATGCAAA
1 TGAAATGTAATGCAAA
21261082 AAGAGGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGCA
Found at i:21263214 original size:30 final size:31
Alignment explanation
Indices: 21263175--21263234 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
21263165 AGAGGTGGGA
*
21263175 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
21263206 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
21263235 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:21263472 original size:18 final size:18
Alignment explanation
Indices: 21263449--21263483 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21263439 TAGTTTGATA
21263449 TTCGAGTTATTCGAATTG
1 TTCGAGTTATTCGAATTG
*
21263467 TTCGAGTTATTCTAATT
1 TTCGAGTTATTCGAATT
21263484 TGAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (18 bp):
TTCGAGTTATTCGAATTG
Found at i:21273629 original size:41 final size:41
Alignment explanation
Indices: 21273572--21273677 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
21273562 GGAAGTTATC
*
21273572 TGAAAAGGTTAAAAAGGACAATATCCGACAAA-GATACCAAA
1 TGAAAAGGTTGAAAAGGACAATATCCGA-AAAGGATACCAAA
*
21273613 TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATATCAAA
1 TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATACCAAA
* * *
21273654 TGAATAGGTTGAAAATGACGATAT
1 TGAAAAGGTTGAAAAGGACAATAT
21273678 TTGAAGAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 3 0.05
41 56 0.95
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (41 bp):
TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATACCAAA
Found at i:21280722 original size:29 final size:29
Alignment explanation
Indices: 21280690--21280753 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
21280680 CTGAAGTAGG
21280690 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
21280719 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
21280748 -AAGTCT
1 AAAGTCT
21280754 GCAAAGAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (29 bp):
AAAGTCTTATGGGACTATTTTATGAGTAC
Found at i:21294978 original size:22 final size:22
Alignment explanation
Indices: 21294948--21295033 Score: 111
Period size: 22 Copynumber: 4.0 Consensus size: 22
21294938 TCTAGGCCAT
**
21294948 AGAG-TTAGTACGTTAGCCATG
1 AGAGCTTAGTACGTTAAACATG
* * *
21294969 AGGGTTTAGTTCGTTAAACATG
1 AGAGCTTAGTACGTTAAACATG
21294991 AGAGCTTAGTACGTTAAACATG
1 AGAGCTTAGTACGTTAAACATG
*
21295013 AGAGCTTAGTACGTGAAACAT
1 AGAGCTTAGTACGTTAAACAT
21295034 CACATCAGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 3 0.05
22 53 0.95
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (22 bp):
AGAGCTTAGTACGTTAAACATG
Found at i:21296731 original size:14 final size:14
Alignment explanation
Indices: 21296712--21296760 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
21296702 TCATTTTTTA
21296712 AATTTTTACATTCT
1 AATTTTTACATTCT
21296726 AATTTTTACATTCT
1 AATTTTTACATTCT
*
21296740 AATTCTTT-TATTCT
1 AATT-TTTACATTCT
21296754 AATTTTT
1 AATTTTT
21296761 TTATTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTACATTCT
Found at i:21296762 original size:14 final size:14
Alignment explanation
Indices: 21296721--21296765 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
21296711 AAATTTTTAC
**
21296721 ATTCTAATTTTTAC
1 ATTCTAATTTTTTT
*
21296735 ATTCTAATTCTTTT
1 ATTCTAATTTTTTT
21296749 ATTCTAATTTTTTT
1 ATTCTAATTTTTTT
21296763 ATT
1 ATT
21296766 TTCTTCTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTCTAATTTTTTT
Found at i:21299936 original size:5 final size:5
Alignment explanation
Indices: 21299926--21299956 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
21299916 ACCCTAGCTC
21299926 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
21299957 CTTCTTCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:21300495 original size:4 final size:4
Alignment explanation
Indices: 21300478--21300512 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
21300468 TTACCTTATT
*
21300478 TTTA TTTG TTTA TTTA TTTA TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21300513 GTTTCTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:21300495 original size:12 final size:12
Alignment explanation
Indices: 21300478--21300512 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
21300468 TTACCTTATT
*
21300478 TTTATTTGTTTA
1 TTTATTTATTTA
21300490 TTTATTTATTTA
1 TTTATTTATTTA
21300502 -TTATTTATTTA
1 TTTATTTATTTA
21300513 GTTTCTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:21300836 original size:3 final size:3
Alignment explanation
Indices: 21300828--21300863 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
21300818 TTTTATTTTC
*
21300828 TAT TAT TAT TAT TAT TAT T-T TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21300864 CTTCTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21300852 original size:17 final size:17
Alignment explanation
Indices: 21300830--21300863 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21300820 TTATTTTCTA
*
21300830 TTATTATTATTATTATT
1 TTATTAGTATTATTATT
21300847 TTATTAGTATTATTATT
1 TTATTAGTATTATTATT
21300864 CTTCTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTAGTATTATTATT
Found at i:21302049 original size:6 final size:6
Alignment explanation
Indices: 21302038--21302101 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 6
21302028 TTTGTTTCTC
* * *
21302038 TTTTTA TTTTTA TTTTTTTA TGTTTA TGTTTA ATTTTA TTTTTA GTTGTTTTA
1 TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA --T-TTTTA
21302091 TTTTTA TTTTT
1 TTTTTA TTTTT
21302102 TTAGACTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 36 0.73
7 1 0.02
8 7 0.14
9 5 0.10
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:21302099 original size:26 final size:25
Alignment explanation
Indices: 21302023--21302100 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 25
21302013 GGATCAGTGA
*
21302023 TTTTATTTGTTTCTCTTTTTATTTTTAT
1 TTTTA-TTGTTT-TATTTTTA-TTTTAT
* *
21302051 TTTT-TTATGTTTATGTTTAATTTTAT
1 TTTTATTGT-TTTAT-TTTTATTTTAT
21302077 TTTTAGTTGTTTTATTTTTATTTT
1 TTTTA-TTGTTTTATTTTTATTTT
21302101 TTTAGACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 23 0.56
27 11 0.27
28 7 0.17
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (25 bp):
TTTTATTGTTTTATTTTTATTTTAT
Found at i:21316038 original size:16 final size:16
Alignment explanation
Indices: 21316019--21316060 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
21316009 TTCATTAGGA
*
21316019 TAATATTTTTATTTTC
1 TAATATTTTTATCTTC
21316035 TAATA-TTTTATCTTC
1 TAATATTTTTATCTTC
21316050 TAATTATTTTT
1 TAA-TATTTTT
21316061 GGATAACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 12 0.52
16 7 0.30
17 4 0.17
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATATTTTTATCTTC
Found at i:21320795 original size:27 final size:27
Alignment explanation
Indices: 21320758--21320812 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21320748 TTCACTCCTA
21320758 TAAAAATGTTTATTCATGTTTCTATAC
1 TAAAAATGTTTATTCATGTTTCTATAC
21320785 TAAAAATGTTTATTCATGTTTCTATAC
1 TAAAAATGTTTATTCATGTTTCTATAC
21320812 T
1 T
21320813 TAGGAGAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (27 bp):
TAAAAATGTTTATTCATGTTTCTATAC
Found at i:21324573 original size:17 final size:17
Alignment explanation
Indices: 21324545--21324596 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
21324535 TTTAGGTAGT
*
21324545 AGAAGAAGAAGAGAAAA
1 AGAAGAAAAAGAGAAAA
* **
21324562 AGAAGATAAAGA-ATAGG
1 AGAAGAAAAAGAGA-AAA
21324579 AGAAGAAAAAGAGAAAA
1 AGAAGAAAAAGAGAAAA
21324596 A
1 A
21324597 ATTGGAGATT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (17 bp):
AGAAGAAAAAGAGAAAA
Found at i:21324581 original size:23 final size:23
Alignment explanation
Indices: 21324556--21324604 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
21324546 GAAGAAGAAG
21324556 AGAAAAAGAAGATAAAGAATAGGAGA
1 AGAAAAAG-AGA-AAA-AATAGGAGA
*
21324582 AGAAAAAGAGAAAAAATTGGAGA
1 AGAAAAAGAGAAAAAATAGGAGA
21324605 TTTCAATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 3 0.14
26 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (23 bp):
AGAAAAAGAGAAAAAATAGGAGA
Found at i:21325634 original size:21 final size:21
Alignment explanation
Indices: 21325608--21325648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21325598 ATGCGGCAAG
21325608 TTAACTGGCCACATCAGCTAA
1 TTAACTGGCCACATCAGCTAA
**
21325629 TTAACTGGCCATGTCAGCTA
1 TTAACTGGCCACATCAGCTA
21325649 TCCCATTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TTAACTGGCCACATCAGCTAA
Found at i:21326825 original size:24 final size:24
Alignment explanation
Indices: 21326781--21326849 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
21326771 TTTCCAAAAT
* *
21326781 ATTTAGTATTTATTAGTATAATAA
1 ATTTAGCATTTATTAGCATAATAA
* *
21326805 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAGCATAATAA
*
21326829 ACTT-GACATTTATTAGCATAA
1 ATTTAG-CATTTATTAGCATAA
21326850 AAGTATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAA
Found at i:21329160 original size:24 final size:23
Alignment explanation
Indices: 21329100--21329160 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
21329090 AAGATCTAGT
*
21329100 ATTTATTAGTATAATATATTTAG
1 ATTTATTAGTATAATATATTTAC
* *
21329123 ATTTACTAGCATAATATATTTGAC
1 ATTTATTAGTATAATATATTT-AC
21329147 ATTTATTAGTATAA
1 ATTTATTAGTATAA
21329161 AAATATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTATTAGTATAATATATTTAC
Found at i:21341793 original size:24 final size:24
Alignment explanation
Indices: 21341764--21341870 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 24
21341754 TTCCACTAGA
21341764 AATAAAAATAAGAACAATGAAA-AT
1 AATAAAAATAA-AACAATGAAATAT
21341788 AATAAAAAT-AAACTAA-GAAATAT
1 AATAAAAATAAAAC-AATGAAATAT
** *
21341811 AGGAATAATAAAACATAT-AAATAT
1 AATAAAAATAAAACA-ATGAAATAT
* *
21341835 AATAACAATAAAAATAATGAAA-AT
1 AATAAAAAT-AAAACAATGAAATAT
21341859 AAT-AAAATAAAA
1 AATAAAAATAAAA
21341871 TAATAGAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
22 11 0.16
23 16 0.24
24 33 0.49
25 8 0.12
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAAAAATAAAACAATGAAATAT
Found at i:21341797 original size:9 final size:9
Alignment explanation
Indices: 21341783--21341865 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 9
21341773 AAGAACAATG
21341783 AAAATAATA
1 AAAATAATA
21341792 AAAATAAACTA
1 AAAAT-AA-TA
21341803 AGAAAT-ATA
1 A-AAATAATA
**
21341812 GGAATAATA
1 AAAATAATA
21341821 AAACAT-AT-
1 AAA-ATAATA
21341829 -AAAT-ATA
1 AAAATAATA
* *
21341836 ATAACAATA
1 AAAATAATA
*
21341845 AAAATAATG
1 AAAATAATA
21341854 AAAATAATA
1 AAAATAATA
21341863 AAA
1 AAA
21341866 TAAAATAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 5 0.09
9 33 0.59
10 5 0.09
11 3 0.05
12 4 0.07
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:21341845 original size:15 final size:14
Alignment explanation
Indices: 21341827--21341873 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
21341817 AATAAAACAT
21341827 ATAAATATAATAACA
1 ATAAATATAATAA-A
*
21341842 ATAAAAATAATGAAA
1 ATAAATATAAT-AAA
*
21341857 AT-AATAAAATAAA
1 ATAAATATAATAAA
21341870 ATAA
1 ATAA
21341874 TAGAACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 13 0.48
16 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
ATAAATATAATAAA
Found at i:21341883 original size:23 final size:24
Alignment explanation
Indices: 21341764--21341883 Score: 81
Period size: 24 Copynumber: 5.1 Consensus size: 24
21341754 TTCCACTAGA
* * *
21341764 AATAAAAATAAGAACAATGAAAAT
1 AATAACAATAAAAATAATGAAAAT
* *
21341788 AATAAAAAT-AAACTAA-GAAATAT
1 AATAACAATAAAAATAATGAAA-AT
** *
21341811 AGGAATAATAAAACAT-AT-AAATAT
1 AATAACAATAAAA-ATAATGAAA-AT
21341835 AATAACAATAAAAATAATGAAAAT
1 AATAACAATAAAAATAATGAAAAT
*
21341859 AATAA-AAT-AAAATAATAGAACAT
1 AATAACAATAAAAATAAT-GAAAAT
21341882 AA
1 AA
21341884 ACATGAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
22 12 0.15
23 24 0.31
24 38 0.49
25 4 0.05
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAACAATAAAAATAATGAAAAT
Found at i:21348441 original size:18 final size:17
Alignment explanation
Indices: 21348414--21348447 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21348404 ATTAGAATGT
*
21348414 AAAAATTAAATTAAAAC
1 AAAAATTAAAATAAAAC
21348431 AAAAATATAAAATAAAA
1 AAAAAT-TAAAATAAAA
21348448 TAAACAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATTAAAATAAAAC
Found at i:21355887 original size:15 final size:16
Alignment explanation
Indices: 21355858--21355896 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21355848 TTTTTATTTT
*
21355858 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
21355874 TATTTTT-ATAAAATA
1 TATTTTTAATAAAATA
21355889 TATATTTT
1 TAT-TTTT
21355897 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:21355932 original size:42 final size:41
Alignment explanation
Indices: 21355825--21355937 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
21355815 CCGGCCCAGC
** *
21355825 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAAT
1 CCGAATTATATATTAAATATATA-TTTT-TTTGGACTTTTAAT
* * *
21355868 -C-AAATATATTTTTATAAAATATATATTTTTTGGACTTTTAAT
1 CCGAATTATA-TATTA-AATATATAT-TTTTTTGGACTTTTAAT
21355910 CCGAATTATATATTAAATATATATTTTT
1 CCGAATTATATATTAAATATATATTTTT
21355938 ATTTTAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
41 10 0.18
42 25 0.45
43 15 0.27
44 6 0.11
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (41 bp):
CCGAATTATATATTAAATATATATTTTTTTGGACTTTTAAT
Found at i:21371762 original size:18 final size:18
Alignment explanation
Indices: 21371738--21371781 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
21371728 CACAGTTTGG
*
21371738 CAAATTAATACAGTTCAC
1 CAAATTAATACAGATCAC
*
21371756 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
21371774 CAAATTAA
1 CAAATTAA
21371782 CATAGTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:21378910 original size:16 final size:16
Alignment explanation
Indices: 21378889--21378921 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21378879 AAGGTTGTTG
21378889 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
21378905 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
21378921 A
1 A
21378922 CTCTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AACTGAAATAGAGTTT
Found at i:21381166 original size:19 final size:19
Alignment explanation
Indices: 21381144--21381286 Score: 112
Period size: 19 Copynumber: 7.4 Consensus size: 19
21381134 ATGCACCTCA
21381144 TGTGCCAATATGCACTTTG
1 TGTGCCAATATGCACTTTG
* *
21381163 TGTGCCAGTATGCGCTTTG
1 TGTGCCAATATGCACTTTG
** *
21381182 TGCACCAGGA-ATGCGCTTTG
1 TGTGCCA--ATATGCACTTTG
* *
21381202 TGTGCCAAGATGCACTTCG
1 TGTGCCAATATGCACTTTG
** * *
21381221 TGTGCCAGGATGTACTTCG
1 TGTGCCAATATGCACTTTG
21381240 TGTGCCAATAT--ACGTTTCG
1 TGTGCCAATATGCAC-TTT-G
*
21381259 TGTGCCAATAATGCACTTCG
1 TGTGCCAAT-ATGCACTTTG
21381279 TGTGCCAA
1 TGTGCCAA
21381287 GTTGCACATT
Statistics
Matches: 101, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 66 0.65
20 26 0.26
21 2 0.02
22 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (19 bp):
TGTGCCAATATGCACTTTG
Found at i:21381247 original size:38 final size:39
Alignment explanation
Indices: 21381128--21381293 Score: 122
Period size: 39 Copynumber: 4.3 Consensus size: 39
21381118 CACTTCATAC
* * * * *
21381128 GCCATGATGCACCTCATGTGCCAA-TATGCACTTTGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* * ** * * *
21381166 GCC-AGTATGCGCTTTGTGCACCAGGAATGCGCTTTGTGT
1 GCCAAG-ATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* *
21381205 GCCAAGATGCACTTCGTGTGCC-AGGATGTACTTCGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* * ** *
21381243 GCCAATATACGTTTCGTGTGCCAATAATGCACTTCGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
*
21381282 GCCAAGTTGCAC
1 GCCAAGATGCAC
21381294 ATTATGTGCT
Statistics
Matches: 93, Mismatches: 31, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
37 1 0.01
38 43 0.46
39 47 0.51
40 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (39 bp):
GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
Found at i:21384458 original size:27 final size:25
Alignment explanation
Indices: 21384441--21384489 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
21384431 ATTTAATTAG
21384441 ATAA-ATATTATTTTATTAATATTTTA
1 ATAAGATATTATTTTATT-AT-TTTTA
*
21384467 ATAAGATATTTTTTTATTATTTT
1 ATAAGATATTATTTTATTATTTT
21384490 ATTTAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 6 0.29
27 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATAAGATATTATTTTATTATTTTTA
Found at i:21384657 original size:13 final size:13
Alignment explanation
Indices: 21384639--21384665 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21384629 AAAAGAATTT
21384639 CCATAGCTACCAA
1 CCATAGCTACCAA
21384652 CCATAGCTACCAA
1 CCATAGCTACCAA
21384665 C
1 C
21384666 AGTGTAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (13 bp):
CCATAGCTACCAA
Found at i:21384986 original size:21 final size:20
Alignment explanation
Indices: 21384948--21385010 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
21384938 ATTCAATTTC
21384948 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
21384965 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
21384986 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
21385005 TGCAAT
1 T-CAAT
21385011 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:21385232 original size:51 final size:50
Alignment explanation
Indices: 21385172--21385309 Score: 163
Period size: 50 Copynumber: 2.7 Consensus size: 50
21385162 ATGTTCGGTT
*
21385172 CACATAGTAGCCTGCACATAGTACTACACACGTGA-TTGAA-ACTATCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCT-AACA-T-TCCAGTA
* * * * * * *
21385223 CGCATAGTAGCCTGCACATAGTTCTACAAATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCCAGTA
21385273 CACATAGTAGCCTGCACATAGTACTACACACGTGACC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC
21385310 ATCACTTTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 38 0.53
51 32 0.44
52 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCCAGTA
Found at i:21388230 original size:33 final size:32
Alignment explanation
Indices: 21388181--21388242 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
21388171 CATGGCAATG
* *
21388181 TTTTAATGTAAGACCATAATTGGGCTATGGCA
1 TTTTAATGAAAGACCATAACTGGGCTATGGCA
*
21388213 TTTTAATGAAAAGACCATAACTGGGTTATG
1 TTTTAATG-AAAGACCATAACTGGGCTATG
21388243 ACACCTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (32 bp):
TTTTAATGAAAGACCATAACTGGGCTATGGCA
Found at i:21389423 original size:13 final size:13
Alignment explanation
Indices: 21389405--21389442 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
21389395 TGCAAATGAA
21389405 TCATTTCTCATTT
1 TCATTTCTCATTT
21389418 TCATTTCT-ATTT
1 TCATTTCTCATTT
*
21389430 CCATTTC-CATTT
1 TCATTTCTCATTT
21389442 T
1 T
21389443 GAGAAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:21389494 original size:45 final size:46
Alignment explanation
Indices: 21389443--21389532 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
21389433 TTTCCATTTT
* * *
21389443 GAGAAAACTACATTTATTTTCAAAT-TATTTCATTTCTCTATTTCG
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
* * *
21389488 GAGAAAACCATAATCATTTTTAAATGTTTTTCATTTCTCTATTTC
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTC
21389533 TATTCATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (46 bp):
GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
Found at i:21392438 original size:20 final size:20
Alignment explanation
Indices: 21392413--21392453 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
21392403 TAAGGTATAT
21392413 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
21392433 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
21392453 G
1 G
21392454 CATTTGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (20 bp):
GTGTATGAAAACTAGTGAAA
Found at i:21394335 original size:20 final size:20
Alignment explanation
Indices: 21394310--21394347 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21394300 ACAATTTAAA
21394310 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
21394330 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
21394348 ATGTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:21398077 original size:16 final size:16
Alignment explanation
Indices: 21398056--21398090 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21398046 TATATGTTTA
*
21398056 TATAAAAATAATATTG
1 TATAAAAAAAATATTG
*
21398072 TATAAAAAAAATTTTG
1 TATAAAAAAAATATTG
21398088 TAT
1 TAT
21398091 TAATCTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (16 bp):
TATAAAAAAAATATTG
Found at i:21399330 original size:44 final size:44
Alignment explanation
Indices: 21399269--21399430 Score: 159
Period size: 44 Copynumber: 3.7 Consensus size: 44
21399259 GATCATTTTG
* *
21399269 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTAT-TACTTTA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGACTTCA
* * *
21399313 ATCCGCTCCAATACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTCA
* * * * *
21399357 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCCATCTTCG
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-CGA-CTTCA
* *
21399402 ATCTG-TCCCACTGCAACTTCAGGGGGATA
1 ATCCGCT-CCACTGCAACTTCAGGGAGATA
21399431 AGACCTGCTT
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
43 4 0.04
44 66 0.67
45 29 0.29
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTCA
Found at i:21410660 original size:16 final size:16
Alignment explanation
Indices: 21410639--21410669 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21410629 AAGCTGTCGA
21410639 AAATAATTTTTTTTAT
1 AAATAATTTTTTTTAT
21410655 AAATAATTTTTTTTA
1 AAATAATTTTTTTTA
21410670 AAAACAGGGA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AAATAATTTTTTTTAT
Found at i:21414921 original size:25 final size:24
Alignment explanation
Indices: 21414887--21414934 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
21414877 ATGTCTTCTC
21414887 CAACAATCAAACAGTGGGAGGCCTT
1 CAACAATCAAACA-TGGGAGGCCTT
* *
21414912 CAACAGTCAAACATTGGAGGCCT
1 CAACAATCAAACATGGGAGGCCT
21414935 CGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (24 bp):
CAACAATCAAACATGGGAGGCCTT
Found at i:21415542 original size:2 final size:2
Alignment explanation
Indices: 21415535--21415586 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
21415525 TTATAACTTT
21415535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21415577 -A TA TGA TA TA
1 TA TA T-A TA TA
21415587 AAACTTAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21421347 original size:2 final size:2
Alignment explanation
Indices: 21421342--21421373 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21421332 AATTGAAAAA
21421342 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21421374 TAGAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21426793 original size:2 final size:2
Alignment explanation
Indices: 21426750--21426776 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21426740 CCAGTTCTTG
21426750 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21426777 GTACCTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21429852 original size:59 final size:60
Alignment explanation
Indices: 21429779--21429896 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
21429769 TATACTAGTA
* *
21429779 GTCACTCAACTATTAGTGAATTCCTTTTTT-GACACTCAATTATGAAAAGTTACAAAATG
1 GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAATG
* * * * *
21429838 GTCACTCAATTATTAGTAAATTTCTTTTTTAGTCACTCAACTATTAAAAGTTATAAAAT
1 GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAAT
21429897 TTTTACTCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 27 0.53
60 24 0.47
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (60 bp):
GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAATG
Found at i:21430168 original size:19 final size:19
Alignment explanation
Indices: 21430144--21430197 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
21430134 AATCTTCGAG
21430144 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21430163 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
21430182 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
21430198 AGATGTGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21430711 original size:33 final size:34
Alignment explanation
Indices: 21430653--21430720 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
21430643 NNNNNNGTTC
* *
21430653 AATTAGTCTTTTTTCATTTTCTTTATTTTTTATT
1 AATTAGTCTTTTTTCATTTTCTTTATATTTAATT
*
21430687 AATTAGTTTTTTATTC-TTTT-TTTATATTTAATT
1 AATTAGTCTTTT-TTCATTTTCTTTATATTTAATT
21430720 A
1 A
21430721 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 12 0.40
34 15 0.50
35 3 0.10
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (34 bp):
AATTAGTCTTTTTTCATTTTCTTTATATTTAATT
Found at i:21430717 original size:29 final size:28
Alignment explanation
Indices: 21430671--21430727 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
21430661 TTTTTTCATT
*
21430671 TTCTTTATTTTTTATTAATTAGTTTTTTA
1 TTCTTTATTTTATATTAATTA-TTTTTTA
21430700 TTCTTT-TTTTATATTTAATTATTTTTTA
1 TTCTTTATTTTATA-TTAATTATTTTTTA
21430728 AAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (28 bp):
TTCTTTATTTTATATTAATTATTTTTTA
Found at i:21430797 original size:4 final size:4
Alignment explanation
Indices: 21430788--21430845 Score: 53
Period size: 4 Copynumber: 13.5 Consensus size: 4
21430778 TATAATATAA
* *
21430788 TTAT TTAT TTAT TTAT TTAT ATGTAA TTAT TTAT TTAT CTATAT GTAT
1 TTAT TTAT TTAT TTAT TTAT -T-TAT TTAT TTAT TTAT -T-TAT TTAT
*
21430836 ATAT TTAT TT
1 TTAT TTAT TT
21430846 TAGTATACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 37 0.82
5 3 0.07
6 5 0.11
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:21430852 original size:22 final size:22
Alignment explanation
Indices: 21430792--21430845 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
21430782 ATATAATTAT
*
21430792 TTATTTATTTATTTATATGTAA
1 TTATTTATTTATCTATATGTAA
21430814 TTATTTATTTATCTATATGT-A
1 TTATTTATTTATCTATATGTAA
21430835 TATATTTATTT
1 T-TATTTATTT
21430846 TAGTATACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TTATTTATTTATCTATATGTAA
Found at i:21438375 original size:44 final size:44
Alignment explanation
Indices: 21438286--21438901 Score: 602
Period size: 44 Copynumber: 14.0 Consensus size: 44
21438276 GCAGATCAGT
* * *
21438286 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * * *
21438330 GAAGATGTAGATCTTGTCTTCCCATATTGGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * *
21438374 GAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * *
21438418 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * *
21438462 GAAGATGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* *
21438505 GAAGATAGCAGATCATGTCTTCCTATATTGGTAGTGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * *
21438550 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * *
21438594 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * *
21438638 AAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * * *
21438682 GAAGATTCAGATCTTATCTTCCCATACTGGTAGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * * *
21438726 GAAGAAAGCAGACCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * * *
21438770 AAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * *
21438814 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
* * * *
21438858 GAAGAAAGCAGATCTTGTCTTCATTTATTGGCA-TGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
21438902 AAAAATAGCA
Statistics
Matches: 460, Mismatches: 96, Indels: 32
0.78 0.16 0.05
Matches are distributed among these distances:
42 1 0.00
43 103 0.22
44 255 0.55
45 101 0.22
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATC
Found at i:21438542 original size:132 final size:132
Alignment explanation
Indices: 21438286--21438911 Score: 812
Period size: 132 Copynumber: 4.7 Consensus size: 132
21438276 GCAGATCAGT
* * * * * * *
21438286 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGTAGATCTTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
*** * * * * * * * * *
21438349 TCCCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGT
65 TCATGTATTGG-CGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGT
*
21438413 AGATC
128 GGATC
* * * * * *
21438418 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* *
21438481 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCATGTCTTCCTATATTGGTAGTGAAGTG
65 TCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTG
21438546 GATC
129 GATC
* *
21438550 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
*
21438615 CATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
21438680 TC
131 TC
* * *
21438682 GAAGATTCAGATCTTATCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGACCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* *
21438747 CATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
21438812 TC
131 TC
*
21438814 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * *
21438879 CATTTATTGGCATGAAGTAGATCAAAAATAGCA
66 CATGTATTGGCGTGAAGTAGATCAAAGATAGCA
21438912 AGTCTTGCCT
Statistics
Matches: 456, Mismatches: 35, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
131 59 0.13
132 328 0.72
133 69 0.15
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
CATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
TC
Found at i:21438854 original size:220 final size:220
Alignment explanation
Indices: 21438301--21438888 Score: 716
Period size: 220 Copynumber: 2.7 Consensus size: 220
21438291 TAGCAGGTCC
* * * * * *
21438301 TGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGTAGATCTTGTCTTCCCATATTGGTGGCG
1 TGTCTTCATATATTGGTAGTGAAGTAGATCAAAAATGCAGATCCTGTCTTCCCATATTGGTGGCG
* *
21438365 GAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGATCGAAGATAGCAGG
66 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGG
* ** * * *
21438430 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCATGTATTGGCGT
131 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCACATACTGGAGC
* *
21438495 GAAGTAGATCGAAGATAGCAGATCA
196 GAAGTAGATCGAAGAAAGCAGACCA
* * * * * * *
21438520 TGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGTG
1 TGTCTTCATATATTGGTAGTGAAGTAGATCAAAAATGCAGATCCTGTCTTCCCATATTGGTGGCG
* *
21438585 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGG
66 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGG
* *
21438650 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATTCAGATCTTATCTTCCCATACTGGTAG
131 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCACATACTGG-AG
*
21438715 CGAAGTAGATCGAAGAAAGCAGACCT
195 CGAAGTAGATCGAAGAAAGCAGACCA
* * * * *
21438741 TGTCTTCATGTATTGG-CGTGAAGTAGATCAAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-
1 TGTCTTCATATATTGGTAGTGAAGTAGATCAAAAAT-GCAGATCCTGTCTTCCCATATTGGTGGC
* * ** * * * *
21438804 GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
65 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCGAAGATAGCA
* * * *
21438868 GATCTTGTCTTCATTTATTGG
129 GGTCCTGTCTTCCTATATTGG
21438889 CATGAAGTAG
Statistics
Matches: 323, Mismatches: 42, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
219 40 0.12
220 224 0.69
221 59 0.18
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (220 bp):
TGTCTTCATATATTGGTAGTGAAGTAGATCAAAAATGCAGATCCTGTCTTCCCATATTGGTGGCG
AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGG
TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCACATACTGGAGC
GAAGTAGATCGAAGAAAGCAGACCA
Found at i:21439121 original size:44 final size:44
Alignment explanation
Indices: 21439047--21439153 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
21439037 TGGCAAATTT
* * *
21439047 TATCTCCCTAAAGTTACAGTGGAACAGATTAAAGCC-GATAATCC
1 TATCTCCCTGAAGTTACAGTGGAACAGATTAAAACCTG-GAATCC
* * *
21439091 TATCTCCCTGAAGTTGCAGT-GAAGCGGATTAAAACCTGGAATCT
1 TATCTCCCTGAAGTTACAGTGGAA-CAGATTAAAACCTGGAATCC
*
21439135 TATCTCTCTGAAGTTACAG
1 TATCTCCCTGAAGTTACAG
21439154 AGAGCAGAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 3 0.06
44 49 0.92
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAACAGATTAAAACCTGGAATCC
Found at i:21439605 original size:19 final size:19
Alignment explanation
Indices: 21439581--21439657 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
21439571 AATCTTCGAG
21439581 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATGT
*
21439600 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATGT
*
21439619 GATATGTAATCTTAGAAGATGT
1 GATATGCAATCTT---AGATGT
*
21439641 GATTTTGCAATCTTAGA
1 GA-TATGCAATCTTAGA
21439658 GATTTAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 30 0.61
20 3 0.06
22 7 0.14
23 9 0.18
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATGT
Found at i:21439624 original size:38 final size:40
Alignment explanation
Indices: 21439581--21439657 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
21439571 AATCTTCGAG
21439581 GATATGCAATCTT-AGATGTGA-TATGCAATCTTAGATAT
1 GATATGCAATCTTAAGATGTGATTATGCAATCTTAGATAT
* *
21439619 GATATGTAATCTTAGAAGATGTGATTTTGCAATCTTAGA
1 GATATGCAATCTT--AAGATGTGATTATGCAATCTTAGA
21439658 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.36
41 8 0.24
42 13 0.39
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (40 bp):
GATATGCAATCTTAAGATGTGATTATGCAATCTTAGATAT
Found at i:21440191 original size:33 final size:33
Alignment explanation
Indices: 21440134--21440200 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
21440124 TTACAGTTCA
* *
21440134 AATTAGTCTTTTTCATTTTCTTTATTTTTTATT
1 AATTAGTCTTTTTCATTTTCTTTATATTTAATT
* *
21440167 AATTAGT-TTTTTTATTCTTTTTTATATTTAATT
1 AATTAGTCTTTTTCATT-TTCTTTATATTTAATT
21440200 A
1 A
21440201 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (33 bp):
AATTAGTCTTTTTCATTTTCTTTATATTTAATT
Found at i:21440309 original size:21 final size:22
Alignment explanation
Indices: 21440272--21440324 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
21440262 ATATAATTAT
*
21440272 TTATTTATTTATTTATATGTAA
1 TTATTTATTTATCTATATGTAA
21440294 TTATTT-TTTATCTATATGT-A
1 TTATTTATTTATCTATATGTAA
21440314 TATATTTATTT
1 T-TATTTATTT
21440325 TAGTATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 9 0.32
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
TTATTTATTTATCTATATGTAA
Found at i:21440317 original size:29 final size:28
Alignment explanation
Indices: 21440242--21440318 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 28
21440232 CATATACGCA
*
21440242 TATTTATTT-TTTGTAGTATA-ATATAAT
1 TATTTATTTATTTAT-GTATATATATAAT
*
21440269 TATTTATTTATTTAT-T-TATATGTAAT
1 TATTTATTTATTTATGTATATATATAAT
21440295 TATTT-TTTATCTATATGTATATAT
1 TATTTATTTAT-T-TATGTATATAT
21440319 TTATTTTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
25 7 0.17
26 13 0.31
27 12 0.29
28 5 0.12
29 5 0.12
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (28 bp):
TATTTATTTATTTATGTATATATATAAT
Found at i:21444217 original size:38 final size:38
Alignment explanation
Indices: 21444142--21444217 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
21444132 TGGCGACATT
* **
21444142 ATGAAAGTGGTTATCTATAGGCTCTACGCAGTGACACC
1 ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
*
21444180 ATGAAAATGGTTATCTATAGGCTCTACGGAGCAACACC
1 ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
21444218 TTGGAAGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (38 bp):
ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
Found at i:21455004 original size:12 final size:13
Alignment explanation
Indices: 21454987--21455015 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21454977 TTTCACATTT
21454987 TTTTATTTTCA-A
1 TTTTATTTTCACA
21454999 TTTTATTTTCACA
1 TTTTATTTTCACA
21455012 TTTT
1 TTTT
21455016 TCTGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTTTCACA
Found at i:21458050 original size:24 final size:24
Alignment explanation
Indices: 21458017--21458070 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21458007 TTTCTAGAAG
*
21458017 ATTTAGTATTTATTAGTATAATAT
1 ATTTAATATTTATTAGTATAATAT
* *
21458041 ATTTAATATTTATTAGTATAGTTT
1 ATTTAATATTTATTAGTATAATAT
21458065 ATTTAA
1 ATTTAA
21458071 CTTACTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (24 bp):
ATTTAATATTTATTAGTATAATAT
Found at i:21469248 original size:2 final size:2
Alignment explanation
Indices: 21469236--21469271 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
21469226 TTTATTCTTT
21469236 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21469272 TAGATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21470627 original size:11 final size:10
Alignment explanation
Indices: 21470608--21470691 Score: 52
Period size: 11 Copynumber: 8.4 Consensus size: 10
21470598 TCAGACGTGG
21470608 TTTTTAATAA
1 TTTTTAATAA
21470618 TTTTTAAATAA
1 TTTTT-AATAA
*
21470629 TTTTT--TTA
1 TTTTTAATAA
*
21470637 TTTTGAA-AA
1 TTTTTAATAA
* *
21470646 TAAATTTGAT-A
1 T--TTTTAATAA
21470657 TTTCTT-ATAA
1 TTT-TTAATAA
21470667 TTTTTAATAA
1 TTTTTAATAA
21470677 TTTTTAAATAA
1 TTTTT-AATAA
21470688 TTTT
1 TTTT
21470692 GTACCAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
8 6 0.11
9 7 0.12
10 20 0.35
11 24 0.42
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:21470691 original size:20 final size:20
Alignment explanation
Indices: 21470609--21470691 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
21470599 CAGACGTGGT
21470609 TTTTAATAATTTTTAAATAA
1 TTTTAATAATTTTTAAATAA
* * *
21470629 TTTT-TTTATTTTGAAAATAA
1 TTTTAATAATTTT-TAAATAA
* *
21470649 ATTTGAT-ATTTCTT--ATAA
1 TTTTAATAATTT-TTAAATAA
21470667 TTTTTAATAATTTTTAAATAA
1 -TTTTAATAATTTTTAAATAA
21470688 TTTT
1 TTTT
21470692 GTACCAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
18 4 0.08
19 13 0.27
20 25 0.52
21 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAATAATTTTTAAATAA
Found at i:21474841 original size:19 final size:20
Alignment explanation
Indices: 21474806--21474864 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
21474796 GATAATTTTA
*
21474806 AATTTTCTATTTCTATTTCTT
1 AATTTT-TATTTTTATTTCTT
21474827 -ATTTTTATTTTTATTT-TT
1 AATTTTTATTTTTATTTCTT
* *
21474845 AATTATAATTTTTATTTCTT
1 AATTTTTATTTTTATTTCTT
21474865 TTTAGCACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 24 0.73
20 7 0.21
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (20 bp):
AATTTTTATTTTTATTTCTT
Found at i:21474844 original size:7 final size:6
Alignment explanation
Indices: 21474807--21474861 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
21474797 ATAATTTTAA
* * *
21474807 ATTTTCT ATTTCT ATTTCTT ATTTTT ATTTTT ATTTTT AATTATA ATTTTT
1 ATTTT-T ATTTTT ATTT-TT ATTTTT ATTTTT ATTTTT -ATTTTT ATTTTT
21474858 ATTT
1 ATTT
21474862 CTTTTTAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 27 0.68
7 13 0.32
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:21478293 original size:23 final size:25
Alignment explanation
Indices: 21478258--21478333 Score: 92
Period size: 23 Copynumber: 3.3 Consensus size: 25
21478248 AATGTTGTTG
*
21478258 ATCAATGGTAGCTTTA-G-CTACAT
1 ATCAGTGGTAGCTTTACGACTACAT
*
21478281 TTCAGTGGTAGC--TACGACTACAT
1 ATCAGTGGTAGCTTTACGACTACAT
21478304 ATCAGTGGTAGC-TT-CGACTACAT
1 ATCAGTGGTAGCTTTACGACTACAT
21478327 ATCAGTG
1 ATCAGTG
21478334 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 43 0.91
24 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (25 bp):
ATCAGTGGTAGCTTTACGACTACAT
Found at i:21485458 original size:18 final size:17
Alignment explanation
Indices: 21485425--21485463 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
21485415 TTTTATAAAT
21485425 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
21485443 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
21485460 TGTG
1 TGTG
21485464 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:21485714 original size:23 final size:23
Alignment explanation
Indices: 21485681--21485756 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
21485671 AGTGTTGTTG
21485681 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
21485704 TTGAGTGGTAGCTACGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
21485727 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
21485750 ATCAGTG
1 ATCAGTG
21485757 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:21487496 original size:23 final size:23
Alignment explanation
Indices: 21487470--21487545 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
21487460 ATAAGTGTCA
* *
21487470 CACTGATATATAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21487493 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21487516 CACTG-TAATGTAGCCGTAGCTAC
1 CACTGAT-ATGTAGCCGAAGCTAC
21487539 CACTGAT
1 CACTGAT
21487546 CAATAACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21490725 original size:13 final size:13
Alignment explanation
Indices: 21490709--21490734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21490699 AAGAAAAGAA
21490709 AAGAAGAAGGGGC
1 AAGAAGAAGGGGC
21490722 AAGAAGAAGGGGC
1 AAGAAGAAGGGGC
21490735 TGATCCGTAT
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:0.08, G:0.46, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGGGGC
Found at i:21502981 original size:16 final size:17
Alignment explanation
Indices: 21502960--21502995 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
21502950 GGGTGGATTA
*
21502960 TTTCGAGTT-TGAGTTT
1 TTTCGAGTTATGACTTT
21502976 TTTCGAGTTATGACTTT
1 TTTCGAGTTATGACTTT
21502993 TTT
1 TTT
21502996 AGGTTCGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.14, C:0.08, G:0.19, T:0.58
Consensus pattern (17 bp):
TTTCGAGTTATGACTTT
Found at i:21513147 original size:2 final size:2
Alignment explanation
Indices: 21513140--21513170 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21513130 AAAATACAAC
21513140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21513171 TAAAACTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21521323 original size:13 final size:14
Alignment explanation
Indices: 21521300--21521328 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21521290 GATTTTTGTA
21521300 AAAACTATTTTTTT
1 AAAACTATTTTTTT
21521314 AAAA-TATTTTTTT
1 AAAACTATTTTTTT
21521327 AA
1 AA
21521329 TCAAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AAAACTATTTTTTT
Found at i:21529242 original size:47 final size:44
Alignment explanation
Indices: 21529182--21529270 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 44
21529172 GACTCCATGG
21529182 ATTTTGAAATTATA-TATTTTAACATGATTTTTAATATTTTTTAATA
1 ATTTTGAAATTATATTATTTTAA-AT-ATTTTTAA-ATTTTTTAATA
21529228 ATTTTGATAATTATATTTATTTTAAATATTTTTAAATTTTTTA
1 ATTTTGA-AATTATA-TTATTTTAAATATTTTTAAATTTTTTA
21529271 GAATTATTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
46 15 0.38
47 15 0.38
48 2 0.05
49 8 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (44 bp):
ATTTTGAAATTATATTATTTTAAATATTTTTAAATTTTTTAATA
Found at i:21530177 original size:28 final size:28
Alignment explanation
Indices: 21530124--21530179 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
21530114 GGCATAAGTG
* * *
21530124 TATATATTATAAATTTTTAAAGTTAAAA
1 TATATATTATAAATATTAAAAATTAAAA
21530152 TATATATTAT-AATATTAAAATATTAAAA
1 TATATATTATAAATATTAAAA-ATTAAAA
21530180 GTTAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TATATATTATAAATATTAAAAATTAAAA
Found at i:21530196 original size:5 final size:5
Alignment explanation
Indices: 21530188--21530221 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
21530178 AAGTTAAGTA
21530188 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
21530222 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:21530203 original size:36 final size:37
Alignment explanation
Indices: 21530124--21530206 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 37
21530114 GGCATAAGTG
* *
21530124 TATATATTATAAATTTTTAAAGTTAAAATATATATTA
1 TATATATTATAAATATTAAAAGTTAAAATATATATTA
*
21530161 TA-ATATTA-AAATATTAAAAGTT-AAGTATATATTA
1 TATATATTATAAATATTAAAAGTTAAAATATATATTA
21530195 TATTATATTATA
1 TA-TATATTATA
21530207 TTATATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 13 0.32
35 12 0.30
36 12 0.30
37 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATATTATAAATATTAAAAGTTAAAATATATATTA
Found at i:21530994 original size:24 final size:24
Alignment explanation
Indices: 21530967--21531013 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21530957 ATTGAAATGG
21530967 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
21530991 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
21531014 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:21531590 original size:31 final size:33
Alignment explanation
Indices: 21531555--21531622 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
21531545 CAAATGGTGA
* *
21531555 GAATTGAGTATGGAATGAATGATGT-ATT-TAT
1 GAATTGAATATGGAATGAATAATGTCATTGTAT
* *
21531586 GAATTGAATATTGAATGACTAATGTCATTGTAT
1 GAATTGAATATGGAATGAATAATGTCATTGTAT
21531619 GAAT
1 GAAT
21531623 AAATGTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 21 0.68
32 3 0.10
33 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (33 bp):
GAATTGAATATGGAATGAATAATGTCATTGTAT
Found at i:21532805 original size:26 final size:26
Alignment explanation
Indices: 21532765--21532817 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
21532755 AGTATTTACT
*
21532765 TAAAGAGGCTTTATGATTGAGGGTGG
1 TAAAGAGGCTATATGATTGAGGGTGG
21532791 TAAAGAGGCTATATGATTGAGGGTGG
1 TAAAGAGGCTATATGATTGAGGGTGG
21532817 T
1 T
21532818 GAATGAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.30
Consensus pattern (26 bp):
TAAAGAGGCTATATGATTGAGGGTGG
Found at i:21533349 original size:6 final size:6
Alignment explanation
Indices: 21533338--21533371 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
21533328 CTTAAAACAC
21533338 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAA
21533372 CACTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:21533540 original size:20 final size:20
Alignment explanation
Indices: 21533471--21533540 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
21533461 GTTTCTTTTG
* *
21533471 AATCGATTTTTTATTGTCTTA
1 AATCGATTCTTTGTTGT-TTA
*
21533492 AATTGATTCTTTGTTGTTTA
1 AATCGATTCTTTGTTGTTTA
*
21533512 AATCAATTCTTTGTTGTTTA
1 AATCGATTCTTTGTTGTTTA
*
21533532 ACTCGATTC
1 AATCGATTC
21533541 AAACGTCAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (20 bp):
AATCGATTCTTTGTTGTTTA
Found at i:21548214 original size:13 final size:13
Alignment explanation
Indices: 21548191--21548223 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21548181 TTGGGCTAGG
21548191 TGTAA-TTGGGTC
1 TGTAATTTGGGTC
*
21548203 TGTAATTTGGGTT
1 TGTAATTTGGGTC
21548216 TGTAATTT
1 TGTAATTT
21548224 TTGCTATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (13 bp):
TGTAATTTGGGTC
Found at i:21550082 original size:25 final size:24
Alignment explanation
Indices: 21550045--21550179 Score: 80
Period size: 25 Copynumber: 5.5 Consensus size: 24
21550035 AAATTGGTGC
21550045 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTT-GCATA
* * **
21550071 TTAATTCTGTCCAAATTAGTGC-T-
1 TTAATGCTGTCC-ATTTTTTGCATA
*
21550094 TAAATGCTGTCCATTTTTTGGCATA
1 TTAATGCTGTCCATTTTTT-GCATA
* **
21550119 TTAATGCTGTCCAAATTAGTGC-T-
1 TTAATGCTGTCC-ATTTTTTGCATA
* * *
21550142 TAAATGCTGTCCATTTTTTTACAAA
1 TTAATGCTGTCCA-TTTTTTGCATA
*
21550167 TCAATGCTGTCCA
1 TTAATGCTGTCCA
21550180 AATGTTGTTA
Statistics
Matches: 81, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
22 5 0.06
23 27 0.33
24 3 0.04
25 34 0.42
26 12 0.15
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (24 bp):
TTAATGCTGTCCATTTTTTGCATA
Found at i:21550103 original size:23 final size:23
Alignment explanation
Indices: 21550077--21550154 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
21550067 CATATTAATT
21550077 CTGTCCAAATTAGTGCTTAAATG
1 CTGTCCAAATTAGTGCTTAAATG
* ** *
21550100 CTGTCC-ATTTTTTGGCATATTAATG
1 CTGTCCAAATTAGT-GC-T-TAAATG
21550125 CTGTCCAAATTAGTGCTTAAATG
1 CTGTCCAAATTAGTGCTTAAATG
21550148 CTGTCCA
1 CTGTCCA
21550155 TTTTTTTACA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
22 4 0.09
23 20 0.47
24 2 0.05
25 13 0.30
26 4 0.09
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (23 bp):
CTGTCCAAATTAGTGCTTAAATG
Found at i:21550103 original size:48 final size:48
Alignment explanation
Indices: 21550026--21550182 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
21550016 TGATGATAAG
* * *
21550026 ATGCTATCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
* *
21550074 ATTCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
* *
21550122 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTA-CAAATCA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA-TTTTTTAGCATATTA
21550170 ATGCTGTCCAAAT
1 ATGCTGTCCAAAT
21550183 GTTGTTACTG
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 93 0.94
49 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (48 bp):
ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
Found at i:21553301 original size:16 final size:17
Alignment explanation
Indices: 21553280--21553312 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21553270 AAAACTAAAA
21553280 AAATA-TTACACTTTCC
1 AAATATTTACACTTTCC
*
21553296 AAATATTTACATTTTCC
1 AAATATTTACACTTTCC
21553313 TATTTTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTACACTTTCC
Found at i:21563482 original size:3 final size:3
Alignment explanation
Indices: 21563474--21563515 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
21563464 GAGTATTTGT
* * *
21563474 CTG CTG CTG CTG CTG CTG TTG CTG TTG CTG TTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
21563516 AATCTGGAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.26, G:0.33, T:0.40
Consensus pattern (3 bp):
CTG
Found at i:21563491 original size:12 final size:12
Alignment explanation
Indices: 21563474--21563515 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
21563464 GAGTATTTGT
*
21563474 CTGCTGCTGCTG
1 CTGCTGTTGCTG
21563486 CTGCTGTTGCTG
1 CTGCTGTTGCTG
*
21563498 TTGCTGTTGCTG
1 CTGCTGTTGCTG
21563510 CTGCTG
1 CTGCTG
21563516 AATCTGGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.33, T:0.40
Consensus pattern (12 bp):
CTGCTGTTGCTG
Found at i:21570549 original size:82 final size:81
Alignment explanation
Indices: 21570397--21570551 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 81
21570387 GCCCTCCCAA
* * * *
21570397 AAAATGAAAATCTTCAATTTAGTCCTCTTATAAATAAAAAAATTATAAATTAATATAAATCGAAA
1 AAAATGAAAATCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATAAATCAAAA
21570462 CTACACTTCACTCCTC
66 CTACACTTCACTCCTC
* * * *
21570478 AAAATGAAAATTTTTCAATTCAATTCTCTTGTAAATAAAGAAATTATAAATAAATATATAAT-AA
1 AAAATGAAAA-TCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATA-AATCAA
*
21570542 AATTACACTT
64 AACTACACTT
21570552 TAACCCCCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 10 0.16
82 50 0.79
83 3 0.05
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (81 bp):
AAAATGAAAATCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATAAATCAAAA
CTACACTTCACTCCTC
Found at i:21577280 original size:9 final size:9
Alignment explanation
Indices: 21577266--21577290 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21577256 TTCAAGTGCT
21577266 CTCAAAATG
1 CTCAAAATG
21577275 CTCAAAATG
1 CTCAAAATG
21577284 CTCAAAA
1 CTCAAAA
21577291 AGCCAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (9 bp):
CTCAAAATG
Found at i:21582138 original size:39 final size:40
Alignment explanation
Indices: 21582095--21582199 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
21582085 TTCCATTATG
21582095 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
21582134 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
21582179 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
21582200 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:21582193 original size:45 final size:44
Alignment explanation
Indices: 21582093--21582202 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
21582083 TTTTCCATTA
21582093 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
21582132 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
21582177 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
21582203 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:21582202 original size:16 final size:16
Alignment explanation
Indices: 21582181--21582234 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
21582171 TTGATTTGCT
*
21582181 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
21582197 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
21582213 AATACACCTTTAATCC
1 ATTACACCTCTAATCC
*
21582229 AATACA
1 ATTACA
21582235 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:21585380 original size:18 final size:18
Alignment explanation
Indices: 21585357--21585391 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21585347 TAAGGCTAAT
21585357 AAAAGAATCTAATCCTGC
1 AAAAGAATCTAATCCTGC
21585375 AAAAGAATCTAATCCTG
1 AAAAGAATCTAATCCTG
21585392 GATTTAAAGG
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:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAGAATCTAATCCTGC
Found at i:21591157 original size:13 final size:13
Alignment explanation
Indices: 21591141--21591165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21591131 AGTACTTCAA
21591141 AAAAAACACTTTG
1 AAAAAACACTTTG
21591154 AAAAAACACTTT
1 AAAAAACACTTT
21591166 TTTTTGGCTA
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:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAACACTTTG
Found at i:21592737 original size:28 final size:28
Alignment explanation
Indices: 21592685--21592754 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
21592675 AAATAAAAAA
*
21592685 TTACCAAAAT-TTTATACATTTTTTTAT
1 TTACCAAAATATATATACATTTTTTTAT
21592712 TTACCAAAATATATATA-ATTTTTTTTAT
1 TTACCAAAATATATATACA-TTTTTTTAT
21592740 TTACCAAAATATATA
1 TTACCAAAATATATA
21592755 AAAAACAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATACATTTTTTTAT
Found at i:21592857 original size:27 final size:27
Alignment explanation
Indices: 21592817--21592874 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 27
21592807 TCCCTGGGTG
21592817 AAGGGAACACTGTTGGCGGCACCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
21592844 AAGGGAAC-CTTGTTGGCGGCACCAAAC
1 AAGGGAACAC-TGTTGGCGGCACCAAAC
21592871 AAGG
1 AAGG
21592875 ATTCCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.33, C:0.24, G:0.31, T:0.12
Consensus pattern (27 bp):
AAGGGAACACTGTTGGCGGCACCAAAC
Found at i:21592886 original size:27 final size:27
Alignment explanation
Indices: 21592817--21592894 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
21592807 TCCCTGGGTG
* *
21592817 AAGGGAACACTGTTGGCGGCACCAAAC
1 AAGGGAACCCTATTGGCGGCACCAAAC
* *
21592844 AAGGGAACCTTGTTGGCGGCACCAAAC
1 AAGGGAACCCTATTGGCGGCACCAAAC
*
21592871 AA-GGATTCCCTATTGGCGGCACCA
1 AAGGGA-ACCCTATTGGCGGCACCA
21592895 CTCGTGTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 42 0.93
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (27 bp):
AAGGGAACCCTATTGGCGGCACCAAAC
Done.