Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008090.1 Hibiscus syriacus cultivar Beakdansim tig00110600_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: 750292
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:274156 original size:105 final size:103
Alignment explanation
Indices: 273974--274181 Score: 364
Period size: 105 Copynumber: 2.0 Consensus size: 103
273964 AGAATATCAT
273974 GTAATCCGGCTCGGTTCGTTCTTGATACTGCAATAAAACGAAACTCGAAGATGACTTGTGTAACA
1 GTAATCCGGCTCGGTTCGTTCTTGATACTGCAATAAAACGAAACTCGAAGATGACTTGTGTAACA
274039 AGCATGATATATATATTGCACAAATGAGTAACTAGTTTGC
66 AGCATG--ATATATATTGCACAAATGAGTAACTAGTTTGC
*
274079 GTAATCTGGCTCGGTTCGTTCTTGATACTGCAATAAAAC-AGAACTCGAAGATGACTTGTGTAAC
1 GTAATCCGGCTCGGTTCGTTCTTGATACTGCAATAAAACGA-AACTCGAAGATGACTTGTGTAAC
*
274143 AAGCATGATATATATTGCACGAATGAGTAACTAGTTTGC
65 AAGCATGATATATATTGCACAAATGAGTAACTAGTTTGC
274182 TATACCTTAT
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 31 0.31
104 1 0.01
105 68 0.68
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (103 bp):
GTAATCCGGCTCGGTTCGTTCTTGATACTGCAATAAAACGAAACTCGAAGATGACTTGTGTAACA
AGCATGATATATATTGCACAAATGAGTAACTAGTTTGC
Found at i:275547 original size:105 final size:105
Alignment explanation
Indices: 275438--275641 Score: 295
Period size: 105 Copynumber: 1.9 Consensus size: 105
275428 GGGACAACAT
* * * * *
275438 TGAAGCAGAAAGTCCTGATGTTGAGGAA-GAAAGTCCTTTCG-TCGGTGAAAAACCACCTGCTGT
1 TGAAGCAGAAAGTCCTAATGTTGAAGAATG-AAGCCCTTTCGCT-GGTGAAAAACCACCTACTAT
*
275501 TGAGGGAGAGAAAATGAGAAGAAAATTACTGGAAGATGGCAC
64 TGAGGGAGAGAAAATGAGAAGAAAATTACTAGAAGATGGCAC
*
275543 TGAAGCAGAAAGTCCTAATGTTGAAGAATGAAGCCCTTTCGCTGGTGAAAAACCACTTACTATTG
1 TGAAGCAGAAAGTCCTAATGTTGAAGAATGAAGCCCTTTCGCTGGTGAAAAACCACCTACTATTG
* *
275608 AGGGAGAGAAGATGAGAAGAAGATTACTAGAAGA
66 AGGGAGAGAAAATGAGAAGAAAATTACTAGAAGA
275642 AGATGTTGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 86 0.98
106 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (105 bp):
TGAAGCAGAAAGTCCTAATGTTGAAGAATGAAGCCCTTTCGCTGGTGAAAAACCACCTACTATTG
AGGGAGAGAAAATGAGAAGAAAATTACTAGAAGATGGCAC
Found at i:275800 original size:189 final size:188
Alignment explanation
Indices: 275543--276218 Score: 829
Period size: 189 Copynumber: 3.6 Consensus size: 188
275533 AAGATGGCAC
* * *
275543 TGAAGCAGAAAGTCCTAATGTTGAAGAATGA-AGCCCTTTCGCTGGTGAAAAACCA-CTTACTAT
1 TGAAGCAAAAAGTCCTAATGTTGAGGAA-GAGAGTCCTTTCGCTGGTGAAAAACCATC-TACTAT
* * *
275606 TGAGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATCGGGAAGTCCGACTGCCG
64 TGAGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATCAGAAAGTCCGACTGCCA
*
275671 ATGAAAACTAATCAGATGATGAGGGAGAGAAGCCAAAAAGGAGATTACTAGAAGACGATGT
129 ATGAAAAC-AATCTGATGATGAGGGAGAGAAGCCAAAAAGGAGATTACTAGAAGACGATGT
* * * *
275732 TGAAGCAAAAAGTCTTAATGTTGAGGAAGAGAGTCCTTTTGCTGGTGAAAAACCATCTATTGTTG
1 TGAAGCAAAAAGTCCTAATGTTGAGGAAGAGAGTCCTTTCGCTGGTGAAAAACCATCTACTATTG
* * *
275797 AGGGGGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATAAGAAAGTCC-A-TCCACAA
66 AGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATCAGAAAGTCCGACTGC-CAA
* * * * *
275860 GTGAAAAAACATCTGACGATGAGGAAGAGAAACCGAAAAGGAGATTACTAGAAGACGATGT
130 -TGAAAACA-ATCTGATGATGAGGGAGAGAAGCCAAAAAGGAGATTACTAGAAGACGATGT
* * * *
275921 TGAAGCAAAAAATCCTAATGTTGAGGAAGAGAGTCCTTTCGCCGGTGAAAAAATACATACTACTG
1 TGAAGCAAAAAGTCCTAATGTTGAGGAAGAGAGTCCTTTCGCTGGTG-AAAAA-CCAT-CTACTA
* ** * ** * * *
275986 TTAAGGGAGAGAAGATGAGAAGAAGAAGATTACTAGAAGATGTTGAATCAAAAAGTCCGCCTGTC
63 TTGAGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATCAGAAAGTCCGACTGCC
* * ** * * *
276051 AATGAAAAACAATTTGATGACGAGGGAGAGAAGTAAAAAAGAAGATTACTAGAAGACAATGA
128 AATG-AAAACAATCTGATGATGAGGGAGAGAAGCCAAAAAGGAGATTACTAGAAGACGATGT
* * * *
276113 TGAAGCAAAAAGTCCTAATGTTGAGGAAGAGAGTCATTTTGCTAGTGAAAAACCACCTACTATTG
1 TGAAGCAAAAAGTCCTAATGTTGAGGAAGAGAGTCCTTTCGCTGGTGAAAAACCATCTACTATTG
* *
276178 AGGGAGAGAAAATGAGAAGAAGATTACTAGAGGAAGATGTT
66 AGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTT
276219 TTGGGAAATA
Statistics
Matches: 411, Mismatches: 65, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
187 2 0.00
188 6 0.01
189 240 0.58
190 8 0.02
191 8 0.02
192 138 0.34
193 8 0.02
194 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.20
Consensus pattern (188 bp):
TGAAGCAAAAAGTCCTAATGTTGAGGAAGAGAGTCCTTTCGCTGGTGAAAAACCATCTACTATTG
AGGGAGAGAAGATGAGAAGAAGATTACTAGAAGAAGATGTTGAATCAGAAAGTCCGACTGCCAAT
GAAAACAATCTGATGATGAGGGAGAGAAGCCAAAAAGGAGATTACTAGAAGACGATGT
Found at i:279786 original size:84 final size:82
Alignment explanation
Indices: 279497--279801 Score: 213
Period size: 84 Copynumber: 3.6 Consensus size: 82
279487 TACTGATGAG
* * *
279497 AAACCATCTAATAATGAGGGAGGGAAACCAAAAAGAAGATTACTAGAAGACAACGTTAAATCAAA
1 AAACCATCTGATGATGAGGGAGAGAAACCAAAAAGAAGATTACTAGAAGACAA-GTTAAATC-AA
* * *
279562 AAAATGGT-TTATCGA-TGAA
64 AAAGT-CTATT-TCCAGTGAA
* * * * * * * * *
279581 AAATCATATGATGACGAGGGAGAGAAGCCGAAAAGAAAATTACAAGGAGACGAAGTTGAAGT-AA
1 AAACCATCTGATGATGAGGGAGAGAAACCAAAAAGAAGATTACTAGAAGAC-AAGTT-AAATCAA
* ** *
279645 AAAGTCCACTCACCGGTGAA
64 AAAGTCTA-TTTCCAGTGAA
* * * * ** ** * *
279665 GAACTACCTGATGTTGAGGGAG-GAATACTGAGTAGAAGATTACTAGAAGATAATGTTAAATCAG
1 AAACCATCTGATGATGAGGGAGAGAA-ACCAAAAAGAAGATTACTAGAAGACAA-GTTAAATCAA
279729 AAAGTCTATTTGCCAGTGAA
64 AAAGTCTATTT-CCAGTGAA
* *
279749 AAACCATCTGATGATGAGGGAGAGAAGCCAAAAAGAAGATTACTGGAAGACAA
1 AAACCATCTGATGATGAGGGAGAGAAACCAAAAAGAAGATTACTAGAAGACAA
279802 CGTTGAAGAA
Statistics
Matches: 160, Mismatches: 51, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
83 16 0.10
84 136 0.85
85 8 0.05
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (82 bp):
AAACCATCTGATGATGAGGGAGAGAAACCAAAAAGAAGATTACTAGAAGACAAGTTAAATCAAAA
AGTCTATTTCCAGTGAA
Found at i:280271 original size:14 final size:15
Alignment explanation
Indices: 280252--280280 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
280242 TAAAAACTTG
280252 AATTTTAAA-TATAA
1 AATTTTAAATTATAA
280266 AATTTTAAATTATAA
1 AATTTTAAATTATAA
280281 TCACTGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAATTATAA
Found at i:281641 original size:14 final size:14
Alignment explanation
Indices: 281622--281651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
281612 AACACAACTA
*
281622 TTCGCAATTCGAAT
1 TTCGCAAATCGAAT
281636 TTCGCAAATCGAAT
1 TTCGCAAATCGAAT
281650 TT
1 TT
281652 GCCAATTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (14 bp):
TTCGCAAATCGAAT
Found at i:284108 original size:81 final size:81
Alignment explanation
Indices: 283948--284110 Score: 186
Period size: 81 Copynumber: 2.0 Consensus size: 81
283938 CTACAAGGGG
* * * * *
283948 AAGTCGAAGAAGAGAGTCCGCTCGCTGGTGAAAAATCACCTGAAAATGAGGGGGAGAAGCCGGGA
1 AAGTCGAAGAAGAGAGTCCGCTCGCTGGTGAAAAATCACCGGAAAACGAGGGAGAGAACCCCGGA
* **
284013 AGATTATCGGGAGACA
66 AAATTATCAAGAGACA
* * * *
284029 AAGTTGAAGAAGAGAGTCCGTTCGGTGGTGAAAAATC-CTCGGATAACGAGGGAGAGAACCCCGG
1 AAGTCGAAGAAGAGAGTCCGCTCGCTGGTGAAAAATCAC-CGGAAAACGAGGGAGAGAACCCCGG
284093 AAAACTTAT-AAGAGACA
65 AAAA-TTATCAAGAGACA
284110 A
1 A
284111 CGTCAGTGAG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 63 0.93
82 4 0.06
ACGTcount: A:0.37, C:0.16, G:0.32, T:0.15
Consensus pattern (81 bp):
AAGTCGAAGAAGAGAGTCCGCTCGCTGGTGAAAAATCACCGGAAAACGAGGGAGAGAACCCCGGA
AAATTATCAAGAGACA
Found at i:290278 original size:13 final size:13
Alignment explanation
Indices: 290260--290284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290250 TGTAATTTGA
290260 AATAAATAAAAAG
1 AATAAATAAAAAG
290273 AATAAATAAAAA
1 AATAAATAAAAA
290285 AACTATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:292496 original size:55 final size:55
Alignment explanation
Indices: 292411--292886 Score: 456
Period size: 51 Copynumber: 8.9 Consensus size: 55
292401 ACCTTCTGTC
* * * * * *
292411 AACGGGTTCGTTCCCTCTTCCT-TCATGGAGTATAAAACTTGAGCAATCATT-TGCA
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATC-TTCT-CA
* * *
292466 AACGAGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCAAAC-ATCTTCTTCT
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTC-TCA
* * *
292520 TACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAAC-ATC-T-TCA
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTCTCA
* * *
292572 AAC-GGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAA-TATC-T-TCA
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTCTCA
* * *
292623 AAC-GGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAA-TATCTTCTTCA
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTC-TCA
* * * * *
292677 AACAGGTTCGTTCCCTCTTTATCT-AGGGAGTATGGAACTCGAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTCT-CA
* *
292732 AATGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-ATCTTCTTCT
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTC-TCA
* * * * *
292786 TACGGGTTTGTTCCCTCTTTATCT-AGGGAGTATGGAACTCGAAC-ATCTTCT--
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTCTCA
* *
292837 AACAGGTTCGCTCCCTCTTTCT-TTAGGGAGTATAGAACTCGAA-AATCTTC
1 AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTC
292887 AAACGTGTAT
Statistics
Matches: 366, Mismatches: 41, Indels: 32
0.83 0.09 0.07
Matches are distributed among these distances:
50 1 0.00
51 135 0.37
52 5 0.01
53 3 0.01
54 101 0.28
55 120 0.33
56 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (55 bp):
AACGGGTTCGCTCCCTCTTTCTCTCAGGGAGTATAGAACTCGAACAATCTTCTCA
Found at i:292969 original size:53 final size:53
Alignment explanation
Indices: 292896--293052 Score: 235
Period size: 53 Copynumber: 2.9 Consensus size: 53
292886 CAAACGTGTA
* *
292896 TGCTCCCTATTTCTTTAGAGAGTATAAGACCCACAATCTTCAACGATCGCGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTC
*
292949 TGC-CTCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGTGTC
1 TGCTC-CCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTC
* *
293002 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCG
1 TGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCG
293053 TTGGGAAACC
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
52 1 0.01
53 75 0.79
54 2 0.02
55 17 0.18
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (53 bp):
TGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTC
Found at i:294074 original size:16 final size:17
Alignment explanation
Indices: 294047--294092 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
294037 TGAACCCTTC
*
294047 TTTTTTCCATTTTTCCA
1 TTTTTTTCATTTTTCCA
**
294064 TTTTTTT-ATTTTTTTA
1 TTTTTTTCATTTTTCCA
294080 TTTTTTTCATTTT
1 TTTTTTTCATTTT
294093 CACTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCATTTTTCCA
Found at i:294075 original size:7 final size:8
Alignment explanation
Indices: 294063--294092 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
294053 CCATTTTTCC
294063 ATTTTTTT
1 ATTTTTTT
294071 ATTTTTTT
1 ATTTTTTT
294079 ATTTTTTT
1 ATTTTTTT
294087 CATTTT
1 -ATTTT
294093 CACTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:304086 original size:16 final size:16
Alignment explanation
Indices: 304065--304102 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
304055 AACCTTATTC
304065 ACATGATATCTACCCA
1 ACATGATATCTACCCA
304081 ACATGATATCTACCCA
1 ACATGATATCTACCCA
304097 ATCATG
1 A-CATG
304103 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:305786 original size:13 final size:13
Alignment explanation
Indices: 305768--305792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305758 TGTAATTTGA
305768 AATAAATAAAAAG
1 AATAAATAAAAAG
305781 AATAAATAAAAA
1 AATAAATAAAAA
305793 AACTATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:307977 original size:21 final size:21
Alignment explanation
Indices: 307951--308049 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 21
307941 TTTAAGGCAT
307951 AAGGGATCGATCCTTTTACCA
1 AAGGGATCGATCCTTTTACCA
*
307972 AAGGGATCGAT-CTTTT-TCA
1 AAGGGATCGATCCTTTTACCA
**** *
307991 AATATTTCGA-CCGTTATACCA
1 AAGGGATCGATCC-TTTTACCA
* ****
308012 AAGGGATTGATCCTTTTTGGG
1 AAGGGATCGATCCTTTTACCA
308033 AAGGGATCGATCCTTTT
1 AAGGGATCGATCCTTTT
308050 GTGAAGGGAT
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
19 9 0.16
20 8 0.14
21 37 0.66
22 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTACCA
Found at i:308055 original size:20 final size:21
Alignment explanation
Indices: 308012--308065 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
308002 CGTTATACCA
*
308012 AAGGGATTGATCCTTTTTGGG
1 AAGGGATCGATCCTTTTTGGG
*
308033 AAGGGATCGATCC-TTTTGTG
1 AAGGGATCGATCCTTTTTGGG
308053 AAGGGATCGATCC
1 AAGGGATCGATCC
308066 CAAACTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTTGGG
Found at i:310307 original size:60 final size:60
Alignment explanation
Indices: 310180--310308 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
310170 ATATTCGAGT
* * * * *
310180 GACCATTTTGTAACTTTTAATAGTAGAGAGAGTCACCAAATCAACATCCTATAGTCAGGG
1 GACCATTTTATAACTTTTAATAGTAGAGAGACTCAACAAAGCAACATCCTATAATCAGGG
* * * * ** *
310240 GATCATTTTATAACTTTTAATAGTCGGGGGACTCAATTAAGCAATATCCTATAATC-GGG
1 GACCATTTTATAACTTTTAATAGTAGAGAGACTCAACAAAGCAACATCCTATAATCAGGG
310299 AGACCATTTT
1 -GACCATTTT
310309 TGCACTTTAC
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
59 3 0.05
60 52 0.95
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTAGAGAGACTCAACAAAGCAACATCCTATAATCAGGG
Found at i:324677 original size:25 final size:25
Alignment explanation
Indices: 324640--324698 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
324630 TTTTTTAAAA
324640 TACAAATATTTTAAATTTAAAATAC
1 TACAAATATTTTAAATTTAAAATAC
*
324665 TATAAATATTTTAAATTTAAAATAC
1 TACAAATATTTTAAATTTAAAATAC
324690 TACAAATAT
1 TACAAATAT
324699 ATGCTAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (25 bp):
TACAAATATTTTAAATTTAAAATAC
Found at i:326510 original size:60 final size:60
Alignment explanation
Indices: 326435--326587 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
326425 ACATTACTGT
* * * * ** *
326435 TTAAACTTTTAAACATTTCAATTTTATCCTAAAACTATGACTCTCATTCTAAATTAGTCC
1 TTAAACTTTTGAACATTTCAATTTTATCCCAAAACTAAGAATAACATTCTAAATTAGACC
* * * *
326495 TTAAACTTTTGAACATTCCAATTTCATCCCCAAACTAAGAATAACATTCTAAATTGGACC
1 TTAAACTTTTGAACATTTCAATTTTATCCCAAAACTAAGAATAACATTCTAAATTAGACC
*
326555 CTAAACTTTTG--CATCTTCAATTTTATCTCCAAA
1 TTAAACTTTTGAACAT-TTCAATTTTATC-CCAAA
326588 TTCATCCAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
58 3 0.04
59 10 0.13
60 63 0.83
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (60 bp):
TTAAACTTTTGAACATTTCAATTTTATCCCAAAACTAAGAATAACATTCTAAATTAGACC
Found at i:343428 original size:27 final size:28
Alignment explanation
Indices: 343373--343439 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
343363 GACCCCCAAT
* * * *
343373 TTTTTATATTCATAATTAGGGCCGTTAA
1 TTTTTATATTTAAAATTAAGGCCGCTAA
343401 TTTTTATATTTAAAATTAAGGCC-CTAA
1 TTTTTATATTTAAAATTAAGGCCGCTAA
343428 TTTTTATTATTT
1 TTTTTA-TATTT
343440 TATGAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (28 bp):
TTTTTATATTTAAAATTAAGGCCGCTAA
Found at i:343637 original size:116 final size:116
Alignment explanation
Indices: 343401--343627 Score: 293
Period size: 117 Copynumber: 2.0 Consensus size: 116
343391 GGGCCGTTAA
* * * *
343401 TTTTTATATTTAAAATTAAGGCCCTAATTTTTATTATTTTATGAAATTTTAGTTTTTGACCCTCT
1 TTTTTATATTTAAAATTAAGGCCCTAATTTTTATAAATTCATAAAATTTTAGTTTTTGACCCTCT
*
343466 TTTTCCATTTATCTTATTAATTCATCTAATTTTGAATTAAATTTAACCAAT
66 TTTTCAATTTATCTTATTAATTCATCTAATTTTGAATTAAATTTAACCAAT
*
343517 TTTTTATATTTATAAA-T-AGTGCCGCTACTTTTTATAAATTCATAAAATATTTAGTTTTT-ACC
1 TTTTTATATTTA-AAATTAAG-GCC-CTAATTTTTATAAATTCATAAAAT-TTTAGTTTTTGACC
* * *
343579 CTTTTTTTCAATTTCTCTTATT-TTTCAT-TCAATTTTGAATTAAATTTAA
62 CTCTTTTTCAATTTATCTTATTAATTCATCT-AATTTTGAATTAAATTTAA
343628 TCGTTTTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
115 3 0.03
116 40 0.41
117 44 0.45
118 10 0.10
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (116 bp):
TTTTTATATTTAAAATTAAGGCCCTAATTTTTATAAATTCATAAAATTTTAGTTTTTGACCCTCT
TTTTCAATTTATCTTATTAATTCATCTAATTTTGAATTAAATTTAACCAAT
Found at i:345154 original size:35 final size:34
Alignment explanation
Indices: 345108--345220 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
345098 AAAACAATCC
*
345108 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
345143 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
345178 TCAATTACATTCTAAAGCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
345213 TCAATTTC
1 TCAATTTC
345221 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:346545 original size:30 final size:30
Alignment explanation
Indices: 346511--346582 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
346501 CCCGAAGGAC
*
346511 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
346541 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
346571 CTGTCCATAGGT
1 CTATCCAGAGGT
346583 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:346689 original size:32 final size:32
Alignment explanation
Indices: 346570--346697 Score: 138
Period size: 31 Copynumber: 4.1 Consensus size: 32
346560 ATCCTCGGCA
* * * *
346570 ACTGTCCATAGGTTCCGAAGAACCTTGGTAA-
1 ACTGTCCATATGTTCCTAAGAACATAGGTAAT
*
346601 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCTAAGAACATAGGTAAT
**
346632 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCTAAGAACATAGGTAAT
* *
346664 TCTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCTAAGAACATAGGTAAT
346695 ACT
1 ACT
346698 CTCGACTCTT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.01
31 53 0.66
32 26 0.32
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCTAAGAACATAGGTAAT
Found at i:347958 original size:64 final size:64
Alignment explanation
Indices: 347851--348071 Score: 243
Period size: 64 Copynumber: 3.5 Consensus size: 64
347841 TAATGAAGGT
* * * * ** *
347851 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATACATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGGG
*
347915 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
* ** **
347979 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCCTTATTAATGGG
**
348042 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
348072 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
63 3 0.02
64 127 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:349428 original size:35 final size:34
Alignment explanation
Indices: 349380--349491 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
349370 ATTCCTCCTT
* *
349380 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
349415 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
349450 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
349485 AAATTGA
1 AAATTGA
349492 GAATTGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:356067 original size:18 final size:18
Alignment explanation
Indices: 356040--356079 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
356030 AACCTTGTGA
*
356040 ATATATGTGGAATAAAAT
1 ATATAAGTGGAATAAAAT
356058 ATATAAGTGGAATAAAAT
1 ATATAAGTGGAATAAAAT
356076 ATAT
1 ATAT
356080 TTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (18 bp):
ATATAAGTGGAATAAAAT
Found at i:360038 original size:31 final size:31
Alignment explanation
Indices: 360001--360092 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
359991 TAATCACATC
*
360001 TTAATTAAATAAAAACGAAGATGACCATATA
1 TTAATTAAGTAAAAACGAAGATGACCATATA
* *
360032 TTAATTAAGTAAAAAGGAAGGTGACCATATA
1 TTAATTAAGTAAAAACGAAGATGACCATATA
** * *
360063 TTAATTTGGTAAAAATGAAAATGACCATAT
1 TTAATTAAGTAAAAACGAAGATGACCATAT
360093 CTTATGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (31 bp):
TTAATTAAGTAAAAACGAAGATGACCATATA
Found at i:364010 original size:25 final size:24
Alignment explanation
Indices: 363956--364011 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
363946 TCACATTTTG
*
363956 ATAATTTTATTTTTAAAAAATAAA
1 ATAATTTTATATTTAAAAAATAAA
*
363980 AAAATTATTATATTTATAAAAA-AAA
1 ATAATT-TTATATTTA-AAAAATAAA
*
364005 CTAATTT
1 ATAATTT
364012 CTCTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 6 0.23
25 15 0.58
26 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTTTATATTTAAAAAATAAA
Found at i:365386 original size:12 final size:12
Alignment explanation
Indices: 365369--365399 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
365359 TAGGGTTTAG
365369 GGTTTTAAATTA
1 GGTTTTAAATTA
*
365381 GGTTTTAAGTTA
1 GGTTTTAAATTA
365393 GGTTTTA
1 GGTTTTA
365400 GGGTTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (12 bp):
GGTTTTAAATTA
Found at i:372403 original size:17 final size:19
Alignment explanation
Indices: 372381--372415 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
372371 AACATTAAAC
372381 TTTAAAA-A-TTAATATTA
1 TTTAAAACATTTAATATTA
372398 TTTAAAACATTTAATATT
1 TTTAAAACATTTAATATT
372416 TCATCTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAACATTTAATATTA
Found at i:374034 original size:17 final size:16
Alignment explanation
Indices: 374014--374047 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
374004 TACCTTTACA
374014 TTTTATTTAATTTGTTT
1 TTTTATTTAATTT-TTT
*
374031 TTTTATTTTATTTTTT
1 TTTTATTTAATTTTTT
374047 T
1 T
374048 AATAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTATTTAATTTTTT
Found at i:375368 original size:2 final size:2
Alignment explanation
Indices: 375361--375404 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
375351 CATCAAAGTA
375361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
375403 AT
1 AT
375405 GTAATAATCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375953 original size:3 final size:3
Alignment explanation
Indices: 375932--375994 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
375922 ACACTCAAAA
* *
375932 TAT TAT CAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
375980 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
375995 ATTCTTTTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:376440 original size:20 final size:19
Alignment explanation
Indices: 376415--376469 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
376405 AATTACTTAT
*
376415 TAAAATAATATTACTAATAA
1 TAAAATAATAATACTAA-AA
*
376435 TAAAATAATAATAGTAAAA
1 TAAAATAATAATACTAAAA
* *
376454 TAAAATTATTATACTA
1 TAAAATAATAATACTA
376470 TATTTTAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAATAATAATACTAAAA
Found at i:379037 original size:38 final size:37
Alignment explanation
Indices: 378986--379064 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 37
378976 TAGAACCATT
*
378986 AGAAAGGGCTGTTTTGGAACCATTACCTCCGAAAGATG
1 AGAAAGAGCTGTTTTGGAACCATTACCTCCG-AAGATG
379024 AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAGATG
1 AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAGATG
379061 AGAA
1 AGAA
379065 GGTCCTCTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.25
38 30 0.75
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (37 bp):
AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAGATG
Found at i:390718 original size:2 final size:2
Alignment explanation
Indices: 390713--390741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
390703 CACGCACGTG
390713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
390742 GTCTAATTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:391127 original size:31 final size:31
Alignment explanation
Indices: 391087--391152 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
391077 ACATATAGTC
*
391087 ATTAAATTTATCGAATTGTTATAAAATGATA
1 ATTAAATTTATCAAATTGTTATAAAATGATA
* *
391118 ATTAGATTTATCAAATTGTTATAAAATGATC
1 ATTAAATTTATCAAATTGTTATAAAATGATA
391149 ATTA
1 ATTA
391153 TACTCCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (31 bp):
ATTAAATTTATCAAATTGTTATAAAATGATA
Found at i:394977 original size:10 final size:10
Alignment explanation
Indices: 394962--394988 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
394952 CGCTCGATTA
394962 TATGTTCATT
1 TATGTTCATT
394972 TATGTTCATT
1 TATGTTCATT
394982 TATGTTC
1 TATGTTC
394989 GAACAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (10 bp):
TATGTTCATT
Found at i:405935 original size:29 final size:26
Alignment explanation
Indices: 405903--405956 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
405893 AAAAGTTAGG
405903 AATATTTTTATAAATATAATAATATTTTT
1 AATATTTTTATAAA-A-AATAA-ATTTTT
405932 AATATTTTTATAAAAAATAAATTTT
1 AATATTTTTATAAAAAATAAATTTT
405957 AAAATTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
27 5 0.20
28 1 0.04
29 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATTTTTATAAAAAATAAATTTTT
Found at i:407240 original size:28 final size:28
Alignment explanation
Indices: 407208--407273 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
407198 AACCGGTGTA
407208 GATTGAACCGGACTAGACAACGATTTCC
1 GATTGAACCGGACTAGACAACGATTTCC
407236 GATTGAACCGGACTAGACAACGATTTCC
1 GATTGAACCGGACTAGACAACGATTTCC
407264 GATTGAACCG
1 GATTGAACCG
407274 ACCGGTCTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (28 bp):
GATTGAACCGGACTAGACAACGATTTCC
Found at i:407709 original size:52 final size:52
Alignment explanation
Indices: 407631--407738 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
407621 GATAAACGAC
407631 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
1 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
407683 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
1 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
407735 GATG
1 GATG
407739 TAAAGAGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.35, T:0.29
Consensus pattern (52 bp):
GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
Found at i:410555 original size:149 final size:143
Alignment explanation
Indices: 410072--410684 Score: 911
Period size: 143 Copynumber: 4.2 Consensus size: 143
410062 GCATTTGCCA
* *
410072 TTTGCTTGATTGATCATGTTTCGAACCCCACTTGAATGCACATATTTGAAATTTTGAATATAGTC
1 TTTG-TTGATTGATTATGTTTCGAATCCCACTTGAATGCAC--A--T---A-TTTGAATATAGTC
*
410137 TT-CAGTTGATTTTTTTTA-----CTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCA
57 TTGAAGTTGATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCA
410196 CTCATCTTGAGGTATATTGCAT
122 CTCATCTTGAGGTATATTGCAT
* * *
410218 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATGGTATTGAAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
* *
410283 ATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTG
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCACTCATCTTG
410348 AGGTATATTGCAT
131 AGGTATATTGCAT
* *
410361 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGGAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
*
410426 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATTGTTACCAGTGCCACTC
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCGTT---A---CCACTC
410491 ATCTTGAGGTATATTGCAT
125 ATCTTGAGGTATATTGCAT
410510 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
410575 --TTTTTTTACTTTTCTTCTTTCGATGATGTTG-CTGGGAATCATATATCGTTACCACTCATCTT
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTC-GGGAATCATATATCGTTACCACTCATCTT
*
410637 GAGGTATATTGCGT
130 GAGGTATATTGCAT
410651 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
410685 GGAATATTGT
Statistics
Matches: 436, Mismatches: 18, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
137 13 0.03
138 15 0.03
141 59 0.14
143 174 0.40
144 1 0.00
145 33 0.08
146 6 0.01
147 47 0.11
149 88 0.20
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (143 bp):
TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCACTCATCTTG
AGGTATATTGCAT
Found at i:410678 original size:290 final size:284
Alignment explanation
Indices: 410072--410684 Score: 925
Period size: 290 Copynumber: 2.1 Consensus size: 284
410062 GCATTTGCCA
* *
410072 TTTGCTTGATTGATCATGTTTCGAACCCCACTTGAATGCACATATTTGAAATTTTGAATATAGTC
1 TTTG-TTGATTGATTATGTTTCGAATCCCACTTGAATGCACA-A-TT--AATTTTGAATATAGTC
410137 TTCAGTTGATTTTTTTTACTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCACTCATC
61 TTCAGTTGATTTTTTTTACTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCACTCATC
*
410202 TTGAGGTATATTGCATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAA
126 TTGAGGTATATTGCATTTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAA
*
410267 TATGGTATTGAAGTTGATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATC
191 TATAGTATTGAAGTTGATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATC
410332 CTTACCACTCATCTTGAGGTATATTGCAT
256 CTTACCACTCATCTTGAGGTATATTGCAT
* *
410361 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCAC-A-T-A-TTTGAATATAGTCTTGGA
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACAATTAATTTTGAATATAGTCTT-CA
*
410422 GTTGATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATTGTTACCAGTGCC
65 GTTGATTTTTTTTA-----CTTCTTTCGATGATGTTGTCGGGAATCATATATCGTT---A---CC
410487 ACTCATCTTGAGGTATATTGCATTTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACAT
119 ACTCATCTTGAGGTATATTGCATTTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACAT
*
410552 ATTTGAATATAGTCTTGAAGTTG-TTTTTT-TACTTTTCTTCTTTCGATGATGTTG-CTGGGAAT
184 ATTTGAATATAGTATTGAAGTTGATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTC-GGGAAT
* *
410614 CATATATCGTTACCACTCATCTTGAGGTATATTGCGT
248 CATATATCCTTACCACTCATCTTGAGGTATATTGCAT
410651 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
410685 GGAATATTGT
Statistics
Matches: 300, Mismatches: 11, Indels: 25
0.89 0.03 0.07
Matches are distributed among these distances:
280 15 0.05
281 16 0.05
284 1 0.00
286 37 0.12
288 33 0.11
289 6 0.02
290 99 0.33
291 6 0.02
292 87 0.29
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (284 bp):
TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACAATTAATTTTGAATATAGTCTTCAG
TTGATTTTTTTTACTTCTTTCGATGATGTTGTCGGGAATCATATATCGTTACCACTCATCTTGAG
GTATATTGCATTTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAG
TATTGAAGTTGATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTAC
CACTCATCTTGAGGTATATTGCAT
Found at i:415854 original size:21 final size:21
Alignment explanation
Indices: 415821--415862 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
415811 GTAAAAATCC
*
415821 TTAAGTGACTAACAATTATCG
1 TTAACTGACTAACAATTATCG
*
415842 TTAACTGATTAACAATTATCG
1 TTAACTGACTAACAATTATCG
415863 CTTGAGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (21 bp):
TTAACTGACTAACAATTATCG
Found at i:417106 original size:3 final size:3
Alignment explanation
Indices: 417098--417131 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
417088 AACTTAAATA
417098 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
417132 CAATTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:423093 original size:60 final size:60
Alignment explanation
Indices: 422957--423093 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
422947 AATAGTTAGT
* * * *
422957 GACCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAACATTCTATAGTTAGAG
1 GACCATTATGTAACTTTTAATAGTCGAAAGACTTAATAAAACAACATTCTATAGTAAGAG
* * * *
423017 GATCATTTTGTAACTTTTAATAGTCGAAAGACTTAATAAAATAATA-TCATATAGTCAAG-G
1 GACCATTATGTAACTTTTAATAGTCGAAAGACTTAATAAAACAACATTC-TATAGT-AAGAG
423077 GACCATATATGT-ACTTT
1 GACCAT-TATGTAACTTT
423094 ACCCCTTACT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 2 0.03
60 58 0.88
61 6 0.09
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
GACCATTATGTAACTTTTAATAGTCGAAAGACTTAATAAAACAACATTCTATAGTAAGAG
Found at i:423507 original size:50 final size:49
Alignment explanation
Indices: 423410--423512 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 49
423400 TATGTGATAA
* * * *
423410 AATTTAATAAAAAATATATTTTATTGAAATTCATCACTCTGACGTGACG
1 AATTTAATAAAAAATATATTTTATTAAAACTCATCACTCTAAAGTGACG
* * *
423459 AATTTAAATAAAAAATATTTTTTATTAAAACTCGTCACATC-AAAGTGACT
1 AATTT-AATAAAAAATATATTTTATTAAAACTCATCAC-TCTAAAGTGACG
423509 AATT
1 AATT
423513 CCATTAACAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 5 0.11
50 38 0.84
51 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (49 bp):
AATTTAATAAAAAATATATTTTATTAAAACTCATCACTCTAAAGTGACG
Found at i:434090 original size:17 final size:16
Alignment explanation
Indices: 434054--434087 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
434044 TTTATAGATG
434054 AAGAAAAATAAAATAA
1 AAGAAAAATAAAATAA
434070 AAGAAAAA-AATAATAA
1 AAGAAAAATAA-AATAA
434086 AA
1 AA
434088 AGATTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGAAAAATAAAATAA
Found at i:434096 original size:21 final size:21
Alignment explanation
Indices: 434072--434111 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
434062 TAAAATAAAA
434072 GAAAA-AAATAATAAAAAGATT
1 GAAAAGAAAT-ATAAAAAGATT
*
434093 GAAAAGAAATTTAAAAAGA
1 GAAAAGAAATATAAAAAGA
434112 AAGTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
GAAAAGAAATATAAAAAGATT
Found at i:434959 original size:21 final size:21
Alignment explanation
Indices: 434929--434978 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
434919 GCGTTACATT
434929 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* *
434950 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
434971 TCGCGTTG
1 TCGCGTTG
434979 TGATTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:435044 original size:6 final size:6
Alignment explanation
Indices: 435033--435061 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
435023 CGTATTACCA
435033 CGACCC CGACCC CGACCC CGA-CC CGACCC
1 CGACCC CGACCC CGACCC CGACCC CGACCC
435062 GACACGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.66, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:435714 original size:41 final size:41
Alignment explanation
Indices: 435665--435842 Score: 232
Period size: 41 Copynumber: 4.3 Consensus size: 41
435655 TTTTTTTTTA
*
435665 ACTATCGCAACGAATTTAGAAAATCTCAACGACAACTGTAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAG
* * * ** *
435706 ACTTTCGCAACAACAACTGTAGACTATCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAA-TTTAGAAAATCGCAACGACAACTGTAG
*
435750 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAG
* *
435791 ACTATCGCAACGAATTTGGAAAATCGCAACGAC-ATTGTAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAG
435831 ACTATCGCAACG
1 ACTATCGCAACG
435843 CGAAATGCAA
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 18 0.15
41 65 0.55
42 2 0.02
43 2 0.02
44 32 0.27
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAG
Found at i:435716 original size:22 final size:22
Alignment explanation
Indices: 435691--435842 Score: 147
Period size: 22 Copynumber: 7.2 Consensus size: 22
435681 TAGAAAATCT
*
435691 CAACGACAACTGTAGACTTTCG
1 CAACGACAACTGTAGACTATCG
*
435713 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
*
435735 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
435757 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
435776 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
435798 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
*
435817 CAACGAC-ATTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
435838 CAACG
1 CAACG
435843 CGAAATGCAA
Statistics
Matches: 105, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
19 26 0.25
20 5 0.05
21 15 0.14
22 59 0.56
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Found at i:440155 original size:3 final size:3
Alignment explanation
Indices: 440147--440181 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
440137 GCAAAACGGC
440147 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
440182 AGGAAAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:440869 original size:4 final size:4
Alignment explanation
Indices: 440862--440911 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
440852 TGGAAGTAAG
* * *
440862 TACA TACA TACA TATA TGCCTA TACA TAAA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA T-AC-A TACA TACA TACA TACA TACA TACA TACA
440912 CATGATTGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
4 35 0.92
5 1 0.03
6 2 0.05
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:441651 original size:30 final size:31
Alignment explanation
Indices: 441617--441677 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
441607 AAATTAAGAC
441617 GTTTTAAGATGTATTAAAAAGAT-ACCGGAA
1 GTTTTAAGATGTATTAAAAAGATAACCGGAA
441647 GTTTTAAGATGTATTAAAAAGATAACCGGAA
1 GTTTTAAGATGTATTAAAAAGATAACCGGAA
441678 AACGATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.30
Consensus pattern (31 bp):
GTTTTAAGATGTATTAAAAAGATAACCGGAA
Found at i:462441 original size:30 final size:30
Alignment explanation
Indices: 462405--462461 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
462395 TTTTATTTCG
*
462405 TGTAGAAAAGGAAAGAAATAGAATATAAAT
1 TGTAGAAAAAGAAAGAAATAGAATATAAAT
*
462435 TGTAGAAAAAGAAATAAATAGAATATA
1 TGTAGAAAAAGAAAGAAATAGAATATA
462462 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (30 bp):
TGTAGAAAAAGAAAGAAATAGAATATAAAT
Found at i:462464 original size:2 final size:2
Alignment explanation
Indices: 462457--462485 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
462447 AATAAATAGA
462457 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
462486 AATAAAGAAA
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:463460 original size:3 final size:3
Alignment explanation
Indices: 463452--463477 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
463442 AACGTTCAAT
463452 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
463478 TACTGATAGA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:466155 original size:14 final size:14
Alignment explanation
Indices: 466136--466168 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
466126 AATTTGTTTA
*
466136 TTTATTTATATTTG
1 TTTATTTATATTCG
466150 TTTATTTATATTCG
1 TTTATTTATATTCG
466164 TTTAT
1 TTTAT
466169 GTTCTCTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTATTTATATTCG
Found at i:466357 original size:24 final size:24
Alignment explanation
Indices: 466307--466358 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
466297 TCAAAATAAT
* * * * *
466307 TTTATATTCGTTTGTTTGTGTTTA
1 TTTACATTCGTTCGTTTATATTCA
466331 TTTACATTCGTTCGTTTATATTCA
1 TTTACATTCGTTCGTTTATATTCA
466355 TTTA
1 TTTA
466359 TCATAACTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTACATTCGTTCGTTTATATTCA
Found at i:469175 original size:20 final size:20
Alignment explanation
Indices: 469081--469449 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
469071 GATTTTCCAT
* ** *
469081 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
469101 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
469121 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
469141 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
469161 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
469181 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
469201 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
469221 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
469241 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
469261 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
469281 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
469301 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
469321 AATCGCAAC-AATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
469341 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
469361 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
469381 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
469401 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
469421 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
469441 AATCACAAC
1 AATCGCAAC
469450 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:470171 original size:24 final size:24
Alignment explanation
Indices: 470132--470178 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
470122 AAATTTGGTC
470132 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
470156 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
470179 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:470369 original size:12 final size:12
Alignment explanation
Indices: 470352--470376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
470342 ATATAATCCT
470352 GAAGAAGAAAAA
1 GAAGAAGAAAAA
470364 GAAGAAGAAAAA
1 GAAGAAGAAAAA
470376 G
1 G
470377 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:472673 original size:19 final size:19
Alignment explanation
Indices: 472651--472943 Score: 401
Period size: 19 Copynumber: 16.4 Consensus size: 19
472641 CGGAAAATAC
*
472651 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
472670 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
472684 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
472704 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
472718 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472737 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472756 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
472775 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
472789 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472808 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472827 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472846 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472865 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472884 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472903 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
472917 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
472936 AATCGCAA
1 AATCGCAA
472944 CGAGAGAATC
Statistics
Matches: 247, Mismatches: 6, Indels: 42
0.84 0.02 0.14
Matches are distributed among these distances:
14 40 0.16
15 2 0.01
16 11 0.04
17 10 0.04
18 3 0.01
19 168 0.68
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:472788 original size:71 final size:71
Alignment explanation
Indices: 472651--472910 Score: 404
Period size: 71 Copynumber: 3.6 Consensus size: 71
472641 CGGAAAATAC
* *
472651 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
472711 ACGAGAG
65 ACGAGAG
472718 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
472783 CGAGAG
66 CGAGAG
472789 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
472854 TGCGAAATGAA
66 --CG--A-GAG
472865 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
472911 CGAAAGAATC
Statistics
Matches: 180, Mismatches: 3, Indels: 11
0.93 0.02 0.06
Matches are distributed among these distances:
67 25 0.14
69 1 0.01
71 87 0.48
72 16 0.09
73 2 0.01
75 1 0.01
76 48 0.27
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGAG
Found at i:472922 original size:14 final size:14
Alignment explanation
Indices: 472903--472957 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
472893 GCGAAATGAA
472903 AATCGCAACGAAAG
1 AATCGCAACGAAAG
472917 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
472934 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
472950 AATCGCAA
1 AATCGCAA
472958 TGCGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:472981 original size:52 final size:55
Alignment explanation
Indices: 472651--472965 Score: 389
Period size: 52 Copynumber: 5.9 Consensus size: 55
472641 CGGAAAATAC
* *
472651 AATCGCAACGCGAAATGAAAATCCCAA-C--ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGC-GAAATGAA
*
472704 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
*
472756 AATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAA
472808 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
472865 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
*
472917 AATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAAT
472966 TATAAACGCA
Statistics
Matches: 238, Mismatches: 6, Indels: 39
0.84 0.02 0.14
Matches are distributed among these distances:
47 10 0.04
48 10 0.04
49 6 0.03
50 3 0.01
51 2 0.01
52 91 0.38
53 25 0.11
54 5 0.02
55 7 0.03
56 2 0.01
57 77 0.32
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAA
Found at i:473016 original size:19 final size:19
Alignment explanation
Indices: 472972--473068 Score: 134
Period size: 20 Copynumber: 5.4 Consensus size: 19
472962 AAATTATAAA
472972 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
472991 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
473011 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
473027 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
473044 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
473062 CGCATTG
1 CGCATTG
473069 TGATAGTCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
18 15 0.21
19 16 0.23
20 19 0.27
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:473195 original size:14 final size:14
Alignment explanation
Indices: 473178--473214 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
473168 CATCAATTAC
473178 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
473192 ACAAATCATCTTTT
1 ACAAATCAACTTTT
473206 ACAAATCAA
1 ACAAATCAA
473215 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:475172 original size:19 final size:19
Alignment explanation
Indices: 475132--475260 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
475122 TAGTTTACTT
* *
475132 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
475152 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
475171 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
475190 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
475204 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
475223 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
475237 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
475256 TCGCA
1 TCGCA
475261 TTGCAATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:475211 original size:33 final size:32
Alignment explanation
Indices: 475168--475260 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
475158 CGCGAAACCA
**
475168 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
475200 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
475233 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
475261 TTGCAATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:475258 original size:52 final size:52
Alignment explanation
Indices: 475132--475260 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
475122 TAGTTTACTT
**
475132 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
475184 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
475237 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
475261 TTGCAATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:475278 original size:19 final size:19
Alignment explanation
Indices: 475256--475374 Score: 105
Period size: 19 Copynumber: 6.8 Consensus size: 19
475246 GAAACCAAAA
*
475256 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
475275 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
475291 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
475308 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
475324 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
475341 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
*
475360 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
475375 AAGTTTCGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.14
16 15 0.18
17 15 0.18
19 42 0.50
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:475297 original size:14 final size:14
Alignment explanation
Indices: 475278--475334 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
475268 TTTCATTTCG
475278 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
475292 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
475309 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
475325 CGTTGCGATT
1 CGTTGCGATT
475335 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:475308 original size:33 final size:33
Alignment explanation
Indices: 475261--475353 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
475251 CAAAATCGCA
* *
475261 TTGCAATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
475294 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
475327 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
475354 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:475382 original size:20 final size:19
Alignment explanation
Indices: 475325--475390 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
475315 GCGATTCTGT
475325 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
475344 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
475363 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
475383 TGTTGCGA
1 CGTTGCGA
475391 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:475592 original size:92 final size:93
Alignment explanation
Indices: 475434--476087 Score: 1248
Period size: 92 Copynumber: 7.1 Consensus size: 93
475424 TTGAATGGAT
*
475434 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACATTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475499 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475527 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475591 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475619 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475683 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475711 -AATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475774 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475867 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475895 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
475959 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
475987 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
476051 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
476079 AAATTTACT
1 AAATTTACT
476088 AAGCAATCTA
Statistics
Matches: 555, Mismatches: 2, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
91 101 0.18
92 324 0.58
93 130 0.23
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:477811 original size:14 final size:14
Alignment explanation
Indices: 477792--477881 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
477782 TTGAAATGAA
477792 AATCGCAACGAGAG
1 AATCGCAACGAGAG
477806 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
477823 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
477839 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
477858 AATCGCATCGAGAG
1 AATCGCAACGAGAG
477872 AATCGCAACG
1 AATCGCAACG
477882 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:477829 original size:33 final size:33
Alignment explanation
Indices: 477784--477898 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
477774 TCTTTTGGTT
477784 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
477817 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
477850 GAAATGAAAATCGCATCGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
477883 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
477899 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:477830 original size:19 final size:18
Alignment explanation
Indices: 477791--477903 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
477781 GTTGAAATGA
477791 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
477806 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
477823 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
477839 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
477856 AAAATCGC-A-TCGAGA-G
1 -AAATCGCAACGCGAGATG
*
477872 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
477889 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
477904 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 15 0.19
17 12 0.16
18 1 0.01
19 26 0.34
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:477934 original size:14 final size:14
Alignment explanation
Indices: 477915--477969 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
477905 TTTGGTTTCG
477915 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
477929 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
477948 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
477962 CGTTGCGA
1 CGTTGCGA
477970 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:477947 original size:33 final size:33
Alignment explanation
Indices: 477899--477969 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
477889 AAAATCGCAA
**
477899 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
477932 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
477965 TGCGA
1 TGCGA
477970 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:477977 original size:33 final size:33
Alignment explanation
Indices: 477910--477991 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
477900 GCGATTTTGG
***
477910 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
477943 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
477976 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
477992 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:477996 original size:20 final size:20
Alignment explanation
Indices: 477922--478010 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
477912 TCGCGTTGCG
477922 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
477942 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
477955 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
477975 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
477995 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
478011 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:478132 original size:33 final size:33
Alignment explanation
Indices: 478090--478160 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
478080 AATACTAACT
*
478090 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
478123 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
478156 TGAAA
1 TGAAA
478161 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:478567 original size:20 final size:20
Alignment explanation
Indices: 478542--478734 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
478532 CTTTAAATAT
478542 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
478562 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
478584 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
478603 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
478623 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
478643 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
478663 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
478683 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
478703 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
478723 CGCGTTGCGATT
1 CGCGTTGCGATT
478735 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:478729 original size:60 final size:60
Alignment explanation
Indices: 478542--478734 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
478532 CTTTAAATAT
**
478542 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
478603 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
478663 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
478723 CGCGTTGCGATT
1 CGCGTTGCGATT
478735 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:478815 original size:20 final size:20
Alignment explanation
Indices: 478790--478841 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
478780 AAGAATCGCG
*
478790 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
478810 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
478830 TTGCGATTCTGG
1 TTGCGATTCTGG
478842 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:480792 original size:93 final size:93
Alignment explanation
Indices: 480633--480825 Score: 368
Period size: 93 Copynumber: 2.1 Consensus size: 93
480623 ATTAAAAGTT
*
480633 TAAAACGGATCAAAACGGATAGTTTAGGTATCAAATGCATAATTTACCCTATAATTAAACAATCA
1 TAAAACGGATCAAAACGGATAGTTTAGGTATCAAATGCACAATTTACCCTATAATTAAACAATCA
480698 AAACTTAGAAGTCATGGCTCTTCTCACA
66 AAACTTAGAAGTCATGGCTCTTCTCACA
480726 TAAAACGGATCAAAACGGATAGTTTAGGTATCAAATGCACAATTTACCCTATAATTAAACAATCA
1 TAAAACGGATCAAAACGGATAGTTTAGGTATCAAATGCACAATTTACCCTATAATTAAACAATCA
480791 AAACTTAGAAGTCATGGCTCTTCTCACA
66 AAACTTAGAAGTCATGGCTCTTCTCACA
*
480819 TATAACG
1 TAAAACG
480826 TGTACGGTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (93 bp):
TAAAACGGATCAAAACGGATAGTTTAGGTATCAAATGCACAATTTACCCTATAATTAAACAATCA
AAACTTAGAAGTCATGGCTCTTCTCACA
Found at i:486821 original size:5 final size:5
Alignment explanation
Indices: 486811--487154 Score: 634
Period size: 5 Copynumber: 68.8 Consensus size: 5
486801 TTCGGATATC
* * * * * *
486811 AACAT AACAT AACAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
486861 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
486911 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
486961 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
487011 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
487061 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
487111 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACA
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACA
487155 GACAAACATA
Statistics
Matches: 337, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 337 1.00
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (5 bp):
AACAT
Found at i:502511 original size:23 final size:21
Alignment explanation
Indices: 502457--502538 Score: 80
Period size: 20 Copynumber: 3.9 Consensus size: 21
502447 TTTTGGTGCA
502457 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
* **
502477 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
502498 GAAGGGGAATCGATTCCCCCACA-
1 G-A-GGGAATCGATTCCCCC-CAT
*
502521 G-GGGAATCGATACCCCCC
1 GAGGGAATCGATTCCCCCC
502539 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 25 0.49
21 8 0.16
22 1 0.02
23 16 0.31
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:508402 original size:17 final size:17
Alignment explanation
Indices: 508359--508410 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
508349 TATAAAGTAG
*
508359 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
508376 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
508391 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
508408 AAA
1 AAA
508411 TTTGTCTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:514436 original size:78 final size:80
Alignment explanation
Indices: 514303--514449 Score: 219
Period size: 78 Copynumber: 1.9 Consensus size: 80
514293 CTTCGAATAG
* *
514303 TCGAGGGACTCAACAAAGTATCACACCCTTATAGTCAAGCGGCCGTTTATATACTTTACCCTGAT
1 TCGAGGGACTCAACAAAGTAT-ACACCCTTATAGTCAAGCGACCGTTTATATACTTTACCCTAAT
514368 ATAAATTAGTTTTTTT
65 ATAAATTAGTTTTTTT
* *
514384 TCGAGGGACTCAACAAAGTAT-TACCC-TATAGTCGATG-GACCGTTTATATACTTTACCCTAAT
1 TCGAGGGACTCAACAAAGTATACACCCTTATAGTC-AAGCGACCGTTTATATACTTTACCCTAAT
514446 ATAA
65 ATAA
514450 CTTAAGATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
78 34 0.56
79 6 0.10
81 21 0.34
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (80 bp):
TCGAGGGACTCAACAAAGTATACACCCTTATAGTCAAGCGACCGTTTATATACTTTACCCTAATA
TAAATTAGTTTTTTT
Found at i:516060 original size:6 final size:7
Alignment explanation
Indices: 516043--516068 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
516033 TCTTTGTTAC
516043 TTTTTTA
1 TTTTTTA
516050 TTTTTTA
1 TTTTTTA
516057 TTTTTTA
1 TTTTTTA
516064 TTTTT
1 TTTTT
516069 GTAAGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:516647 original size:13 final size:13
Alignment explanation
Indices: 516625--516687 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
516615 TAGTACTTAC
*
516625 TATAACAAATAAT
1 TATAATAAATAAT
516638 TATAATAAATAACT
1 TATAATAAATAA-T
*
516652 GTCA-AAAAAATAAT
1 -T-ATAATAAATAAT
*
516666 TATAATAAATAAAA
1 TATAATAAAT-AAT
516680 TATAATAA
1 TATAATAA
516688 TACCCTAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.02
13 18 0.44
14 12 0.29
15 9 0.22
16 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (13 bp):
TATAATAAATAAT
Found at i:516720 original size:21 final size:21
Alignment explanation
Indices: 516696--516735 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
516686 AATACCCTAG
*
516696 ATCATAAACTCTAAGCCTTAA
1 ATCATAAACTCTAAACCTTAA
516717 ATCATAAACTCTAAACCTT
1 ATCATAAACTCTAAACCTT
516736 GAACCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (21 bp):
ATCATAAACTCTAAACCTTAA
Found at i:517178 original size:2 final size:2
Alignment explanation
Indices: 517171--517209 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
517161 TGACTCAAAA
517171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
517210 GATAAAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:517302 original size:2 final size:2
Alignment explanation
Indices: 517295--517319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
517285 ATATAATTGA
517295 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 A
517320 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:518365 original size:16 final size:16
Alignment explanation
Indices: 518340--518383 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
518330 AAACAGTTTT
518340 AAATAGTTAAATGATA
1 AAATAGTTAAATGATA
*
518356 AAATATTTAAATGATA
1 AAATAGTTAAATGATA
518372 AAATAGTTAAAT
1 AAATAGTTAAAT
518384 AGAGGATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AAATAGTTAAATGATA
Found at i:523291 original size:60 final size:60
Alignment explanation
Indices: 523197--523357 Score: 173
Period size: 60 Copynumber: 2.7 Consensus size: 60
523187 GATGAATTTG
* ** **
523197 GGGATAAAGTTAGAATATTCAAAAGTTTGGGGACTAATTTAGAAAT-A-GGGTCATAGTTTA
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAG-AATGAGGGGT-ATAGTTTA
* * *
523257 GGGATAAAATTAGAATGCACAAAAGTTTAAGGACTAGTTTAGAATGAGGGGTATAGTTTG
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAGAATGAGGGGTATAGTTTA
** * * *
523317 GGGATAAAATTAGAATATGCAGAAGTTAAAGGACCAATTTA
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTA
523358 ATATGACAGT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
59 3 0.04
60 77 0.92
61 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (60 bp):
GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAGAATGAGGGGTATAGTTTA
Found at i:525340 original size:2 final size:2
Alignment explanation
Indices: 525333--525360 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
525323 CAACCACTAT
525333 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
525361 ACACTGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:526701 original size:36 final size:36
Alignment explanation
Indices: 526654--526729 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
526644 TGAAAGCATT
*
526654 TTTAATCATTCATAACTAAACTCTATCAATTCAATA
1 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
526690 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
1 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
526726 TTTA
1 TTTA
526730 TTCTTCTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (36 bp):
TTTAATCATTCATAACTAAACCCTATCAATTCAATA
Found at i:531557 original size:12 final size:12
Alignment explanation
Indices: 531540--531605 Score: 105
Period size: 12 Copynumber: 5.5 Consensus size: 12
531530 CAGTTGTTGG
531540 TGCCAATGTCGA
1 TGCCAATGTCGA
*
531552 TGCCAATGTCGG
1 TGCCAATGTCGA
*
531564 TGCAAATGTCGA
1 TGCCAATGTCGA
*
531576 TGCCAATGTCGG
1 TGCCAATGTCGA
531588 TGCCAATGTCGA
1 TGCCAATGTCGA
531600 TGCCAA
1 TGCCAA
531606 AGATGACGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (12 bp):
TGCCAATGTCGA
Found at i:531571 original size:24 final size:24
Alignment explanation
Indices: 531538--531605 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
531528 TGCAGTTGTT
531538 GGTGCCAATGTCGATGCCAATGTC
1 GGTGCCAATGTCGATGCCAATGTC
*
531562 GGTGCAAATGTCGATGCCAATGTC
1 GGTGCCAATGTCGATGCCAATGTC
531586 GGTGCCAATGTCGATGCCAA
1 GGTGCCAATGTCGATGCCAA
531606 AGATGACGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (24 bp):
GGTGCCAATGTCGATGCCAATGTC
Found at i:532699 original size:42 final size:42
Alignment explanation
Indices: 532650--532770 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 42
532640 ATTATATATA
532650 TATATATATATATATATAATATTTTATAA---TT-T-TT-A-
1 TATATATATATATATATAATATTTTATAATTTTTATATTAAT
532685 TAT-TA-AT-TATATATAATATTTTAT-ATTTTTATATTAAT
1 TATATATATATATATATAATATTTTATAATTTTTATATTAAT
*
532723 TATATATATAATATATATAATA-TTTATATTTTTTATATTAAT
1 TATATATAT-ATATATATAATATTTTATAATTTTTATATTAAT
532765 TATATA
1 TATATA
532771 ATAAAAACCC
Statistics
Matches: 73, Mismatches: 1, Indels: 17
0.80 0.01 0.19
Matches are distributed among these distances:
31 1 0.01
32 17 0.23
33 2 0.03
34 4 0.05
35 4 0.05
36 2 0.03
37 1 0.01
38 3 0.04
39 2 0.03
40 2 0.03
41 5 0.07
42 30 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (42 bp):
TATATATATATATATATAATATTTTATAATTTTTATATTAAT
Found at i:532770 original size:2 final size:2
Alignment explanation
Indices: 532642--532751 Score: 66
Period size: 2 Copynumber: 61.5 Consensus size: 2
532632 CCTCCCCGAT
* *
532642 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
532681 TT TA TA T- TA -A T- TA TA TA TA -A TA T- TT TA TA TT TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
532718 T- TA -A T- TA TA TA TA TA -A TA TA TA TA -A TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
532752 TTTTTATATT
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
1 13 0.15
2 74 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:533191 original size:25 final size:25
Alignment explanation
Indices: 533142--533191 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
533132 GCTTGGTTTT
**
533142 TTCTCAGGATCGGGTCGGGTTCGGG
1 TTCTCAGGATCGGGTCGGGGACGGG
*
533167 TTCTCGGGATCGGGTCGGGGACGGG
1 TTCTCAGGATCGGGTCGGGGACGGG
533192 ACAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.20, G:0.48, T:0.24
Consensus pattern (25 bp):
TTCTCAGGATCGGGTCGGGGACGGG
Found at i:536955 original size:19 final size:19
Alignment explanation
Indices: 536933--536976 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
536923 AAGATGGATG
536933 GTGGGTATCAAGTTGGGTA
1 GTGGGTATCAAGTTGGGTA
536952 GTGGGTATCAAGTTGGGTA
1 GTGGGTATCAAGTTGGGTA
536971 GTGGGT
1 GTGGGT
536977 GTGAGGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.18, C:0.05, G:0.45, T:0.32
Consensus pattern (19 bp):
GTGGGTATCAAGTTGGGTA
Found at i:538133 original size:21 final size:20
Alignment explanation
Indices: 538080--538135 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
538070 GAATCGGCTG
*
538080 CCGGCCCTGCAGCATCCGCTA
1 CCGG-CCTGCAGCATCCACTA
*
538101 CCGGCGCAGCAGCATCCACTA
1 CCGGC-CTGCAGCATCCACTA
538122 CCGGTCCTGCAGCA
1 CCGG-CCTGCAGCA
538136 ACCTTCAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.12
Consensus pattern (20 bp):
CCGGCCTGCAGCATCCACTA
Found at i:540167 original size:14 final size:15
Alignment explanation
Indices: 540139--540172 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
540129 CGGTTCGGTT
540139 CGGTTTGGCTTTAAA
1 CGGTTTGGCTTTAAA
540154 CGGTTTGG-TTTAAA
1 CGGTTTGGCTTTAAA
540168 -GGTTT
1 CGGTTT
540173 CATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 6 0.32
15 8 0.42
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (15 bp):
CGGTTTGGCTTTAAA
Found at i:542795 original size:17 final size:16
Alignment explanation
Indices: 542773--542838 Score: 73
Period size: 15 Copynumber: 4.1 Consensus size: 16
542763 CCGTGTCCCG
542773 ACCCGGATATTACGGGT
1 ACCCGGATATT-CGGGT
*
542790 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
542805 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
542822 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
542837 AC
1 AC
542839 TTGATACACG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
15 18 0.43
16 7 0.17
17 17 0.40
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.23
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:542821 original size:32 final size:32
Alignment explanation
Indices: 542773--542838 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
542763 CCGTGTCCCG
542773 ACCCGGATATTACGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
* *
542805 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
542837 AC
1 AC
542839 TTGATACACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.23
Consensus pattern (32 bp):
ACCCGGATATTACGGGTACCCGGTAATCGGGT
Found at i:544299 original size:28 final size:29
Alignment explanation
Indices: 544212--544316 Score: 140
Period size: 31 Copynumber: 3.6 Consensus size: 29
544202 CTTTTTCATT
544212 TAAGTACCTAAACTATTTTTTGGTCAAAA
1 TAAGTACCTAAACTATTTTTTGGTCAAAA
*
544241 TAAGTACCTAAAGTTATCTTTTTGGTCAAAA
1 TAAGTACCTAAA-CTAT-TTTTTGGTCAAAA
* *
544272 TAAGTACCTAAAATATTTTAT-GTCAAAA
1 TAAGTACCTAAACTATTTTTTGGTCAAAA
* *
544300 TAGGTGCCTAAACTATT
1 TAAGTACCTAAACTATT
544317 CAAACTTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
28 21 0.31
29 16 0.24
30 6 0.09
31 25 0.37
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (29 bp):
TAAGTACCTAAACTATTTTTTGGTCAAAA
Found at i:548870 original size:24 final size:22
Alignment explanation
Indices: 548819--548870 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
548809 TAACTAACCT
*
548819 TAAAATTTATAGAAATTGACTA
1 TAAAATTTATAGAAATTAACTA
548841 TAAAATTTATAGAAATTAACTCTA
1 TAAAATTTATAGAAATTAA--CTA
548865 TAAAAT
1 TAAAAT
548871 CAGATCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 18 0.67
24 9 0.33
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (22 bp):
TAAAATTTATAGAAATTAACTA
Found at i:550209 original size:24 final size:24
Alignment explanation
Indices: 550182--550238 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
550172 TAGCATGTTT
550182 AAAAATAAAACTT-AAAATAAAATA
1 AAAAATAAAACTTGAAAAT-AAATA
**
550206 AAAACGAAAACTTGAAAATAAATA
1 AAAAATAAAACTTGAAAATAAATA
550230 AAAGAATAA
1 AAA-AATAA
550239 CTTTATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (24 bp):
AAAAATAAAACTTGAAAATAAATA
Found at i:550509 original size:26 final size:26
Alignment explanation
Indices: 550456--550531 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
550446 CAAAAGGTGC
* *
550456 TGACTAGATCTTCTAGAAAACTGCTGT
1 TGACTGGACCTTCTAG-AAACTGCTGT
550483 TGACTGGACCTTCTAGAAACTGCTGT
1 TGACTGGACCTTCTAGAAACTGCTGT
*
550509 TGATTGGACCTTCTAGAAACTGC
1 TGACTGGACCTTCTAGAAACTGC
550532 CACGTCAGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 32 0.70
27 14 0.30
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (26 bp):
TGACTGGACCTTCTAGAAACTGCTGT
Found at i:557326 original size:16 final size:16
Alignment explanation
Indices: 557305--557335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
557295 TTCTGAAAAA
557305 ATTAAAAAAAATAAAT
1 ATTAAAAAAAATAAAT
*
557321 ATTAAAATAAATAAA
1 ATTAAAAAAAATAAA
557336 AAATGATAGT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAAAAAATAAAT
Found at i:557547 original size:46 final size:46
Alignment explanation
Indices: 557481--557586 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
557471 TTAGGATTTG
* **
557481 GAGAGAGAGAGAGAGAAGCAGCATTTAAAGCATTACATAGGGGCTA
1 GAGAGAGAGAGAGAAAAGCAGCATGCAAAGCATTACATAGGGGCTA
557527 GAGAGAGAGAGAGAAAAGCAGCATGCAAAGCATTACATAGGGGCTA
1 GAGAGAGAGAGAGAAAAGCAGCATGCAAAGCATTACATAGGGGCTA
557573 GAGAGAGGAGAGAG
1 GAGAGA-GAGAGAG
557587 GGACTGCAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 49 0.88
47 7 0.12
ACGTcount: A:0.42, C:0.10, G:0.36, T:0.11
Consensus pattern (46 bp):
GAGAGAGAGAGAGAAAAGCAGCATGCAAAGCATTACATAGGGGCTA
Done.