Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 78 of 356
Found at i:24528967 original size:38 final size:38
Alignment explanation
Indices: 24528916--24528990 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
24528906 AAATACTAAA
24528916 GGCAGATAATATAAAGCGACAAAAGATTGATCAATAAT
1 GGCAGATAATATAAAGCGACAAAAGATTGATCAATAAT
24528954 GGCAGATAATATAAAGCGACAAAAGATTGATCAATAA
1 GGCAGATAATATAAAGCGACAAAAGATTGATCAATAA
24528991 AATCAAGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.20
Consensus pattern (38 bp):
GGCAGATAATATAAAGCGACAAAAGATTGATCAATAAT
Found at i:24530216 original size:6 final size:6
Alignment explanation
Indices: 24530207--24530243 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
24530197 CATGGTTATA
* *
24530207 GTAGAG GTAGAG GTAGAG GTAGAG GCAGAG GCAGAG G
1 GTAGAG GTAGAG GTAGAG GTAGAG GTAGAG GTAGAG G
24530244 CAGAAGAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (6 bp):
GTAGAG
Found at i:24530244 original size:6 final size:6
Alignment explanation
Indices: 24530209--24530247 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
24530199 TGGTTATAGT
* * *
24530209 AGAGGT AGAGGT AGAGGT AGAGGC AGAGGC AGAGGC AGA
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGA
24530248 AGAAGGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.49, T:0.08
Consensus pattern (6 bp):
AGAGGC
Found at i:24530244 original size:12 final size:12
Alignment explanation
Indices: 24530209--24530247 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
24530199 TGGTTATAGT
*
24530209 AGAGGTAGAGGT
1 AGAGGTAGAGGC
24530221 AGAGGTAGAGGC
1 AGAGGTAGAGGC
*
24530233 AGAGGCAGAGGC
1 AGAGGTAGAGGC
24530245 AGA
1 AGA
24530248 AGAAGGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.49, T:0.08
Consensus pattern (12 bp):
AGAGGTAGAGGC
Found at i:24537119 original size:22 final size:22
Alignment explanation
Indices: 24537069--24537110 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24537059 CCCAATTTTA
24537069 TTAT-TTATTTATTTTTAATTG
1 TTATATTATTTATTTTTAATTG
24537090 TTATATTATTTATTTTTAATT
1 TTATATTATTTATTTTTAATT
24537111 TACTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTATATTATTTATTTTTAATTG
Found at i:24537172 original size:16 final size:17
Alignment explanation
Indices: 24537145--24537188 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
24537135 ATTCTTATAC
*
24537145 TTATATTTTTAATTTTT
1 TTATACTTTTAATTTTT
24537162 TTATA-TTTTAATTTTT
1 TTATACTTTTAATTTTT
*
24537178 ATATACTTTTA
1 TTATACTTTTA
24537189 TTATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATACTTTTAATTTTT
Found at i:24537227 original size:14 final size:13
Alignment explanation
Indices: 24537158--24537237 Score: 52
Period size: 14 Copynumber: 5.5 Consensus size: 13
24537148 TATTTTTAAT
24537158 TTTTTTATATTTTAA
1 TTTTTT-TATTTT-A
24537173 TTTTTATATACTTTTA
1 TTTTT-T-TA-TTTTA
*
24537189 TTATTTTAATTTTTA
1 TT-TTTTTA-TTTTA
**
24537204 TTTTGCTATTTATA
1 TTTTTTTATTT-TA
*
24537218 TTTTTTTATTTTG
1 TTTTTTTATTTTA
24537231 TTTTTTT
1 TTTTTTT
24537238 TACTATTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.21
14 14 0.26
15 13 0.25
16 8 0.15
17 7 0.13
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:24537346 original size:24 final size:24
Alignment explanation
Indices: 24537291--24537346 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
24537281 TGAGATTATT
* *
24537291 ATTATTTTTTAACTTTCTTTTTAA
1 ATTATTTTTTAACTTTCTCTTCAA
* **
24537315 ATTTTTTTTTTTCTTTCTCTTCAA
1 ATTATTTTTTAACTTTCTCTTCAA
*
24537339 CTTATTTT
1 ATTATTTT
24537347 CATTATTATC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTATTTTTTAACTTTCTCTTCAA
Found at i:24545539 original size:12 final size:12
Alignment explanation
Indices: 24545506--24545546 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
24545496 CTAGGGAAAT
*
24545506 AAAAATGATATA
1 AAAAATGATTTA
24545518 AAAAAT-ATTTA
1 AAAAATGATTTA
24545529 AAAAATGATTTTA
1 AAAAATGA-TTTA
24545542 AAAAA
1 AAAAA
24545547 ATAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 7 0.27
13 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (12 bp):
AAAAATGATTTA
Found at i:24548113 original size:3 final size:3
Alignment explanation
Indices: 24548105--24548136 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24548095 AACAAATAGG
24548105 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
24548137 GGACTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:24549978 original size:44 final size:44
Alignment explanation
Indices: 24549925--24550881 Score: 380
Period size: 44 Copynumber: 20.8 Consensus size: 44
24549915 CCTTTATTTT
* * *
24549925 AATCCACTCCACTGTAATCTCAGGTAGATAGGATTACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
*
24549969 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * *
24550013 AATCTGCTCCATTGTAATCTCAGGGAGATAAGATCTGA-AATTTTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** ** **
24550059 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * *
24550103 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * *
24550157 AATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * **
24550201 AATCTACTCCGCTGTAATTTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* **
24550245 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * *
24550289 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * *
24550343 AATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * **
24550387 AATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * **
24550431 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * *
24550475 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * *
24550529 AATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * **
24550573 AATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* **
24550617 AATCTACTCCACTGTAACCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * * *
24550661 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAAATAAGATCCT-TTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * *
24550715 AATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * **
24550759 AATCTACTTCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * * **
24550803 AATCTGCTCCACTATAACCTCAGGGAGATAAGATCTAAAATTCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTA-TCTTC
**
24550849 GGTCTACTCCACTGTAATCTCAGGGAGATAAGA
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGA
24550882 CCTGTATAAT
Statistics
Matches: 726, Mismatches: 117, Indels: 138
0.74 0.12 0.14
Matches are distributed among these distances:
42 4 0.01
43 8 0.01
44 477 0.66
45 13 0.02
46 73 0.10
47 8 0.01
49 4 0.01
50 1 0.00
51 7 0.01
52 4 0.01
53 8 0.01
54 107 0.15
55 12 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
Found at i:24550247 original size:232 final size:232
Alignment explanation
Indices: 24549822--24550280 Score: 755
Period size: 232 Copynumber: 2.0 Consensus size: 232
24549812 GAAATTTATG
*
24549822 TTTTCAGTGTGTTCCACTGCAACATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
1 TTTTCAGTCTGTTCCACTGCAACATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
*
24549887 CTCTACTGTAACTTCAGAGAGATAATATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGTAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGTAG
* * *
24549952 ATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTCAATC
131 ATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATC
*
24550017 TGCTCCATTGTAATCTCAGGGAGATAAGATCTGAAAT
196 TGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT
* *
24550054 TTTTCGGTCTGTTCCACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCT
1 TTTTCAGTCTGTTCCACTGCAA-CATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCT
*
24550118 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGAG
65 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATC-TCAG-G
* *
24550182 -AGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATTTCAGAGAGATAAGATCT-CTGGCTTC
128 TAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGAT-TACTAGCTTC
24550245 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
192 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
24550281 CTGGCTTCAA
Statistics
Matches: 212, Mismatches: 11, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
231 1 0.00
232 208 0.98
233 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (232 bp):
TTTTCAGTCTGTTCCACTGCAACATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGTAG
ATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATC
TGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT
Found at i:24550287 original size:186 final size:186
Alignment explanation
Indices: 24549975--24550838 Score: 1489
Period size: 186 Copynumber: 4.6 Consensus size: 186
24549965 CTTCAATCTA
* * * * * ** *
24549975 CTCCGCTGTAA-TCTCAGGGAGATAAGATTACTATCTTCAATCTGCTCCATTGTAATCTCAGGGA
1 CTCCACTGTAACT-TCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGA
* ** ** * *
24550039 GATAAGATCTGAAAT-TTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
65 GATAAGATCT---CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTC
24550103 AATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
127 AATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
*
24550163 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATTTCAGAGAG
1 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
*
24550228 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
24550293 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
131 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
24550349 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
1 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
24550414 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
24550479 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
131 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
24550535 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
1 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
*
24550600 ATAAGATCTCTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
*
24550665 TGATGTGATCTACTCTACTGTAACTTCAGAGAAATAAGATCCTTTATTTTAATCCG
131 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
*
24550721 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTTCGCTGTAATCTCAGAGAG
1 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
*
24550786 ATAAGATCTCTGGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATCT
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
24550839 AAAATTCTTC
Statistics
Matches: 652, Mismatches: 22, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
185 1 0.00
186 587 0.90
188 63 0.10
189 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (186 bp):
CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATC
TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
Found at i:24550557 original size:98 final size:98
Alignment explanation
Indices: 24550388--24550577 Score: 233
Period size: 98 Copynumber: 1.9 Consensus size: 98
24550378 ACTAGCTTCA
* * *
24550388 ATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCTCA
* *
24550453 GGGAGATAAGATCT-CTGGCTTCAATCTGATGTG
66 GAGAGATAAGAT-TACTAGCTTCAATCTGATGTG
* * * * *
24550486 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACTT
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACCT
*
24550549 CAGAGAGATAGGATTACTAGCTTCAATCT
64 CAGAGAGATAAGATTACTAGCTTCAATCT
24550578 ACTCCGCTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
97 3 0.04
98 75 0.96
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (98 bp):
ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCTCA
GAGAGATAAGATTACTAGCTTCAATCTGATGTG
Found at i:24563760 original size:18 final size:18
Alignment explanation
Indices: 24563739--24563788 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
24563729 AAGATAACGT
*
24563739 TGGAGATGAAGATGTAGG
1 TGGAGATGGAGATGTAGG
24563757 TGGAGATGGAGATGTAGG
1 TGGAGATGGAGATGTAGG
24563775 TGGAGATGGAGATG
1 TGGAGATGGAGATG
24563789 GAGATAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (18 bp):
TGGAGATGGAGATGTAGG
Found at i:24563766 original size:6 final size:6
Alignment explanation
Indices: 24563739--24563793 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
24563729 AAGATAACGT
* * * * *
24563739 TGGAGA TGAAGA TGTAGG TGGAGA TGGAGA TGTAGG TGGAGA TGGAGA
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA
24563787 TGGAGA T
1 TGGAGA T
24563794 AAAGATGATG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (6 bp):
TGGAGA
Found at i:24563799 original size:12 final size:12
Alignment explanation
Indices: 24563739--24563800 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
24563729 AAGATAACGT
24563739 TGGAGATGAAGA
1 TGGAGATGAAGA
* * *
24563751 TGTAGGTGGAGA
1 TGGAGATGAAGA
* *
24563763 TGGAGATGTAGG
1 TGGAGATGAAGA
*
24563775 TGGAGATGGAGA
1 TGGAGATGAAGA
*
24563787 TGGAGATAAAGA
1 TGGAGATGAAGA
24563799 TG
1 TG
24563801 ATGAGCCAGA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.45, T:0.21
Consensus pattern (12 bp):
TGGAGATGAAGA
Found at i:24565590 original size:29 final size:32
Alignment explanation
Indices: 24565534--24565603 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
24565524 AATAATTCTA
24565534 AAAAAAATCTTTAAAATATATATAAATTATGT
1 AAAAAAATCTTTAAAATATATATAAATTATGT
* * *
24565566 AAAAATATTTTTAAAA-ATA-A-AAATTATGA
1 AAAAAAATCTTTAAAATATATATAAATTATGT
24565595 ATAAAAAAT
1 A-AAAAAAT
24565604 TTCTAGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.27
30 7 0.21
31 3 0.09
32 14 0.42
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (32 bp):
AAAAAAATCTTTAAAATATATATAAATTATGT
Found at i:24566742 original size:26 final size:26
Alignment explanation
Indices: 24566702--24566751 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
24566692 AAGTTTTGGC
24566702 TTTAATAAAACTTGG-TTTGATTTAT
1 TTTAATAAAACTTGGCTTTGATTTAT
*
24566727 TTTAATGAAAATTTGGCTTTGATTT
1 TTTAAT-AAAACTTGGCTTTGATTT
24566752 CTTAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (26 bp):
TTTAATAAAACTTGGCTTTGATTTAT
Found at i:24567247 original size:23 final size:23
Alignment explanation
Indices: 24567217--24567260 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
24567207 TTAAAGTATA
*
24567217 AATATGAAAA-ATTTGAAGGGCT
1 AATATGAAAATATTTAAAGGGCT
24567239 AATAGTGAAAATATTTAAAGGG
1 AATA-TGAAAATATTTAAAGGG
24567261 TGGAAGGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (23 bp):
AATATGAAAATATTTAAAGGGCT
Found at i:24567741 original size:19 final size:19
Alignment explanation
Indices: 24567717--24567754 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24567707 AATATCAAGT
24567717 TAGATTCATGAAAATAGAA
1 TAGATTCATGAAAATAGAA
24567736 TAGATTCATGAAAATAGAA
1 TAGATTCATGAAAATAGAA
24567755 GTTGGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
TAGATTCATGAAAATAGAA
Found at i:24568527 original size:16 final size:18
Alignment explanation
Indices: 24568495--24568527 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
24568485 TGGAAATTAA
24568495 GGGATAAATTATATATTT
1 GGGATAAATTATATATTT
24568513 GGGA-AAATT-TATATT
1 GGGATAAATTATATATT
24568528 AGAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (18 bp):
GGGATAAATTATATATTT
Found at i:24573077 original size:45 final size:45
Alignment explanation
Indices: 24573010--24573115 Score: 149
Period size: 45 Copynumber: 2.4 Consensus size: 45
24573000 AACCCTCGAC
* *
24573010 TTGGATCCTCATTCATAGACCCTCGAAATTACTTAAGGTGTTGAT
1 TTGGATCCTCATTCATAAACCCTCAAAATTACTTAAGGTGTTGAT
* * ** *
24573055 TTGGATCCTCACTCATAAACCCTTAAAATTGTTTAATGTGTTGAT
1 TTGGATCCTCATTCATAAACCCTCAAAATTACTTAAGGTGTTGAT
24573100 TTGGATCCTCATTCAT
1 TTGGATCCTCATTCAT
24573116 CTGGATCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TTGGATCCTCATTCATAAACCCTCAAAATTACTTAAGGTGTTGAT
Found at i:24574339 original size:21 final size:22
Alignment explanation
Indices: 24574315--24574355 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24574305 AAAACTTAAA
24574315 TAACAT-GAAACCAAAAGCATT
1 TAACATAGAAACCAAAAGCATT
* *
24574336 TAACATAGAAATCTAAAGCA
1 TAACATAGAAACCAAAAGCA
24574356 AGAAACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.20
Consensus pattern (22 bp):
TAACATAGAAACCAAAAGCATT
Found at i:24578089 original size:25 final size:25
Alignment explanation
Indices: 24578039--24578090 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
24578029 GATTTTTAAA
* *
24578039 AAAAATATATTTAACATTTTATATT
1 AAAAATATATTTAACATTATAAATT
*
24578064 AAAAATATATTT-TCATTATACAATT
1 AAAAATATATTTAACATTATA-AATT
24578089 AA
1 AA
24578091 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAAATATATTTAACATTATAAATT
Found at i:24582489 original size:21 final size:21
Alignment explanation
Indices: 24582462--24582503 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24582452 TATAATGTAC
* *
24582462 ATTTTTATATTAATTTTTTTGG
1 ATTTTAAT-TTAATTATTTTGG
24582484 ATTTTAATTTAATTATTTTG
1 ATTTTAATTTAATTATTTTG
24582504 ATTAATTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
ATTTTAATTTAATTATTTTGG
Found at i:24585429 original size:29 final size:30
Alignment explanation
Indices: 24585376--24585446 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
24585366 TTTTTATAAA
* *
24585376 TTTAAAATTTAGTCTATGT-ACTTTTA-TT
1 TTTAAAATTTAATCTATGTAATTTTTAGTT
* *
24585404 TTTAAAAATTTAATCTCTTTAATTTTTAGTT
1 TTT-AAAATTTAATCTATGTAATTTTTAGTT
24585435 TTTAAAATTTAA
1 TTTAAAATTTAA
24585447 GTTTAATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 13 0.36
30 15 0.42
31 5 0.14
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTAAAATTTAATCTATGTAATTTTTAGTT
Found at i:24589640 original size:66 final size:66
Alignment explanation
Indices: 24589509--24589633 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
24589499 CAAAAATGCC
* * * *
24589509 GCTATAGATCGAGAATTAGTGGCGCTTTTTAAAAATCGCCGCTATAGATCGAGCATTAGAAACGC
1 GCTATAGATCGAGAATTAGCGACGCTTTTAAAAAATCGCCGCTATAGATCGACCATTAGAAACGC
24589574 T
66 T
* * *
24589575 GCTATAGATTGAGCATTAGCGACGCTTTTCAAAAAAT-GCCGCTATAGGTCGACCATTAG
1 GCTATAGATCGAGAATTAGCGACGCTTTT-AAAAAATCGCCGCTATAGATCGACCATTAG
24589634 CGACGCTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 45 0.88
67 6 0.12
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (66 bp):
GCTATAGATCGAGAATTAGCGACGCTTTTAAAAAATCGCCGCTATAGATCGACCATTAGAAACGC
T
Found at i:24589932 original size:189 final size:189
Alignment explanation
Indices: 24589563--24589939 Score: 551
Period size: 189 Copynumber: 2.0 Consensus size: 189
24589553 TAGATCGAGC
* * * *
24589563 ATTAGAAACGCTGCTATAGATTGAGCATTAGCGACGCTTTTCAAAAAATGCCGCTATAGGTCGAC
1 ATTAGAAACGCTGCTATAGATCGAGCATTAGCGACGCTTTTCAAAAAACGCCACTACAGGTCGAC
*
24589628 CATTAGCGACGCTTTCTGAAAAACGCTGAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAG
66 CATTAGCGACGCTTTCTGAAAAACGCCGAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAG
* * *
24589693 CTTTACTGGCATTAGCGGCGCATTCCTAAAAACGCCGCTATAGATCGAGCATTAGCGGT
131 CTTTAATGGCATTAGCAGCGCATTCCTAAAAACGCCGCCATAGATCGAGCATTAGCGGT
* * *
24589752 ATTA-AAATGCTGCTATAGATCGAGCATTAGCGGCGCTTCTT-GAAAAACGCCACTACAGGTCGA
1 ATTAGAAACGCTGCTATAGATCGAGCATTAGCGACGCTT-TTCAAAAAACGCCACTACAGGTCGA
* * *
24589815 CCATTAGCGGCGCTTTCTGAAAAACGCCGCAAAAAAATTAAGCACAATGTCGTCGTTTTATGTTG
65 CCATTAGCGACGCTTTCTGAAAAACGCCG-AAAAAAATTAAGCACAACGTCGTCATTTTATGTTG
* ** * *
24589880 AGCTTTAATGGCATTAGCAGCGCTTTTTTAAAATCGCTGCCATAGATCGAGCATTAGCGG
129 AGCTTTAATGGCATTAGCAGCGCATTCCTAAAAACGCCGCCATAGATCGAGCATTAGCGG
24589940 CGCTTTTCGA
Statistics
Matches: 167, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
188 76 0.46
189 91 0.54
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (189 bp):
ATTAGAAACGCTGCTATAGATCGAGCATTAGCGACGCTTTTCAAAAAACGCCACTACAGGTCGAC
CATTAGCGACGCTTTCTGAAAAACGCCGAAAAAAATTAAGCACAACGTCGTCATTTTATGTTGAG
CTTTAATGGCATTAGCAGCGCATTCCTAAAAACGCCGCCATAGATCGAGCATTAGCGGT
Found at i:24590037 original size:21 final size:21
Alignment explanation
Indices: 24590008--24590118 Score: 93
Period size: 21 Copynumber: 5.3 Consensus size: 21
24589998 ATTAGTGTCA
* *
24590008 TTAGAGTTTATGGGTTATGGT
1 TTAGGGTTTATGGTTTATGGT
**
24590029 TTAGGGTTTATGGTTTATAAT
1 TTAGGGTTTATGGTTTATGGT
*
24590050 TTAGGGCTTA-GAGTTTATGGT
1 TTAGGGTTTATG-GTTTATGGT
* *
24590071 TTGGGGTTTATGGTTTGA-GAT
1 TTAGGGTTTATGGTTT-ATGGT
* *
24590092 TTAAGGTTTAAGGTTTA-GGAT
1 TTAGGGTTTATGGTTTATGG-T
24590113 TTAGGG
1 TTAGGG
24590119 GTAAATATGG
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
20 3 0.04
21 66 0.93
22 2 0.03
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTATGGT
Found at i:24590039 original size:14 final size:14
Alignment explanation
Indices: 24590013--24590118 Score: 74
Period size: 14 Copynumber: 7.6 Consensus size: 14
24590003 TGTCATTAGA
24590013 GTTTATGGG-TTATG
1 GTTTA-GGGTTTATG
24590027 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
*** *
24590041 GTTTATAATTTAGG
1 GTTTAGGGTTTATG
* *
24590055 GCTTAGAGTTTATG
1 GTTTAGGGTTTATG
*
24590069 GTTTGGGGTTTATG
1 GTTTAGGGTTTATG
* *
24590083 GTTT-GAGATTTAAG
1 GTTTAG-GGTTTATG
*
24590097 GTTTAAGGTTTA-G
1 GTTTAGGGTTTATG
24590110 GATTTAGGG
1 G-TTTAGGG
24590119 GTAAATATGG
Statistics
Matches: 72, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
13 6 0.08
14 66 0.92
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:24590085 original size:7 final size:7
Alignment explanation
Indices: 24590013--24590108 Score: 61
Period size: 7 Copynumber: 13.7 Consensus size: 7
24590003 TGTCATTAGA
24590013 GTTTATG
1 GTTTATG
*
24590020 GGTTATG
1 GTTTATG
*
24590027 GTTTAGG
1 GTTTATG
24590034 GTTTATG
1 GTTTATG
*
24590041 GTTTATA
1 GTTTATG
* *
24590048 ATTTAGG
1 GTTTATG
*
24590055 GCTTA-G
1 GTTTATG
24590061 AGTTTATG
1 -GTTTATG
**
24590069 GTTTGGG
1 GTTTATG
24590076 GTTTATG
1 GTTTATG
24590083 GTTTGA-G
1 GTTT-ATG
* *
24590090 ATTTAAG
1 GTTTATG
*
24590097 GTTTAAG
1 GTTTATG
24590104 GTTTA
1 GTTTA
24590109 GGATTTAGGG
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
6 2 0.03
7 64 0.94
8 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (7 bp):
GTTTATG
Found at i:24590628 original size:15 final size:15
Alignment explanation
Indices: 24590608--24590655 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
24590598 ACTATTTTAA
24590608 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
24590623 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* *
24590637 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
24590652 GGTT
1 GGTT
24590656 GGGGTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:24590628 original size:22 final size:20
Alignment explanation
Indices: 24590548--24590652 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 20
24590538 ATTGAATTAA
* *
24590548 TTATCATTATAGTTTAAGGT
1 TTATGATTATGGTTTAAGGT
* *
24590568 TTATGATTTAGGGTTTAAAGT
1 TTATGA-TTATGGTTTAAGGT
**
24590589 TTATGAGTTACTATTTTAAGGT
1 TTATGA-TTA-TGGTTTAAGGT
* *
24590611 TTATGGATTATGGGTTTAGGGA
1 TTAT-GATTAT-GGTTTAAGGT
*
24590633 TTATGGTTTATGGTTTAAGG
1 TTAT-GATTATGGTTTAAGG
24590653 GTTGGGGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.08
21 29 0.44
22 30 0.45
23 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.48
Consensus pattern (20 bp):
TTATGATTATGGTTTAAGGT
Found at i:24590646 original size:7 final size:7
Alignment explanation
Indices: 24590554--24590649 Score: 52
Period size: 7 Copynumber: 13.4 Consensus size: 7
24590544 TTAATTATCA
*
24590554 TTATAGT
1 TTATGGT
*
24590561 TTAAGGT
1 TTATGGT
*
24590568 TTATGAT
1 TTATGGT
*
24590575 TTAGGGT
1 TTATGGT
**
24590582 TTAAAGT
1 TTATGGT
24590589 TTATGAGT
1 TTATG-GT
24590597 TACTAT--T
1 T--TATGGT
*
24590604 TTAAGGT
1 TTATGGT
*
24590611 TTATGGA
1 TTATGGT
24590618 TTATGGGT
1 TTAT-GGT
* *
24590626 TTAGGGA
1 TTATGGT
24590633 TTATGGT
1 TTATGGT
24590640 TTATGGT
1 TTATGGT
24590647 TTA
1 TTA
24590650 AGGGTTGGGG
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
5 2 0.03
7 52 0.80
8 8 0.12
10 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:24590686 original size:21 final size:21
Alignment explanation
Indices: 24590637--24590683 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24590627 TAGGGATTAT
* *
24590637 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGCTTAAGGGTTGG
*
24590658 GGTTTAAGGCTTAATGGTTAGG
1 GGTTTAAGGCTTAAGGGTT-GG
24590680 GGTT
1 GGTT
24590684 AAGTGTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (21 bp):
GGTTTAAGGCTTAAGGGTTGG
Found at i:24591479 original size:114 final size:114
Alignment explanation
Indices: 24591238--24591583 Score: 509
Period size: 114 Copynumber: 3.1 Consensus size: 114
24591228 GGCATTTTTA
* *
24591238 GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGTATAAACGCCACAAAAGGTTATTCTG
1 GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGGATAAACGCCACTAAAGGTTATTCTG
* * * * *
24591303 -TTACA-CCAAACGAAGTCATTTTGTTGGATTTTTAGTGGCGTTTTAAG
66 TTTATATCAAAACGACGTCGTTTTGTTGGATTTTTAGTGGCGTTTTAGG
* * * * * *
24591350 GTAAAACACAGCAATAGGCTGGATTTAGCGGCGCTAGGGGATAAACGCCATTAACGGTTATTTTG
1 GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGGATAAACGCCACTAAAGGTTATTCTG
* *
24591415 TTTATATCAAAACGACGTCGTTTTGTTGGATTTTTAATGGCATTTTAGG
66 TTTATATCAAAACGACGTCGTTTTGTTGGATTTTTAGTGGCGTTTTAGG
* *
24591464 GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGGATAAATGCCACTAAAAGTTATTCTG
1 GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGGATAAACGCCACTAAAGGTTATTCTG
*
24591529 TTTATATCAAAACGACGTCGTTTTGTTGGATTTTT-GTGGTGTTTTAGG
66 TTTATATCAAAACGACGTCGTTTTGTTGGATTTTTAGTGGCGTTTTAGG
24591577 GTAAAAC
1 GTAAAAC
24591584 ACCTTTAGCC
Statistics
Matches: 206, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
112 57 0.28
113 21 0.10
114 128 0.62
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (114 bp):
GTAAAACGCCGCAATAGGTTGGATTTAGCGGCGCTAGGGGATAAACGCCACTAAAGGTTATTCTG
TTTATATCAAAACGACGTCGTTTTGTTGGATTTTTAGTGGCGTTTTAGG
Found at i:24594357 original size:9 final size:9
Alignment explanation
Indices: 24594300--24594460 Score: 96
Period size: 9 Copynumber: 17.9 Consensus size: 9
24594290 GTGTTAAAAT
*
24594300 TTACATAAG
1 TTACATAAC
24594309 TTACATAAC
1 TTACATAAC
*
24594318 GTACATAA-
1 TTACATAAC
* * *
24594326 ATATATATC
1 TTACATAAC
*
24594335 ATACCATAAC
1 TTA-CATAAC
*
24594345 TTACATAAT
1 TTACATAAC
24594354 TTACATAAC
1 TTACATAAC
*
24594363 ATACATAA-
1 TTACATAAC
* * *
24594371 ATATATATC
1 TTACATAAC
*
24594380 ATATCATAAC
1 TTA-CATAAC
24594390 TTACATAAC
1 TTACATAAC
* *
24594399 TTACATTAT
1 TTACATAAC
24594408 TTACATAAC
1 TTACATAAC
*
24594417 GTACATAA-
1 TTACATAAC
* * *
24594425 ATATAT-AT
1 TTACATAAC
24594433 TATATCATAAC
1 T-TA-CATAAC
24594444 TTACATAAC
1 TTACATAAC
24594453 TTACATAA
1 TTACATAA
24594461 GTAACTGTAA
Statistics
Matches: 118, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
7 1 0.01
8 15 0.13
9 84 0.71
10 16 0.14
11 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:24594360 original size:54 final size:54
Alignment explanation
Indices: 24594300--24594462 Score: 218
Period size: 54 Copynumber: 3.2 Consensus size: 54
24594290 GTGTTAAAAT
24594300 TTACATAAGTTACATAACGTACAT--A-A-ATAT-ATATCAT-AC---CATAAC
1 TTACATAAGTTACATAACGTACATAAATATATATCATATCATAACTTACATAAC
* *
24594345 TTACATAATTTACATAACATACATAAATATATATCATATCATAACTTACATAAC
1 TTACATAAGTTACATAACGTACATAAATATATATCATATCATAACTTACATAAC
* * *
24594399 TTACATTATTTACATAACGTACATAAATATATATTATATCATAACTTACATAAC
1 TTACATAAGTTACATAACGTACATAAATATATATCATATCATAACTTACATAAC
24594453 TTACATAAGT
1 TTACATAAGT
24594463 AACTGTAACT
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
45 22 0.22
47 1 0.01
48 1 0.01
49 4 0.04
50 7 0.07
51 2 0.02
54 65 0.64
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (54 bp):
TTACATAAGTTACATAACGTACATAAATATATATCATATCATAACTTACATAAC
Found at i:24594368 original size:45 final size:45
Alignment explanation
Indices: 24594300--24594460 Score: 187
Period size: 45 Copynumber: 3.4 Consensus size: 45
24594290 GTGTTAAAAT
*
24594300 TTACATAAGTTACATAACGTACATAAATATATATCATACCATAAC
1 TTACATAATTTACATAACGTACATAAATATATATCATACCATAAC
*
24594345 TTACATAATTTACATAACATACATAAATATATATCATATCATAACTTACATAAC
1 TTACATAATTTACATAACGTACAT--A-A-ATAT-ATATCAT-AC---CATAAC
* * *
24594399 TTACATTATTTACATAACGTACATAAATATATATTATATCATAAC
1 TTACATAATTTACATAACGTACATAAATATATATCATACCATAAC
*
24594444 TTACATAACTTACATAA
1 TTACATAATTTACATAA
24594461 GTAACTGTAA
Statistics
Matches: 99, Mismatches: 8, Indels: 18
0.79 0.06 0.14
Matches are distributed among these distances:
45 43 0.43
47 1 0.01
48 2 0.02
49 10 0.10
50 11 0.11
51 3 0.03
52 1 0.01
54 28 0.28
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (45 bp):
TTACATAATTTACATAACGTACATAAATATATATCATACCATAAC
Found at i:24600329 original size:43 final size:43
Alignment explanation
Indices: 24600281--24600436 Score: 179
Period size: 43 Copynumber: 3.6 Consensus size: 43
24600271 TTTTTTAGCA
*
24600281 GCGTTTGTGGCAAAAGCGCCGCTAAAAAACATGACCTTTGGCG
1 GCGTTTGTGGCAAAAACGCCGCTAAAAAACATGACCTTTGGCG
* * *
24600324 GCGTTTGTGTCAAAAACGCCGCTAAAGAACATGACCTTTGGTG
1 GCGTTTGTGGCAAAAACGCCGCTAAAAAACATGACCTTTGGCG
** * * * * *
24600367 GCGCTTT-TATCAAAAATGTCGTTAAAGAACATGACCTTTAGCG
1 GCG-TTTGTGGCAAAAACGCCGCTAAAAAACATGACCTTTGGCG
* *
24600410 GCATTTGTGGCAAAAGCGCCGCTAAAA
1 GCGTTTGTGGCAAAAACGCCGCTAAAA
24600437 GTCATGTTAT
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 3 0.03
43 87 0.94
44 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (43 bp):
GCGTTTGTGGCAAAAACGCCGCTAAAAAACATGACCTTTGGCG
Found at i:24600949 original size:86 final size:85
Alignment explanation
Indices: 24600582--24601031 Score: 469
Period size: 87 Copynumber: 5.3 Consensus size: 85
24600572 TATTGCAGTG
* * * * * * * *
24600582 TCTGTTAAATGGCGGGATTAAATCTCGAAACAGA--TTATTCAA-TTAAATTCTAATTTGGAAAC
1 TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTCTATTTTGGAAAT
* *
24600644 AACATCAAAATTGAATAAAA
66 AAAATCAAAATGGAATAAAA
* ** *
24600664 TCTGTTAAACGAAGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTTCT-TGTTT-GAC
1 TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAA-TTCTAT-TTTGGA-
*
24600727 AACAAAATCAAGAATGGAATAAAA
63 AATAAAATCAA-AATGGAATAAAA
* * * * *
24600751 TCTATTGAACAGCGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATACTCTTTTGGAAAC
1 TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTCTATTTTGGAAA-
* *
24600816 AAAAATAAAGAATGGAATAAAA
65 TAAAATCAA-AATGGAATAAAA
* * *
24600838 TCTGTTGAACGACGAGAATAAATCCCGAAATAGATTTTATTTAATTTTAATTCTAATTTTGGAAA
1 TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTCT-ATTTTGGAAA
*
24600903 TAAAATCAAAATAGAATAAAA
65 TAAAATCAAAATGGAATAAAA
* * * * * **
24600924 TTTATTGAACGGTGGGAATAAATCCCGAAACAAATTTTATTTAACTTTAATTCTCGTTTGGAAAT
1 TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTCTATTTTGGAAAT
* *
24600989 AAAATAAAAATGAAATAAAA
66 AAAATCAAAATGGAATAAAA
**
24601009 TCTGTTGAACCACGGGAATAAAT
1 TCTGTTGAACGGCGGGAATAAAT
24601032 AATAAATCCC
Statistics
Matches: 309, Mismatches: 48, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
82 28 0.09
84 7 0.02
85 50 0.16
86 82 0.27
87 133 0.43
88 9 0.03
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (85 bp):
TCTGTTGAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTCTATTTTGGAAAT
AAAATCAAAATGGAATAAAA
Found at i:24601216 original size:22 final size:21
Alignment explanation
Indices: 24601189--24601230 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
24601179 TAGCGAACAA
24601189 AAATATATAAATATAAATAAAC
1 AAATATATAAATA-AAATAAAC
* *
24601211 AAATATTTATATAAAATAAA
1 AAATATATAAATAAAATAAA
24601231 TTAAGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATATAAATAAAATAAAC
Found at i:24601712 original size:20 final size:20
Alignment explanation
Indices: 24601671--24601719 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
24601661 AGGGGTAATT
* *
24601671 AAATCAATTTGATTAAAGTC
1 AAATCAAATTGACTAAAGTC
24601691 AAATCAAATTGACTAGAA-TC
1 AAATCAAATTGACTA-AAGTC
*
24601711 AAATAAAAT
1 AAATCAAAT
24601720 CAAGATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGACTAAAGTC
Found at i:24603467 original size:40 final size:40
Alignment explanation
Indices: 24603383--24603515 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
24603373 TTTTGAGCCT
* *
24603383 TCGAGGCATTAGCGACGCTTTTTCAAGAAATGCCGCTATAGA
1 TCGA-GCATTAGCGACGCTTTTTGAA-AAACGCCGCTATAGA
*
24603425 TCGAG-ATTTAGCGGCGCTTTTTGAAAAACGCCGCTATAGA
1 TCGAGCA-TTAGCGACGCTTTTTGAAAAACGCCGCTATAGA
*
24603465 TCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGG
1 TCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGA
*
24603505 TCAAGCATTAG
1 TCGAGCATTAG
24603516 TGGCGTTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
40 61 0.73
41 18 0.22
42 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (40 bp):
TCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGA
Found at i:24603526 original size:40 final size:40
Alignment explanation
Indices: 24603383--24603532 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
24603373 TTTTGAGCCT
* * *
24603383 TCGAGGCATTAGCGACGCTTTTTCAAGAAATGCCGCTATAGA
1 TCGA-GCATTAGCGGCGCTTTTTGAA-AAACGCCGCTATAGA
24603425 TCGAG-ATTTAGCGGCGCTTTTTGAAAAACGCCGCTATAGA
1 TCGAGCA-TTAGCGGCGCTTTTTGAAAAACGCCGCTATAGA
* *
24603465 TCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGG
1 TCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGA
* * * *
24603505 TCAAGCATTAGTGGCGTTTTTTAAAAAA
1 TCGAGCATTAGCGGCGCTTTTTGAAAAA
24603533 ATCCGTAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 74 0.77
41 18 0.19
42 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (40 bp):
TCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGA
Found at i:24603533 original size:81 final size:82
Alignment explanation
Indices: 24603383--24603532 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 82
24603373 TTTTGAGCCT
* * *
24603383 TCGAGGCATTAGCGACGCTTTTTCAAGAAATGCCGCTATAGATCGAGATTTAGCGGCGCTTTTTG
1 TCGAGGCATTAGCGACGCTTTTTCAAGAAACGCCGCTATAGATCAAGATTTAGCGGCGCTTTTTA
24603448 AAAAACGCCGCTATAGA
66 AAAAACGCCGCTATAGA
* * * *
24603465 TCGA-GCATTAGCGACGCTTTTTGAA-AAACGCCGCTATAGGTCAAGCA-TTAGTGGCGTTTTTT
1 TCGAGGCATTAGCGACGCTTTTTCAAGAAACGCCGCTATAGATCAAG-ATTTAGCGGCGCTTTTT
24603527 AAAAAA
65 AAAAAA
24603533 ATCCGTAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 35 0.58
81 21 0.35
82 4 0.07
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (82 bp):
TCGAGGCATTAGCGACGCTTTTTCAAGAAACGCCGCTATAGATCAAGATTTAGCGGCGCTTTTTA
AAAAACGCCGCTATAGA
Found at i:24604001 original size:15 final size:15
Alignment explanation
Indices: 24603981--24604017 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24603971 AATATTTTAA
24603981 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
24603996 GGTTTAGGGATTATG
1 GGTTTATGGATTATG
*
24604011 AGTTTAT
1 GGTTTAT
24604018 AGTTTAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:24604036 original size:37 final size:37
Alignment explanation
Indices: 24603995--24604067 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
24603985 TATGGATTAT
*
24603995 GGGTTTAGGGATTATGAGTTTATAGTTTAAGGTTTAG
1 GGGTTTAGGGATTATGAGTTAATAGTTTAAGGTTTAG
* * *
24604032 GGGTTTATGGTTTATGAGTTAATATTTTAAGGTTTA
1 GGGTTTAGGGATTATGAGTTAATAGTTTAAGGTTTA
24604068 TGGATTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.47
Consensus pattern (37 bp):
GGGTTTAGGGATTATGAGTTAATAGTTTAAGGTTTAG
Found at i:24604323 original size:15 final size:15
Alignment explanation
Indices: 24604300--24604425 Score: 75
Period size: 15 Copynumber: 8.5 Consensus size: 15
24604290 AGTTAATGGC
24604300 TAAGGGTTTAGGGGT
1 TAAGGGTTTAGGGGT
* **
24604315 TAGGGGTTTAGGATT
1 TAAGGGTTTAGGGGT
*
24604330 TAA-GGTTTAGAGGT
1 TAAGGGTTTAGGGGT
* *
24604344 TAAAGGTTTAGGAGT
1 TAAGGGTTTAGGGGT
*
24604359 TATA-TG-TTAGGGGTT
1 TA-AGGGTTTAGGGG-T
*
24604374 TAAGGGTTAATGGGGCT
1 TAAGGGTTTA-GGGG-T
*
24604391 T--GGG-TTAGAGGT
1 TAAGGGTTTAGGGGT
*
24604403 TAAGGGTTTAGGAGT
1 TAAGGGTTTAGGGGT
*
24604418 TAGGGGTT
1 TAAGGGTT
24604426 AAGGCATTAA
Statistics
Matches: 83, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
12 2 0.02
13 3 0.04
14 23 0.28
15 46 0.55
16 3 0.04
17 6 0.07
ACGTcount: A:0.23, C:0.01, G:0.40, T:0.36
Consensus pattern (15 bp):
TAAGGGTTTAGGGGT
Found at i:24604336 original size:29 final size:30
Alignment explanation
Indices: 24604304--24604378 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 30
24604294 AATGGCTAAG
** *
24604304 GGTTTAGGGGTTAGGGGTTTAGGATTTA-A
1 GGTTTAGGGGTTAAAGGTTTAGGAGTTATA
*
24604333 GGTTTAGAGGTTAAAGGTTTAGGAGTTATA
1 GGTTTAGGGGTTAAAGGTTTAGGAGTTATA
* *
24604363 TG-TTAGGGGTTTAAGG
1 GGTTTAGGGGTTAAAGG
24604379 GTTAATGGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (30 bp):
GGTTTAGGGGTTAAAGGTTTAGGAGTTATA
Found at i:24604626 original size:16 final size:16
Alignment explanation
Indices: 24604573--24604626 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
24604563 ATATTAAATA
*
24604573 ATTTCAAATTTTAAAG
1 ATTTCAAATTTTCAAG
24604589 ATTTCAAATTTTC-A-
1 ATTTCAAATTTTCAAG
24604603 A--T--AATTTTCAAG
1 ATTTCAAATTTTCAAG
24604615 ATTTCAAATTTT
1 ATTTCAAATTTT
24604627 ATCTAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 1 0.03
12 2 0.06
14 2 0.06
15 1 0.03
16 18 0.58
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTCAAATTTTCAAG
Found at i:24607211 original size:13 final size:14
Alignment explanation
Indices: 24607195--24607223 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24607185 TTATAAATAT
24607195 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
24607208 TTATAATGGTTTAA
1 TTATAATGGTTTAA
24607222 TT
1 TT
24607224 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:24610246 original size:24 final size:22
Alignment explanation
Indices: 24610194--24610249 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
24610184 AACGAGAAAA
*
24610194 GAAATAAAAATAAAATAATAAC
1 GAAATAAAAATAAAAAAATAAC
24610216 GACAATAATAAATAATAAAAATACAC
1 GA-AATAA-AAATAA-AAAAATA-AC
24610242 -AAATAAAA
1 GAAATAAAA
24610250 GGGCATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.07
23 7 0.24
24 11 0.38
25 7 0.24
26 2 0.07
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (22 bp):
GAAATAAAAATAAAAAAATAAC
Found at i:24622967 original size:21 final size:21
Alignment explanation
Indices: 24622933--24622973 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24622923 AGATGAGCGA
* * *
24622933 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTAGAGTG
24622954 TACTCCAAAACAGGTAGAGT
1 TACTCCAAAACAGGTAGAGT
24622974 TTAAGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:24626340 original size:15 final size:16
Alignment explanation
Indices: 24626320--24626359 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
24626310 AAAATAACTT
24626320 AATATTCTATATT-AA
1 AATATTCTATATTAAA
24626335 AATATTCT-T-TTAAA
1 AATATTCTATATTAAA
*
24626349 AATATTATATA
1 AATATTCTATA
24626360 ATAGTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTCTATATTAAA
Found at i:24627289 original size:23 final size:23
Alignment explanation
Indices: 24627247--24627310 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 23
24627237 AAAAAATTTA
*
24627247 TAATATTATTAATTAGTTTTGATAGT
1 TAATATTATTAATTA-TTTTCA-A-T
24627273 TAATATTATTAA-T-TTTTCAAT
1 TAATATTATTAATTATTTTCAAT
24627294 TAA-ATTATTAAATTATT
1 TAATATTATT-AATTATT
24627311 ACATAGTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 6 0.18
21 6 0.18
22 2 0.06
23 7 0.21
25 1 0.03
26 12 0.35
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TAATATTATTAATTATTTTCAAT
Found at i:24630462 original size:13 final size:13
Alignment explanation
Indices: 24630444--24630469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24630434 CACACAAATC
24630444 TCATATCATAATA
1 TCATATCATAATA
24630457 TCATATCATAATA
1 TCATATCATAATA
24630470 ATCAATCCAC
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:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATATCATAATA
Found at i:24633874 original size:17 final size:16
Alignment explanation
Indices: 24633829--24633880 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
24633819 AATCACTTTT
* *
24633829 ATATTAAATTAATATA
1 ATATTATATTAAAATA
*
24633845 ATATT-TATCAAAATAA
1 ATATTATATTAAAAT-A
24633861 ATATTATATTAAAATTA
1 ATATTATATTAAAA-TA
24633878 ATA
1 ATA
24633881 ATAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.21
16 11 0.38
17 11 0.38
18 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTATATTAAAATA
Found at i:24633880 original size:21 final size:22
Alignment explanation
Indices: 24633855--24633902 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
24633845 ATATTTATCA
24633855 AAATAAATATTATATTAAAATTAAT
1 AAATAAATA-T-TATTAAAA-TAAT
24633880 -AATAAATATTATTAAAATAAT
1 AAATAAATATTATTAAAATAAT
24633901 AA
1 AA
24633903 TAAGATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 1 0.05
24 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATAAATATTATTAAAATAAT
Found at i:24633903 original size:21 final size:24
Alignment explanation
Indices: 24633856--24633905 Score: 79
Period size: 21 Copynumber: 2.2 Consensus size: 24
24633846 TATTTATCAA
24633856 AATAAATATTATATTAAAATTAAT
1 AATAAATATTATATTAAAATTAAT
24633880 AATAAATA-T-TATTAAAA-TAAT
1 AATAAATATTATATTAAAATTAAT
24633901 AATAA
1 AATAA
24633906 GATAAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 1 0.04
24 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAAATATTATATTAAAATTAAT
Found at i:24636019 original size:752 final size:752
Alignment explanation
Indices: 24634575--24636085 Score: 2914
Period size: 752 Copynumber: 2.0 Consensus size: 752
24634565 ATATCCAGAA
24634575 GCATCGTTCTGATAATTCACAATTACTTAATCATGGAGTCAATCTACAAGAAATACCATGATTGA
1 GCATCGTTCTGATAATTCACAATTACTTAATCATGGAGTCAATCTACAAGAAATACCATGATTGA
24634640 AAACTCCTTATTGTATACTCTTTACGAAAGTAATTCACCCAACTGCTTTGTTCAATGACCTCGTC
66 AAACTCCTTATTGTATACTCTTTACGAAAGTAATTCACCCAACTGCTTTGTTCAATGACCTCGTC
24634705 ATGTGTGCGTTACCCTCATATAATATCCTTGATTCCTTTGAGTTAAATCCATTTACTCAATACAA
131 ATGTGTGCGTTACCCTCATATAATATCCTTGATTCCTTTGAGTTAAATCCATTTACTCAATACAA
24634770 TCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGTCACTGTCAACAAATG
196 TCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGTCACTGTCAACAAATG
24634835 ATAAATTGCCCATTCGAGAAGTAACAACCCGTGGCCACATTTCATATTTATCAATCCACACAATG
261 ATAAATTGCCCATTCGAGAAGTAACAACCCGTGGCCACATTTCATATTTATCAATCCACACAATG
24634900 CCAATGAAAGGATATCATTTACTCTTTAATTGAGCTATGGATTCCACTGTTGCTAGTAAAGCCAT
326 CCAATGAAAGGATATCATTTACTCTTTAATTGAGCTATGGATTCCACTGTTGCTAGTAAAGCCAT
*
24634965 GCCATACACAAGTCATGTACCCAACATACCGACTATGGGCTTGATCATTTTTAGAACATAAGTAT
391 GCCATACACAAGTCATGTACCCAACATACCGACTATAGGCTTGATCATTTTTAGAACATAAGTAT
*
24635030 ACACTCATATTAAAGTACATGAGTTGCATATGCATGGTCAGTGACTAACACAAGATTTAGGTAAA
456 ACACTCATATTAAAGTACATGAGTTGCATACGCATGGTCAGTGACTAACACAAGATTTAGGTAAA
24635095 TTACACTATGAACGTCACAAGTAAATTAATTCACAAAAAGATTCAGAATTAATTCATCTTGAGTT
521 TTACACTATGAACGTCACAAGTAAATTAATTCACAAAAAGATTCAGAATTAATTCATCTTGAGTT
24635160 GTAACAGTCGATTTTTTAGTGGTGTCAGGAATAGTAGTTTCAGGATAAAAAATCTAACGTGTCAA
586 GTAACAGTCGATTTTTTAGTGGTGTCAGGAATAGTAGTTTCAGGATAAAAAATCTAACGTGTCAA
*
24635225 TTCATAAAATTTATTAGCTAAATATTTATGAGGTCATTAGTGTAATACTAAAATTTGGTTATGAG
651 TTCATAAAATTTATTAGCTAAATATTTACGAGGTCATTAGTGTAATACTAAAATTTGGTTATGAG
24635290 ATTATAATATTTAAATAGTTACTTAGTAAAAAGGACT
716 ATTATAATATTTAAATAGTTACTTAGTAAAAAGGACT
24635327 GCATCGTTCTGATAATTCACAATTACTTAATCATGGAGTCAATCTACAAGAAATACCATGATTGA
1 GCATCGTTCTGATAATTCACAATTACTTAATCATGGAGTCAATCTACAAGAAATACCATGATTGA
*
24635392 AAACTCCTTATTGTATACTCTTTACGAAAGTAATTCATCCAACTGCTTTGTTCAATGACCTCGTC
66 AAACTCCTTATTGTATACTCTTTACGAAAGTAATTCACCCAACTGCTTTGTTCAATGACCTCGTC
24635457 ATGTGTGCGTTACCCTCATATAATATCCTTGATTCCTTTGAGTTAAATCCATTTACTCAATACAA
131 ATGTGTGCGTTACCCTCATATAATATCCTTGATTCCTTTGAGTTAAATCCATTTACTCAATACAA
24635522 TCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGTCACTGTCAACAAATG
196 TCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGTCACTGTCAACAAATG
*
24635587 ATAAATTGCTCATTCGAGAAGTAACAACCCGTGGCCACATTTCATATTTATCAATCCACACAATG
261 ATAAATTGCCCATTCGAGAAGTAACAACCCGTGGCCACATTTCATATTTATCAATCCACACAATG
*
24635652 CCAATGAGAGGATATCATTTACTCTTTAATTGAGCTATGGATTCCACTGTTGCTAGTAAAGCCAT
326 CCAATGAAAGGATATCATTTACTCTTTAATTGAGCTATGGATTCCACTGTTGCTAGTAAAGCCAT
24635717 GCCATACACAAGTCATGTACCCAACATACCGACTATAGGCTTGATCATTTTTAGAACATAAGTAT
391 GCCATACACAAGTCATGTACCCAACATACCGACTATAGGCTTGATCATTTTTAGAACATAAGTAT
*
24635782 ACACTCATATTAAAGTACATGAGTTGCATACGCATGGTCAGTGACTAATACAAGATTTAGGTAAA
456 ACACTCATATTAAAGTACATGAGTTGCATACGCATGGTCAGTGACTAACACAAGATTTAGGTAAA
*
24635847 TTACACTATGAACGTCACAAGTGAATTAATTCACAAAAAGATTCAGAATTAATTCATCTTGAGTT
521 TTACACTATGAACGTCACAAGTAAATTAATTCACAAAAAGATTCAGAATTAATTCATCTTGAGTT
* *
24635912 GTAACAGTCGATTTTTTTGTGGTGTCAGGAATAGTAGTTTCAGGATAAAAAATCTGACGTGTCAA
586 GTAACAGTCGATTTTTTAGTGGTGTCAGGAATAGTAGTTTCAGGATAAAAAATCTAACGTGTCAA
*
24635977 TTCATAAAATTTATTAGTTAAATATTTACGAGGTCATTAGTGTAATACTAAAATTTGGTTATGAG
651 TTCATAAAATTTATTAGCTAAATATTTACGAGGTCATTAGTGTAATACTAAAATTTGGTTATGAG
24636042 ATTATAATATTTAAATAGTTACTTAGTAAAAAGGACT
716 ATTATAATATTTAAATAGTTACTTAGTAAAAAGGACT
*
24636079 GAATCGT
1 GCATCGT
24636086 AAAAGCTATA
Statistics
Matches: 747, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
752 747 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (752 bp):
GCATCGTTCTGATAATTCACAATTACTTAATCATGGAGTCAATCTACAAGAAATACCATGATTGA
AAACTCCTTATTGTATACTCTTTACGAAAGTAATTCACCCAACTGCTTTGTTCAATGACCTCGTC
ATGTGTGCGTTACCCTCATATAATATCCTTGATTCCTTTGAGTTAAATCCATTTACTCAATACAA
TCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGTCACTGTCAACAAATG
ATAAATTGCCCATTCGAGAAGTAACAACCCGTGGCCACATTTCATATTTATCAATCCACACAATG
CCAATGAAAGGATATCATTTACTCTTTAATTGAGCTATGGATTCCACTGTTGCTAGTAAAGCCAT
GCCATACACAAGTCATGTACCCAACATACCGACTATAGGCTTGATCATTTTTAGAACATAAGTAT
ACACTCATATTAAAGTACATGAGTTGCATACGCATGGTCAGTGACTAACACAAGATTTAGGTAAA
TTACACTATGAACGTCACAAGTAAATTAATTCACAAAAAGATTCAGAATTAATTCATCTTGAGTT
GTAACAGTCGATTTTTTAGTGGTGTCAGGAATAGTAGTTTCAGGATAAAAAATCTAACGTGTCAA
TTCATAAAATTTATTAGCTAAATATTTACGAGGTCATTAGTGTAATACTAAAATTTGGTTATGAG
ATTATAATATTTAAATAGTTACTTAGTAAAAAGGACT
Found at i:24639015 original size:39 final size:39
Alignment explanation
Indices: 24638961--24639039 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
24638951 GATGATCCGC
*
24638961 AACAAATGCTAAATCATCAAATGACATGATATAACTCTA
1 AACAAATACTAAATCATCAAATGACATGATATAACTCTA
*
24639000 AACAAATACTAAATCATCAAATGACGTGATATAACTCTA
1 AACAAATACTAAATCATCAAATGACATGATATAACTCTA
24639039 A
1 A
24639040 CTCTGTAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (39 bp):
AACAAATACTAAATCATCAAATGACATGATATAACTCTA
Found at i:24640294 original size:53 final size:53
Alignment explanation
Indices: 24640222--24640363 Score: 214
Period size: 53 Copynumber: 2.7 Consensus size: 53
24640212 TTCAAATATC
* *
24640222 ATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATT
1 ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATT
*
24640275 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATT
1 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
** *
24640328 GCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
24640364 GCACACTTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
52 1 0.01
53 81 0.99
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (53 bp):
ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
Found at i:24647792 original size:53 final size:53
Alignment explanation
Indices: 24647711--24647856 Score: 213
Period size: 53 Copynumber: 2.7 Consensus size: 53
24647701 CTTACACGGT
* *
24647711 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
24647766 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
**
24647819 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
24647857 AAGGGCACAC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:24649886 original size:3 final size:3
Alignment explanation
Indices: 24649878--24649904 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
24649868 TCTCCAACTC
24649878 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
24649905 GCTCAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:24651265 original size:39 final size:39
Alignment explanation
Indices: 24651202--24651365 Score: 197
Period size: 39 Copynumber: 4.2 Consensus size: 39
24651192 GAATTTAAAC
* * * * *
24651202 CCGG-TATAATACCAGCTCGAAGCCTGCGGGA-CTTTAGC
1 CCGGATATAATTCCAGCACGTAGCCTGC-GGACCTTAAGT
* * * *
24651240 CCGGACATATTTTCAGCACGTAGCCTGCAGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCCTGCGGACCTTAAGT
* *
24651279 CCGGTTATAATTCCAGCATGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCCTGCGGACCTTAAGT
*
24651318 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCCTGCGGACCTTAAGT
24651357 CCGGATATA
1 CCGGATATA
24651366 CTTCATCACT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
38 6 0.06
39 100 0.94
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACGTAGCCTGCGGACCTTAAGT
Found at i:24660141 original size:18 final size:18
Alignment explanation
Indices: 24660095--24660141 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
24660085 ATTATTCTAA
*
24660095 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
24660112 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
24660130 TAATTTT-TTTAT
1 T-ATTTTATTTAT
24660142 CTTACTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:24662894 original size:17 final size:17
Alignment explanation
Indices: 24662872--24662905 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24662862 GAATTTAAAC
24662872 TTGAGATGCTACTTGAG
1 TTGAGATGCTACTTGAG
*
24662889 TTGAGATGCTATTTGAG
1 TTGAGATGCTACTTGAG
24662906 AAAGAAAATA
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:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (17 bp):
TTGAGATGCTACTTGAG
Found at i:24663015 original size:15 final size:16
Alignment explanation
Indices: 24662991--24663023 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
24662981 TGTTGCGGTT
24662991 AAAAAGTATTTTT-AA
1 AAAAAGTATTTTTGAA
*
24663006 AAAAATTATTTTTGAA
1 AAAAAGTATTTTTGAA
24663022 AA
1 AA
24663024 GTATGATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAAAGTATTTTTGAA
Found at i:24663046 original size:25 final size:26
Alignment explanation
Indices: 24663005--24663053 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
24662995 AGTATTTTTA
* *
24663005 AAAAAATTATTTTTGAAAAGTATGAT
1 AAAAAATTATTTATGAAAAATATGAT
24663031 AAAAAATTA-TTATGAAAAATATG
1 AAAAAATTATTTATGAAAAATATG
24663054 GACAGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (26 bp):
AAAAAATTATTTATGAAAAATATGAT
Found at i:24663049 original size:26 final size:25
Alignment explanation
Indices: 24663005--24663053 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
24662995 AGTATTTTTA
*
24663005 AAAAAATTATTTTTGAAAAGTATGAT
1 AAAAAATTATTTATGAAAA-TATGAT
24663031 AAAAAATTA-TTATGAAAAATATG
1 AAAAAATTATTTATG-AAAATATG
24663054 GACAGTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (25 bp):
AAAAAATTATTTATGAAAATATGAT
Found at i:24675979 original size:46 final size:46
Alignment explanation
Indices: 24675912--24676005 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
24675902 AGTTTTCCTT
24675912 AATAGTTATTACCATTGCCTTTTTAAGCAGTTAAGCCTCACTTCCC
1 AATAGTTATTACCATTGCCTTTTTAAGCAGTTAAGCCTCACTTCCC
24675958 AATAGTTATTACCATTGCCTTTTTAAGCAGTTAAGCCTCACTTCCC
1 AATAGTTATTACCATTGCCTTTTTAAGCAGTTAAGCCTCACTTCCC
24676004 AA
1 AA
24676006 CCAGGTAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (46 bp):
AATAGTTATTACCATTGCCTTTTTAAGCAGTTAAGCCTCACTTCCC
Found at i:24676279 original size:17 final size:17
Alignment explanation
Indices: 24676265--24676298 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24676255 AAATATACAC
24676265 AGTATGACCATATACCT
1 AGTATGACCATATACCT
24676282 AGTATGACCATATACCT
1 AGTATGACCATATACCT
24676299 GCAGCTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
AGTATGACCATATACCT
Found at i:24682070 original size:20 final size:20
Alignment explanation
Indices: 24682028--24682071 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
24682018 AATTTAAATC
* *
24682028 ATTTTTTAATTTTTATTTGT
1 ATTTTGTAATTTATATTTGT
24682048 ATTTTGTAATTTAATATTT-T
1 ATTTTGTAATTT-ATATTTGT
24682068 ATTT
1 ATTT
24682072 GATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTTGTAATTTATATTTGT
Found at i:24689950 original size:14 final size:15
Alignment explanation
Indices: 24689930--24689964 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
24689920 AAAAAAAAAT
*
24689930 TATATTATTAATTTA
1 TATATTAATAATTTA
24689945 -ATATTAATAATTTA
1 TATATTAATAATTTA
24689959 TATATT
1 TATATT
24689965 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTAATAATTTA
Found at i:24693031 original size:2 final size:2
Alignment explanation
Indices: 24693024--24693050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24693014 GGTAATTCCT
24693024 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
24693051 TTAAGCTACG
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:24694055 original size:25 final size:25
Alignment explanation
Indices: 24694008--24694060 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
24693998 AATTATTTTT
* *
24694008 ATTTTATAATTGAAAATAATTATTTA
1 ATTTTATAAATGAAAAGAATTA-TTA
*
24694034 ATTTTATAAAT-AAAAGAGTTATTA
1 ATTTTATAAATGAAAAGAATTATTA
24694058 ATT
1 ATT
24694061 AAAAAGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 8 0.33
26 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
ATTTTATAAATGAAAAGAATTATTA
Found at i:24695273 original size:29 final size:29
Alignment explanation
Indices: 24695240--24695296 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
24695230 TATTTTATTA
*
24695240 TTAATTTTGTTTTTATTTTAAAGGCATTG
1 TTAATTTTGTTATTATTTTAAAGGCATTG
*
24695269 TTAATTTTGTTATTATTTTAGAGGCATT
1 TTAATTTTGTTATTATTTTAAAGGCATT
24695297 TGCTTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.58
Consensus pattern (29 bp):
TTAATTTTGTTATTATTTTAAAGGCATTG
Found at i:24695970 original size:22 final size:20
Alignment explanation
Indices: 24695935--24695978 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
24695925 TTAGGTTTAA
24695935 ATAAATTTATTAATATTTATTT
1 ATAAATTTATTAAT-TTT-TTT
24695957 ATAAATTT-TCTAATTTTTTT
1 ATAAATTTAT-TAATTTTTTT
24695977 AT
1 AT
24695979 TTTGTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATAAATTTATTAATTTTTTT
Found at i:24696859 original size:22 final size:23
Alignment explanation
Indices: 24696819--24696871 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
24696809 TAATTTTGTT
*
24696819 ATTTGAATTATAAAATAAAAATAA
1 ATTTCAATTATAAAATAAAAA-AA
*
24696843 A-TTCAATT-TAAAGTAAAAAAA
1 ATTTCAATTATAAAATAAAAAAA
24696864 ATTTCAAT
1 ATTTCAAT
24696872 ATCTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 6 0.23
24 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (23 bp):
ATTTCAATTATAAAATAAAAAAA
Found at i:24711950 original size:10 final size:10
Alignment explanation
Indices: 24711931--24711962 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
24711921 ATTAAAATGA
*
24711931 AAAAAAGGCT
1 AAAAAGGGCT
24711941 AAAAAGGGCT
1 AAAAAGGGCT
24711951 AAAAAGGGCT
1 AAAAAGGGCT
24711961 AA
1 AA
24711963 TAACAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.09, G:0.25, T:0.09
Consensus pattern (10 bp):
AAAAAGGGCT
Found at i:24716292 original size:6 final size:6
Alignment explanation
Indices: 24716283--24716321 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
24716273 GAAAGATACC
* *
24716283 GTAACA GTAACA TTAACA GTAATA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTA
24716322 TCGGTACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (6 bp):
GTAACA
Found at i:24718532 original size:3 final size:3
Alignment explanation
Indices: 24718526--24718555 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24718516 TGATGAGATT
24718526 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
24718556 CGGGGAGCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24719150 original size:30 final size:30
Alignment explanation
Indices: 24719116--24719173 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
24719106 CTTAACAAGT
24719116 AAATGTCCCTAAAATAATAACAAAATTAAC
1 AAATGTCCCTAAAATAATAACAAAATTAAC
**
24719146 AAATGTCTTTAAAATAATAACAAAATTA
1 AAATGTCCCTAAAATAATAACAAAATTA
24719174 GCAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATGTCCCTAAAATAATAACAAAATTAAC
Found at i:24721555 original size:5 final size:5
Alignment explanation
Indices: 24721545--24721569 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
24721535 TGTTTAAAGG
24721545 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
24721570 TAAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:24722465 original size:21 final size:21
Alignment explanation
Indices: 24722436--24722475 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24722426 AGTTACACGA
*
24722436 CTAGATCACACGGGCATGTCC
1 CTAGATCACACAGGCATGTCC
*
24722457 CTAGGTCACACAGGCATGT
1 CTAGATCACACAGGCATGT
24722476 GCCTTAGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (21 bp):
CTAGATCACACAGGCATGTCC
Found at i:24722849 original size:13 final size:14
Alignment explanation
Indices: 24722831--24722861 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
24722821 AGGCATTCTA
24722831 ATTCTGTAT-TTTG
1 ATTCTGTATGTTTG
24722844 ATTCTGTATGTTTG
1 ATTCTGTATGTTTG
24722858 ATTC
1 ATTC
24722862 CAAAGAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (14 bp):
ATTCTGTATGTTTG
Found at i:24725253 original size:20 final size:20
Alignment explanation
Indices: 24725215--24725262 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
24725205 TAATTTTTAA
* **
24725215 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
24725235 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
24725255 AAA-ATAAA
1 AAAGATAAA
24725263 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:24725306 original size:15 final size:15
Alignment explanation
Indices: 24725286--24725315 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24725276 ATAATCCTAA
*
24725286 TAATTATCTTAATAT
1 TAATTATCCTAATAT
24725301 TAATTATCCTAATAT
1 TAATTATCCTAATAT
24725316 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:24726040 original size:16 final size:17
Alignment explanation
Indices: 24726003--24726044 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
24725993 CTTATATCAA
*
24726003 TAAAA-TAAAATAATTT
1 TAAAATTAAAATAACTT
24726019 TAAAAATTAAAAT-ACTT
1 T-AAAATTAAAATAACTT
24726036 TAAAATTAA
1 TAAAATTAA
24726045 CTTAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTAAAATAACTT
Found at i:24727916 original size:24 final size:24
Alignment explanation
Indices: 24727889--24727939 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
24727879 GACAGCGGTG
*
24727889 GAGATGAATATGAATATGAGG-GTC
1 GAGATGAACATGAATATG-GGAGTC
24727913 GAGATGAACATGAATATGGGAGTC
1 GAGATGAACATGAATATGGGAGTC
24727937 GAG
1 GAG
24727940 GTGCTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.37, C:0.06, G:0.35, T:0.22
Consensus pattern (24 bp):
GAGATGAACATGAATATGGGAGTC
Found at i:24729811 original size:19 final size:19
Alignment explanation
Indices: 24729787--24729884 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
24729777 AATCTTTAAG
24729787 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24729806 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24729825 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24729842 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24729861 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
24729882 GAT
1 GAT
24729885 CTTGTAATAT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:24729817 original size:36 final size:35
Alignment explanation
Indices: 24729777--24729884 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
24729767 ATGGAAATAT
24729777 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
24729813 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
24729849 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
24729885 CTTGTAATAT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:24730419 original size:26 final size:25
Alignment explanation
Indices: 24730389--24730438 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
24730379 GTGCATAGTT
*
24730389 TTATTTTTTTTATATGCTATGTTTAA
1 TTATTTCTTTTATATGCTAT-TTTAA
*
24730415 TTATTTCTTTTATGTGCTATTTTA
1 TTATTTCTTTTATATGCTATTTTA
24730439 TGATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.66
Consensus pattern (25 bp):
TTATTTCTTTTATATGCTATTTTAA
Found at i:24736519 original size:44 final size:44
Alignment explanation
Indices: 24736374--24737075 Score: 522
Period size: 44 Copynumber: 16.0 Consensus size: 44
24736364 CAGAGAAACA
*
24736374 AGATTTGGCATCCCTGTGTTTATAGGGAAC-AGATCGAATATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAG-TCGAAGATAGC
* * * * * * ***
24736418 AGATCTGACA-CTCTTGTGCTTACAGCGAAGC-AGATCGAAGATTTT
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
24736463 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
** * * *
24736506 AGATTTTTCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* ** * * * * ***
24736550 AGATCTAACA-CTCCTGTGATTACAGCGAAGC-AGATTGAAGATTTT
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* *
24736595 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * *
24736638 AAATTTGGCATCCCTGTGTTTATAAGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * **
24736682 AGATCTGACATTCCTGTGATTACAGCGAAGC-AGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* *
24736727 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
**
24736770 AGATTTGGCATCCCTGTGTTTATAGGGAACAAAACGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * ***
24736814 AGATCTGACATTCCTGTGATTACAGCGAAGC-AGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* *
24736859 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
24736902 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * ** **
24736946 AGATCTGACATTCCTGTGATTACAGCAAAGC-AGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
24736991 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
24737034 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATA
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATA
24737076 ACAAATCTGA
Statistics
Matches: 510, Mismatches: 115, Indels: 66
0.74 0.17 0.10
Matches are distributed among these distances:
42 5 0.01
43 51 0.10
44 388 0.76
45 61 0.12
46 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
Found at i:24736611 original size:132 final size:132
Alignment explanation
Indices: 24736374--24737088 Score: 1232
Period size: 132 Copynumber: 5.4 Consensus size: 132
24736364 CAGAGAAACA
* * * * *
24736374 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAATATAGCAGATCTGACACTCTTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
24736439 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
24736504 GC
131 GC
** * * * *
24736506 AGATTTTTCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGTAGATCTAACACTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
24736571 ACAGCGAAGCAGATTGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
66 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
24736636 GC
131 GC
* *
24736638 AAATTTGGCATCCCTGTGTTTATAAGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
24736703 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
66 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
24736768 GC
131 GC
*
24736770 AGATTTGGCATCCCTGTGTTTATAGGGAACAAAACGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
24736835 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
66 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
24736900 GC
131 GC
24736902 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
* * *
24736967 ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
24737032 GC
131 GC
* *
24737034 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAAATCTGACAT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACAT
24737089 CTCCATTTCG
Statistics
Matches: 552, Mismatches: 31, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 552 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
GC
Found at i:24737685 original size:19 final size:19
Alignment explanation
Indices: 24737661--24737772 Score: 156
Period size: 19 Copynumber: 5.8 Consensus size: 19
24737651 AATCTTTAAG
24737661 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24737680 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24737699 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
24737716 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24737735 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
* *
24737756 GATCTTGTAATCTTAGA
1 GAT-ATGCAATCTTAGA
24737773 GATTTAATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
17 17 0.20
19 48 0.56
20 3 0.04
21 9 0.11
22 8 0.09
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:24737692 original size:36 final size:35
Alignment explanation
Indices: 24737651--24737758 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 35
24737641 ATGAAAATAT
*
24737651 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATAC
24737687 AATC-TT-AGATATGATACAATCTTAGATATGATATAC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATAC
*
24737723 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
24737759 CTTGTAATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 27 0.45
37 1 0.02
38 7 0.12
40 10 0.17
41 6 0.10
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATAC
Found at i:24740318 original size:17 final size:19
Alignment explanation
Indices: 24740276--24740319 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
24740266 TCCTAAACAA
24740276 AAAAAACTCTAACCCTCTT
1 AAAAAACTCTAACCCTCTT
*
24740295 AACAAACTCTAA-CC-CTT
1 AAAAAACTCTAACCCTCTT
24740312 AAAAAACT
1 AAAAAACT
24740320 ATAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAACTCTAACCCTCTT
Found at i:24773471 original size:20 final size:19
Alignment explanation
Indices: 24773415--24773485 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
24773405 AAAAAAATAA
24773415 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
* *
24773435 ATTTTAAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
24773454 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
24773474 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
24773486 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 3 0.07
19 25 0.56
20 17 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:24773486 original size:20 final size:20
Alignment explanation
Indices: 24773415--24773485 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
24773405 AAAAAAATAA
*
24773415 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAAAAATT
*
24773435 ATTTT-AAATTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
*
24773454 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTAAAAATT
24773474 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
24773486 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 10 0.22
19 12 0.27
20 23 0.51
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:24782211 original size:27 final size:27
Alignment explanation
Indices: 24782181--24782236 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
24782171 ACTTATAACA
24782181 CATAGCATGAAAATTGATCATTCCCAT
1 CATAGCATGAAAATTGATCATTCCCAT
24782208 CATAGCATGAAAATTGATCATTCCCAT
1 CATAGCATGAAAATTGATCATTCCCAT
24782235 CA
1 CA
24782237 CCTTTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.29
Consensus pattern (27 bp):
CATAGCATGAAAATTGATCATTCCCAT
Found at i:24782747 original size:3 final size:3
Alignment explanation
Indices: 24782739--24782770 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
24782729 CACCAGTTGC
*
24782739 TCT TCT TCT TCT TCT TCT TCT TCT TCT ACT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
24782771 CTCAAGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:24784253 original size:17 final size:18
Alignment explanation
Indices: 24784231--24784268 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
24784221 ATATAAATAT
* *
24784231 ATTTTTTAATATT-ATTA
1 ATTTTTAAAAATTAATTA
24784248 ATTTTTAAAAATTAATTA
1 ATTTTTAAAAATTAATTA
24784266 ATT
1 ATT
24784269 GTAAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTAAAAATTAATTA
Found at i:24785925 original size:15 final size:15
Alignment explanation
Indices: 24785907--24785937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24785897 TTTTAGTGGA
24785907 TTTCATTTTAGTCAC
1 TTTCATTTTAGTCAC
*
24785922 TTTCATTTTGGTCAC
1 TTTCATTTTAGTCAC
24785937 T
1 T
24785938 CAGTTTTTAG
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:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTCATTTTAGTCAC
Found at i:24798050 original size:22 final size:21
Alignment explanation
Indices: 24798001--24798051 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
24797991 ATATAACCAA
*
24798001 AAATAAATAAAAATTGAAAAT
1 AAATAAATAAAAATTAAAAAT
** *
24798022 ACTTAAATCAATAATTAAAAAT
1 AAATAAAT-AAAAATTAAAAAT
24798044 AAATAAAT
1 AAATAAAT
24798052 GATAAAAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATAAAAATTAAAAAT
Found at i:24800904 original size:30 final size:30
Alignment explanation
Indices: 24800868--24800928 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
24800858 TACACCCCAT
*
24800868 TTAGTATGTACCACCTTATTTTGGTCCGTA
1 TTAGTATGTACCACCTTATTCTGGTCCGTA
24800898 TTAGTATGTACCACCTTATTCTGGTCCGTA
1 TTAGTATGTACCACCTTATTCTGGTCCGTA
24800928 T
1 T
24800929 CATAGCCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (30 bp):
TTAGTATGTACCACCTTATTCTGGTCCGTA
Found at i:24804549 original size:23 final size:23
Alignment explanation
Indices: 24804480--24804567 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 23
24804470 ACCTGATCAG
* *
24804480 AATACGACACATAAAGTGCCT-A
1 AATACGACACATGAGGTGCCTGA
24804502 AA-ACGACACATGAGGTGCCTG-
1 AATACGACACATGAGGTGCCTGA
*
24804523 -ATACGACACACGAGGTGCCTGA
1 AATACGACACATGAGGTGCCTGA
* *
24804545 AATACGACACATAAAGTGCCTGA
1 AATACGACACATGAGGTGCCTGA
24804568 TCAGTAAAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.61
22 2 0.04
23 19 0.34
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
AATACGACACATGAGGTGCCTGA
Found at i:24804566 original size:44 final size:42
Alignment explanation
Indices: 24804481--24804568 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 42
24804471 CCTGATCAGA
* * *
24804481 ATACGACACATAAAGTGCCTAAAACGACACATGAGGTGCCTG
1 ATACGACACACAAAGTGCCTAAAACGACACATAAAGTGCCTG
* *
24804523 ATACGACACACGAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCT-AAA-ACGACACATAAAGTGCCTG
24804567 AT
1 AT
24804569 CAGTAAAGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 17 0.44
43 3 0.08
44 19 0.49
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (42 bp):
ATACGACACACAAAGTGCCTAAAACGACACATAAAGTGCCTG
Found at i:24805496 original size:22 final size:21
Alignment explanation
Indices: 24805471--24805511 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
24805461 TTTCTTTCTT
24805471 TTCTTTGATTCTTTTTATTTCA
1 TTCTTTGATTC-TTTTATTTCA
*
24805493 TTCTTTTATTCTTTTATTT
1 TTCTTTGATTCTTTTATTT
24805512 ACTTTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (21 bp):
TTCTTTGATTCTTTTATTTCA
Found at i:24805736 original size:23 final size:23
Alignment explanation
Indices: 24805709--24805765 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
24805699 AAATTAGTTA
*
24805709 TTTTATTACAAGTGTA-C-ATAT
1 TTTTATTACAAATGTACCAATAT
24805730 CTATTTATTACAAATGTACCAATAT
1 -T-TTTATTACAAATGTACCAATAT
24805755 TTTTATTACAA
1 TTTTATTACAA
24805766 TTGTCATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 24 0.77
24 2 0.06
25 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (23 bp):
TTTTATTACAAATGTACCAATAT
Found at i:24806006 original size:3 final size:3
Alignment explanation
Indices: 24805998--24806059 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
24805988 TAATGAAACC
* ** *
24805998 ATA ATA ATA ATA ATA ATA ATA ATA AT- TTA AT- ATA A-A ACC ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24806043 ATA ATTA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA A
24806060 AATCTTAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24813047 original size:20 final size:20
Alignment explanation
Indices: 24813009--24813047 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24812999 ATTTCAAATA
*
24813009 TAAGGAAATAAAATGTAACC
1 TAAGGAAATAAAATATAACC
24813029 TAAGGTAAATAAAA-ATAAC
1 TAAGG-AAATAAAATATAAC
24813048 TATTTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (20 bp):
TAAGGAAATAAAATATAACC
Found at i:24814999 original size:16 final size:16
Alignment explanation
Indices: 24814978--24815011 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24814968 CGACGTGTTG
24814978 CTATAAATCACAAACT
1 CTATAAATCACAAACT
24814994 CTATAAATCACAAACT
1 CTATAAATCACAAACT
24815010 CT
1 CT
24815012 TTACCTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
CTATAAATCACAAACT
Found at i:24820106 original size:29 final size:28
Alignment explanation
Indices: 24820057--24820112 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
24820047 CTTGTCATTT
24820057 ATTTCACATTTCAACCTCTAAATTTTCAC
1 ATTTCACATTTCAACCTCT-AATTTTCAC
24820086 ATTTCACAATTT-AATCC-CTAATTTTCA
1 ATTTCAC-ATTTCAA-CCTCTAATTTTCA
24820113 TTTTTACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTCACATTTCAACCTCTAATTTTCAC
Found at i:24825183 original size:31 final size:33
Alignment explanation
Indices: 24825124--24825190 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
24825114 AGAATAATAT
24825124 TTAAATATATATTAAAATATTTTTTATTTTGATA
1 TTAAATATATATTAAAATA-TTTTTATTTTGATA
* *
24825158 TTAAAT-TGTATTAAAATA-TTTTATTTTGTTA
1 TTAAATATATATTAAAATATTTTTATTTTGATA
24825189 TT
1 TT
24825191 GTCATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 14 0.45
33 11 0.35
34 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (33 bp):
TTAAATATATATTAAAATATTTTTATTTTGATA
Found at i:24831635 original size:17 final size:17
Alignment explanation
Indices: 24831613--24831646 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24831603 ATTGACAATG
24831613 TTATAAAAAATAATTAA
1 TTATAAAAAATAATTAA
*
24831630 TTATAAAAAGTAATTAA
1 TTATAAAAAATAATTAA
24831647 AAATAATTAT
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:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTATAAAAAATAATTAA
Found at i:24831668 original size:33 final size:33
Alignment explanation
Indices: 24831622--24831688 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
24831612 GTTATAAAAA
*
24831622 ATAATTAATTATAA-AAAGTAATTAAAAATAATT
1 ATAATTAATTATAATAAA-TAATTAAAAACAATT
*
24831655 ATAATTTAA-TATAATAAATAATTTAAAACAATT
1 ATAA-TTAATTATAATAAATAATTAAAAACAATT
24831688 A
1 A
24831689 ATTAAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
ATAATTAATTATAATAAATAATTAAAAACAATT
Found at i:24835466 original size:12 final size:11
Alignment explanation
Indices: 24835438--24835482 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
24835428 TCATTAATAA
24835438 ATAAACGAGTC
1 ATAAACGAGTC
*
24835449 ATAAACGAGCTT
1 ATAAACGAG-TC
24835461 ATAAACGAGTC
1 ATAAACGAGTC
*
24835472 AATAAATGAGT
1 -ATAAACGAGT
24835483 TTGCTCGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (11 bp):
ATAAACGAGTC
Done.