Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 21
Found at i:59 original size:23 final size:24
Alignment explanation
Indices: 16--71 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
6 TAATAGGTCT
* *
16 ATTTATTATTAATTATCAAAA-TA
1 ATTTATTATAAATTATAAAAAGTA
39 ATTTATTATAACATT-TAAAAAGTA
1 ATTTATTATAA-ATTATAAAAAGTA
*
63 ATCTATTAT
1 ATTTATTAT
72 TTTTTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTTATTATAAATTATAAAAAGTA
Found at i:211 original size:15 final size:16
Alignment explanation
Indices: 191--220 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
181 ATCATTACAG
191 GTCAGGTT-AAAACAT
1 GTCAGGTTGAAAACAT
206 GTCAGGTTGAAAACA
1 GTCAGGTTGAAAACA
221 GGTCGGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
GTCAGGTTGAAAACAT
Found at i:15394 original size:55 final size:55
Alignment explanation
Indices: 15335--15928 Score: 433
Period size: 55 Copynumber: 10.9 Consensus size: 55
15325 TAAGTGAGAT
* * *
15335 TTGAAAAATCTTCGAAGGACGAGTACGCTCCCTATTCTATCAGAGAGTATAAGAC
1 TTGAAAAATCTTCGAAGAACGAGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * *
15390 TTGAAATAATCTTCGGAA-AACGGGT-CTGCTCTCTATTCTTTTAGGGAGTATAGGAC
1 TTGAAA-AATCTTC-GAAGAACGAGTAC-GCTCCCTATTCTTTCAGGGAGTATAAGAC
* ** * *
15446 TTGAATAATCTTCAGAA-AAC-AGATTTGCCCCCTATTCTTTCAGGGAGTATAGGAC
1 TTGAAAAATCTTC-GAAGAACGAG-TACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * * * * *
15501 TTGAACAATCTTCGGAGAATGGGT-CTGCTCCCTACTCTTTTAGGGAGTATATGAC
1 TTGAAAAATCTTCGAAGAACGAGTAC-GCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * *
15556 TTGAACAATATTCGGAA-AAC-AGGTTCGTTCCCTATTCTTTCAGGGAGTAT-AGAC
1 TTGAAAAATCTTC-GAAGAACGA-GTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * *
15610 TTGAACAATCTTCGTAGAACGGGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
1 TTGAAAAATCTTCGAAGAACGAGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
*
15665 TT-AAACAATCTTCGTAGAAC-AGGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
1 TTGAAA-AATCTTCGAAGAACGA-GTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * ** *
15720 TT-AAACAATCTTCGAAAAATGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGGAC
1 TTGAAA-AATCTTCGAAGAACGAGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * *
15775 TCGAACAATCTTC-AATAAACGTGT-CTGCT-CC----C--TCAGGGAGTATAAGAC
1 TTGAAAAATCTTCGAA-GAACGAGTAC-GCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * * * *
15823 TCGAACAATCTTCAGCA-AACGTGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
1 TTGAAAAATCTTC-GAAGAACGAGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
* * * * * * *
15878 TCGAACAATCTTTAGTA-AACGTGT-CTGCTCCCTATTATTTTAGGGAGTATA
1 TTGAAAAATC-TTCGAAGAACGAGTAC-GCTCCCTATTCTTTCAGGGAGTATA
15929 GAACACAAAC
Statistics
Matches: 450, Mismatches: 57, Indels: 64
0.79 0.10 0.11
Matches are distributed among these distances:
48 38 0.08
49 3 0.01
50 2 0.00
53 3 0.01
54 54 0.12
55 298 0.66
56 49 0.11
57 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (55 bp):
TTGAAAAATCTTCGAAGAACGAGTACGCTCCCTATTCTTTCAGGGAGTATAAGAC
Found at i:15551 original size:110 final size:110
Alignment explanation
Indices: 15360--15928 Score: 603
Period size: 110 Copynumber: 5.2 Consensus size: 110
15350 AGGACGAGTA
* * * *
15360 CGCTCCCTATTCTATCAGAGAGTATAAGACTTGAAATAATCTTCGGAAAACGGGTCTGCTCTCTA
1 CGCTCCCTATTCTTTCAGGGAGTATAAGACTTG-AACAATCTTCGGAAAACGGGTCTGCTCCCTA
* * *
15425 TTCTTTTAGGGAGTATAGGACTTGAATAATCTTCAGAAAACAGATT
65 TTCTTTCAGGGAGTATAGGACTTGAACAATCTTCAGAAAACAGGTT
* * * * * *
15471 TGCCCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGGAGAATGGGTCTGCTCCCTAC
1 CGCTCCCTATTCTTTCAGGGAGTATAAGACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTAT
* * * *
15536 TCTTTTAGGGAGTATATGACTTGAACAATATTCGGAAAACAGGTT
66 TCTTTCAGGGAGTATAGGACTTGAACAATCTTCAGAAAACAGGTT
* * *
15581 CGTTCCCTATTCTTTCAGGGAGTAT-AGACTTGAACAATCTTCGTAGAACGGGTAC-GCTCCCTA
1 CGCTCCCTATTCTTTCAGGGAGTATAAGACTTGAACAATCTTCGGAAAACGGGT-CTGCTCCCTA
* * * *
15644 TTCTTTCAGGGAGTATAAGACTTAAACAATCTTC-GTAGAACAGGTA
65 TTCTTTCAGGGAGTATAGGACTTGAACAATCTTCAG-AAAACAGGTT
* * * *
15690 CGCTCCCTATTCTTTCAGGGAGTATAAGACTTAAACAATCTTCGAAAAATGGGTTTGCTCCCTAT
1 CGCTCCCTATTCTTTCAGGGAGTATAAGACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTAT
*
15755 TCTTTCAGGGAGTATAGGACTCGAACAATCTTCA-ATAAAC--GTGT
66 TCTTTCAGGGAGTATAGGACTTGAACAATCTTCAGA-AAACAGGT-T
* * * *
15799 CTGCT-CC----C--TCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGT-TCGCTCCCT
1 C-GCTCCCTATTCTTTCAGGGAGTATAAGACTTGAACAATCTTCGGAAAACGGGTCT-GCTCCCT
* * *
15856 ATTCTTTCAGGGAGTATAGGACTCGAACAATCTTTAGTAAAC--GTGT
64 ATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCAGAAAACAGGT-T
* *
15902 CTGCTCCCTATTATTTTAGGGAGTATA
1 C-GCTCCCTATTCTTTCAGGGAGTATA
15929 GAACACAAAC
Statistics
Matches: 391, Mismatches: 50, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
102 1 0.00
103 88 0.23
104 2 0.01
105 1 0.00
108 3 0.01
109 98 0.25
110 170 0.43
111 28 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (110 bp):
CGCTCCCTATTCTTTCAGGGAGTATAAGACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTAT
TCTTTCAGGGAGTATAGGACTTGAACAATCTTCAGAAAACAGGTT
Found at i:15783 original size:219 final size:211
Alignment explanation
Indices: 15363--15928 Score: 602
Period size: 219 Copynumber: 2.6 Consensus size: 211
15353 ACGAGTACGC
* * * *
15363 TCCCTATTCTATCAGAGAGTATAAGACTTGAAATAATCTTCGGAAAACGGGTCTGCTCTCTATTC
1 TCCCTATTCTATCAGGGAGTATAAGACTTG-AACAATCTTC-GCAAACGGGTC-GCTCCCTATTC
* * * * * *
15428 TTTTAGGGAGTATAGGACTTGAATAATCTTCAGAAAACAGATTTGCCCCCTATTCTTTCAGGGAG
63 TTTCAGGGAGTATAGGACTTGAACAATCTTC-GTAAACAG-GTCGCTCCCTATTCTTTCAGGGAG
* * * * * * *
15493 TATAGGACTTGAACAATCTTCGGAGAATGGGTCTGCTCCCTACTCTTTTAGGGAGTATATGACTT
126 TATAAGACTTAAACAATCTTCGAAAAATGGGTCTGCTCCCTACTCTTTCAGGGAGTATAGGACTC
*
15558 GAACAATATTCGGAA-AACAGGTTCG
191 GAACAATATTC--AATAA-ACG-T-G
* *
15583 TTCCCTATTCTTTCAGGGAGTAT-AGACTTGAACAATCTTCGTAGAACGGGTACGCTCCCTATTC
1 -TCCCTATTCTATCAGGGAGTATAAGACTTGAACAATCTTCGCA-AACGGGT-CGCTCCCTATTC
* *
15647 TTTCAGGGAGTATAAGACTTAAACAATCTTCGTAGAACAGGTACGCTCCCTATTCTTTCAGGGAG
63 TTTCAGGGAGTATAGGACTTGAACAATCTTCGTA-AACAGGT-CGCTCCCTATTCTTTCAGGGAG
* *
15712 TATAAGACTTAAACAATCTTCGAAAAATGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGGACTC
126 TATAAGACTTAAACAATCTTCGAAAAATGGGTCTGCTCCCTACTCTTTCAGGGAGTATAGGACTC
*
15777 GAACAATCTTCAATAAACGTG
191 GAACAATATTCAATAAACGTG
** ** * *
15798 T--CTGCTCCCTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTTCGCTCCCTATTCT
1 TCCCTATTCTATCAGGGAGTATAAGACTTGAACAATCTTC-GCAAACG-GGTCGCTCCCTATTCT
* * * *
15861 TTCAGGGAGTATAGGACTCGAACAATCTTTAGTAAAC-GTGTCTGCTCCCTATTATTTTAGGGAG
64 TTCAGGGAGTATAGGACTTGAACAATC-TTCGTAAACAG-GTC-GCTCCCTATTCTTTCAGGGAG
15925 TATA
126 TATA
15929 GAACACAAAC
Statistics
Matches: 297, Mismatches: 37, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
212 17 0.06
213 85 0.29
214 10 0.03
215 1 0.00
216 1 0.00
217 4 0.01
218 7 0.02
219 144 0.48
220 8 0.03
221 20 0.07
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (211 bp):
TCCCTATTCTATCAGGGAGTATAAGACTTGAACAATCTTCGCAAACGGGTCGCTCCCTATTCTTT
CAGGGAGTATAGGACTTGAACAATCTTCGTAAACAGGTCGCTCCCTATTCTTTCAGGGAGTATAA
GACTTAAACAATCTTCGAAAAATGGGTCTGCTCCCTACTCTTTCAGGGAGTATAGGACTCGAACA
ATATTCAATAAACGTG
Found at i:15815 original size:48 final size:48
Alignment explanation
Indices: 15759--15910 Score: 189
Period size: 48 Copynumber: 3.0 Consensus size: 48
15749 CCCTATTCTT
*
15759 TCAGGGAGTATAGGACTCGAACAATCTTCAATAAACGTGTCTGCTCCC
1 TCAGGGAGTATAGGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
* *
15807 TCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGT-TCGCTCCCTATTC
1 TCAGGGAGTATAGGACTCGAACAATCTTCAGTAAACGTGTCT-GCT-CC----C
*
15860 TTTCAGGGAGTATAGGACTCGAACAATCTTTAGTAAACGTGTCTGCTCCC
1 --TCAGGGAGTATAGGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
15910 T
1 T
15911 ATTATTTTAG
Statistics
Matches: 89, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
47 1 0.01
48 41 0.46
49 2 0.02
50 1 0.01
53 1 0.01
54 2 0.02
55 40 0.45
56 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (48 bp):
TCAGGGAGTATAGGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
Found at i:15944 original size:55 final size:55
Alignment explanation
Indices: 15807--15946 Score: 158
Period size: 55 Copynumber: 2.5 Consensus size: 55
15797 GTCTGCTCCC
* * *
15807 TCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTTCGCTCCCTATTCTT
1 TCAGGGAGTATAGA-ACACAAACAATCTTCAGCAAACGTGTTCGCTCCCTATTATT
* * * * *
15862 TCAGGGAGTATAGGACTCGAACAATCTTTAGTAAACGTG-TCTGCTCCCTATTATT
1 TCAGGGAGTATAGAACACAAACAATCTTCAGCAAACGTGTTC-GCTCCCTATTATT
* *
15917 TTAGGGAGTATAGAACACAAACCATCTTCA
1 TCAGGGAGTATAGAACACAAACAATCTTCA
15947 TAAAATGAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
54 2 0.03
55 71 0.97
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (55 bp):
TCAGGGAGTATAGAACACAAACAATCTTCAGCAAACGTGTTCGCTCCCTATTATT
Found at i:15944 original size:158 final size:157
Alignment explanation
Indices: 15485--15950 Score: 388
Period size: 158 Copynumber: 2.9 Consensus size: 157
15475 CCCTATTCTT
* ** * ** * *
15485 TCAGGGAGTATAGGACTTGAACAATCTTCGGAGAATGGGT-CTGCTCCCTACTCTTTTAGGGAGT
1 TCAGGGAGTATAAGACTCAAACAATCTTCGCAGAACAGGTAC-GCTCCCTATTCTTTCAGGGAGT
* ** * * * * * * **
15549 ATATGACTTGAACAATATTCGGAAAACAGGT-TCGTTCCCTATTCTTTCAGGGAGTATAG-ACTT
65 ATAAGACTCAAACAATCTTAGAAAAACGGGTCT-GCTCCCTATTATTTCAGGGAGTATAGAACAC
* * *
15612 GAACAATCTTCGTAGAACGGGTAC-GCTCCCTATTC
129 AAACAATCTTCATA-AACGTGT-CTGCT-CC----C
* *
15647 TTTCAGGGAGTATAAGACTTAAACAATCTTCGTAGAACAGGTACGCTCCCTATTCTTTCAGGGAG
1 --TCAGGGAGTATAAGACTCAAACAATCTTCGCAGAACAGGTACGCTCCCTATTCTTTCAGGGAG
* * * * * * *
15712 TATAAGACTTAAACAATCTTCGAAAAATGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGGACTC
64 TATAAGACTCAAACAATCTTAGAAAAACGGGTCTGCTCCCTATTATTTCAGGGAGTATAGAACAC
*
15777 GAACAATCTTCAATAAACGTGTCTGCTCCC
129 AAACAATCTTC-ATAAACGTGTCTGCTCCC
* *
15807 TCAGGGAGTATAAGACTCGAACAATCTTCAGCA-AAC-GTGTTCGCTCCCTATTCTTTCAGGGAG
1 TCAGGGAGTATAAGACTCAAACAATCTTC-GCAGAACAG-GTACGCTCCCTATTCTTTCAGGGAG
* * * * *
15870 TATAGGACTCGAACAATCTTTAG-TAAACGTGTCTGCTCCCTATTATTTTAGGGAGTATAGAACA
64 TATAAGACTCAAACAATC-TTAGAAAAACGGGTCTGCTCCCTATTATTTCAGGGAGTATAGAACA
*
15934 CAAACCATCTTCATAAA
128 CAAACAATCTTCATAAA
15951 ATGAGTCTAC
Statistics
Matches: 259, Mismatches: 35, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
157 6 0.02
158 112 0.43
159 5 0.02
160 1 0.00
164 108 0.42
165 25 0.10
166 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (157 bp):
TCAGGGAGTATAAGACTCAAACAATCTTCGCAGAACAGGTACGCTCCCTATTCTTTCAGGGAGTA
TAAGACTCAAACAATCTTAGAAAAACGGGTCTGCTCCCTATTATTTCAGGGAGTATAGAACACAA
ACAATCTTCATAAACGTGTCTGCTCCC
Found at i:16046 original size:36 final size:36
Alignment explanation
Indices: 15999--16070 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
15989 TCGAGATTGA
* * *
15999 TTTGCTTCACTACTCTTTCGTGAAGGTTTAAGATGG
1 TTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGG
16035 TTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGG
1 TTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGG
16071 CCCGGAGTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGG
Found at i:16200 original size:37 final size:37
Alignment explanation
Indices: 16159--16264 Score: 176
Period size: 37 Copynumber: 2.9 Consensus size: 37
16149 GATGGCTTGC
*
16159 TTCACTACTCTTCTGTGAAGGCTTAAGATTGATTTGA
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGATTTGA
*
16196 TTCACTACTCTTCCGTGAAGGCTTAAGATTGATTTGC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGATTTGA
* *
16233 TTCACTGCTCTTCCGTTAAGGCTTAAGATTGA
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGA
16265 CTTGCCCCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATTGATTTGA
Found at i:18194 original size:97 final size:99
Alignment explanation
Indices: 18047--18224 Score: 263
Period size: 97 Copynumber: 1.8 Consensus size: 99
18037 TTGTAATTCG
* * * *
18047 CCTTTATCAGGCTAGTTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTTA-TCTAGAGGG
1 CCTTTACCAGGCTAGCTGAATCTTATCAATAAAGTCAGGGCGTTTAACCAA-TTACACTAGAGGG
**
18111 ACAGTTCAAGCTTTATTGTATATATATTATAATCA
65 ACAACTCAAGCTTTATTGTATATATATTATAATCA
*
18146 CCTTTACCAGGCTAGCT-AATCTTATCAATAAAG-CAGGGTGTTTAACCAATTACACTAGAGGGA
1 CCTTTACCAGGCTAGCTGAATCTTATCAATAAAGTCAGGGCGTTTAACCAATTACACTAGAGGGA
18209 CAACTCAAGCTTTATT
66 CAACTCAAGCTTTATT
18225 ATAAACATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
96 3 0.04
97 38 0.54
98 15 0.21
99 15 0.21
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (99 bp):
CCTTTACCAGGCTAGCTGAATCTTATCAATAAAGTCAGGGCGTTTAACCAATTACACTAGAGGGA
CAACTCAAGCTTTATTGTATATATATTATAATCA
Found at i:22316 original size:22 final size:22
Alignment explanation
Indices: 22284--22336 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
22274 CACATTCTAA
22284 ATGTC-ATTTGTACTAAATCCT
1 ATGTCAATTTGTACTAAATCCT
22305 ATGTCAATTTGTACTAAATCCT
1 ATGTCAATTTGTACTAAATCCT
22327 ATGTCAATTT
1 ATGTCAATTT
22337 AAAGGCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (22 bp):
ATGTCAATTTGTACTAAATCCT
Found at i:23219 original size:2 final size:2
Alignment explanation
Indices: 23208--23237 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
23198 ATTTGGCATT
23208 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23238 TATTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27576 original size:24 final size:24
Alignment explanation
Indices: 27559--27637 Score: 106
Period size: 24 Copynumber: 3.2 Consensus size: 24
27549 ATCAAAACAT
27559 AATCCAGGTCAAGTATCAGATCAAA
1 AATCCAGGTCAAGTATCAGATC-AA
*
27584 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAGATCAA
* *
27608 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
27632 AATCCA
1 AATCCA
27638 AGTAAGATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
23 2 0.04
24 28 0.55
25 19 0.37
26 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:27859 original size:16 final size:17
Alignment explanation
Indices: 27828--27860 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27818 CAATAACTGA
27828 CAGAATCATAAGTTATT
1 CAGAATCATAAGTTATT
*
27845 CAGAAT-ATAATTTATT
1 CAGAATCATAAGTTATT
27861 AGGATCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (17 bp):
CAGAATCATAAGTTATT
Found at i:36427 original size:13 final size:13
Alignment explanation
Indices: 36405--36434 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36395 CTTGTGTCTA
36405 AAATAACTGTTTG
1 AAATAACTGTTTG
*
36418 AAATATCTGTTTG
1 AAATAACTGTTTG
36431 AAAT
1 AAAT
36435 CTCATGTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (13 bp):
AAATAACTGTTTG
Found at i:37729 original size:26 final size:26
Alignment explanation
Indices: 37673--37753 Score: 139
Period size: 26 Copynumber: 3.2 Consensus size: 26
37663 CGAAGTACAT
*
37673 TACACATAAGGTTGTGCCCA-CATAA
1 TACACATAAGGTCGTGCCCACCATAA
37698 TACACATAAGGTCGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCATAA
37724 TACACATAAGGTCGTGCCCACCAT-A
1 TACACATAAGGTCGTGCCCACCATAA
37749 TACAC
1 TACAC
37754 TTAGTGTCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
25 25 0.46
26 29 0.54
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.21
Consensus pattern (26 bp):
TACACATAAGGTCGTGCCCACCATAA
Found at i:38688 original size:30 final size:31
Alignment explanation
Indices: 38630--38698 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
38620 AACCATTAAC
* * *
38630 AACTTTTCAAAAATTGTTGAATTGGTCCCCT
1 AACTTTTCAAAAATTATAGAATTGGTCCCCA
*
38661 AACTTTTTAAAAATTATAGAA-TGGTCCCCA
1 AACTTTTCAAAAATTATAGAATTGGTCCCCA
38691 AACTTTTC
1 AACTTTTC
38699 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (31 bp):
AACTTTTCAAAAATTATAGAATTGGTCCCCA
Found at i:39316 original size:11 final size:11
Alignment explanation
Indices: 39300--39324 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39290 TTCCATGCTA
39300 AATTTACCTTT
1 AATTTACCTTT
39311 AATTTACCTTT
1 AATTTACCTTT
39322 AAT
1 AAT
39325 GAATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTACCTTT
Found at i:43488 original size:64 final size:64
Alignment explanation
Indices: 43420--43541 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
43410 GCACTCTTTT
* *
43420 AATAATGAA-ACATCGAATGCAATTGGTGCA-TCGATGCATAAGGAGTGCATCGATGCATCCCAG
1 AATAAT-AATACATCGAATACAATTGATGCACT-GATGCATAAGGAGTGCATCGATGCATCCCAG
43483 C
64 C
** * * *
43484 AATAATAATACATCGAATACCTTTTATGCACTGATGCATCAGTAGTGCATCGATGCAT
1 AATAATAATACATCGAATACAATTGATGCACTGATGCATAAGGAGTGCATCGATGCAT
43542 AGCTTCATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
63 2 0.04
64 46 0.94
65 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
AATAATAATACATCGAATACAATTGATGCACTGATGCATAAGGAGTGCATCGATGCATCCCAGC
Found at i:43867 original size:12 final size:12
Alignment explanation
Indices: 43849--43884 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43839 TATATATGTT
43849 CATGTGATATGA
1 CATGTGATATGA
*
43861 TATGTGATATGA
1 CATGTGATATGA
*
43873 CCTGTGATATGA
1 CATGTGATATGA
43885 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:49911 original size:12 final size:12
Alignment explanation
Indices: 49896--49927 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
49886 TATGTTCATA
*
49896 TGATATGATATG
1 TGATATGACATG
49908 TGATATGACATG
1 TGATATGACATG
49920 TGATATGA
1 TGATATGA
49928 GAACATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (12 bp):
TGATATGACATG
Found at i:49952 original size:23 final size:26
Alignment explanation
Indices: 49908--49960 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 26
49898 ATATGATATG
49908 TGATATGACATGTGATATGAGA-ACA
1 TGATATGACATGTGATATGAGATACA
*
49933 TGATATGA-A-GTTATATGAGATACA
1 TGATATGACATGTGATATGAGATACA
49957 TGAT
1 TGAT
49961 CACAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.32
Consensus pattern (26 bp):
TGATATGACATGTGATATGAGATACA
Found at i:52969 original size:64 final size:64
Alignment explanation
Indices: 52901--53022 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
52891 GCACTCTTTT
* * *
52901 AATAATGAA-ACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGC
1 AATAAT-AATACATCGAATACAATTGATGCACCGATGCATAAGGAGTGCATCGATGCATCCCAGC
** * * *
52965 AATAATAATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 AATAATAATACATCGAATACAATTGATGCACCGATGCATAAGGAGTGCATCGATGCAT
53023 ACCTTCATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (64 bp):
AATAATAATACATCGAATACAATTGATGCACCGATGCATAAGGAGTGCATCGATGCATCCCAGC
Found at i:53349 original size:12 final size:12
Alignment explanation
Indices: 53334--53367 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53324 TATGTTCATA
53334 TGATATGATATG
1 TGATATGATATG
**
53346 TGATATGACCTG
1 TGATATGATATG
53358 TGATATGATA
1 TGATATGATA
53368 ACATGATATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (12 bp):
TGATATGATATG
Found at i:59835 original size:40 final size:40
Alignment explanation
Indices: 59789--59893 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
59779 ATCGTAGTGC
*
59789 TACACATAAGGCCGTGCCCACCATATGCACCGAAGTACAT
1 TACACATAAGGTCGTGCCCACCATATGCACCGAAGTACAT
* * * *
59829 TACACATAAGGTCATGACCAACATATGCACTGAAGTACAT
1 TACACATAAGGTCGTGCCCACCATATGCACCGAAGTACAT
* *
59869 TAAACGTAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
59894 ATACACATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATGCACCGAAGTACAT
Found at i:59911 original size:26 final size:25
Alignment explanation
Indices: 59875--59924 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
59865 ACATTAAACG
59875 TAAGGTCGTGCCCACCATAATACACA
1 TAAGGTCGTGCCCACCAT-ATACACA
59901 TAAGGTCGTGCCCACCATATACAC
1 TAAGGTCGTGCCCACCATATACAC
59925 TTAGTGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (25 bp):
TAAGGTCGTGCCCACCATATACACA
Found at i:62678 original size:2 final size:2
Alignment explanation
Indices: 62671--62699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62661 TATAAATTGA
62671 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 A
62700 CACATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64471 original size:104 final size:106
Alignment explanation
Indices: 64273--64472 Score: 253
Period size: 104 Copynumber: 1.9 Consensus size: 106
64263 TGAAACTTGA
* * *
64273 TGTTAAAGACAACACTACTCATCTACATTGAAGAGATTTGGTCACTTTTGAAGATGATACTATTC
1 TGTTAAAGACAACACTACTCATCCACATTGAAGAGATTTGGCCACTTTTGAAGATGACACTATTC
**
64338 CTTATCATTGAGGAAATCTTGTCAATCTGGAGATAATATGG
66 CTTATCATTGAGGAAATCGGGTCAATCTGGAGATAATATGG
* * ** * *
64379 TGTTGAAGACGACACTACTCATCCATGTTGAAGAG-TTATGGCCAC-TTT-CATATGACACTATT
1 TGTTAAAGACAACACTACTCATCCACATTGAAGAGATT-TGGCCACTTTTGAAGATGACACTATT
* *
64441 CCTTCTCATTGAGGAAGTCGGGTCAATCTGGA
65 CCTTATCATTGAGGAAATCGGGTCAATCTGGA
64473 TAATTTAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
104 39 0.49
105 5 0.06
106 36 0.45
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (106 bp):
TGTTAAAGACAACACTACTCATCCACATTGAAGAGATTTGGCCACTTTTGAAGATGACACTATTC
CTTATCATTGAGGAAATCGGGTCAATCTGGAGATAATATGG
Found at i:68023 original size:18 final size:19
Alignment explanation
Indices: 67997--68034 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
67987 GAACTTGAAA
67997 ATTTAAAAATAATAT-TAT
1 ATTTAAAAATAATATCTAT
*
68015 ATTTTAAAATAATATCTAT
1 ATTTAAAAATAATATCTAT
68034 A
1 A
68035 ATATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAAAATAATATCTAT
Found at i:68089 original size:16 final size:16
Alignment explanation
Indices: 68070--68310 Score: 84
Period size: 16 Copynumber: 14.4 Consensus size: 16
68060 TTTAGAAAAC
68070 TATATATATTTTTAAA
1 TATATATATTTTTAAA
* *
68086 TATATATA-ATATAACA
1 TATATATATTTTTAA-A
*
68102 TATATACTA--CTT-AA
1 TATATA-TATTTTTAAA
* * *
68116 TATTATATATATATATA
1 TA-TATATATTTTTAAA
*
68133 TATATATATATTTAAA
1 TATATATATTTTTAAA
* *
68149 AATTATATATTTTCAAA
1 TA-TATATATTTTTAAA
* **
68166 -CTATAT-TTTAAAAA
1 TATATATATTTTTAAA
68180 CTATATATATTTTAATATATA
1 -TATATATATTTT--TA-A-A
*
68201 TATATATATATTTAAA
1 TATATATATTTTTAAA
68217 -ATTATATTATTTTTAAAA
1 TA-TATA-TATTTTT-AAA
* * *
68235 TATAACATATATTAAAA
1 TAT-ATATATTTTTAAA
68252 CTATATA-ATTTTTTAAAA
1 -TATATATA-TTTTT-AAA
* *
68270 TATATATATATATATATA
1 TATATATAT-T-TTTAAA
*
68288 TATATATATATTTAAA
1 TATATATATTTTTAAA
*
68304 AATATAT
1 TATATAT
68311 TATATAATAC
Statistics
Matches: 168, Mismatches: 32, Indels: 50
0.67 0.13 0.20
Matches are distributed among these distances:
14 11 0.07
15 15 0.09
16 51 0.30
17 42 0.25
18 30 0.18
19 6 0.04
20 12 0.07
21 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATATTTTTAAA
Found at i:68138 original size:33 final size:35
Alignment explanation
Indices: 68085--68158 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 35
68075 ATATTTTTAA
*
68085 ATATATATAATATAACATATATACTACTT-AATATT
1 ATATATATAATATAACATATATA-TACTTAAAAATT
* *
68120 ATATATAT-ATAT-ATATATATATATTTAAAAATT
1 ATATATATAATATAACATATATATACTTAAAAATT
68153 ATATAT
1 ATATAT
68159 TTTCAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 4 0.11
33 19 0.54
34 4 0.11
35 8 0.23
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (35 bp):
ATATATATAATATAACATATATATACTTAAAAATT
Found at i:68158 original size:2 final size:2
Alignment explanation
Indices: 68070--68143 Score: 59
Period size: 2 Copynumber: 38.5 Consensus size: 2
68060 TTTAGAAAAC
* * * *
68070 TA TA TA TA TT TT TA AA TA TA TA TA -A TA TA -A CA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
68111 CT- TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68144 TTAAAAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
1 5 0.08
2 52 0.85
3 4 0.07
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:68170 original size:13 final size:14
Alignment explanation
Indices: 68137--68185 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
68127 TATATATATA
*
68137 TATATATTTAAAAAT
1 TATAT-TTTAAAAAC
**
68152 TATATATTTTCAAAC
1 TATAT-TTTAAAAAC
68167 TATATTTTAAAAAC
1 TATATTTTAAAAAC
68181 TATAT
1 TATAT
68186 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATTTTAAAAAC
Found at i:68198 original size:14 final size:14
Alignment explanation
Indices: 68070--68203 Score: 56
Period size: 14 Copynumber: 8.6 Consensus size: 14
68060 TTTAGAAAAC
68070 TATATATATTTTTAAA
1 TATATATA-TTTT-AA
* *
68086 TATATATAATATAA
1 TATATATATTTTAA
* *
68100 CATATATACTACTTAA
1 TATATATA-T-TTTAA
68116 TATTATATATATATATATA
1 TA-TATATAT-T-T-TA-A
*
68135 TATATATATTTAAA
1 TATATATATTTTAA
*
68149 AATTATATATTTTCAA
1 TA-TATATATTTT-AA
*
68165 -ACTATAT-TTTAAAAA
1 TA-TATATATTT--TAA
68180 CTATATATATTTTAA
1 -TATATATATTTTAA
68195 TATATATAT
1 TATATATAT
68204 ATATATATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
14 23 0.25
15 22 0.24
16 22 0.24
17 12 0.13
18 9 0.10
19 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATATATTTTAA
Found at i:68252 original size:72 final size:72
Alignment explanation
Indices: 68093--68309 Score: 213
Period size: 68 Copynumber: 3.1 Consensus size: 72
68083 AAATATATAT
**
68093 AATATAACATATA-TACTACT-TA-ATATTATATATATATATATATATATATATTTAAAAATTAT
1 AATATAACATATATTAAAACTATATATATT-T-TA-ATATATATATATATATATTTAAAAATTAT
68155 ATATTTTCAA
63 ATATTTTCAA
*
68165 ACTAT---AT-T-TTAAAAACTATATATATTTTAATATATATATATATATATTT-AAAATTATAT
1 AATATAACATATATT-AAAACTATATATATTTTAATATATATATATATATATTTAAAAATTATA-
*
68224 TATTTTTAA
64 TATTTTCAA
* * * * *
68233 AATATAACATATATTAAAACTATATAATTTTTTAAAATATATATATATATATATATATA-TATAT
1 AATATAACATATATTAAAACTATAT-ATATTTTAATATATATATATATATATTTAAAAATTATAT
*
68297 A-TTTAAA
65 ATTTTCAA
68304 AATATA
1 AATATA
68310 TTATATAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
67 9 0.07
68 34 0.28
69 8 0.07
70 3 0.02
71 18 0.15
72 17 0.14
73 31 0.25
74 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (72 bp):
AATATAACATATATTAAAACTATATATATTTTAATATATATATATATATATTTAAAAATTATATA
TTTTCAA
Found at i:68274 original size:2 final size:2
Alignment explanation
Indices: 68269--68316 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
68259 ATTTTTTAAA
* * *
68269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68311 -T AT AT A
1 AT AT AT A
68317 ATACTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70824 original size:36 final size:35
Alignment explanation
Indices: 70767--70884 Score: 123
Period size: 35 Copynumber: 3.3 Consensus size: 35
70757 GCACGTAAAA
*
70767 CTTCTCCAAGAGATGTATTTCCAAATGACATGATG
1 CTTCACCAAGAGATGTATTTCCAAATGACATGATG
*
70802 CTTCACCAAGA-ATTGTCATTTCCAAATGACATTATG
1 CTTCACCAAGAGA-TGT-ATTTCCAAATGACATGATG
* * * * *
70838 CTTTACCAAAAGATATATTTTC-AATAGACATGATA
1 CTTCACCAAGAGATGTATTTCCAAAT-GACATGATG
*
70873 ATTCACCAAGAG
1 CTTCACCAAGAG
70885 GTGCCTCCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 4 0.06
35 34 0.50
36 29 0.43
37 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (35 bp):
CTTCACCAAGAGATGTATTTCCAAATGACATGATG
Found at i:72523 original size:20 final size:21
Alignment explanation
Indices: 72494--72534 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
72484 CTACATGCAT
*
72494 ATGAGTATTTTC-AAATAAAA
1 ATGAGAATTTTCAAAATAAAA
72514 ATGAGAATTTTCAAAATAAAA
1 ATGAGAATTTTCAAAATAAAA
72535 CTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (21 bp):
ATGAGAATTTTCAAAATAAAA
Found at i:73181 original size:30 final size:30
Alignment explanation
Indices: 73145--73213 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
73135 CATATCCGGA
73145 TTAGCACTAGAGCGTAAGCTTAGTGGAAGT
1 TTAGCACTAGAGCGTAAGCTTAGTGGAAGT
73175 TTAGCACTAGAGCGTAAGCTTAGTGGAAGT
1 TTAGCACTAGAGCGTAAGCTTAGTGGAAGT
73205 TTAGCACTA
1 TTAGCACTA
73214 CATTGTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (30 bp):
TTAGCACTAGAGCGTAAGCTTAGTGGAAGT
Found at i:82052 original size:55 final size:55
Alignment explanation
Indices: 81937--82533 Score: 702
Period size: 55 Copynumber: 10.9 Consensus size: 55
81927 TATACAAAAC
* * *** * * * *
81937 TTCATCAACCCATGATGAATTCTGTG-GGCTGCACACATAGTACTTGTATGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* *
81991 TTCATCAACTCATGACGAATTCCGTGAATATTCACACAAAGTGCCTGTAAGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * *
82046 ATCATCAACTCATGATGAATTTTCGTGAATATGCACACAAATTGCCTGTACA-GTGA
1 TTCATCAACTCATGATGAA-TTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
** * * *
82102 TTCATCAACTCATGATGAATTATGTGAATAAGCACACAAAGTGCCAGTACA-TTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
* ** *
82157 TTCATCAACTCATGATGAATTCCGTGACTATGCACACAAAGTTTCTGTACGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
*
82212 TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTACA-GTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
* * *
82267 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTACCTGTATGATGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * *
82322 TTCA--AACTCATGATGAATTTCGTGAATATGCACAAAAAGTGCATGTATGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * *
82375 TTCATCAACTCATGATGAATTCCGTGAATATGTACACAAAGTGCTTTTACGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * * * *
82430 TTCATCAACTCATGAAGAATTCTGTGAATATGCACACAAAGTACATGTATGATGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * * *
82485 TTCATCAACTCATGATAAATTCCTTGAGTATACACACATAGTGCCTGTA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA
82534 GTACACATAG
Statistics
Matches: 466, Mismatches: 69, Indels: 15
0.85 0.13 0.03
Matches are distributed among these distances:
53 48 0.10
54 23 0.05
55 345 0.74
56 49 0.11
57 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
Found at i:82415 original size:218 final size:218
Alignment explanation
Indices: 81937--82533 Score: 760
Period size: 218 Copynumber: 2.7 Consensus size: 218
81927 TATACAAAAC
* * *** * *
81937 TTCATCAACCCATGATGAATTCTGTG-GGCTGCACACATAGTAC-TTGTATGGTGATTCATCAAC
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGT-CTTTGTACGGTGATTCATCAAC
* * * *
82000 TCATGACGAATTCCGTGAATATTCACACAAAGTGCCTGTAAGGTGAATCATCAACTCATGATGAA
65 TCATGAAGAATTCTGTGAATATGCACACAAAGTGCCTGTAA-GTGATTCATCAACTCATGATGAA
* *
82065 TTTTCGTGAATATGCACACAAATTGCCTGTACAGTGATTCATCAACTCATGATGAATTATGTGAA
129 -TTCCGTGAATATGCACACAAAGTGCCTGTACAGTGATTCA-CAACTCATGATGAATTATGTGAA
* *
82130 TAAGCACACAAAGTGCCAGTACATTGA
192 TAAGCACAAAAAGTGCCAGTACAGTGA
*
82157 TTCATCAACTCATGATGAATTCCGTGACTATGCACACAAAGT-TTCTGTACGGTGATTCATCAAC
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTCTT-TGTACGGTGATTCATCAAC
*
82221 TCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTACAGTGATTCATCAACTCATGATGAA
65 TCATGAAGAATTCTGTGAATATGCACACAAAGTGCCTGTA-AGTGATTCATCAACTCATGATGAA
* *
82286 TTCCGTGAATATGCACACAAAGTACCTGTA-TGATGATTCA-AACTCATGATGAATT-TCGTGAA
129 TTCCGTGAATATGCACACAAAGTGCCTGTACAG-TGATTCACAACTCATGATGAATTAT-GTGAA
* **
82348 TATGCACAAAAAGTG-CATGTATGGTGA
192 TAAGCACAAAAAGTGCCA-GTACAGTGA
*
82375 TTCATCAACTCATGATGAATTCCGTGAATATGTACACAAAGTGCTTT-TACGGTGATTCATCAAC
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGT-CTTTGTACGGTGATTCATCAAC
* * * *
82439 TCATGAAGAATTCTGTGAATATGCACACAAAGTACATGTATGATGATTCATCAACTCATGATAAA
65 TCATGAAGAATTCTGTGAATATGCACACAAAGTGCCTGTAAG-TGATTCATCAACTCATGATGAA
* * * *
82504 TTCCTTGAGTATACACACATAGTGCCTGTA
129 TTCCGTGAATATGCACACAAAGTGCCTGTA
82534 GTACACATAG
Statistics
Matches: 335, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
217 4 0.01
218 179 0.53
219 2 0.01
220 61 0.18
221 88 0.26
222 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (218 bp):
TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTCTTTGTACGGTGATTCATCAACT
CATGAAGAATTCTGTGAATATGCACACAAAGTGCCTGTAAGTGATTCATCAACTCATGATGAATT
CCGTGAATATGCACACAAAGTGCCTGTACAGTGATTCACAACTCATGATGAATTATGTGAATAAG
CACAAAAAGTGCCAGTACAGTGA
Found at i:83090 original size:20 final size:21
Alignment explanation
Indices: 83041--83097 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
83031 TTTGATGTTT
* *
83041 CTAGGTATCGATAC-CCCTTA
1 CTAGGTATCGATACTGCCTCA
83061 CTATGGTATCGATACTGCCTCA
1 CTA-GGTATCGATACTGCCTCA
83083 -TAGGTATCGATACTG
1 CTAGGTATCGATACTG
83098 ATTGAATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.48
21 13 0.39
22 4 0.12
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (21 bp):
CTAGGTATCGATACTGCCTCA
Found at i:89364 original size:55 final size:55
Alignment explanation
Indices: 89252--89754 Score: 645
Period size: 55 Copynumber: 9.3 Consensus size: 55
89242 TTCTGTGGGC
* * *
89252 TGCACACATAGTGCATGTAC-GTGATTCATCAA--CATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
** * * *
89304 TGCACACAAAGTTACTGTACGGTGATTCATCAACTCGTGATAAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
89359 TGCACACAAAATGCCTATACGGTGTTTCATCAACTC-------A-TTCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
89406 TGCACACAAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* *
89461 TGCACACAAAGTGCCTATACGGTGATTCATCAACTCATGATGAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
89516 TGCACACAAAGTGCCTATACGGTGATTCATCAACCCATGATGAATTCCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
89571 TGCACACAAAGTGCTTGTACGATGATTCATCAACTCATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
89626 TGCATACAAAGTGCCTGTACGGTGATTCATCAACTCATTATGAA-TTC-TGTAGATT
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTG-A-ATA
* *
89681 TGCACACAATGTGCCTGTAGGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
89736 TGCACACAAAGTACCTGTA
1 TGCACACAAAGTGCCTGTA
89755 GTACACATAG
Statistics
Matches: 391, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
47 40 0.10
48 1 0.00
52 16 0.04
53 14 0.04
54 4 0.01
55 310 0.79
56 4 0.01
57 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (55 bp):
TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
Found at i:96576 original size:55 final size:55
Alignment explanation
Indices: 96464--96966 Score: 645
Period size: 55 Copynumber: 9.3 Consensus size: 55
96454 TTCTGTGGGC
* * *
96464 TGCACACATAGTGCATGTAC-GTGATTCATCAA--CATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
** * * *
96516 TGCACACAAAGTTACTGTACGGTGATTCATCAACTCGTGATAAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
96571 TGCACACAAAATGCCTATACGGTGTTTCATCAACTC-------A-TTCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
96618 TGCACACAAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* *
96673 TGCACACAAAGTGCCTATACGGTGATTCATCAACTCATGATGAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
96728 TGCACACAAAGTGCCTATACGGTGATTCATCAACCCATGATGAATTCCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
96783 TGCACACAAAGTGCTTGTACGATGATTCATCAACTCATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
96838 TGCATACAAAGTGCCTGTACGGTGATTCATCAACTCATTATGAA-TTC-TGTAGATT
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTG-A-ATA
* *
96893 TGCACACAATGTGCCTGTAGGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
96948 TGCACACAAAGTACCTGTA
1 TGCACACAAAGTGCCTGTA
96967 GTACACATAG
Statistics
Matches: 391, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
47 40 0.10
48 1 0.00
52 16 0.04
53 14 0.04
54 4 0.01
55 310 0.79
56 4 0.01
57 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (55 bp):
TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
Found at i:108193 original size:24 final size:22
Alignment explanation
Indices: 108166--108214 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
108156 ATAAAAAACA
*
108166 CAAAAATGCACAAAGAAAGAAAAT
1 CAAAAAGGCACAAAG-AA-AAAAT
* *
108190 CAAACAGGCACAGAGAAAAAAT
1 CAAAAAGGCACAAAGAAAAAAT
108212 CAA
1 CAA
108215 GCTTGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.63, C:0.16, G:0.14, T:0.06
Consensus pattern (22 bp):
CAAAAAGGCACAAAGAAAAAAT
Found at i:112259 original size:20 final size:21
Alignment explanation
Indices: 112211--112260 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
112201 AATCCTTCGA
*
112211 TATCGATACTCCTACGAAGAG
1 TATCGATACTCCTACCAAGAG
* * *
112232 TATTGATACTCC-ACCTATAG
1 TATCGATACTCCTACCAAGAG
112252 TATCGATAC
1 TATCGATAC
112261 CAAAAGTGGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (21 bp):
TATCGATACTCCTACCAAGAG
Found at i:115949 original size:11 final size:12
Alignment explanation
Indices: 115933--115961 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
115923 AATATGCTTC
115933 AATGGTAAT-GA
1 AATGGTAATGGA
115944 AATGGTAATGGA
1 AATGGTAATGGA
115956 AATGGT
1 AATGGT
115962 GTAGGCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (12 bp):
AATGGTAATGGA
Found at i:123157 original size:37 final size:37
Alignment explanation
Indices: 123116--123193 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
123106 AGAAAAGGAA
*
123116 AGAACTGAAGGTTCAGAAAGGCATCGATCAAACAATG
1 AGAACTGAAGGTTCAGAAAGGCATCGATCAAACAACG
*
123153 AGAACTGAAGGTTCAGAAAGGCATCGGTCAAACAACG
1 AGAACTGAAGGTTCAGAAAGGCATCGATCAAACAACG
123190 AGAA
1 AGAA
123194 ATTAATGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.14
Consensus pattern (37 bp):
AGAACTGAAGGTTCAGAAAGGCATCGATCAAACAACG
Found at i:131820 original size:16 final size:15
Alignment explanation
Indices: 131776--131816 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
131766 TAAATAGAAT
131776 AAGAAATTAATG--A
1 AAGAAATTAATGATA
*
131789 AAGAAATGAATTGATA
1 AAGAAATTAA-TGATA
131805 AAGAAATTAATG
1 AAGAAATTAATG
131817 GATAGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 2 0.09
16 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (15 bp):
AAGAAATTAATGATA
Found at i:133865 original size:3 final size:3
Alignment explanation
Indices: 133848--133913 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
133838 ACTAATTTTT
* * * *
133848 TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
133895 TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
133914 AAAAATAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:139421 original size:15 final size:15
Alignment explanation
Indices: 139403--139434 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
139393 GATCAATACC
139403 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
139418 TTTTGCATACATTCA
1 TTTTGCATACATGCA
139433 TT
1 TT
139435 ATTCAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:149318 original size:23 final size:20
Alignment explanation
Indices: 149273--149321 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
149263 TGAGTAACCC
*
149273 GTTGACTTTGACCGTTGATT
1 GTTGACTTTGACCGTTGACT
149293 GTTGACTTTGACCTGAGTTGACT
1 GTTGACTTTGACC---GTTGACT
149316 GTTGAC
1 GTTGAC
149322 CATTAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
23 12 0.48
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (20 bp):
GTTGACTTTGACCGTTGACT
Found at i:154186 original size:14 final size:14
Alignment explanation
Indices: 154159--154199 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
154149 GCAAGCACTC
154159 AAAAGAAA-AAAAG
1 AAAAGAAAGAAAAG
154172 AATAA-AAAGAAAAG
1 AA-AAGAAAGAAAAG
154186 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
154200 TTGAAAGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAAGAAAAG
Found at i:161615 original size:24 final size:24
Alignment explanation
Indices: 161586--161632 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
161576 TGGTTGGTTG
161586 AATGGT-TATTTAAACTTTATTTTT
1 AATGGTATATTT-AACTTTATTTTT
*
161610 AATGGTATATTTAAGTTTATTTT
1 AATGGTATATTTAACTTTATTTT
161633 GGTTCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (24 bp):
AATGGTATATTTAACTTTATTTTT
Found at i:168892 original size:19 final size:21
Alignment explanation
Indices: 168855--168897 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
168845 TAACTTTTTC
168855 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
168875 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
168895 TTT
1 TTT
168898 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:168903 original size:19 final size:20
Alignment explanation
Indices: 168854--168903 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
168844 TTAACTTTTT
*
168854 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
168874 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
168893 CTTTTACCTTT
1 CTTTTACCTTT
168904 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:179659 original size:74 final size:74
Alignment explanation
Indices: 179575--179722 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
179565 CAACTCCTTC
179575 TATGATGGAAATGAGCAAAAAGTTGATGTTAATATACCTCCTACAGTGATAGAATCAGACGCAAC
1 TATGATGGAAATGAGCAAAAAGTTGATGTTAATATACCTCCTACAGTGATAGAATCAGACGCAAC
179640 TAGCATCTT
66 TAGCATCTT
179649 TATGATGGAAATGAGCAAAAAGTTGATGTTAATATACCTCCTACAGTGATAGAATCAGACGCAAC
1 TATGATGGAAATGAGCAAAAAGTTGATGTTAATATACCTCCTACAGTGATAGAATCAGACGCAAC
179714 TAGCATCTT
66 TAGCATCTT
179723 GATCTACCTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (74 bp):
TATGATGGAAATGAGCAAAAAGTTGATGTTAATATACCTCCTACAGTGATAGAATCAGACGCAAC
TAGCATCTT
Found at i:180159 original size:5 final size:6
Alignment explanation
Indices: 180141--180188 Score: 60
Period size: 6 Copynumber: 7.3 Consensus size: 6
180131 CTTTGGATTC
180141 TTCTTT TTCTTT TTCTTT TTCTTT TTCTATTT TTCCCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC--TTT TT--CTTT TTCTTT TT
180189 TTCAACAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 27 0.71
8 10 0.26
10 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:180182 original size:16 final size:16
Alignment explanation
Indices: 180161--180191 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
180151 TTTTCTTTTT
180161 CTTTTTCTATTTTTCC
1 CTTTTTCTATTTTTCC
*
180177 CTTTTTCTTTTTTTC
1 CTTTTTCTATTTTTC
180192 AACAAAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
CTTTTTCTATTTTTCC
Found at i:183280 original size:14 final size:14
Alignment explanation
Indices: 183261--183288 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
183251 ATTATTCATA
183261 TTGGTGGCATTTTT
1 TTGGTGGCATTTTT
183275 TTGGTGGCATTTTT
1 TTGGTGGCATTTTT
183289 GGAAATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.29, T:0.57
Consensus pattern (14 bp):
TTGGTGGCATTTTT
Found at i:191134 original size:6 final size:6
Alignment explanation
Indices: 191123--191156 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
191113 ATTAGGATAG
* *
191123 TATTGT TATTGT TATTGT TATTTT TATTAT TATT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATT
191157 TTCAACCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (6 bp):
TATTGT
Found at i:192980 original size:19 final size:17
Alignment explanation
Indices: 192943--192982 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
192933 CAAAGAGATA
*
192943 ATTTTTTTCAAAAAAAT
1 ATTTATTTCAAAAAAAT
192960 ATTTATTTCATAAATAAAT
1 ATTTATTTCA-AAA-AAAT
192979 ATTT
1 ATTT
192983 CATCCTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTATTTCAAAAAAAT
Found at i:197364 original size:21 final size:20
Alignment explanation
Indices: 197326--197364 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
197316 CATTGCAGGA
**
197326 ATTTATGGCCTCGTCAAAAG
1 ATTTATGGCCTCCACAAAAG
197346 ATTTCATGGCCTCCACAAA
1 ATTT-ATGGCCTCCACAAA
197365 TACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:204606 original size:200 final size:204
Alignment explanation
Indices: 204256--204659 Score: 780
Period size: 200 Copynumber: 2.0 Consensus size: 204
204246 ACGCATACAC
204256 AATAACAAGGAATCCTGACTAGGGAAGGGACTTGACTGATATGACTGTTGAATATGTTGAGGCTA
1 AATAACAAGGAATCCTGACTAGGGAAGGGACTTGACTGATATGACTGTTGAATATGTTGAGGCTA
204321 AACATTTTTACTAAGGGCTGAAATCTCAAACCATATGATTTTCTTAACACTGTTTTGCCATGAAA
66 AACATTTTTACTAAGGGCTGAAATCTCAAACCATATGATTTTCTTAACACTGTTTTGCCATGAAA
204386 TTTTTTATTTTCTTCTAGTTATTATACATTGCTTGAGGACAAGC-ATAGCTTAAGTTTA-GGG-G
131 TTTTTTATTTTCTTCTAGTTATTATACATTGCTTGAGGACAAGCAATAGCTTAAGTTTAGGGGTG
204448 ATAACTCCG
196 ATAACTCCG
204457 AATAAC-AGGAATCCTGACTAGGGAAGGGACTTGACTGATATGACTGTTGAATATGTTGAGGCTA
1 AATAACAAGGAATCCTGACTAGGGAAGGGACTTGACTGATATGACTGTTGAATATGTTGAGGCTA
204521 AACATTTTTACTAAGGGCTGAAATCTCAAACCATATGATTTTCTTAACACTGTTTTGCCATGAAA
66 AACATTTTTACTAAGGGCTGAAATCTCAAACCATATGATTTTCTTAACACTGTTTTGCCATGAAA
204586 TTTTTTATTTTCTTCTAGTTATTATACATTGCTTGAGGACAAGCAATAGCTTAAGTTTAGGGGTG
131 TTTTTTATTTTCTTCTAGTTATTATACATTGCTTGAGGACAAGCAATAGCTTAAGTTTAGGGGTG
204651 ATAACTCCG
196 ATAACTCCG
204660 TAAAAAGACT
Statistics
Matches: 200, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
200 167 0.83
201 20 0.10
202 3 0.01
203 10 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (204 bp):
AATAACAAGGAATCCTGACTAGGGAAGGGACTTGACTGATATGACTGTTGAATATGTTGAGGCTA
AACATTTTTACTAAGGGCTGAAATCTCAAACCATATGATTTTCTTAACACTGTTTTGCCATGAAA
TTTTTTATTTTCTTCTAGTTATTATACATTGCTTGAGGACAAGCAATAGCTTAAGTTTAGGGGTG
ATAACTCCG
Found at i:212417 original size:17 final size:18
Alignment explanation
Indices: 212390--212423 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
212380 CTATGATACT
212390 GATACCCATTTCAATATC
1 GATACCCATTTCAATATC
*
212408 GATA-CCATTTCTATAT
1 GATACCCATTTCAATAT
212424 TTTGTGTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (18 bp):
GATACCCATTTCAATATC
Found at i:212531 original size:94 final size:94
Alignment explanation
Indices: 212363--212540 Score: 216
Period size: 94 Copynumber: 1.9 Consensus size: 94
212353 CACTACCCTG
* ** * *
212363 GTATCGATACTTCTATACTATGATACTGATACCCATTTCAATATCGATACCATTTCTATATTTTG
1 GTATCGATACTACTATACTATGATACCAATACCCATTTCAATATCGATACCATTTCTACATTCTG
* *
212428 TGTTGCATGGTATCGATACCCTTCAATTA
66 TGATACATGGTATCGATACCCTTCAATTA
* * * * *
212457 GTATCGATACTACTATATTGTGGTACCAATACTCCCTTTCAGTATCGATACCATTT-TGACATTC
1 GTATCGATACTACTATACTATGATACCAATAC-CCATTTCAATATCGATACCATTTCT-ACATTC
212521 TG-GATACATGGTATCGATAC
64 TGTGATACATGGTATCGATAC
212541 TTCTCCTTGT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
94 43 0.61
95 27 0.39
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (94 bp):
GTATCGATACTACTATACTATGATACCAATACCCATTTCAATATCGATACCATTTCTACATTCTG
TGATACATGGTATCGATACCCTTCAATTA
Found at i:217555 original size:20 final size:20
Alignment explanation
Indices: 217530--217569 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
217520 TTCCCCTTCA
*
217530 AAGGGGGAATCGGTTCCCTC
1 AAGGGGGAATCGATTCCCTC
*
217550 AAGGGGGGATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
217570 TGCACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Found at i:221694 original size:6 final size:6
Alignment explanation
Indices: 221683--221707 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
221673 TGCCATTTCC
221683 TCGTCA TCGTCA TCGTCA TCGTCA T
1 TCGTCA TCGTCA TCGTCA TCGTCA T
221708 TCGAATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TCGTCA
Found at i:227841 original size:26 final size:26
Alignment explanation
Indices: 227811--227863 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
227801 ATACCGTAAT
227811 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
227837 GCATCCTTTCATGTATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
227863 G
1 G
227864 ATTCGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:238222 original size:473 final size:473
Alignment explanation
Indices: 237329--238291 Score: 1901
Period size: 473 Copynumber: 2.0 Consensus size: 473
237319 AGTGTGACAC
*
237329 TGAG-ATTAATGATACTACAATTGTGAAGGATTTAACTGTTAACATACAGGGAGACAAGTGTTAA
1 TGAGCATTGATGATACTACAATTGTGAAGGATTTAACTGTTAACATACAGGGAGACAAGTGTTAA
237393 ACTATGAATGTGGATTTAAAGAAGTCCTCTTCAAACAGCTCCGATACCTCTCTAACAAACGAGGA
66 ACTATGAATGTGGATTTAAAGAAGTCCTCTTCAAACAGCTCCGATACCTCTCTAACAAACGAGGA
237458 GCAGGAGGCAAAGGTATATTTTGTTTATACGATCCAACATCCCTACTTCCTCATATGTTATCATT
131 GCAGGAGGCAAAGGTATATTTTGTTTATACGATCCAACATCCCTACTTCCTCATATGTTATCATT
237523 TTGATTTTTGATAGATTTCGATATTTGCAGATTACTGAAATAAGAAGGCTGATAGGACCATTGCC
196 TTGATTTTTGATAGATTTCGATATTTGCAGATTACTGAAATAAGAAGGCTGATAGGACCATTGCC
237588 TGAGAAGTTAGCCATCTATTGCTCTGATGCAGCCATCATTAGATATTTAAGGTCAAGGAACAGGA
261 TGAGAAGTTAGCCATCTATTGCTCTGATGCAGCCATCATTAGATATTTAAGGTCAAGGAACAGGA
237653 ATGTGAAGAAGGCAACTAAAATGCTGAAACAAACCTTGAATTGGAGAGCTGAATACAAACAGGAA
326 ATGTGAAGAAGGCAACTAAAATGCTGAAACAAACCTTGAATTGGAGAGCTGAATACAAACAGGAA
237718 GAGATTCGCTGGGTATGCTACAATTCATCCTCCATTGATTTATACGTAGTTTCTTAAATAAAGTT
391 GAGATTCGCTGGGTATGCTACAATTCATCCTCCATTGATTTATACGTAGTTTCTTAAATAAAGTT
237783 AGAAATGCTTGCAGGACT
456 AGAAATGCTTGCAGGACT
237801 TGAGCATTGATGATACTACAATTGTGAAGGATTTAACTGTTAACATACAGGGAGACAAGTGTTAA
1 TGAGCATTGATGATACTACAATTGTGAAGGATTTAACTGTTAACATACAGGGAGACAAGTGTTAA
237866 ACTATGAATGTGGATTTAAAGAAGTCCTCTTCAAACAGCTCCGATACCTCTCTAACAAACGAGGA
66 ACTATGAATGTGGATTTAAAGAAGTCCTCTTCAAACAGCTCCGATACCTCTCTAACAAACGAGGA
237931 GCAGGAGGCAAAGGTATATTTTGTTTATACGATCCAACATCCCTACTTCCTCATATGTTATCATT
131 GCAGGAGGCAAAGGTATATTTTGTTTATACGATCCAACATCCCTACTTCCTCATATGTTATCATT
237996 TTGATTTTTGATAGATTTCGATATTTGCAGATTACTGAAATAAGAAGGCTGATAGGACCATTGCC
196 TTGATTTTTGATAGATTTCGATATTTGCAGATTACTGAAATAAGAAGGCTGATAGGACCATTGCC
238061 TGAGAAGTTAGCCATCTATTGCTCTGATGCAGCCATCATTAGATATTTAAGGTCAAGGAACAGGA
261 TGAGAAGTTAGCCATCTATTGCTCTGATGCAGCCATCATTAGATATTTAAGGTCAAGGAACAGGA
238126 ATGTGAAGAAGGCAACTAAAATGCTGAAACAAACCTTGAATTGGAGAGCTGAATACAAACAGGAA
326 ATGTGAAGAAGGCAACTAAAATGCTGAAACAAACCTTGAATTGGAGAGCTGAATACAAACAGGAA
238191 GAGATTCGCTGGGTATGCTACAATTCATCCTCCATTGATTTATACGTAGTTTCTTAAATAAAGTT
391 GAGATTCGCTGGGTATGCTACAATTCATCCTCCATTGATTTATACGTAGTTTCTTAAATAAAGTT
238256 AGAAATGCTTGCAGGACT
456 AGAAATGCTTGCAGGACT
*
238274 TGAGCATTGAAGATACTA
1 TGAGCATTGATGATACTA
238292 GGAATTGCCA
Statistics
Matches: 488, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
472 4 0.01
473 484 0.99
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (473 bp):
TGAGCATTGATGATACTACAATTGTGAAGGATTTAACTGTTAACATACAGGGAGACAAGTGTTAA
ACTATGAATGTGGATTTAAAGAAGTCCTCTTCAAACAGCTCCGATACCTCTCTAACAAACGAGGA
GCAGGAGGCAAAGGTATATTTTGTTTATACGATCCAACATCCCTACTTCCTCATATGTTATCATT
TTGATTTTTGATAGATTTCGATATTTGCAGATTACTGAAATAAGAAGGCTGATAGGACCATTGCC
TGAGAAGTTAGCCATCTATTGCTCTGATGCAGCCATCATTAGATATTTAAGGTCAAGGAACAGGA
ATGTGAAGAAGGCAACTAAAATGCTGAAACAAACCTTGAATTGGAGAGCTGAATACAAACAGGAA
GAGATTCGCTGGGTATGCTACAATTCATCCTCCATTGATTTATACGTAGTTTCTTAAATAAAGTT
AGAAATGCTTGCAGGACT
Found at i:238865 original size:40 final size:40
Alignment explanation
Indices: 238810--238931 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
238800 ACGGTATTAG
238810 AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
1 AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
238850 AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
1 AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
*
238890 AGTTAATGTGTGAAAATTATCCCTACACCAGAGTAACTAA
1 AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
238930 AG
1 AG
238932 AAACACATAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (40 bp):
AGTTAATGTGTGAAAATTATCCCTACACTAGAGTAACTAA
Found at i:240527 original size:33 final size:33
Alignment explanation
Indices: 240489--240553 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
240479 AGCTTTAAAC
240489 TATTTGAGTCTAGTCGAACACAACAATACTCAT
1 TATTTGAGTCTAGTCGAACACAACAATACTCAT
* *
240522 TATTTGAGTCTAGTCGAACTCAGCAATACTCA
1 TATTTGAGTCTAGTCGAACACAACAATACTCA
240554 CGCTTTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (33 bp):
TATTTGAGTCTAGTCGAACACAACAATACTCAT
Found at i:246922 original size:14 final size:14
Alignment explanation
Indices: 246905--246931 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
246895 CGGCTCTTAG
246905 CCCTTACATCTTCA
1 CCCTTACATCTTCA
246919 CCCTTACATCTTC
1 CCCTTACATCTTC
246932 GCCTTGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (14 bp):
CCCTTACATCTTCA
Found at i:257492 original size:26 final size:27
Alignment explanation
Indices: 257434--257512 Score: 101
Period size: 26 Copynumber: 3.0 Consensus size: 27
257424 TGTTACTTCA
*
257434 ATCAAGTTGCTCGAACCATACCCTG--
1 ATCAAGTTGCTCGAACCATGCCCTGCT
* * *
257459 ATAAAGTTGTTCGAATCATG-CCTGCT
1 ATCAAGTTGCTCGAACCATGCCCTGCT
257485 ATCAAGTTGCTCGAACCATGCCCTGCT
1 ATCAAGTTGCTCGAACCATGCCCTGCT
257512 A
1 A
257513 CCCTAACACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 4 0.09
25 16 0.36
26 17 0.39
27 7 0.16
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (27 bp):
ATCAAGTTGCTCGAACCATGCCCTGCT
Found at i:257698 original size:27 final size:27
Alignment explanation
Indices: 257667--257780 Score: 104
Period size: 27 Copynumber: 4.0 Consensus size: 27
257657 GAAATGTTAG
* * *
257667 GGTAACAGCGCATGGTTCGAGCAACTT
1 GGTAACAGGGCATGATTCGAACAACTT
257694 GGTAACAGGGCATTG-TTCGAACAACTTGAT
1 GGTAACAGGGCA-TGATTCGAACAAC-T--T
* *
257724 CAAGGTAACAGGGCATGATTTGAGCAACTT
1 ---GGTAACAGGGCATGATTCGAACAACTT
*
257754 GGTAACAGAGCATGATTCGAACAACTT
1 GGTAACAGGGCATGATTCGAACAACTT
257781 TATCGAGGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
27 44 0.61
28 3 0.04
30 2 0.03
32 3 0.04
33 20 0.28
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (27 bp):
GGTAACAGGGCATGATTCGAACAACTT
Found at i:257760 original size:60 final size:60
Alignment explanation
Indices: 257667--257790 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 60
257657 GAAATGTTAG
* *
257667 GGTAACAGCGCATGGTTCGAGCAACTTGGTAACAGGGCATTG-TTCGAACAACTTGATCAA
1 GGTAACAGCGCATGATTCGAGCAACTTGGTAACAGAGCA-TGATTCGAACAACTTGATCAA
* * * *
257727 GGTAACAGGGCATGATTTGAGCAACTTGGTAACAGAGCATGATTCGAACAACTTTATCGA
1 GGTAACAGCGCATGATTCGAGCAACTTGGTAACAGAGCATGATTCGAACAACTTGATCAA
257787 GGTA
1 GGTA
257791 GTAGGAAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 2 0.04
60 55 0.96
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (60 bp):
GGTAACAGCGCATGATTCGAGCAACTTGGTAACAGAGCATGATTCGAACAACTTGATCAA
Found at i:260993 original size:131 final size:131
Alignment explanation
Indices: 260830--261198 Score: 452
Period size: 131 Copynumber: 2.8 Consensus size: 131
260820 ATAATTTTAA
* * * *
260830 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATTCCTTAAAATA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
* * * * ** *
260895 ATCATTTATTACCCCAATTGAAATGAAGAGATATTACTATTTCGTCTTAAAATTCAATATTGATT
66 ATCATTTATTGCTCCAATCGAAATGAAGAGATATTACTATTACGTCTTAAAAAGCAATATTAATT
260960 C
131 C
* * * * * *
260961 GAGTGAAAATGATAATATCTAATGATTTCCAATTGAAAATAAAGGACCTCTCATACCTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
* * *
261026 TTCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTACGTCTTAAAAAGCAATGTTAATT
66 ATCATTTATTGCTCCAATCGAAATGAAGAGATATTACTATTACGTCTTAAAAAGCAATATTAATT
261091 C
131 C
* * * * * *
261092 GAGAG-AAATCGATATTATCGAATTATTTCCAATCAAGAATAAATAACCTCTCATGCCTTAAACC
1 GAGAGAAAAT-GATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAAC
* * * *
261156 AGTCATTTATTGCTCCAACCGAAATGAAAAGATATTAATATTA
65 AATCATTTATTGCTCCAATCGAAATGAAGAGATATTACTATTA
261199 TCAATATCGA
Statistics
Matches: 201, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
130 4 0.02
131 197 0.98
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (131 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
ATCATTTATTGCTCCAATCGAAATGAAGAGATATTACTATTACGTCTTAAAAAGCAATATTAATT
C
Found at i:263258 original size:3 final size:3
Alignment explanation
Indices: 263250--263299 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
263240 TAAAGCCTGA
263250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
263298 AA
1 AA
263300 CGGGACAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:271861 original size:131 final size:128
Alignment explanation
Indices: 271635--272000 Score: 480
Period size: 128 Copynumber: 2.8 Consensus size: 128
271625 AATAATTTTA
* * *
271635 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTTTCATGCCTTAAAAC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * *
271700 AATCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATAAAATATTGAT
66 AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTC-T-TAAAAAT-AAATATTGAT
271765 T
128 T
* * * * * *
271766 AGAGTGAAAACAATAATATCTAATGATTTCCAGTCAAGAATAAATGACCTCTCATACCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * *
271831 ATTCATTTATTGCTCCAATTGAAATGAAGAGATATCATTATTTCTTAAAAATAAATATTGATT
66 AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTCTTAAAAATAAATATTGATT
* * * *
271894 CGAGAGAAATCGATAATATCAAATTATTTCCAATCGAGAATAAATGACCCCTCATGCCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* *** *
271959 AGTCATTTATTACTCCAACCAAAATGAAAAGATATTACTATT
66 AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATT
272001 CTCAATATCG
Statistics
Matches: 201, Mismatches: 34, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
128 100 0.50
129 6 0.03
130 1 0.00
131 94 0.47
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (128 bp):
AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTCTTAAAAATAAATATTGATT
Found at i:271948 original size:128 final size:131
Alignment explanation
Indices: 271635--271976 Score: 474
Period size: 131 Copynumber: 2.6 Consensus size: 131
271625 AATAATTTTA
* * *
271635 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTTTCATGCCTTAAAAC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * *
271700 AATCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATAAAATATTGAT
66 AATCATTTATTACTCCAATTGAAATAAAGAGATATCACTATTTCGTCTAAAAATAAAATATTGAT
271765 T
131 T
* * * * * *
271766 AGAGTGAAAACAATAATATCTAATGATTTCCAGTCAAGAATAAATGACCTCTCATACCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * *
271831 ATTCATTTATTGCTCCAATTGAAATGAAGAGATATCATTATTTC-T-TAAAAAT-AAATATTGAT
66 AATCATTTATTACTCCAATTGAAATAAAGAGATATCACTATTTCGTCTAAAAATAAAATATTGAT
271893 T
131 T
* * * *
271894 CGAGAGAAATCGATAATATCAAATTATTTCCAATCGAGAATAAATGACCCCTCATGCCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
*
271959 AGTCATTTATTACTCCAA
66 AATCATTTATTACTCCAA
271977 CCAAAATGAA
Statistics
Matches: 183, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
128 82 0.45
129 6 0.03
130 1 0.01
131 94 0.51
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (131 bp):
AGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
AATCATTTATTACTCCAATTGAAATAAAGAGATATCACTATTTCGTCTAAAAATAAAATATTGAT
T
Found at i:273653 original size:18 final size:18
Alignment explanation
Indices: 273630--273683 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
273620 ATATAACCCG
273630 ATTTTTACAGATTTTTTT
1 ATTTTTACAGATTTTTTT
273648 ATTTTTACAGATTTTTTT
1 ATTTTTACAGATTTTTTT
273666 ATTTTTACAGATTTTTTT
1 ATTTTTACAGATTTTTTT
273684 CTCCTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (18 bp):
ATTTTTACAGATTTTTTT
Found at i:275472 original size:17 final size:18
Alignment explanation
Indices: 275450--275488 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
275440 TAGATTATTT
275450 ATTTAATTATT-TCTTTC
1 ATTTAATTATTGTCTTTC
* *
275467 ATTTAATTCTTGTCTTTT
1 ATTTAATTATTGTCTTTC
275485 ATTT
1 ATTT
275489 TAAAAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTAATTATTGTCTTTC
Found at i:275553 original size:22 final size:22
Alignment explanation
Indices: 275535--275578 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
275525 TACTATTATT
* *
275535 TATTATTTTATCTTTTATTTTA
1 TATTATTATACCTTTTATTTTA
*
275557 TTTTATTATACCTTTTATTTTA
1 TATTATTATACCTTTTATTTTA
275579 CATTTTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTATTATACCTTTTATTTTA
Found at i:275677 original size:37 final size:37
Alignment explanation
Indices: 275626--275719 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 37
275616 CACTTCTTTT
* **
275626 TTTTATTTTGTTTTATCTTTATTTTCCCACTTTTTTAT-
1 TTTTATTAT-TTTTATCTTTATTTTAACA-TTTTTTATA
* *
275664 TTTTTTTATTTTTATCTTCTCTTTTAACATTTTTTATA
1 TTTTATTATTTTTATCTT-TATTTTAACATTTTTTATA
275702 TTTTATTATTTTT-TCTTT
1 TTTTATTATTTTTATCTTT
275720 TCTGAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.02
37 21 0.44
38 26 0.54
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.73
Consensus pattern (37 bp):
TTTTATTATTTTTATCTTTATTTTAACATTTTTTATA
Found at i:283902 original size:270 final size:270
Alignment explanation
Indices: 283421--284009 Score: 923
Period size: 270 Copynumber: 2.2 Consensus size: 270
283411 GGATATCCAA
* * * * *
283421 TTCAAAGCTCAACTTCACAACGAA-AGAGCCACATATGATTTTAACCTCACAACGAAGGATATCG
1 TTCAAAGCTCAACTTCACAACGAAGA-AGCCACCTACGATTTAAACTTCACAACAAAGGATATCG
* * *
283485 TACCCAAAATATCGACCCAACTTCAAAACGAATGAGTCATCTGTAACGCAACAATGAAAAACCAG
65 TACCCAAAAAATCGACCCAACTTCAAAACGAATGAGTCATATGTAACACAACAATGAAAAACCAG
* *
283550 TTTCATACCAAAGTCTTCAAGTCAAATTTCAGCTTCACAACGAAGTATATTGGGCTAGAAGACGA
130 TTTCATACCAAAGTATTCAAGTCAAATTTCAGCTTCACAACGAAGTATATTGGGCTAGAAGAAGA
*
283615 TACATGAGCGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATCATGCTCA
195 TACAAGAGCGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATCATGCTCA
283680 GGATTTTTCAG
260 GGATTTTTCAG
283691 TTCAAAGCTCAACTTCACAACGAAGAAGCCACCTACGATTTAAACTTCACAACAAAGGATATCGT
1 TTCAAAGCTCAACTTCACAACGAAGAAGCCACCTACGATTTAAACTTCACAACAAAGGATATCGT
* * ** * * *
283756 ACCCAAAAAATTGACCCAGCTTCACGACTAATGAGTCATATGTAACATAACAATGAAAAACCGGT
66 ACCCAAAAAATCGACCCAACTTCAAAACGAATGAGTCATATGTAACACAACAATGAAAAACCAGT
* * *
283821 TTCATACCAAAGTATTCAGGTCAAATTTTAGCTTCACGACGAAGTATATTGGGCTAGAAGAAGAT
131 TTCATACCAAAGTATTCAAGTCAAATTTCAGCTTCACAACGAAGTATATTGGGCTAGAAGAAGAT
*
283886 ACAAGAGCGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATCGTGCTCAG
196 ACAAGAGCGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATCATGCTCAG
283951 GATTTTTCAG
261 GATTTTTCAG
*
283961 TTCAAAGCTCAACTTCACAACGAATG-AGCCA-CTAACGATTTCAACTTCA
1 TTCAAAGCTCAACTTCACAACGAA-GAAGCCACCT-ACGATTTAAACTTCA
284010 TGAAGAATGA
Statistics
Matches: 293, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
269 2 0.01
270 289 0.99
271 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (270 bp):
TTCAAAGCTCAACTTCACAACGAAGAAGCCACCTACGATTTAAACTTCACAACAAAGGATATCGT
ACCCAAAAAATCGACCCAACTTCAAAACGAATGAGTCATATGTAACACAACAATGAAAAACCAGT
TTCATACCAAAGTATTCAAGTCAAATTTCAGCTTCACAACGAAGTATATTGGGCTAGAAGAAGAT
ACAAGAGCGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATCATGCTCAG
GATTTTTCAG
Found at i:284632 original size:85 final size:87
Alignment explanation
Indices: 284512--284670 Score: 216
Period size: 85 Copynumber: 1.9 Consensus size: 87
284502 TTTTATCTTT
** *
284512 GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAGGATATTATTTTAAAAATTAT-
1 GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATAAAAGATATTATTTTAAAAATTATC
284576 TTTA-TTTTATCTTTGTTTTAG
66 TTTAGTTTTATCTTTGTTTTAG
* * * * *
284597 GTATTTTAGTTTAAATAG-TTTTAAGTGTTTTAATTAGGATAAAAGATATTTTTTTAGAAATTAT
1 GTATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGGATAAAAGATATTATTTTAAAAATTAT
284661 CTTTAGTTTT
65 CTTTAGTTTT
284671 TTTTAGGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 3 0.05
85 52 0.83
86 4 0.06
87 4 0.06
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.53
Consensus pattern (87 bp):
GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATAAAAGATATTATTTTAAAAATTATC
TTTAGTTTTATCTTTGTTTTAG
Found at i:285161 original size:18 final size:18
Alignment explanation
Indices: 285119--285161 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
285109 CTTTAGATTA
* *
285119 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATAT
* *
285137 TTCATTTAATTCTTATAT
1 TTTATTTAATTATTATAT
285155 TTTATTT
1 TTTATTT
285162 TAAAAATAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:285254 original size:12 final size:12
Alignment explanation
Indices: 285209--285256 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
285199 CTATTATTTA
*
285209 TTATTTTATCTT
1 TTATTTTACCTT
285221 TTATTTTA--TT
1 TTATTTTACCTT
*
285231 TTATTATACCTT
1 TTATTTTACCTT
*
285243 TAATTTTACCTT
1 TTATTTTACCTT
285255 TT
1 TT
285257 TTTCTCTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 9 0.30
12 21 0.70
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTTACCTT
Found at i:287836 original size:20 final size:20
Alignment explanation
Indices: 287811--287850 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
287801 ACAGGAAAGA
287811 TTAAGAAAAACCTCACACAG
1 TTAAGAAAAACCTCACACAG
287831 TTAAGAAAAACCTCACACAG
1 TTAAGAAAAACCTCACACAG
287851 CCTAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.10, T:0.15
Consensus pattern (20 bp):
TTAAGAAAAACCTCACACAG
Found at i:292291 original size:22 final size:22
Alignment explanation
Indices: 292247--292291 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
292237 AATGATGATG
* * *
292247 TAAATGAAACCAATATGTGACA
1 TAAATGAAACCAAAACGTAACA
292269 TAAATGAAACCAAAACGTAACA
1 TAAATGAAACCAAAACGTAACA
292291 T
1 T
292292 TATATATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (22 bp):
TAAATGAAACCAAAACGTAACA
Found at i:292885 original size:3 final size:3
Alignment explanation
Indices: 292877--292902 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
292867 ATACATCCAA
292877 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
292903 CTCTCTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:293822 original size:40 final size:41
Alignment explanation
Indices: 293776--294161 Score: 112
Period size: 37 Copynumber: 9.4 Consensus size: 41
293766 TAATAATAAT
*
293776 AACTATATAATATA-AAAAAATTT-AAAAATGTTTTTTTAAA
1 AACTATATAATATATAAAAAATTTCAAAAATG-TTTTTAAAA
* ** * *
293816 AACTATATATTATATATGAATTTTCAAAACTGTTTTTAAAA
1 AACTATATAATATATAAAAAATTTCAAAAATGTTTTTAAAA
* * * * *
293857 AACTATATAATTTTTAAAAATGTTTTTTAAAAACTATATAATTTTCAAAA
1 AACTATATAATATATAAAAA----ATTTCAAAA--ATGT--TTTT-AAAA
* * * * * *
293907 ATATTTTAAAAAGTATATATTATATAAGTTTTCAAAAATATTTTT-TAA
1 A-ACTAT-ATAA-TATATA--A-A-AA-ATTTCAAAAATGTTTTTAAAA
* ** *
293955 AACTATAT-AT-TATATAATTTTTCAAAAATCTTTTT--AA
1 AACTATATAATATATAAAAAATTTCAAAAATGTTTTTAAAA
** **
293992 AACTATAT-AT-TATATGATTTTTCAAAAATGTTTTTTAAAA
1 AACTATATAATATATAAAAAATTTCAAAAATG-TTTTTAAAA
* *
294032 AACTATAT-AT-TAT-ATAATTTCTCAAAAATG-TTTT-AAA
1 AACTATATAATATATAAAAAATT-TCAAAAATGTTTTTAAAA
*** *
294069 AACTATATAATATATAAATGTTTTC-AAAATG-TTTT-CAA
1 AACTATATAATATATAAAAAATTTCAAAAATGTTTTTAAAA
* ** * * *
294107 AACTATAT-AT-TAT-ATATTTTTTAAAAAT-ATTTTCAAA
1 AACTATATAATATATAAAAAATTTCAAAAATGTTTTTAAAA
294144 AACTATATAATATATAAA
1 AACTATATAATATATAAA
294162 TTTTCGAAAA
Statistics
Matches: 272, Mismatches: 43, Indels: 62
0.72 0.11 0.16
Matches are distributed among these distances:
35 5 0.02
36 12 0.04
37 53 0.19
38 49 0.18
39 13 0.05
40 43 0.16
41 29 0.11
42 6 0.02
43 4 0.01
44 1 0.00
45 9 0.03
46 1 0.00
47 5 0.02
48 3 0.01
49 4 0.01
50 9 0.03
51 3 0.01
52 7 0.03
53 4 0.01
54 8 0.03
55 1 0.00
56 1 0.00
57 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (41 bp):
AACTATATAATATATAAAAAATTTCAAAAATGTTTTTAAAA
Found at i:293825 original size:42 final size:41
Alignment explanation
Indices: 293779--293865 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
293769 TAATAATAAC
*
293779 TATATAATATAAAAAAATTT-AAAAATGTTTTTTTAAAAACTA
1 TATATAATAT-AAAAAATTTCAAAAATG-TTTTTAAAAAACTA
* ** * *
293821 TATATTATATATGAATTTTCAAAACTGTTTTTAAAAAACTA
1 TATATAATATAAAAAATTTCAAAAATGTTTTTAAAAAACTA
293862 TATA
1 TATA
293866 ATTTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (41 bp):
TATATAATATAAAAAATTTCAAAAATGTTTTTAAAAAACTA
Found at i:293870 original size:31 final size:31
Alignment explanation
Indices: 293828--293963 Score: 130
Period size: 31 Copynumber: 4.2 Consensus size: 31
293818 CTATATATTA
*
293828 TATATGAATTTTCAAAACTGTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTTAAAAAAC
* *
293860 TATATAATTTTTAAAAATGTTTTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAAC
* * *
293891 TATATAATTTTCAAAAATATTTTAAAAAGTATATAT
1 TATATAATTTTCAAAAATGTTTT-TAAA--A-A-AC
* *
293927 TATATAAGTTTTCAAAAATATTTTT-TAAAAC
1 TATATAA-TTTTCAAAAATGTTTTTAAAAAAC
293958 TATATA
1 TATATA
293964 TTATATAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
31 51 0.59
32 8 0.09
33 1 0.01
34 1 0.01
35 2 0.02
36 8 0.09
37 16 0.18
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAAC
Found at i:293941 original size:37 final size:37
Alignment explanation
Indices: 293891--294236 Score: 342
Period size: 37 Copynumber: 9.2 Consensus size: 37
293881 TTTTAAAAAC
*
293891 TATATAA-TTTTCAAAAATATTTTAAAAAGTATATAT
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAT
* *
293927 TATATAAGTTTTCAAAAATATTTTTTAAAACTATATAT
1 TATATAATTTTTCAAAAATA-TTTTAAAAACTATATAT
* *
293965 TATATAATTTTTCAAAAATCTTTTTAAAACTATATAT
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAT
* *
294002 TATATGATTTTTCAAAAATGTTTTTTAAAAAACTATATAT
1 TATATAATTTTTCAAAAA--TATTTT-AAAAACTATATAT
* * *
294042 TATATAATTTCTCAAAAATGTTTTAAAAACTATATAA
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAT
* *
294079 TATATAAATGTTTTC-AAAATGTTTTCAAAACTATATAT
1 TATAT-AAT-TTTTCAAAAATATTTTAAAAACTATATAT
* *
294117 TATAT-ATTTTTTAAAAATATTTTCAAAAACTATATAA
1 TATATAATTTTTCAAAAATATTTT-AAAAACTATATAT
* * * * *
294154 TATATAAATTTTCGAAAATTGTTTTCTGAAAATTATATAT
1 TATATAATTTTTC-AAAAAT-ATTT-TAAAAACTATATAT
* * * *
294194 TATAT--TTTGTCAAAAACATTTTCACAAACTATATTAC
1 TATATAATTTTTCAAAAATATTTT-AAAAACTATA-TAT
294231 TATATA
1 TATATA
294237 CATATATATG
Statistics
Matches: 260, Mismatches: 34, Indels: 30
0.80 0.10 0.09
Matches are distributed among these distances:
35 5 0.02
36 28 0.11
37 90 0.35
38 76 0.29
39 14 0.05
40 46 0.18
41 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATAATTTTTCAAAAATATTTTAAAAACTATATAT
Found at i:293971 original size:38 final size:37
Alignment explanation
Indices: 293806--294198 Score: 339
Period size: 38 Copynumber: 10.6 Consensus size: 37
293796 TTTAAAAATG
* *
293806 TTTTTTTAAAAACTATATATTATATATGAATTTTCAAAAC
1 TTTTTTT-AAAACTATATATTATATA--ATTTTTCAAAAA
* *
293846 TGTTTTT-AAA--A-A-ACTATATAATTTTT-AAAAA
1 TTTTTTTAAAACTATATATTATATAATTTTTCAAAAA
*
293877 TGTTTTTT--AA--A-A-ACTATATAA-TTTTCAAAAA
1 T-TTTTTTAAAACTATATATTATATAATTTTTCAAAAA
* * * *
293908 TATTTTAAAAAGTATATATTATATAAGTTTTCAAAAA
1 TTTTTTTAAAACTATATATTATATAATTTTTCAAAAA
293945 TATTTTTTAAAACTATATATTATATAATTTTTCAAAAA
1 T-TTTTTTAAAACTATATATTATATAATTTTTCAAAAA
* *
293983 TCTTTTTAAAACTATATATTATATGATTTTTCAAAAA
1 TTTTTTTAAAACTATATATTATATAATTTTTCAAAAA
*
294020 TGTTTTTTAAAAAACTATATATTATATAATTTCTCAAAAA
1 T-TTTTTT--AAAACTATATATTATATAATTTTTCAAAAA
* * *
294060 TGTTTTAAAAACTATATAATATATAAATGTTTTC-AAAA
1 TTTTTTTAAAACTATATATTATAT-AAT-TTTTCAAAAA
* * *
294098 TGTTTTCAAAACTATATATTATAT-ATTTTTTAAAAA
1 TTTTTTTAAAACTATATATTATATAATTTTTCAAAAA
** * * *
294134 TATTTTCAAAAACTATATAATATATAAATTTTCGAAAA
1 T-TTTTTTAAAACTATATATTATATAATTTTTCAAAAA
*
294172 TTGTTTTCTGAAAATTATATATTATAT
1 TT-TTTT-T-AAAACTATATATTATAT
294199 TTTGTCAAAA
Statistics
Matches: 297, Mismatches: 35, Indels: 42
0.79 0.09 0.11
Matches are distributed among these distances:
30 8 0.03
31 24 0.08
32 12 0.04
34 8 0.03
35 6 0.02
36 16 0.05
37 82 0.28
38 83 0.28
39 8 0.03
40 50 0.17
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TTTTTTTAAAACTATATATTATATAATTTTTCAAAAA
Found at i:293999 original size:75 final size:75
Alignment explanation
Indices: 293891--294236 Score: 373
Period size: 75 Copynumber: 4.6 Consensus size: 75
293881 TTTTAAAAAC
* *
293891 TATATAA-TTTTCAAAAATATTTTAAAAAGTATATATTATATAAGTTTTCAAAAATATTTTTT-A
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAATATATAAGTTTTCAAAAAT-TTTTTTAA
293954 AAACTATATAT
65 AAACTATATAT
* * * * *
293965 TATATAATTTTTCAAAAATCTTTTTAAAACTATATATTATATGATTTTTCAAAAATGTTTTTTAA
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAATATATAAGTTTTCAAAAAT-TTTTTT-A
294030 AAAACTATATAT
64 AAAACTATATAT
* * * *
294042 TATATAATTTCTCAAAAATGTTTTAAAAACTATATAATATATAAATGTTTTC-AAAA-TGTTTTC
1 TATATAATTTTTCAAAAATATTTTAAAAACTATATAATATAT-AA-GTTTTCAAAAATTTTTTTA
294105 AAAACTATATAT
64 AAAACTATATAT
* * *
294117 TATAT-ATTTTTTAAAAATATTTTCAAAAACTATATAATATATAAATTTTCGAAAATTGTTTTCT
1 TATATAATTTTTCAAAAATATTTT-AAAAACTATATAATATATAAGTTTTCAAAAATT-TTTT-T
* *
294181 GAAAATTATATAT
63 AAAAACTATATAT
* * * *
294194 TATAT--TTTGTCAAAAACATTTTCACAAACTATATTACTATATA
1 TATATAATTTTTCAAAAATATTTT-AAAAACTATA-TAATATATA
294237 CATATATATG
Statistics
Matches: 235, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
73 5 0.02
74 28 0.12
75 85 0.36
76 32 0.14
77 75 0.32
78 5 0.02
79 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (75 bp):
TATATAATTTTTCAAAAATATTTTAAAAACTATATAATATATAAGTTTTCAAAAATTTTTTTAAA
AACTATATAT
Found at i:294100 original size:11 final size:11
Alignment explanation
Indices: 294084--294108 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
294074 TATAATATAT
294084 AAATGTTTTCA
1 AAATGTTTTCA
294095 AAATGTTTTCA
1 AAATGTTTTCA
294106 AAA
1 AAA
294109 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:294243 original size:2 final size:2
Alignment explanation
Indices: 294231--294305 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
294221 ACTATATTAC
* *
294231 TA TA TA CA TA TA TA TG TA TA TA TA TA -A 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
294272 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
294306 ACAAAATAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:295131 original size:84 final size:83
Alignment explanation
Indices: 294968--295607 Score: 633
Period size: 84 Copynumber: 7.7 Consensus size: 83
294958 CGACTTAAGC
* * * * *
294968 TATGTTGCAAATGATGTTGTCTTTGAGCTGAGTGTAATCGAACTCGAATGTC--TT--TGGCAGA
1 TATGCTGCAAATGATG-TG-CCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGA
295029 TAACCCTTCTAGCCTTGAGT
64 TAACCCTTCTAGCCTTGAGT
* * *
295049 TATACTGCAAATGACGTGCCTATGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGAG-AGA
1 TATGCTGCAAATGATGTGCCT-TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG-GCAGA
295113 TAACCCTTCTAGCCTTGAGT
64 TAACCCTTCTAGCCTTGAGT
* * * * * * *
295133 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGG-CCTTTGGTTGGCAA
1 TATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGGCAG
* * * *
295197 ATAGCCCTTCTCGACTTAAGT
63 ATAACCCTTCTAGCCTTGAGT
* * * *
295218 TATGCTGCAAATAATGTGCCTTTGAGCTGAGCGTAGTCAAACTCAAAGGTC-TTTGATGGCAGAT
1 TATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGAT
295282 AACCCTTCTAGCCTTGAGT
65 AACCCTTCTAGCCTTGAGT
* * * * *
295301 TATGCTACAAATGATATGCCTTGGAGGTTAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
1 TATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGAT
295366 AACCCTTCTAGCCTTGAGT
65 AACCCTTCTAGCCTTGAGT
* * * * * * *
295385 TATGTTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGT---AGA
1 TATGCTGCAAATGATGT-GCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGA
* * ** * *
295446 TAGCCCTTCTCGATTTAAGC
64 TAACCCTTCTAGCCTTGAGT
295466 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-TTTTGGTTGGCAGA
1 TATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGGCAGA
* * *
295530 TAACCCTTCTCGACTT-AAT
64 TAACCCTTCTAGCCTTGAGT
* * *
295549 TATGCTGCAAATGATGTGCATTGGAGCTAAGCGTAGTCGAACTCGAAGG-CCTTTGGTGG
1 TATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
295608 GCAAGATTCC
Statistics
Matches: 460, Mismatches: 76, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
79 2 0.00
80 58 0.13
81 47 0.10
82 7 0.02
83 116 0.25
84 141 0.31
85 89 0.19
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (83 bp):
TATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATA
ACCCTTCTAGCCTTGAGT
Found at i:295295 original size:252 final size:247
Alignment explanation
Indices: 294947--295606 Score: 907
Period size: 252 Copynumber: 2.7 Consensus size: 247
294937 TCTTCAGCAG
* * * * *
294947 ATAGTCCTTCTCGACTTAAGCTATGTTGCAAATGATGTTGTCTTTGAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG-TGCCTTTGAGCTGAGCGTAGTCGAACT
* * *
295012 CGAATGTC-TT-TGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGACGTGCCTAT-GA
65 CGAAGGTCTTTGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT-TGGA
* * *
295074 GCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGAGAGATAACCCTTCTAGCCTTGAGTTATGCT
129 GCTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
*
295139 GTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGGCCTTTGGTTGGCAA
194 GTAAATGATGTACCCTCGAAGCTGAGTGCAATCGAACTCGAAGGCCTTTGG-T---AA
* * *
295197 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCTTTGAGCTGAGCGTAGTCAAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTC
* * *
295262 AAAGGTCTTTGATGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGAG
66 GAAGGTCTTTG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAG
* * *
295327 GTTAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTG
130 CTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * * *
295392 TAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAG
195 TAAATGATGTACCCTCGAAGCTGAGTGCAATCGAACTCGAAGGCCTTTGGTAA
* *
295445 ATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTC
* * * * *
295510 GAAGGTTTTTGGTTGGCAGATAACCCTTCTCGACTT-AATTATGCTGCAAATGATGTGCATTGGA
66 GAAGGTCTTT-G-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
295574 GCTAAGCGTAGTCGAACTCGAAGG-CCTTTGGTG
129 GCTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
295607 GGCAAGATTC
Statistics
Matches: 364, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
247 8 0.02
248 115 0.32
249 51 0.14
250 35 0.10
251 2 0.01
252 153 0.42
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (247 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGC
TAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
AAATGATGTACCCTCGAAGCTGAGTGCAATCGAACTCGAAGGCCTTTGGTAA
Found at i:295919 original size:110 final size:110
Alignment explanation
Indices: 295712--296473 Score: 1121
Period size: 110 Copynumber: 7.0 Consensus size: 110
295702 ATCCAAATAT
* * *
295712 TTGTGTTGTTTCAAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACT-T---TGAAACT-AGA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA-A
* ** * *
295772 AAGTTATATGTTGACAACCAGCCGCCCCTTCGTTGTGAAGTTGAGC
65 AAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * * * *
295818 TTGTGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAATTTAAGTTGACTCTGAATGAAACTAAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * *
295883 AGTTGTTTGTTGACAGTCAATCGCCCCTTAGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * * * *
295928 TTGTTTTGTATCGAGTCTAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
295993 AGTGT-TTTGTTGACAGTCAGTCGCCCATTCGCTGTGAAGTTGAGC
66 AGT-TATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * * *
296038 TTGAGTTGTCTCGAGTTCAATATCCTTCACTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
296103 AGTTATTTGTTGACAGTCAGTCGCCCATTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
*
296148 TTGAGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
296213 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
296258 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
296323 AGTTATTTGTTGACAGTCAGTTGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * * * *
296368 TTGTGTTGTCTCGAGTCTAATATCATTCGTTGTGAAGTTGAAATTGACTATGAATGGAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
296433 AGTTGTTTGTTG--A--CAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
296474 AACCACCATC
Statistics
Matches: 601, Mismatches: 48, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
106 69 0.11
107 1 0.00
108 1 0.00
109 1 0.00
110 527 0.88
111 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
Found at i:300222 original size:16 final size:16
Alignment explanation
Indices: 300203--300268 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
300193 GTTAAAAAGG
300203 AAAAATATAAAATAAT
1 AAAAATATAAAATAAT
300219 -AAAATATAATAATAAT
1 AAAAATATAA-AATAAT
*
300235 -AAAATAAATAAATAAAT
1 AAAAATATA-AAAT-AAT
* *
300252 AGAGATA-AAAATAAT
1 AAAAATATAAAATAAT
300267 AA
1 AA
300269 TGAAAATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
15 13 0.31
16 20 0.48
17 5 0.12
18 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATATAAAATAAT
Found at i:300224 original size:5 final size:5
Alignment explanation
Indices: 300216--300309 Score: 50
Period size: 5 Copynumber: 18.4 Consensus size: 5
300206 AATATAAAAT
* *
300216 AATAA AATAT AATAA TAATAA AAT-A AAT-A AAT-A AATAGA GATAAA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AATA-A AAT-AA
* * * ** *
300261 AATAA TAATGAA AATAT GATAA AACAA ACCAA AATAA AATGA AATAA AA
1 AATAA -AAT-AA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
300310 AATTAAATGA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
4 12 0.17
5 37 0.54
6 17 0.25
7 3 0.04
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:300240 original size:8 final size:8
Alignment explanation
Indices: 300204--300246 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
300194 TTAAAAAGGA
300204 AAAAT-AT
1 AAAATAAT
300211 AAAATAAT
1 AAAATAAT
300219 AAAAT-AT
1 AAAATAAT
300226 AATAATAAT
1 AA-AATAAT
300235 AAAATAAAT
1 AAAAT-AAT
300244 AAA
1 AAA
300247 TAAATAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 9 0.28
8 13 0.41
9 10 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATAAT
Found at i:300317 original size:12 final size:13
Alignment explanation
Indices: 300296--300329 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
300286 AAACCAAAAT
300296 AAAATGAAAT-AA
1 AAAATGAAATGAA
*
300308 AAAATTAAATGAA
1 AAAATGAAATGAA
300321 AAAATGAAA
1 AAAATGAAA
300330 AAATTGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAATGAAATGAA
Found at i:301513 original size:4 final size:4
Alignment explanation
Indices: 301504--301552 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
301494 CAACAAAAAG
*
301504 AAAT AAAT AAAT AAA- AAAT -AAT -AAT AAAT GAAT AAAT --AT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
301547 AAAT AA
1 AAAT AA
301553 TAATAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 9 0.23
4 28 0.72
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:301529 original size:17 final size:17
Alignment explanation
Indices: 301509--301562 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
301499 AAAAGAAATA
301509 AATAAATAAAAAATAAT
1 AATAAATAAAAAATAAT
* *
301526 AATAAAT-GAATA-AAT
1 AATAAATAAAAAATAAT
*
301541 -ATAAATAAATAATAAT
1 AATAAATAAAAAATAAT
301557 AATAAA
1 AATAAA
301563 AACTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
16 6 0.21
17 12 0.41
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAAATAAAAAATAAT
Found at i:301537 original size:14 final size:14
Alignment explanation
Indices: 301504--301562 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
301494 CAACAAAAAG
301504 AAATAAAT-A-AAT
1 AAATAAATAATAAT
301516 AAA-AAATAATAAT
1 AAATAAATAATAAT
*
301529 AAATGAATAA-ATAT
1 AAATAAATAATA-AT
301543 AAATAAATAATAAT
1 AAATAAATAATAAT
301557 -AATAAA
1 AAATAAA
301563 AACTATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 13 0.32
14 18 0.45
15 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:301538 original size:25 final size:28
Alignment explanation
Indices: 301504--301562 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
301494 CAACAAAAAG
301504 AAATAAAT-AA-ATAAA-AAATAATAAT
1 AAATAAATAAATATAAATAAATAATAAT
*
301529 AAATGAATAAATATAAATAAATAATAAT
1 AAATAAATAAATATAAATAAATAATAAT
301557 -AATAAA
1 AAATAAA
301563 AACTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 2 0.07
27 10 0.34
28 10 0.34
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATAAATAAATATAAATAAATAATAAT
Found at i:301668 original size:31 final size:31
Alignment explanation
Indices: 301615--301749 Score: 139
Period size: 30 Copynumber: 4.2 Consensus size: 31
301605 CTATATATTA
**
301615 TATATAAATTTTCAAACCTGTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTTAAAAAAC
*
301647 TATATAATTTTTAAAAATGTTTTT-AAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAAC
* *
301677 TATATAATTTTCAAAAATGTTTTAAAAATTATATAT
1 TATATAATTTTCAAAAATGTTTT-TAAA--A-A-AC
*
301713 TATATAAGTTTTCAAAAATGTTTTT-TAAAAC
1 TATATAA-TTTTCAAAAATGTTTTTAAAAAAC
301744 TATATA
1 TATATA
301750 TTATATAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
30 28 0.32
31 23 0.26
32 8 0.09
33 1 0.01
34 1 0.01
35 2 0.02
36 8 0.09
37 16 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAAC
Found at i:301757 original size:38 final size:37
Alignment explanation
Indices: 301677--302009 Score: 286
Period size: 37 Copynumber: 9.2 Consensus size: 37
301667 TTTTAAAAAC
* *
301677 TATATAA-TTTTCAAAAATGTTTTAAAAATTATATAT
1 TATATAAGTTTTCAAAAATGTTTTTAAAACTATATAT
301713 TATATAAGTTTTCAAAAATGTTTTTTAAAACTATATAT
1 TATATAAGTTTTCAAAAATG-TTTTTAAAACTATATAT
*
301751 TATATAATTTTTCAAAAATGTTTTTAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTTAAAACTATATAT
*
301788 TATATAATTTTTCAAAAATGTTTTTTAAAAAACTATATAT
1 TATATAAGTTTTCAAAAATG-TTTTT--AAAACTATATAT
* *
301828 TATATAAGTTTTC-AAAATATTTTAAAAACTATATA-
1 TATATAAGTTTTCAAAAATGTTTTTAAAACTATATAT
*
301863 -ATAT-A----T---AAATGTTTTCAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTTAAAACTATATAT
** * * *
301891 TATATATTTTTTAAAAATA--TTTTCAAAACTATATAA
1 TATATAAGTTTTCAAAA-ATGTTTTTAAAACTATATAT
* * *
301927 TATATAAATTTTCGAAAATTGTTTTCTGAAAATTATATAT
1 TATATAAGTTTTC-AAAAATGTTTT-T-AAAACTATATAT
* * *
301967 TATAT---TTTATCAAAAATATTTTCACAAACTATATTAC
1 TATATAAGTTT-TCAAAAATGTTTTTA-AAACTATA-TAT
302004 TATATA
1 TATATA
302010 CATATATATG
Statistics
Matches: 250, Mismatches: 22, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
27 19 0.08
29 5 0.02
33 1 0.00
34 5 0.02
35 1 0.00
36 51 0.20
37 74 0.30
38 50 0.20
39 5 0.02
40 39 0.16
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTTAAAACTATATAT
Found at i:301785 original size:75 final size:75
Alignment explanation
Indices: 301677--301882 Score: 308
Period size: 75 Copynumber: 2.7 Consensus size: 75
301667 TTTTAAAAAC
*
301677 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTATATAAGTTTTCAAAAATGTTTTTT-AA
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTTTTAAA
301741 AACTATATAT
66 AACTATATAT
* *
301751 TATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTTAA
1 TATATAA-TTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTTTT-A
301816 AAAACTATATAT
64 AAAACTATATAT
* *
301828 TATATAAGTTTTC-AAAATATTTTAAAAACTATATAATATATAAATGTTTTCAAAA
1 TATATAA-TTTTCAAAAATGTTTTAAAAACTATATATTATAT-AA-GTTTTCAAAA
301883 CTATATATTA
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
74 7 0.06
75 52 0.44
76 25 0.21
77 26 0.22
78 9 0.08
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (75 bp):
TATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTTTTAAA
AACTATATAT
Found at i:301887 original size:63 final size:63
Alignment explanation
Indices: 301816--301935 Score: 204
Period size: 63 Copynumber: 1.9 Consensus size: 63
301806 TGTTTTTTAA
*
301816 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAACTATATATTATATAAGTTTTAAAAATATTTTAAAAACTATATAATATATAAATGTTTTC
** *
301879 AAAACTATATATTATATATTTTTTAAAAATATTTTCAAAACTATATAATATATAAAT
1 AAAACTATATATTATATAAGTTTTAAAAATATTTTAAAAACTATATAATATATAAAT
301936 TTTCGAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (63 bp):
AAAACTATATATTATATAAGTTTTAAAAATATTTTAAAAACTATATAATATATAAATGTTTTC
Found at i:301897 original size:36 final size:36
Alignment explanation
Indices: 301857--301932 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
301847 TTTTAAAAAC
* * *
301857 TATATAATATATAAATGTTTTCAAAACTATATATTA
1 TATATAATATAAAAATATTTTCAAAACTATATAATA
** *
301893 TATATTTTTTAAAAATATTTTCAAAACTATATAATA
1 TATATAATATAAAAATATTTTCAAAACTATATAATA
301929 TATA
1 TATA
301933 AATTTTCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (36 bp):
TATATAATATAAAAATATTTTCAAAACTATATAATA
Found at i:301907 original size:25 final size:27
Alignment explanation
Indices: 301842--301896 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
301832 TAAGTTTTCA
*
301842 AAATATTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATAATATAT
* *
301869 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATAATATAT
301896 A
1 A
301897 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATAATATAT
Found at i:302016 original size:2 final size:2
Alignment explanation
Indices: 302004--302070 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
301994 ACTATATTAC
* * *
302004 TA TA TA CA TA TA TA TG TA TA TA TA TG TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
302044 AA TA -A 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
302071 ACAAAATAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:302045 original size:139 final size:136
Alignment explanation
Indices: 301738--302045 Score: 293
Period size: 139 Copynumber: 2.2 Consensus size: 136
301728 AAATGTTTTT
** * * * *
301738 TAAAACTATATATTATATA-ATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTCA
1 TAAAACTATATATTATATATA-TAAT-AAAAATATTTTCAAAACTATATAATATATAAATTTTCA
*
301802 AAAATGTTTTTTAAAAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATAT
64 AAAATGTTTTCTAAAAAACTATATATTATAT-A-TTTTCAAAATATTTTAAAAACTATATAATAT
* *
301867 ATAAATGTTT
127 ATAAATATTA
* **
301877 TCAAAACTATATATTATATATTTTTTAAAAATATTTTCAAAACTATATAATATATAAATTTTCGA
1 T-AAAACTATATATTATATATATAATAAAAATATTTTCAAAACTATATAATATATAAATTTTC-A
* * * * *
301942 AAATTGTTTTCT-GAAAATTATATATTATAT-TTTATCAAAAATATTTTCACAAACTATATTACT
64 AAAATGTTTTCTAAAAAACTATATATTATATATTT-TC-AAAATATTTT-AAAAACTATA-TAAT
*
302005 ATATACATA-TA
125 ATATAAATATTA
**
302016 TATGTA-TATATATGTATATATATAATAAAA
1 TA-AAACTATATAT-TATATATATAATAAAA
302046 TAATATATAT
Statistics
Matches: 141, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
136 3 0.02
137 2 0.01
138 18 0.13
139 75 0.53
140 43 0.30
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (136 bp):
TAAAACTATATATTATATATATAATAAAAATATTTTCAAAACTATATAATATATAAATTTTCAAA
AATGTTTTCTAAAAAACTATATATTATATATTTTCAAAATATTTTAAAAACTATATAATATATAA
ATATTA
Found at i:302058 original size:31 final size:31
Alignment explanation
Indices: 302020--302079 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
302010 CATATATATG
* *
302020 TATATATATGTATATATATAATAAAATAATA
1 TATATATATATATATATATAACAAAATAATA
302051 TATATATATATATATATATAACAAAATAA
1 TATATATATATATATATATAACAAAATAA
302080 CTCCGGGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
TATATATATATATATATATAACAAAATAATA
Done.