Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007200.1 Hibiscus syriacus cultivar Beakdansim tig00018999_pilon, whole genome shotgun sequence
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: 414581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:167454 original size:18 final size:18
Alignment explanation
Indices: 167428--167472 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
167418 TCACATAATG
*
167428 TAAGATTACCGGCGGGAA
1 TAAGATTACCAGCGGGAA
*
167446 TATGATTACCAGCGGGAA
1 TAAGATTACCAGCGGGAA
167464 TAAGATTAC
1 TAAGATTAC
167473 TGGGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGCGGGAA
Found at i:170362 original size:12 final size:12
Alignment explanation
Indices: 170319--170369 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
170309 AATTTAAGGT
170319 TAAAAAATAATAA
1 TAAAAAAT-ATAA
*
170332 GAAAAATATATAA
1 TAAAAA-ATATAA
* *
170345 TTAAAAATATCA
1 TAAAAAATATAA
170357 T-AAAAATATAA
1 TAAAAAATATAA
170368 TA
1 TA
170370 TTTTTTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 13 0.42
14 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
TAAAAAATATAA
Found at i:172064 original size:37 final size:37
Alignment explanation
Indices: 171978--172078 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
171968 TTCATCCTAT
* *
171978 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
* *
172015 TAGGATTCAAACTCCTAAAAATAGGATATAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
** * * *
172052 TATTATTTAAACTGCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
172079 CCAGAAGCAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:172777 original size:29 final size:30
Alignment explanation
Indices: 172745--172817 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
172735 TTTATATTTC
172745 TATGATTACTATTTTTTCAGTTAATATTA-
1 TATGATTACTATTTTTTCAGTTAATATTAT
* * *
172774 TATG-TATA-TTTATTTTTCATTTATTATTAT
1 TATGAT-TACTAT-TTTTTCAGTTAATATTAT
*
172804 TATTATTACTATTT
1 TATGATTACTATTT
172818 AGTATTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
28 3 0.09
29 21 0.62
30 7 0.21
31 3 0.09
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (30 bp):
TATGATTACTATTTTTTCAGTTAATATTAT
Found at i:172890 original size:22 final size:22
Alignment explanation
Indices: 172795--172901 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 22
172785 ATTTTTCATT
*
172795 TATTATTATTA-TTAT-TACTATT
1 TATTATT-TTATTTATATA-TATA
* *
172817 TAGTATTTTATTATATTATACATA
1 TATTATTTTATT-TA-TATATATA
*
172841 CATT-TTTATATTTATATATATA
1 TATTATTT-TATTTATATATATA
*
172863 TATTATTTTATTTATACTATTTA
1 TATTATTTTATTTATA-TATATA
172886 T-TTATTTTCA-TTATAT
1 TATTATTTT-ATTTATAT
172902 TTTTAGTTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
21 4 0.06
22 37 0.54
23 17 0.25
24 9 0.13
25 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (22 bp):
TATTATTTTATTTATATATATA
Found at i:174219 original size:19 final size:19
Alignment explanation
Indices: 174195--174231 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
174185 ACCTTACTAA
174195 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
174214 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
174232 ATCATCTGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:177512 original size:7 final size:7
Alignment explanation
Indices: 177500--177544 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
177490 TAAAAAGGGC
177500 AAAAAGA
1 AAAAAGA
177507 AAAAAGAA
1 AAAAAG-A
177515 AAAAAGCA
1 AAAAAG-A
177523 AAAAAGA
1 AAAAAGA
*
177530 AGAAA-A
1 AAAAAGA
177536 AAAAAGA
1 AAAAAGA
177543 AA
1 AA
177545 TAACAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 5 0.15
7 14 0.42
8 14 0.42
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:177519 original size:16 final size:17
Alignment explanation
Indices: 177500--177537 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
177490 TAAAAAGGGC
177500 AAAAAG-AAAAAAGA-A
1 AAAAAGCAAAAAAGAGA
177515 AAAAAGCAAAAAAGAAGA
1 AAAAAGCAAAAAAG-AGA
177533 AAAAA
1 AAAAA
177538 AAAGAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 1 0.05
18 6 0.30
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAGCAAAAAAGAGA
Found at i:178197 original size:22 final size:22
Alignment explanation
Indices: 178169--178245 Score: 154
Period size: 22 Copynumber: 3.5 Consensus size: 22
178159 GCTACCCCAT
178169 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
178191 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
178213 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
178235 CAAACCTTTGA
1 CAAACCTTTGA
178246 CCAAACACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:179341 original size:106 final size:106
Alignment explanation
Indices: 179208--180917 Score: 2735
Period size: 106 Copynumber: 16.1 Consensus size: 106
179198 ATATCGTGCC
* * * *
179208 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
179273 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
179314 ACTCCAGACAACACAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
179379 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
179420 ACTCCAGACAACGCAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
179485 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
179526 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
179591 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
179632 ACTCTAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
179697 AATTTCAGAGCCAATTTCAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
179738 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
179803 AATTTCAGAGCCAATTTTAAATTCACAGA-GAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
* * * *
179844 ACTCCAGACAACTCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAGAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
179909 AAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
179950 ACTCCAGACAACGCAAGTTCAATTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
180015 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
180056 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
180121 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
180162 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
180227 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
180268 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
180333 AATTTCAGAGCCAATTTCAACTTCACAGA-GAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
* *
180374 ACTCCAGACAACTCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
180439 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
180480 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
180545 AATTTTAGAGCCAATTTCATCTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
180586 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
180651 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
180692 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
180757 AATTTCAAAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
180798 ACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * * * *
180862 CGATTCCAGAACCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
180904 ACT-CAGAACAACGC
1 ACTCCAG-ACAACGC
180918 TACTTACTTG
Statistics
Matches: 1486, Mismatches: 112, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
105 6 0.00
106 1478 0.99
107 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:181709 original size:37 final size:37
Alignment explanation
Indices: 181656--181760 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
181646 CCTTTTCGTC
181656 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
181693 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
181730 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
181761 TCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:182319 original size:24 final size:23
Alignment explanation
Indices: 182274--182321 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
182264 TTTTTTGCGT
* *
182274 TATATTATATTATTTTCCTATTA
1 TATATTATATTATATTACTATTA
*
182297 TATATATATATTATATTATTATTA
1 TATAT-TATATTATATTACTATTA
182321 T
1 T
182322 TTTTATCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTATATTATATTACTATTA
Found at i:182379 original size:2 final size:2
Alignment explanation
Indices: 182372--182439 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
182362 TTCCTAACGT
182372 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
182414 TA TA TA T- 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
182440 TCTTATATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:182572 original size:24 final size:25
Alignment explanation
Indices: 182540--182630 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 25
182530 TACTATTTCG
*
182540 TATTTTATTATATTATACATACATT
1 TATTATATTATATTATACATACATT
* * *
182565 T-TTATATTTTTATATATATATATATT
1 TATTATA-TTATAT-TATACATACATT
* **
182591 TATTATTTTAT-TTATACTATTTATT
1 TATTATATTATATTATAC-ATACATT
*
182616 TATTTTCATTATATT
1 TATTAT-ATTATATT
182631 TTTAGCTTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
24 8 0.16
25 18 0.36
26 18 0.36
27 6 0.12
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATATTATATTATACATACATT
Found at i:183768 original size:22 final size:22
Alignment explanation
Indices: 183740--183785 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
183730 GGAGGAGGGG
183740 GCTTCCAGTTGACGTTTCTTCT
1 GCTTCCAGTTGACGTTTCTTCT
183762 GCTTCCAGTTGACGTTTCTTCT
1 GCTTCCAGTTGACGTTTCTTCT
183784 GC
1 GC
183786 AAAGTGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.28, G:0.20, T:0.43
Consensus pattern (22 bp):
GCTTCCAGTTGACGTTTCTTCT
Found at i:185703 original size:39 final size:39
Alignment explanation
Indices: 185552--185705 Score: 141
Period size: 39 Copynumber: 4.0 Consensus size: 39
185542 ACACCCAGTA
* * * **
185552 AAGG-CTTACCCTGTGTACAAAACAGAGGAGCTTGTAGT
1 AAGGTCTTACCCTGTGCACAAAACAGAGGAACCTGCGGT
* * * *
185590 AAAGTCTTATCCC-GTGCACAAAACAGAGTAACATGTGGT
1 AAGGTCTTA-CCCTGTGCACAAAACAGAGGAACCTGCGGT
* * * * *
185629 AAGGACTTACCCTGAGCACAAAGCCGATGAACCTGCGGT
1 AAGGTCTTACCCTGTGCACAAAACAGAGGAACCTGCGGT
* *
185668 AAGGTCTTATCCTGTGCACAAAACAGAGGAGCCTGCGG
1 AAGGTCTTACCCTGTGCACAAAACAGAGGAACCTGCGG
185706 AAAGCGGTAA
Statistics
Matches: 91, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
38 6 0.07
39 82 0.90
40 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (39 bp):
AAGGTCTTACCCTGTGCACAAAACAGAGGAACCTGCGGT
Found at i:186808 original size:16 final size:16
Alignment explanation
Indices: 186787--186825 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
186777 ATCACGAGTC
186787 TTTATTTTTTACCTAA
1 TTTATTTTTTACCTAA
**
186803 TTTATTTTTTATTTAA
1 TTTATTTTTTACCTAA
186819 TTTATTT
1 TTTATTT
186826 CACCATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTTTTACCTAA
Found at i:188996 original size:35 final size:36
Alignment explanation
Indices: 188957--189043 Score: 122
Period size: 35 Copynumber: 2.4 Consensus size: 36
188947 GTAGTGCTCA
* *
188957 ACTCGTGCTCGTTAAAAAA-TTTGATGTTCGACTCG
1 ACTCGTGCTCGTTAAAAAATTTTGATGCTCAACTCG
*
188992 ACTCGTGCTCGTTAAAAAATTTTGCTGCTCAACTCG
1 ACTCGTGCTCGTTAAAAAATTTTGATGCTCAACTCG
*
189028 ACTCGTTTCTCGTTAA
1 ACTCG-TGCTCGTTAA
189044 GCTCGATTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 19 0.41
36 18 0.39
37 9 0.20
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (36 bp):
ACTCGTGCTCGTTAAAAAATTTTGATGCTCAACTCG
Found at i:189054 original size:21 final size:21
Alignment explanation
Indices: 189024--189068 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
189014 TGCTGCTCAA
*
189024 CTCGACTCGTTTCTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
*
189045 CTCGATTCGTTGCTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
189066 CTC
1 CTC
189069 ACTAAAAAAT
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:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (21 bp):
CTCGACTCGTTGCTCGTTAAG
Found at i:189292 original size:43 final size:43
Alignment explanation
Indices: 189211--189333 Score: 174
Period size: 43 Copynumber: 2.9 Consensus size: 43
189201 AATTCCAAAC
* * * *
189211 TAACAAACCATAAATACACCAAACTAGCATATTTAAACTAAAG
1 TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
* *
189254 TAGCAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
1 TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
* *
189297 TAACAATCCACAAGTACATCAAACTAACATATTAAAA
1 TAACAATCCACAAATACACCAAACTAACATATTAAAA
189334 GCATTCTAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.53, C:0.22, G:0.04, T:0.21
Consensus pattern (43 bp):
TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
Found at i:192952 original size:4 final size:4
Alignment explanation
Indices: 192943--192967 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
192933 ATATTCATGC
192943 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
192968 TATATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:192976 original size:10 final size:10
Alignment explanation
Indices: 192961--192990 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
192951 ACATACATAC
192961 ATACATATAT
1 ATACATATAT
192971 ATACATATAT
1 ATACATATAT
*
192981 ATATATATAT
1 ATACATATAT
192991 TAATGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATACATATAT
Found at i:193260 original size:18 final size:18
Alignment explanation
Indices: 193237--193310 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
193227 GAGGGATATC
*
193237 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
193255 AGTGGTCATTCGGGACATAT
1 AGTGGTCATTCGGGAC--AT
193275 CAGTGGTCATTCGGGACAT
1 -AGTGGTCATTCGGGACAT
*
193294 AGTGGTCCTTCGGGACA
1 AGTGGTCATTCGGGACA
193311 AATATTCAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 31 0.61
19 2 0.04
20 2 0.04
21 16 0.31
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:193288 original size:39 final size:39
Alignment explanation
Indices: 193232--193310 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
193222 GAGTCGAGGG
*
193232 ATATCAGTGGTCCTTCGGGACATAGTGGTCATTCGGGAC
1 ATATCAGTGGTCATTCGGGACATAGTGGTCATTCGGGAC
*
193271 ATATCAGTGGTCATTCGGGACATAGTGGTCCTTCGGGAC
1 ATATCAGTGGTCATTCGGGACATAGTGGTCATTCGGGAC
193310 A
1 A
193311 AATATTCAAT
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:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (39 bp):
ATATCAGTGGTCATTCGGGACATAGTGGTCATTCGGGAC
Found at i:199528 original size:19 final size:19
Alignment explanation
Indices: 199500--199550 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
199490 AATGAGATTT
*
199500 GTGTACCGATGCATAGCTA
1 GTGTATCGATGCATAGCTA
199519 GTGTATCGATGCATAGCTA
1 GTGTATCGATGCATAGCTA
* *
199538 ATGCATCGATGCA
1 GTGTATCGATGCA
199551 CACGTTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (19 bp):
GTGTATCGATGCATAGCTA
Found at i:205682 original size:21 final size:22
Alignment explanation
Indices: 205653--205694 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
205643 TGCACATAAT
205653 TCGGATTTTAATCCGATCCGGA
1 TCGGATTTTAATCCGATCCGGA
*
205675 TCGG-TTTTTATCCGATCCGG
1 TCGGATTTTAATCCGATCCGG
205695 TTTTTTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (22 bp):
TCGGATTTTAATCCGATCCGGA
Found at i:206041 original size:21 final size:20
Alignment explanation
Indices: 206013--206063 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
206003 TTACACTTAG
*
206013 GGAACCGATTTCCTATGAGA
1 GGAACCGATTCCCTATGAGA
206033 GGAAACCGATTCCCTATGAGA
1 GG-AACCGATTCCCTATGAGA
*
206054 GGTACCGATT
1 GGAACCGATT
206064 ACCCCATGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (20 bp):
GGAACCGATTCCCTATGAGA
Found at i:206283 original size:13 final size:13
Alignment explanation
Indices: 206262--206316 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
206252 AAGTTCGATA
*
206262 AATTCAAATACTT
1 AATTGAAATACTT
206275 AATTGAAATACTT
1 AATTGAAATACTT
* *
206288 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
206302 AATTGAAATACTT
1 AATTGAAATACTT
206315 AA
1 AA
206317 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:206398 original size:32 final size:33
Alignment explanation
Indices: 206302--206400 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
206292 AACTCAACAT
* * *
206302 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
206335 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
206368 AATTCAAATATTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
206400 A
1 A
206401 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:206419 original size:21 final size:21
Alignment explanation
Indices: 206395--206434 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
206385 ACTTCAAGTT
206395 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
206416 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
206435 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:208749 original size:15 final size:14
Alignment explanation
Indices: 208718--208759 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
208708 TTTCGGATAA
208718 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
208731 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
*
208744 CAAACCAGTTTTTTT
1 -AAACCGGTTTTTTT
208759 A
1 A
208760 TCCGGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.24
13 6 0.24
14 1 0.04
15 12 0.48
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.48
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:214405 original size:22 final size:20
Alignment explanation
Indices: 214377--214438 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
214367 TGCTTATTCT
214377 AATTTTAAATCTTGAAATTCAA
1 AATTTTAAA-CTT-AAATTCAA
* *
214399 AATTTTAGACATTAAATCTTAA
1 AATTTTAAAC-TTAAAT-TCAA
214421 AATTTTAAACCTTAAATT
1 AATTTTAAA-CTTAAATT
214439 GGATACATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 6 0.18
22 27 0.79
23 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTTTAAACTTAAATTCAA
Found at i:216762 original size:2 final size:2
Alignment explanation
Indices: 216750--216786 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
216740 TAATTTTTAT
* *
216750 TA TA AA TA TA TA TA TA TA AA 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
216787 GTATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:217169 original size:22 final size:22
Alignment explanation
Indices: 217141--217188 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
217131 AACCCACCCC
217141 CTCCCTTTCCCCTACCTCCTTT
1 CTCCCTTTCCCCTACCTCCTTT
217163 CTCCCTTTCCCCTACCTCCTTT
1 CTCCCTTTCCCCTACCTCCTTT
217185 CTCC
1 CTCC
217189 TTCCCCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.04, C:0.56, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCCCTTTCCCCTACCTCCTTT
Found at i:220493 original size:20 final size:21
Alignment explanation
Indices: 220468--220524 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
220458 ATACGCCTTA
*
220468 GGGTATCGGTACCAT-CATAG
1 GGGTATCGATACCATGCATAG
*
220488 GGGTATCAATACCATTGCATAG
1 GGGTATCGATACCA-TGCATAG
220510 GGGTATCGATACCAT
1 GGGTATCGATACCAT
220525 TGGGGGGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 18 0.56
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCATGCATAG
Found at i:220802 original size:17 final size:17
Alignment explanation
Indices: 220770--220803 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
220760 TCATATTCGA
*
220770 ATAATTTAATCGAATAT
1 ATAATTTAATAGAATAT
*
220787 ATAATTTAATATAATAT
1 ATAATTTAATAGAATAT
220804 CTTAAAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAATTTAATAGAATAT
Found at i:220936 original size:12 final size:12
Alignment explanation
Indices: 220919--220967 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
220909 CTAATATTGA
*
220919 AAATCATTTTTG
1 AAATCAATTTTG
**
220931 AAATCAA-AATG
1 AAATCAATTTTG
220942 AAATCAATTTTG
1 AAATCAATTTTG
220954 AAATCAATTTTG
1 AAATCAATTTTG
220966 AA
1 AA
220968 TTGAAATTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (12 bp):
AAATCAATTTTG
Found at i:222553 original size:12 final size:12
Alignment explanation
Indices: 222536--222560 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
222526 TAATGGGATT
222536 AGGAATTTGAGG
1 AGGAATTTGAGG
222548 AGGAATTTGAGG
1 AGGAATTTGAGG
222560 A
1 A
222561 TTTGGGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (12 bp):
AGGAATTTGAGG
Found at i:223307 original size:20 final size:21
Alignment explanation
Indices: 223282--223401 Score: 115
Period size: 21 Copynumber: 5.6 Consensus size: 21
223272 AACCCGAAGA
* *
223282 GGGTATCGGTACCA-TCAGGG
1 GGGTATCGATACCATTCAAGG
223302 GGGTATCGATACCCATTCAAGG
1 GGGTATCGATA-CCATTCAAGG
223324 GGGTATCGATACCTATTGC-A-G
1 GGGTATCGATACC-ATT-CAAGG
*
223345 GGGTATCGATACCTATTCAAAGA
1 GGGTATCGATACC-ATTC-AAGG
223368 GGGTATCGATACCATTCTCAA--
1 GGGTATCGATACCA-T-TCAAGG
223389 GGGTATCGATACC
1 GGGTATCGATACC
223402 TAATGCACAA
Statistics
Matches: 88, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.12
21 36 0.41
22 22 0.25
23 17 0.19
24 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACCATTCAAGG
Found at i:223393 original size:44 final size:43
Alignment explanation
Indices: 223302--223403 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
223292 ACCATCAGGG
* * *
223302 GGGTATCGATACCCATTCAAGGGGGTATCGATACCTATTGCAG
1 GGGTATCGATACCTATTCAAGAGGGTATCGATACCTATTGCAA
*
223345 GGGTATCGATACCTATTCAAAGAGGGTATCGATACC-ATTCTCAA
1 GGGTATCGATACCTATTC-AAGAGGGTATCGATACCTATT-GCAA
223389 GGGTATCGATACCTA
1 GGGTATCGATACCTA
223404 ATGCACAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 20 0.38
44 33 0.62
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
GGGTATCGATACCTATTCAAGAGGGTATCGATACCTATTGCAA
Found at i:227263 original size:22 final size:21
Alignment explanation
Indices: 227221--227260 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
227211 GAGTTTATTT
*
227221 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
227242 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
227261 ACAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:229195 original size:20 final size:22
Alignment explanation
Indices: 229170--229246 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 22
229160 ATATGCCTTA
*
229170 GGGTATCGGTACCAT-CATA-G
1 GGGTATCGATACCATGCATAGG
229190 GGGTATCGATACCATTGCATAGG
1 GGGTATCGATACCA-TGCATAGG
*
229213 GGGTATCGATACCAT---TGGG
1 GGGTATCGATACCATGCATAGG
229232 GGGTATCGATACCAT
1 GGGTATCGATACCAT
229247 CCGAACATTC
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
19 18 0.35
20 13 0.25
21 1 0.02
22 5 0.10
23 15 0.29
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (22 bp):
GGGTATCGATACCATGCATAGG
Found at i:229219 original size:23 final size:23
Alignment explanation
Indices: 229170--229246 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
229160 ATATGCCTTA
*
229170 GGGTATCGGTACCA-T-CATA-G
1 GGGTATCGATACCATTGCATAGG
229190 GGGTATCGATACCATTGCATAGG
1 GGGTATCGATACCATTGCATAGG
229213 GGGTATCGATACCATTG----GG
1 GGGTATCGATACCATTGCATAGG
229232 GGGTATCGATACCAT
1 GGGTATCGATACCAT
229247 CCGAACATTC
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
19 17 0.32
20 13 0.25
21 1 0.02
22 4 0.08
23 18 0.34
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (23 bp):
GGGTATCGATACCATTGCATAGG
Found at i:233701 original size:15 final size:14
Alignment explanation
Indices: 233681--233736 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
233671 CATATACAAC
233681 TGTTATTAATGAATT
1 TGTTATTAA-GAATT
233696 TGTTATTAAGAA-T
1 TGTTATTAAGAATT
***
233709 ACATATTAATGAATT
1 TGTTATTAA-GAATT
*
233724 TTTTATTAAGAAT
1 TGTTATTAAGAAT
233737 ACTATATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 7 0.21
14 10 0.30
15 16 0.48
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (14 bp):
TGTTATTAAGAATT
Found at i:233724 original size:28 final size:29
Alignment explanation
Indices: 233684--233743 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 29
233674 ATACAACTGT
233684 TATTAATGAATTTGTTATTAAGAATAC-A
1 TATTAATGAATTTGTTATTAAGAATACTA
*
233712 TATTAATGAATTTTTTATTAAGAATACTA
1 TATTAATGAATTTGTTATTAAGAATACTA
233741 TAT
1 TAT
233744 AAAATAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (29 bp):
TATTAATGAATTTGTTATTAAGAATACTA
Found at i:233753 original size:29 final size:28
Alignment explanation
Indices: 233688--233754 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
233678 AACTGTTATT
* *
233688 AATGAATTTGTTATTAAGAATACATATT
1 AATGAATTTTTTATTAAGAATACATATA
233716 AATGAATTTTTTATTAAGAATACTATATAA
1 AATGAATTTTTTATTAAGAATAC-ATAT-A
233746 AAT-AATTTT
1 AATGAATTTT
233755 AGTGACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 22 0.63
29 10 0.29
30 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (28 bp):
AATGAATTTTTTATTAAGAATACATATA
Found at i:234189 original size:22 final size:22
Alignment explanation
Indices: 234140--234198 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
234130 AACACAAACT
*
234140 TAAAAATATTGTTTTAATATAA
1 TAAAAATATTGTTTTAATAAAA
* *
234162 TTAAAAT-TTAGTTTTATTAAAA
1 TAAAAATATT-GTTTTAATAAAA
* *
234184 TAAAAAAATTATTTT
1 TAAAAATATTGTTTT
234199 GGGTGCCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
TAAAAATATTGTTTTAATAAAA
Found at i:237233 original size:29 final size:29
Alignment explanation
Indices: 237044--237233 Score: 224
Period size: 29 Copynumber: 6.6 Consensus size: 29
237034 CATATTTGAA
*
237044 AATTCCCAAAATGTCATCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
237073 AATT-CCAAGAATGTCACTTTTTTCAAAAA
1 AATTCCCAA-AATGTCACCTTTTTCAAAAT
* *
237102 AAATCCCAAAATGTTA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
237130 AATTCCCATAATGTCA-TTTTTTTAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
237158 AATTCCCAAAATGTCACATTTTCCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
237187 AATTTCCAGAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
237216 AATTTCCAAAATGTCACC
1 AATTCCCAAAATGTCACC
237234 GGGTCGGGTC
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
28 52 0.39
29 79 0.59
30 4 0.03
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:237262 original size:17 final size:17
Alignment explanation
Indices: 237233--237274 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
237223 AAAATGTCAC
237233 CGGGTCGGGTCAACGGGT
1 CGGGTC-GGTCAACGGGT
237251 CGGGTCGGTCAACGGGT
1 CGGGTCGGTCAACGGGT
*
237268 CGAGTCG
1 CGGGTCG
237275 AACTGGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.17
Consensus pattern (17 bp):
CGGGTCGGTCAACGGGT
Found at i:242317 original size:2 final size:2
Alignment explanation
Indices: 242310--242350 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
242300 TATTATAAAG
242310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
242351 CCTTAATTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:243689 original size:20 final size:21
Alignment explanation
Indices: 243664--243715 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
243654 TTTTCCCAAT
*
243664 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
243684 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
243705 TCGCAATGCGA
1 TCGCAATGCGA
243716 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:243729 original size:20 final size:20
Alignment explanation
Indices: 243704--243797 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
243694 AATTGGGAAA
243704 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
243724 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
243744 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
243765 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
243785 TTCGCAACGCGAT
1 ATCGCAATGCGAT
243798 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:244401 original size:19 final size:19
Alignment explanation
Indices: 244379--244563 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
244369 GAAACAAAAA
* *
244379 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
244398 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
244417 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
244436 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
244456 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
244472 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
244489 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
244503 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
244522 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
244542 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
244562 TC
1 TC
244564 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.44
20 48 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:244456 original size:39 final size:38
Alignment explanation
Indices: 244379--244468 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
244369 GAAACAAAAA
*
244379 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
244417 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
244456 TCGCGTTGCGATT
1 TCGCGTTGCGATT
244469 GTCTGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 22 0.44
39 28 0.56
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:244479 original size:39 final size:39
Alignment explanation
Indices: 244379--244479 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
244369 GAAACAAAAA
* * **
244379 TCGCATTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
* **
244417 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
244456 TCGCGTTGCGATTGTCT-GGTCGCG
1 TCGCGTTGCGATT-TCTAGGTCGCG
244480 ATAGTCATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 22 0.39
39 33 0.58
40 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (39 bp):
TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
Found at i:244533 original size:34 final size:33
Alignment explanation
Indices: 244451--244538 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
244441 GTTGCGATTT
* *
244451 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
244484 TCATTTCGCGTTGCGATTCTCTCGTTGTGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
244517 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
244539 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:244540 original size:20 final size:20
Alignment explanation
Indices: 244517--244563 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
244507 GTTGTGATAG
244517 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
244537 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
244557 TCATTTC
1 TCATTTC
244564 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:246624 original size:42 final size:42
Alignment explanation
Indices: 246563--246685 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
246553 GCCCGACTTG
* * * *
246563 CCTATTATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
246605 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
246647 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
246686 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:246643 original size:21 final size:21
Alignment explanation
Indices: 246619--246685 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
246609 TCATTCCTCG
246619 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
246640 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
246661 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
246682 AGAG
1 AGAG
246686 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:248061 original size:14 final size:14
Alignment explanation
Indices: 248042--248077 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
248032 ATTGTTTAAT
248042 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
248056 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
248070 TGATTTGT
1 TGATTTGT
248078 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:248278 original size:19 final size:19
Alignment explanation
Indices: 248256--248373 Score: 58
Period size: 19 Copynumber: 6.7 Consensus size: 19
248246 CGAAATTAAA
248256 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
248275 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
248290 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
248308 TTCGCATTGC-A----AAA
1 TTCGCGTTGCGATTTTCAT
*
248322 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
248341 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
248360 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
248374 AGACATTAAG
Statistics
Matches: 69, Mismatches: 19, Indels: 21
0.63 0.17 0.19
Matches are distributed among these distances:
14 17 0.25
15 1 0.01
16 3 0.04
17 3 0.04
18 1 0.01
19 34 0.49
20 10 0.14
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:248302 original size:33 final size:31
Alignment explanation
Indices: 248259--248353 Score: 127
Period size: 33 Copynumber: 2.9 Consensus size: 31
248249 AATTAAATTC
*
248259 GCGTTGCGATTTTCATTTCGCATTGCGATTCCC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT--A
* *
248292 TCGTTGCGATTTTCATTTCGCATTGCAAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGC--GATTA
248325 GCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
248354 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
31 2 0.04
33 50 0.91
35 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTA
Found at i:250660 original size:12 final size:12
Alignment explanation
Indices: 250643--250667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
250633 TCTTCGGGGA
250643 CTTTTTCTTCTT
1 CTTTTTCTTCTT
250655 CTTTTTCTTCTT
1 CTTTTTCTTCTT
250667 C
1 C
250668 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:250876 original size:24 final size:24
Alignment explanation
Indices: 250842--250895 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
250832 CTGAAACATC
* *
250842 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
250866 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
250890 ATCAAA
1 ATCAAA
250896 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:251972 original size:20 final size:20
Alignment explanation
Indices: 251947--252004 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
251937 ATTCATTTGA
251947 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
251967 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
251987 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
252005 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:252047 original size:14 final size:14
Alignment explanation
Indices: 252028--252081 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
252018 GAAAATCGCA
252028 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
252042 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
252059 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
252075 TTGCGAT
1 TTGCGAT
252082 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:252047 original size:33 final size:33
Alignment explanation
Indices: 252010--252080 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
252000 AAAATCGCAA
252010 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
252043 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
252076 TGCGA
1 TGCGA
252081 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:252081 original size:33 final size:33
Alignment explanation
Indices: 252023--252100 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
252013 GAAATGAAAA
***
252023 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
252056 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
252089 TCGCGTTGCGAT
1 TCGCATTGCGAT
252101 AGTCTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:252203 original size:14 final size:14
Alignment explanation
Indices: 252184--252220 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
252174 CATCAATTAA
252184 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
252198 ACAAATCATCTTTT
1 ACAAATCAACATTT
252212 ACAAATCAA
1 ACAAATCAA
252221 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:254106 original size:19 final size:19
Alignment explanation
Indices: 254063--254160 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
254053 TAGTTTACTT
* *
254063 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
254083 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
*
254102 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
254121 TCGCAA--CG--AT-AAAA
1 TCGCAACGCGAAATGAAAA
254135 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
254153 TCGCAACG
1 TCGCAACG
254161 ACAAAATCGT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 2 0.03
17 2 0.03
18 13 0.20
19 25 0.38
20 12 0.18
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:254136 original size:14 final size:14
Alignment explanation
Indices: 254117--254174 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
254107 ATGCGAAATG
254117 AAAATCGCAACGAT
1 AAAATCGCAACGAT
254131 AAAATCGCAACGCGAAAT
1 AAAATCGCAA--CG--AT
* *
254149 GAAATCGCAACGAC
1 AAAATCGCAACGAT
*
254163 AAAATCGTAACG
1 AAAATCGCAACG
254175 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 4 0.11
18 11 0.31
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:254159 original size:32 final size:33
Alignment explanation
Indices: 254101--254179 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
254091 CGAAATGACT
* *
254101 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
254134 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
254166 ATCGTAACGCGAAA
1 ATCGCAACGCGAAA
254180 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:254227 original size:14 final size:14
Alignment explanation
Indices: 254208--254265 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
254198 TTTCATTTCG
254208 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
254222 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
254238 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
254254 CGTTGCGATTTT
1 CGTTGCGATTTT
254266 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:254277 original size:33 final size:33
Alignment explanation
Indices: 254191--254281 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
254181 ACAAATCGCA
*
254191 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
254224 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
254256 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
254282 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:254288 original size:19 final size:20
Alignment explanation
Indices: 254266--254309 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
254256 TTGCGATTTT
254266 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* * *
254285 CATTTCCTCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
254305 CATTT
1 CATTT
254310 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:254828 original size:18 final size:18
Alignment explanation
Indices: 254802--254846 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
254792 GTCGATCAGA
*
254802 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
254820 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
254838 TGATGGCTC
1 TGATGGCTC
254847 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:256189 original size:20 final size:20
Alignment explanation
Indices: 256164--256206 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
256154 AATAGTTTCT
256164 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
256184 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
256204 GAA
1 GAA
256207 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:256512 original size:22 final size:22
Alignment explanation
Indices: 256485--256528 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
256475 GATGGAGATA
256485 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
256507 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
256529 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:256741 original size:20 final size:20
Alignment explanation
Indices: 256715--256828 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
256705 GATTATGTAT
256715 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
256735 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
256755 TATCGCGTTGAGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
256775 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
256796 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
256816 TATCGCATTGCGA
1 TATCGCGTTGCGA
256829 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 63 0.83
21 13 0.17
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:256832 original size:41 final size:41
Alignment explanation
Indices: 256695--256830 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
256685 CGCTTTGAAA
* *
256695 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * * * *
256736 ATCGCGTTGCGA-AAGTCAGTATCGCGTTGAGAAAGTAAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * *
256776 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
256817 ATCGCATTGCGATT
1 ATCGCATTGCGATT
256831 TTCCCAATTC
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 31 0.42
41 42 0.58
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
Found at i:256850 original size:21 final size:21
Alignment explanation
Indices: 256818--256893 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
256808 ATAGTCAGTA
*
256818 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
256839 TCGCGTTTCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
256859 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
256880 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
256894 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:256862 original size:20 final size:20
Alignment explanation
Indices: 256837--256910 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
256827 GATTTTCCCA
*
256837 ATTCGCGTTTCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
256857 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
256878 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
256898 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
256911 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:256863 original size:41 final size:41
Alignment explanation
Indices: 256818--256910 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
256808 ATAGTCAGTA
*
256818 TCGCATTGCGATTTTCCCAATTCGCGTTTCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
256859 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
256900 TCGCATTGCGA
1 TCGCATTGCGA
256911 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:263492 original size:42 final size:42
Alignment explanation
Indices: 263446--263528 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
263436 AGATTGATGG
263446 TGATGAAGGTAGGGTGATATGAGGTGGAATATGTGATGAAGC
1 TGATGAAGGTAGGGTGATATGAGGTGGAATATGTGATGAAGC
263488 TGATGAAGGTAGGGTGATATGAGGTGGAATATGTGATGAAG
1 TGATGAAGGTAGGGTGATATGAGGTGGAATATGTGATGAAG
263529 ATAGACTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.01, G:0.41, T:0.27
Consensus pattern (42 bp):
TGATGAAGGTAGGGTGATATGAGGTGGAATATGTGATGAAGC
Found at i:265465 original size:14 final size:14
Alignment explanation
Indices: 265446--265477 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
265436 CGTTTGTGAA
265446 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
265460 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
265474 CGTT
1 CGTT
265478 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:265494 original size:24 final size:24
Alignment explanation
Indices: 265447--265497 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
265437 GTTTGTGAAC
* *
265447 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGATTATGTTCATTCAGTTAT
* *
265471 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAGTTAT
265495 GTT
1 GTT
265498 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAGTTAT
Found at i:266555 original size:16 final size:16
Alignment explanation
Indices: 266534--266600 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
266524 GTCTCCAACG
266534 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
266550 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
** *
266566 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
266582 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
266596 TTTAT
1 TTTAT
266601 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
16 40 0.89
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:266573 original size:32 final size:32
Alignment explanation
Indices: 266532--266592 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
266522 GGGTCTCCAA
**
266532 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
*
266564 CGTTTATGTTCGTGCGCGTTTATGTTCGT
1 CGTTTATGTTCGTGCGCATTTATGTTCGT
266593 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.52
Consensus pattern (32 bp):
CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
Found at i:266641 original size:71 final size:71
Alignment explanation
Indices: 266560--266691 Score: 237
Period size: 71 Copynumber: 1.9 Consensus size: 71
266550 TTTATGTTCG
*
266560 TGTTCGTTTATGTTCGTGCGCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAAAA
1 TGTTCGTTTATGTTCGTGCGCGTTTATGTTCATTTATTTATTAAATGAACGAACATGAACAAAAA
266625 AAAATT
66 AAAATT
**
266631 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCATTTATTTATTAAATGAACGAACATGAACA
1 TGTTCGTTTATGTTCGTGCGCGTTTATGTTCATTTATTTATTAAATGAACGAACATGAACA
266692 TACCTCCGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (71 bp):
TGTTCGTTTATGTTCGTGCGCGTTTATGTTCATTTATTTATTAAATGAACGAACATGAACAAAAA
AAAATT
Found at i:266652 original size:16 final size:16
Alignment explanation
Indices: 266631--266661 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
266621 AAAAAAAATT
266631 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
266647 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
266662 ATTTATTTAT
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:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:273451 original size:3 final size:3
Alignment explanation
Indices: 273443--273549 Score: 169
Period size: 3 Copynumber: 35.7 Consensus size: 3
273433 TTAATATATT
* *
273443 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
273491 TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
273539 TAA TAA TAA TA
1 TAA TAA TAA TA
273550 TGGATAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:274116 original size:113 final size:113
Alignment explanation
Indices: 273868--274745 Score: 1501
Period size: 113 Copynumber: 7.8 Consensus size: 113
273858 GAATTATGCC
* * *
273868 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
273932 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
*
273979 AAAATGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
274044 TATGAACTTTTTCTGGAAAAAATGTTCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
*
274092 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
274157 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
274205 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
274270 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAA-GTGATGAATTCAGGT
*
274319 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
274384 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
274432 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
274497 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAA-GTGATGAATTCAGGT
*
274546 -AAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
274610 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
* *
274658 AAAAGGTTGACCAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
274723 TATGAACCTTCTCTGGAAAAGAT
66 TATGAACTTTCTCTGGAAAAGAT
274746 AATCTTTCAA
Statistics
Matches: 725, Mismatches: 37, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
111 4 0.01
112 78 0.11
113 521 0.72
114 122 0.17
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:274727 original size:453 final size:451
Alignment explanation
Indices: 273868--274749 Score: 1568
Period size: 453 Copynumber: 2.0 Consensus size: 451
273858 GAATTATGCC
* * *
273868 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
273933 ATGAACTTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAATGTTGAACAAATTCT
66 ATGAACTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCT
* *
273998 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
**
274063 AAATGTTCCATCAAGTGATGAATTCAGGTAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCT
196 AAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCT
274128 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTG
261 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTG
*
274193 ATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
326 ATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
274258 AGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
391 AGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
*
274319 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
274384 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
65 TATGAAC-TTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
274449 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
129 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
* *
274514 AAAGATAATCCATCAATTTGATGAATTCAGGT-AAAGGTTGAATAAATTCTTCTCATTATGAACT
194 AAAAATAATCCATCAA-GTGATGAATTCAGGTAAAAGGTTGAATAAATTCTTCTCATTATGAACT
274578 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
258 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
*
274643 GTGATGAATTCAGGTAAAAGGTTGACCAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
323 GTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
274708 ATGAGTTCTTTTCATTATGAACCTTCTCTGGAAAAGATAATC
388 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATC
274750 TTTCAAATGA
Statistics
Matches: 410, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
451 4 0.01
452 63 0.15
453 329 0.80
454 14 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (451 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
AAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTG
ATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
AGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
Found at i:275635 original size:82 final size:82
Alignment explanation
Indices: 275382--276285 Score: 1456
Period size: 82 Copynumber: 11.0 Consensus size: 82
275372 TTTACTATGA
* * * *
275382 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-ATCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCT-AAACCAGGTCAGATAACTCAAAGAACAC
275446 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
* * * * * *
275464 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCT-ATATAATCAGATCAAATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATT-GTTCTGCTA-AACCAGGTCAGATAACTCAAAGAACA
275528 CTTCCAGAAGATGCTATTG
64 CTTCCAGAAGATGCTATTG
275547 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
275612 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * *
275629 GTAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
275694 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
275711 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAATCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
275776 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * *
275793 GTAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
275858 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
275875 GCAAATTCATCTTCTAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
275940 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
275957 GCAAATTCATCTTCTAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
276022 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
276039 GCAAATTCATCTTCTAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
276104 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * **
276121 GCAAATTCATCTTCTAAATTCAATGCTTGATTCTG-TCCAACCATATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTG-TTCTGCT-AAACCAGGTCAGATAACTCAAAGAACA
*
276185 CTTCCAGAAGATGCTATTA
64 CTTCCAGAAGATGCTATTG
* * **
276204 GCAAATTCATCTTCCAAATTCAATGATTGATTCTG-TCCAACCATATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTG-TTCTGCT-AAACCAGGTCAGATAACTCAAAGAACA
276268 CTTCCAGAAGATGCTATT
64 CTTCCAGAAGATGCTATT
276286 CTGTCTAACC
Statistics
Matches: 786, Mismatches: 31, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
82 581 0.74
83 205 0.26
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (82 bp):
GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:276296 original size:50 final size:50
Alignment explanation
Indices: 276233--276384 Score: 241
Period size: 50 Copynumber: 3.0 Consensus size: 50
276223 TCAATGATTG
* *
276233 ATTCTGTCCAACCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
* *
276283 ATTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCTAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
* * *
276333 ATTCTGTCTAACCAGATCATATAACTCTAAGAACACTTCCAAAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
276383 AT
1 AT
276385 GAGTCTCTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (50 bp):
ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
Found at i:277195 original size:16 final size:17
Alignment explanation
Indices: 277157--277201 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
277147 AATATAAAAG
*
277157 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
277175 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
277191 AATAAATTGAA
1 AATAAATTGAA
277202 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:277552 original size:10 final size:10
Alignment explanation
Indices: 277539--277586 Score: 69
Period size: 10 Copynumber: 4.5 Consensus size: 10
277529 CCATTTTTTC
277539 TTTTTTTCTT
1 TTTTTTTCTT
277549 TTTTTTTCCTTT
1 TTTTTTT-C-TT
277561 TTTTTTTCTT
1 TTTTTTTCTT
277571 TTTTTTTCTT
1 TTTTTTTCTT
277581 TCTTTT
1 T-TTTT
277587 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 20 0.57
11 6 0.17
12 9 0.26
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:277555 original size:11 final size:11
Alignment explanation
Indices: 277539--277586 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
277529 CCATTTTTTC
277539 TTTTTTTCTTT
1 TTTTTTTCTTT
*
277550 TTTTTTCCTTT
1 TTTTTTTCTTT
277561 TTTTTTTC-TT
1 TTTTTTTCTTT
277571 TTTTTTTCTTT
1 TTTTTTTCTTT
277582 CTTTT
1 -TTTT
277587 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 10 0.30
11 19 0.58
12 4 0.12
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:277564 original size:14 final size:13
Alignment explanation
Indices: 277532--277586 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
277522 TGACCCCCCA
*
277532 TTTTTTCTTTTT-
1 TTTTTTTTTTTTC
*
277544 TTCTTTTTTTTTC
1 TTTTTTTTTTTTC
*
277557 -CTTTTTTTTTTC
1 TTTTTTTTTTTTC
277569 TTTTTTTTTCTTTC
1 TTTTTTTTT-TTTC
277583 TTTT
1 TTTT
277587 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 20 0.57
13 7 0.20
14 8 0.23
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:289881 original size:11 final size:11
Alignment explanation
Indices: 289865--289895 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
289855 TCTATTTTCC
289865 TTTTTTTCTTT
1 TTTTTTTCTTT
289876 TTTTTTTCTTT
1 TTTTTTTCTTT
*
289887 TTTTGTTCT
1 TTTTTTTCT
289896 GTCTCTGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:290428 original size:3 final size:3
Alignment explanation
Indices: 290420--290515 Score: 156
Period size: 3 Copynumber: 31.7 Consensus size: 3
290410 TTAATATATT
*
290420 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
290468 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
290514 TA
1 TA
290516 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:293631 original size:29 final size:29
Alignment explanation
Indices: 293610--293667 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
293600 AAACTTTGAA
293610 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
293639 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
293668 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:293657 original size:30 final size:30
Alignment explanation
Indices: 293610--293669 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
293600 AAACTTTGAA
293610 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
293639 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
293670 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:293808 original size:20 final size:19
Alignment explanation
Indices: 293781--293838 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
293771 TGTTTAATGA
293781 AAAAGATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
*
293800 AAAAGGATACTAATTGTTA-
1 AAAA-GATACCAATTGTTAC
293819 AAAAGATAACCAATTGTTAC
1 AAAAGAT-ACCAATTGTTAC
293839 CAATTGTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 18 0.53
20 13 0.38
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Found at i:294958 original size:23 final size:24
Alignment explanation
Indices: 294927--294977 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
294917 TAAATCAAAA
*
294927 TTTTCTTTTTCAAAACTATAAAT-
1 TTTTATTTTTCAAAACTATAAATC
* * *
294950 TTTTATTTTTGAAAGCTCTAAATC
1 TTTTATTTTTCAAAACTATAAATC
294974 TTTT
1 TTTT
294978 TTCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTATTTTTCAAAACTATAAATC
Found at i:296190 original size:20 final size:22
Alignment explanation
Indices: 296165--296204 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
296155 AGTCGTATAT
296165 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
296185 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
296205 TTTTGCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:296329 original size:18 final size:19
Alignment explanation
Indices: 296284--296334 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
296274 CGTTGTAGCC
296284 AGGGGGTATAGATACCCCT
1 AGGGGGTATAGATACCCCT
* *
296303 AGAGGGTATGGATACCCCT
1 AGGGGGTATAGATACCCCT
296322 -GGGGGTATAGATA
1 AGGGGGTATAGATA
296335 TCATCCGAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
AGGGGGTATAGATACCCCT
Found at i:296496 original size:29 final size:29
Alignment explanation
Indices: 296475--296532 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
296465 AAACTTTGAA
296475 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
296504 TAAGTTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
296533 TACCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 14 0.54
31 2 0.08
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:303710 original size:26 final size:26
Alignment explanation
Indices: 303681--303732 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
303671 GGTTAAAACC
303681 CCACAATATAACATTATCAATTGTAA
1 CCACAATATAACATTATCAATTGTAA
303707 CCACAATATAACATTATCAATTGTAA
1 CCACAATATAACATTATCAATTGTAA
303733 ACAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (26 bp):
CCACAATATAACATTATCAATTGTAA
Found at i:307373 original size:42 final size:41
Alignment explanation
Indices: 307327--307420 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
307317 TTTTTGTCGT
307327 GGCAAGAAAAATATGCAAGAGTAAACAAATAAAAATTGCTAA
1 GGCAAGAAAAAT-TGCAAGAGTAAACAAATAAAAATTGCTAA
** *
307369 GGCAA-AAATTAATTGCAAGAGTAAGTAAATAAAAGTTGCTAA
1 GGCAAGAAA--AATTGCAAGAGTAAACAAATAAAAATTGCTAA
307411 GGC--GAAAAAT
1 GGCAAGAAAAAT
307421 GTTTGAGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 3 0.07
41 6 0.13
42 34 0.74
43 3 0.07
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (41 bp):
GGCAAGAAAAATTGCAAGAGTAAACAAATAAAAATTGCTAA
Found at i:310633 original size:20 final size:21
Alignment explanation
Indices: 310608--310650 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
310598 TCAATCATTA
*
310608 ATTTTTTAAAAT-TAATTTTT
1 ATTTTTTAAAATATAAATTTT
310628 ATTTTTTAAAATATAAATTTT
1 ATTTTTTAAAATATAAATTTT
310649 AT
1 AT
310651 GTGGCATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTTAAAATATAAATTTT
Found at i:323353 original size:18 final size:18
Alignment explanation
Indices: 323330--323382 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
323320 ACACTCCTAC
323330 AAAAGTATCAATACTTAT
1 AAAAGTATCAATACTTAT
* * *
323348 AAAAGTTTCGATACTTTCT
1 AAAAGTATCAATAC-TTAT
*
323367 ACAAGTATCAATACTT
1 AAAAGTATCAATACTT
323383 TTTAAACATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (18 bp):
AAAAGTATCAATACTTAT
Found at i:323380 original size:19 final size:19
Alignment explanation
Indices: 323330--323388 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
323320 ACACTCCTAC
323330 AAAAGTATCAATAC-TTAT
1 AAAAGTATCAATACTTTAT
* * *
323348 AAAAGTTTCGATACTTTCT
1 AAAAGTATCAATACTTTAT
* *
323367 ACAAGTATCAATACTTTTT
1 AAAAGTATCAATACTTTAT
323386 AAA
1 AAA
323389 CATTCTGGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (19 bp):
AAAAGTATCAATACTTTAT
Found at i:330403 original size:22 final size:22
Alignment explanation
Indices: 330378--330432 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
330368 CTGTTAATAT
* *
330378 CAGGAGTTATTTAATTTAATTA
1 CAGGAGTTATATAATATAATTA
* * *
330400 CAGGGGTTACATAATATAATTT
1 CAGGAGTTATATAATATAATTA
*
330422 CGGGAGTTATA
1 CAGGAGTTATA
330433 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATAATATAATTA
Found at i:333728 original size:3 final size:3
Alignment explanation
Indices: 333722--333759 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
333712 GTGACCAAAC
333722 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
333760 GTTGAGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:339613 original size:22 final size:23
Alignment explanation
Indices: 339583--339627 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
339573 AATATTAAAT
*
339583 AAATCAAATGAAAA-AAAATAATA
1 AAATCAAAT-AAAATAAAAGAATA
339606 AAAT-AAATAAAATAAAAGAATA
1 AAATCAAATAAAATAAAAGAATA
339628 TTAAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATCAAATAAAATAAAAGAATA
Found at i:340600 original size:17 final size:16
Alignment explanation
Indices: 340555--340601 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 16
340545 ATGATAAAAT
340555 TAATAATATTAT-ATA
1 TAATAATATTATAATA
340570 T-ATAAT-TATATAATA
1 TAATAATAT-TATAATA
340585 TAATAATATTACTAATA
1 TAATAATATTA-TAATA
340602 AAAGGACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.04
14 8 0.30
15 5 0.19
16 7 0.26
17 6 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATAATATTATAATA
Found at i:340600 original size:25 final size:21
Alignment explanation
Indices: 340552--340602 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
340542 CAAATGATAA
*
340552 AATTAATAATATTATATATAT
1 AATTAATAATATAATATATAT
340573 AATTATATAATATAATA-ATAT
1 AATTA-ATAATATAATATATAT
* *
340594 TACTAATAA
1 AATTAATAA
340603 AAGGACGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATAATATAATATATAT
Found at i:344532 original size:18 final size:18
Alignment explanation
Indices: 344509--344543 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
344499 CAACGGTCGG
344509 GTCGGGTCGGGTCAACGA
1 GTCGGGTCGGGTCAACGA
344527 GTCGGGTCGGGTCAACG
1 GTCGGGTCGGGTCAACG
344544 GGTCAGGTAA
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:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GTCGGGTCGGGTCAACGA
Found at i:344534 original size:23 final size:22
Alignment explanation
Indices: 344496--344539 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
344486 ACCGGTCAAC
344496 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
344518 GGTCAACGAGTCGGGTCGGGTC
1 GGTCAACG-GTCGGGTCGGGTC
344540 AACGGGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Done.