Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 117 of 190
Found at i:18352391 original size:127 final size:125
Alignment explanation
Indices: 18352175--18352503 Score: 331
Period size: 127 Copynumber: 2.6 Consensus size: 125
18352165 TCATAAAACT
* * ** * **
18352175 TTTGAATGCTCCTACAATCAGTGGCCATGAAACTT-TGAATTTAAAAAGGTTCACCTGGAGGTCT
1 TTTGAATGCTCCTACAATTAGAGGCCATGAAACTTAAAAATTTAAAAAAGTTCACCCAGAGGTCT
* * * * * *** * * * *
18352239 TGAAGATTGTGCCCGGAGGTTTTAAAGATTATGCTTGGAGGTTTTAGGAATTTCAAAATC
66 TGAAAATTATGCCCGAAGGTCTTAAAGATTATACCCAGAGGTCTTAGAAATCTCAAAATA
* *
18352299 TTTGAATGCTCCTCCGATTAGAGGCCATGAAACATTAAAAATTTTAAAAAAGTTCACCCAGA-GT
1 TTTGAATGCTCCTACAATTAGAGGCCATGAAAC-TTAAAAA-TTTAAAAAAGTTCACCCAGAGGT
*
18352363 CCTTGAAAATTATGCCCGAAGGTCTTAAAGATTATACCCAGAGGTCTTATAAATCTCAAAATA
64 -CTTGAAAATTATGCCCGAAGGTCTTAAAGATTATACCCAGAGGTCTTAGAAATCTCAAAATA
* * * * * *
18352426 TTTGAATGCTCATTCAATTAGAAGCCATGAAACTTTAAAAATTT-AAAATGTTTTACCCGGAGGT
1 TTTGAATGCTCCTACAATTAGAGGCCATGAAAC-TTAAAAATTTAAAAAAG-TTCACCCAGAGGT
*
18352490 CTTAAAAATTATGC
64 CTTGAAAATTATGC
18352504 TTGGAGGTCC
Statistics
Matches: 168, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
124 29 0.17
125 7 0.04
126 28 0.17
127 104 0.62
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (125 bp):
TTTGAATGCTCCTACAATTAGAGGCCATGAAACTTAAAAATTTAAAAAAGTTCACCCAGAGGTCT
TGAAAATTATGCCCGAAGGTCTTAAAGATTATACCCAGAGGTCTTAGAAATCTCAAAATA
Found at i:18352697 original size:104 final size:103
Alignment explanation
Indices: 18352403--18352707 Score: 382
Period size: 103 Copynumber: 2.9 Consensus size: 103
18352393 ATTATACCCA
* * * * *
18352403 GAGGTCTTATAAATCTCAAAATATTTGAATGCTCATTCAATTAGAA-GCCATGAAACTTTAAAAA
1 GAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAA-TA-AAGGCCATGAAACTTTAAAAA
* *
18352467 TTTAAAATGTTTTACCCGGAGGTCTTAAAAATTATGCTTG
64 TTTAAAATGTTTTACCCAGAGGTCTTGAAAATTATGCTTG
* *
18352507 GAGGTCCTACAAATCTT-AAATCTTTGAATGCTCCTCCAATAAGAGGCCATAAAACTTTAAAAAT
1 GAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAATAA-AGGCCATGAAACTTTAAAAAT
* *
18352571 TTAAATTGTTTTGCCCAGAGGTCTTGAAAATTATGCTTG
65 TTAAAATGTTTTACCCAGAGGTCTTGAAAATTATGCTTG
* *
18352610 GAGGTCTTA-AAGATTTTAAAATCTTTGAATGCTCCTCCAATCAAAGGCCGTGAAACTTTAAAAA
1 GAGGTCTTACAA-ATCTTAAAATCTTTGAATGCTCCTCCAAT-AAAGGCCATGAAACTTTAAAAA
* * * * *
18352674 TTAAAAAAGGTTCACCCAAAGGTCTTGAAAATTA
64 TTTAAAATGTTTTACCCAGAGGTCTTGAAAATTA
18352708 GGCCCAGAGG
Statistics
Matches: 174, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
101 1 0.01
102 5 0.03
103 84 0.48
104 82 0.47
105 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (103 bp):
GAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAATAAAGGCCATGAAACTTTAAAAATT
TAAAATGTTTTACCCAGAGGTCTTGAAAATTATGCTTG
Found at i:18352713 original size:22 final size:22
Alignment explanation
Indices: 18352688--18352729 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18352678 AAAAGGTTCA
18352688 CCCAAAGGTCTTGAAA-ATTAGG
1 CCCAAAGGTCTT-AAAGATTAGG
*
18352710 CCCAGAGGTCTTAAAGATTA
1 CCCAAAGGTCTTAAAGATTA
18352730 TACCTAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (22 bp):
CCCAAAGGTCTTAAAGATTAGG
Found at i:18352728 original size:104 final size:103
Alignment explanation
Indices: 18352381--18352722 Score: 359
Period size: 104 Copynumber: 3.3 Consensus size: 103
18352371 ATTATGCCCG
* * * * * *
18352381 AAGGTCTT-AAAGATTATACCCAGAGGTCTTATAAATCTCAAAATATTTGAATGCTCATTCAATT
1 AAGGTCTTGAAA-ATTATGCCCAGAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAA-T
*
18352445 AGAA-GCCATGAAACTTTAAAAATTTAAAATGTTTTACCCG
64 A-AAGGCCATGAAACTTTAAAAATTTAAAATGTTTTACCCA
* * *** *
18352485 GAGGTCTTAAAAATTATGCTTGGAGGTCCTACAAATCTT-AAATCTTTGAATGCTCCTCCAATAA
1 AAGGTCTTGAAAATTATGCCCAGAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAATAA
* * *
18352549 GAGGCCATAAAACTTTAAAAATTTAAATTGTTTTGCCCA
66 -AGGCCATGAAACTTTAAAAATTTAAAATGTTTTACCCA
* *** *
18352588 GAGGTCTTGAAAATTATGCTTGGAGGTCTTA-AAGATTTTAAAATCTTTGAATGCTCCTCCAATC
1 AAGGTCTTGAAAATTATGCCCAGAGGTCTTACAA-ATCTTAAAATCTTTGAATGCTCCTCCAAT-
* * * * *
18352652 AAAGGCCGTGAAACTTTAAAAATTAAAAAAGGTTCACCCA
64 AAAGGCCATGAAACTTTAAAAATTTAAAATGTTTTACCCA
*
18352692 AAGGTCTTGAAAATTAGGCCCAGAGGTCTTA
1 AAGGTCTTGAAAATTATGCCCAGAGGTCTTA
18352723 AAGATTATAC
Statistics
Matches: 201, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
101 1 0.00
102 5 0.02
103 84 0.42
104 106 0.53
105 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (103 bp):
AAGGTCTTGAAAATTATGCCCAGAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCCAATAA
AGGCCATGAAACTTTAAAAATTTAAAATGTTTTACCCA
Found at i:18352808 original size:126 final size:125
Alignment explanation
Indices: 18352583--18352965 Score: 478
Period size: 126 Copynumber: 3.1 Consensus size: 125
18352573 AAATTGTTTT
* * * *
18352583 GCCCAGAGGTCTTGAAAATTATGCTTGGAGGTCTTA-AAGATTTTAAAATCTTTGAATGCTCCTC
1 GCCCAGAGGTCTTGAAAATTATGCCTAGAGGTCTTACAA-ATCTCAAAATCTTTGAATGCTCCTC
* * * * *
18352647 CAATCAAAGGCCGTGAAACTTTAAAAATTAAAAAAGGTTCACCCAAAGGTCTTGAAAATTA
65 CAATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACTCAAAGGTCTTGAAAATTA
*
18352708 GGCCCAGAGGTCTT-AAAGATTATACCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCT
1 -GCCCAGAGGTCTTGAAA-ATTATGCCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCT
* *
18352772 CCAATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCGCTCGAAGGTCTTGAAAATT-
64 CCAATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACTCAAAGGTCTTGAAAATTA
* * *
18352833 -----G-TGTCTTGAAAATTAGGCCTAGAGGTCTTACAAATCTCAAAATCTTTGAATACTCCTCC
1 GCCCAGAGGTCTTGAAAATTATGCCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCC
* * * *
18352892 AATTAGAGGCCATGAAACTTTAAAATTTTAAAAAAGTTCACTTAAAGGTCTTAAAAATTA
66 AATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACTCAAAGGTCTTGAAAATTA
* *
18352952 TGCTCGGAGGTCTT
1 -GCCCAGAGGTCTT
18352966 AGAGATTTTA
Statistics
Matches: 223, Mismatches: 23, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
118 103 0.46
119 4 0.02
125 4 0.02
126 110 0.49
127 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (125 bp):
GCCCAGAGGTCTTGAAAATTATGCCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCC
AATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACTCAAAGGTCTTGAAAATTA
Found at i:18352868 original size:118 final size:114
Alignment explanation
Indices: 18352717--18353154 Score: 407
Period size: 118 Copynumber: 3.8 Consensus size: 114
18352707 AGGCCCAGAG
*
18352717 GTCTTAAAGATTATAC-CTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATTAGA
1 GTCTTAAA-ATTATGCTC-AGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATTAGA
18352781 GGCCATGAAACTTTAAAAATTTAAAAAGGTTCGCTCGAAGGTCTTGAAAATTGT
64 GGCCATGAAACTTTAAAAATTTAAAAAGGTT--CTCGAA-GTCTTGAAAATTGT
* *
18352835 GTCTTGAAAATTAGGC-CTAGAGGTCTTACAAATCTCAAAATCTTTGAATACTCCTCCAATTAGA
1 GTCTT-AAAATTATGCTC-AGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATTAGA
* *
18352899 GGCCATGAAACTTTAAAATTTTAAAAAAG-T-TC--A--CTT--AAA--G-
64 GGCCATGAAACTTTAAAAATTTAAAAAGGTTCTCGAAGTCTTGAAAATTGT
* * * * * * *
18352939 GTCTTAAAAATTATGCTCGGAGGTCTTAGAGATTTTAAAATCTTTGAATGCTCCTCCAATAAAAG
1 GTCTT-AAAATTATGCTCAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATTAGAG
* * * * *
18353004 GGCATGAAACTTTAAAAATTTAAAATGTTTTACCCAGAAGTATTGAAAATTATGCCT
65 GCCATGAAACTTTAAAAATTTAAAAAG-GTT-CTC-GAAGTCTTGAAAA-T-TG--T
* * * * *
18353061 GAAAGTCTTAGAGATTATGCTCGGAGGTCTTACAAATCTCAAAATCTTTTAATGCTCCTCAAATC
1 ----GTCTTA-AAATTATGCTCAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATT
18353126 AGAGGCCATGAAACTTTAAAAATTTAAAA
61 AGAGGCCATGAAACTTTAAAAATTTAAAA
18353155 TGTTTTACTC
Statistics
Matches: 263, Mismatches: 32, Indels: 42
0.78 0.09 0.12
Matches are distributed among these distances:
104 76 0.29
105 2 0.01
106 1 0.00
107 3 0.01
108 1 0.00
109 3 0.01
111 1 0.00
112 1 0.00
113 2 0.01
114 2 0.01
115 3 0.01
117 1 0.00
118 84 0.32
119 4 0.02
125 1 0.00
126 78 0.30
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (114 bp):
GTCTTAAAATTATGCTCAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATTAGAGG
CCATGAAACTTTAAAAATTTAAAAAGGTTCTCGAAGTCTTGAAAATTGT
Found at i:18352893 original size:348 final size:332
Alignment explanation
Indices: 18352248--18353154 Score: 1041
Period size: 348 Copynumber: 2.7 Consensus size: 332
18352238 TTGAAGATTG
* * * * * *
18352248 TGCCCGGAGGTTTTAAAGATTATGCTTGGAGGT-TTTAGGAATTTCAAAATCTTTGAATGCTCCT
1 TGCCCAGAGGTCTTAAAAATTATGCTTGGAGGTCTTAAAG-ATTTTAAAATCTTTGAATGCTCCT
* * * * *
18352312 CCGATTAGAGGCCATGAAACATTAAAAATTTTAAAAAA-GTTCACCCAGAGTCCTTGAAAATTAT
65 CCAATAAAAGGCCATGAAACTTTAAAAA--TTAAAAAAGGTTCACCCAAAGT-CTTGAAAATTAT
* * * * *
18352376 GCCCGAAGGTCTTAAAGATTATACCCAGAGGTCTTATAAATCTCAAAATATTTGAATGCTCATTC
127 GCCCGAAGGTCTTAAAGATTATACCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCC
* * * * *
18352441 AATTAGAAGCCATGAAACTTTAAAAATTTAAAATGTTTTACCCGGAGGTCTTAAAAATTATGCTT
192 AATTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACCCGAAGGTCTTAAAAATTATGCTT
* *
18352506 GGAGGTCCTACAAATCTTAAATCTTTGAATGCTCCTCCAATAAGAGGCCATAAAACTTTAAAAAT
257 GGAGGTCCTACAAATCTAAAATCTTTGAATACTCCTCCAATAAGAGGCCATAAAACTTTAAAAAT
**
18352571 TT-AAATTGTTT
322 TTAAAAAAG-TT
*
18352582 TGCCCAGAGGTCTTGAAAATTATGCTTGGAGGTCTTAAAGATTTTAAAATCTTTGAATGCTCCTC
1 TGCCCAGAGGTCTTAAAAATTATGCTTGGAGGTCTTAAAGATTTTAAAATCTTTGAATGCTCCTC
* * *
18352647 CAATCAAAGGCCGTGAAACTTTAAAAATTAAAAAAGGTTCACCCAAAGGTCTTGAAAATTAGGCC
66 CAATAAAAGGCCATGAAACTTTAAAAATTAAAAAAGGTTCACCCAAA-GTCTTGAAAATTATGCC
18352712 C-AGAGGTCTTAAAGATTATACCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAA
130 CGA-AGGTCTTAAAGATTATACCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAA
* * * *
18352776 TTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCGCTCGAAGGTCTTGAAAATTGTGTCTTG
194 TTAGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACCCGAAGGTCTTAAAAATTATG-C---
* * *
18352841 AAAATTAGGCCTAGAGGTCTTACAAATCTCAAAATCTTTGAATACTCCTCCAATTAGAGGCCATG
255 ----TT--G----GAGGTCCTACAAATCT-AAAATCTTTGAATACTCCTCCAATAAGAGGCCATA
*
18352906 AAACTTTAAAATTTTAAAAAAGTT
309 AAACTTTAAAAATTTAAAAAAGTT
** ** * * *
18352930 CACTTAAAGGTCTTAAAAATTATGCTCGGAGGTCTTAGAGATTTTAAAATCTTTGAATGCTCCTC
1 TGCCCAGAGGTCTTAAAAATTATGCTTGGAGGTCTTAAAGATTTTAAAATCTTTGAATGCTCCTC
* * * * * *
18352995 CAATAAAAGGGCATGAAACTTTAAAAATTTAAAATGTTTTACCCAGAAGTATTGAAAATTATGCC
66 CAATAAAAGGCCATGAAACTTTAAAAATTAAAAAAGGTTCACCCA-AAGTCTTGAAAATTATGCC
* * * * * * *
18353060 TGAAAGTCTTAGAGATTAT-GCTCGGAGGTCTTACAAATCTCAAAATCTTTTAATGCTCCTCAAA
130 CGAAGGTCTTAAAGATTATACCT-AGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAA
*
18353124 TCAGAGGCCATGAAACTTTAAAAATTTAAAA
194 TTAGAGGCCATGAAACTTTAAAAATTTAAAA
18353155 TGTTTTACTC
Statistics
Matches: 489, Mismatches: 61, Indels: 32
0.84 0.10 0.05
Matches are distributed among these distances:
332 9 0.02
333 132 0.27
334 78 0.16
335 4 0.01
341 2 0.00
343 1 0.00
347 17 0.03
348 239 0.49
349 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (332 bp):
TGCCCAGAGGTCTTAAAAATTATGCTTGGAGGTCTTAAAGATTTTAAAATCTTTGAATGCTCCTC
CAATAAAAGGCCATGAAACTTTAAAAATTAAAAAAGGTTCACCCAAAGTCTTGAAAATTATGCCC
GAAGGTCTTAAAGATTATACCTAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTCCAATT
AGAGGCCATGAAACTTTAAAAATTTAAAAAGGTTCACCCGAAGGTCTTAAAAATTATGCTTGGAG
GTCCTACAAATCTAAAATCTTTGAATACTCCTCCAATAAGAGGCCATAAAACTTTAAAAATTTAA
AAAAGTT
Found at i:18353053 original size:104 final size:104
Alignment explanation
Indices: 18352871--18353076 Score: 247
Period size: 104 Copynumber: 2.0 Consensus size: 104
18352861 TACAAATCTC
* * * **
18352871 AAAATCTTTGAATACTCCTCCAATTAGAGGCCATGAAACTTTAAAATTTTAAAAAAGTTCACTTA
1 AAAATCTTTGAATACTCCTCCAATAAAAGGCCATGAAACTTTAAAAATTTAAAAAAGTTCACCCA
* * *
18352936 AAGGTCTTAAAAATTATG-CTCGGAGGTCTTAGAGATTTT
66 AAGGTATTAAAAATTATGCCT-GAAAGTCTTAGAGATTTT
* * * *
18352975 AAAATCTTTGAATGCTCCTCCAATAAAAGGGCATGAAACTTTAAAAATTT-AAAATGTTTTACCC
1 AAAATCTTTGAATACTCCTCCAATAAAAGGCCATGAAACTTTAAAAATTTAAAAAAG-TTCACCC
*
18353039 AGAA-GTATTGAAAATTATGCCTGAAAGTCTTAGAGATT
65 A-AAGGTATTAAAAATTATGCCTGAAAGTCTTAGAGATT
18353077 ATGCTCGGAG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
103 5 0.06
104 77 0.90
105 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (104 bp):
AAAATCTTTGAATACTCCTCCAATAAAAGGCCATGAAACTTTAAAAATTTAAAAAAGTTCACCCA
AAGGTATTAAAAATTATGCCTGAAAGTCTTAGAGATTTT
Found at i:18353214 original size:82 final size:84
Alignment explanation
Indices: 18353080--18353244 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 84
18353070 AGAGATTATG
* * * * * *
18353080 CTCGGAGGTCTTACAAATCTCAAAATCTTTTAATGCTCCTCAAATCAGAGGCCATGAAACT-T-T
1 CTCGAAGGTATTACAAATCTCAAAATCTTTGAATACTCCTCAAATCAAAGGCCATGAAACTATAA
*
18353143 AAAAATTTAAAATGTTTTA
66 AAAAATTAAAAATGTTTTA
* * *
18353162 CTCGAAGGTATTACAGATTTCAAAATCTTTGAATACTCCTCCAATCAAAGGCCATGAAACTATAA
1 CTCGAAGGTATTACAAATCTCAAAATCTTTGAATACTCCTCAAATCAAAGGCCATGAAACTATAA
18353227 AAAAATTAAAAATGTTTT
66 AAAAATTAAAAATGTTTT
18353245 TCCCTAAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 53 0.75
83 1 0.01
84 17 0.24
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (84 bp):
CTCGAAGGTATTACAAATCTCAAAATCTTTGAATACTCCTCAAATCAAAGGCCATGAAACTATAA
AAAAATTAAAAATGTTTTA
Found at i:18353911 original size:15 final size:15
Alignment explanation
Indices: 18353891--18353920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18353881 TATCTTTCTT
*
18353891 GTGATGCAGATGCAA
1 GTGATGCAAATGCAA
18353906 GTGATGCAAATGCAA
1 GTGATGCAAATGCAA
18353921 ATATCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (15 bp):
GTGATGCAAATGCAA
Found at i:18353924 original size:41 final size:42
Alignment explanation
Indices: 18353862--18354045 Score: 166
Period size: 45 Copynumber: 4.4 Consensus size: 42
18353852 AGTGCAAATA
* *
18353862 CAAGTGATGCAAA--CATGAATATC-TTTCTTGTGATGCAGATG
1 CAAGTGATGCAAATGCA--AATATCTTTTCTTATGATGTAGATG
18353903 CAAGTGATGCAAATGCAAATATCTTTTTTTCTTATGATGTAGATG
1 CAAGTGATGCAAATGCAAATATC---TTTTCTTATGATGTAGATG
* *
18353948 CAAGTGATGCAAATGCAAATGTCTTTTTTCTTATGATATAGATG
1 CAAGTGATGCAAATGCAAATATC--TTTTCTTATGATGTAGATG
* * *
18353992 CAAGT-ATG--AATGCAAATGTCCTTTT-TTGTGATGTAGATA
1 CAAGTGATGCAAATGCAAATAT-CTTTTCTTATGATGTAGATG
* *
18354031 CAAGTAAGGCAAATG
1 CAAGTGATGCAAATG
18354046 TCTTTTTTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
39 16 0.13
40 6 0.05
41 30 0.24
42 5 0.04
43 5 0.04
44 25 0.20
45 38 0.30
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (42 bp):
CAAGTGATGCAAATGCAAATATCTTTTCTTATGATGTAGATG
Found at i:18353949 original size:45 final size:44
Alignment explanation
Indices: 18353885--18354045 Score: 197
Period size: 45 Copynumber: 3.8 Consensus size: 44
18353875 CATGAATATC
* * *
18353885 TTTCTTGTGATGCAGATGCAAGTGATGCAAATGCAAATATCTTTT
1 TTTCTTATGATGTAGATGCAAGTGATGCAAATGCAAATGTC-TTT
18353930 TTTCTTATGATGTAGATGCAAGTGATGCAAATGCAAATGTCTTT
1 TTTCTTATGATGTAGATGCAAGTGATGCAAATGCAAATGTCTTT
* *
18353974 TTTCTTATGATATAGATGCAAGT-ATG--AATGCAAATGTC-CT
1 TTTCTTATGATGTAGATGCAAGTGATGCAAATGCAAATGTCTTT
* * * *
18354014 TTT-TTGTGATGTAGATACAAGTAAGGCAAATG
1 TTTCTTATGATGTAGATGCAAGTGATGCAAATG
18354046 TCTTTTTTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
39 16 0.15
40 6 0.06
41 12 0.12
42 4 0.04
43 3 0.03
44 25 0.24
45 38 0.37
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (44 bp):
TTTCTTATGATGTAGATGCAAGTGATGCAAATGCAAATGTCTTT
Found at i:18354053 original size:36 final size:38
Alignment explanation
Indices: 18353962--18354054 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 38
18353952 TGATGCAAAT
* *
18353962 GCAAATGTCTTTTTTCTTATGATATAGATGCAAGTATGAAT
1 GCAAATGTC-TTTTT-TTATGATATAGATACAAG-ATGAAG
* * *
18354003 GCAAATGTCCTTTTTTGTGATGTAGATACAAG-T-AAG
1 GCAAATGTCTTTTTTTATGATATAGATACAAGATGAAG
18354039 GCAAATGTCTTTTTTT
1 GCAAATGTCTTTTTTT
18354055 TTTTTGTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 17 0.37
37 1 0.02
39 15 0.33
40 4 0.09
41 9 0.20
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (38 bp):
GCAAATGTCTTTTTTTATGATATAGATACAAGATGAAG
Found at i:18354146 original size:34 final size:34
Alignment explanation
Indices: 18354122--18354447 Score: 151
Period size: 34 Copynumber: 9.9 Consensus size: 34
18354112 GCTTAATTCT
*
18354122 TTCTTTGAAGGCTAGCTAAACTAGGCTTAAAATA
1 TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
* *
18354156 TTCTTTGAAGGCCAGTTAAACT-GAGCTT---ACA
1 TTCTTTGAAGGCCAGCTAAACTAG-GCTTAAAATA
* * * * * * *
18354187 TTCATTGGAGGCTAGCTTATCTGGGCTTAAAATC
1 TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
** * *
18354221 TTCTTTGAAGGCCAGCTAATTTGGGCTT---ACA
1 TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
* * * *
18354252 TTCATT-AGAGGCCAACTAATCTAGGCTTAAAATC
1 TTCTTTGA-AGGCCAGCTAAACTAGGCTTAAAATA
* * * *
18354286 TTTTTTGAAGGTCAGCTAAACTGGGCTT---ACA
1 TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
* * * * *
18354317 TTCATTAGAA-GCTAGTTAATCTAGG-TTTAAATA
1 TTC-TTTGAAGGCCAGCTAAACTAGGCTTAAAATA
** * * * *
18354350 TTTCTTTGAAGGCCATTTAAATTGGGTTTAATAT-
1 -TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
* * * *
18354384 TTC-ATCAAGGGCCAGCTAATCTAGGCTTAAAATC
1 TTCTTTGAA-GGCCAGCTAAACTAGGCTTAAAATA
* *
18354418 TTCTTTGAAGGCCAGCTAAATTGGGCTTAA
1 TTCTTTGAAGGCCAGCTAAACTAGGCTTAA
18354448 TACTCAAGAA
Statistics
Matches: 210, Mismatches: 62, Indels: 40
0.67 0.20 0.13
Matches are distributed among these distances:
30 3 0.01
31 58 0.28
32 9 0.04
33 28 0.13
34 103 0.49
35 9 0.04
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (34 bp):
TTCTTTGAAGGCCAGCTAAACTAGGCTTAAAATA
Found at i:18354217 original size:65 final size:65
Alignment explanation
Indices: 18354130--18354446 Score: 377
Period size: 65 Copynumber: 4.8 Consensus size: 65
18354120 CTTTCTTTGA
* * * * * *
18354130 AGGCTAGCTAAACTAGGCTTAAAATATTCTTTGAAGGCCAGTTAAACTGAGCTTACATTCATTGG
1 AGGCTAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTACATTCATTAG
* * *
18354195 AGGCTAGCTTATCTGGGCTTAAAATCTTCTTTGAAGGCCAGCTAATTTGGGCTTACATTCATTAG
1 AGGCTAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTACATTCATTAG
* * * * *
18354260 AGGCCAACTAATCTAGGCTTAAAATCTTTTTTGAAGGTCAGCTAAACTGGGCTTACATTCATTAG
1 AGGCTAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTACATTCATTAG
* * * ** * *
18354325 AAGCTAGTTAATCTAGGTTTAAATAT-TTCTTTGAAGGCCATTTAAATTGGGTTTAATATTTCAT
1 AGGCTAGCTAATCTAGGCTTAAA-ATCTTCTTTGAAGGCCAGCTAAATTGGGCTT-ACA-TTCAT
*
18354389 CA-
63 TAG
*
18354391 AGGGCCAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTA
1 A-GGCTAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTA
18354447 ATACTCAAGA
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
65 153 0.73
66 8 0.04
67 49 0.23
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AGGCTAGCTAATCTAGGCTTAAAATCTTCTTTGAAGGCCAGCTAAATTGGGCTTACATTCATTAG
Found at i:18355387 original size:11 final size:10
Alignment explanation
Indices: 18355289--18355384 Score: 54
Period size: 10 Copynumber: 9.3 Consensus size: 10
18355279 CATTCATTTC
18355289 TTTTTCTTTT
1 TTTTTCTTTT
18355299 TTTTTCCTTTAT
1 TTTTT-CTTT-T
18355311 TTTATTCTTCCTT
1 TTT-TTCTT--TT
*
18355324 TTTTTC-ATT
1 TTTTTCTTTT
*
18355333 TTTTTCTTTCC
1 TTTTTCTTT-T
*
18355344 CTTTTC-TTT
1 TTTTTCTTTT
*
18355353 TTTTAC-TTT
1 TTTTTCTTTT
*
18355362 TTTTTGTTTT
1 TTTTTCTTTT
* *
18355372 TTCTTATTTT
1 TTTTTCTTTT
18355382 TTT
1 TTT
18355385 CTTTTGGATC
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
9 19 0.29
10 21 0.32
11 9 0.14
12 10 0.15
13 6 0.09
14 1 0.02
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:18355389 original size:16 final size:15
Alignment explanation
Indices: 18355285--18355389 Score: 59
Period size: 16 Copynumber: 6.5 Consensus size: 15
18355275 CACCCATTCA
18355285 TTTCTTTTTCTTTTTT
1 TTTC-TTTTCTTTTTT
* *
18355301 TTTCCTTTATTTTATT
1 TTTCTTTTCTTTT-TT
* *
18355317 CTTCCTTTTTTTCATTTT
1 -TTTCTTTTCTT--TTTT
* *
18355335 TTTCTTTCCCTTTTCT
1 TTTCTTT-TCTTTTTT
*
18355351 TTT-TTTACTTTTTT
1 TTTCTTTTCTTTTTT
*
18355365 TTGTTTTTTCTTATTTT
1 TT-TCTTTTCTT-TTTT
18355382 TTTCTTTT
1 TTTCTTTT
18355390 GGATCTTGTC
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
14 8 0.12
15 11 0.16
16 23 0.34
17 20 0.29
18 4 0.06
19 2 0.03
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:18356821 original size:15 final size:14
Alignment explanation
Indices: 18356787--18356820 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
18356777 TGTTTTTGCC
18356787 TTTTTTTGTTTATA
1 TTTTTTTGTTTATA
*
18356801 TTTTTTTGTTT-TG
1 TTTTTTTGTTTATA
18356814 TTTTTTT
1 TTTTTTT
18356821 TACTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTTTTGTTTATA
Found at i:18358500 original size:30 final size:30
Alignment explanation
Indices: 18358464--18358533 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
18358454 TGTGCATAAC
18358464 ATGGGATGCATATACTATCCATCAATGTGA
1 ATGGGATGCATATACTATCCATCAATGTGA
* * ** *
18358494 ATGGGATACATGTACTATCCATTGATGTGG
1 ATGGGATGCATATACTATCCATCAATGTGA
18358524 ATGGGATGCA
1 ATGGGATGCA
18358534 ATGCATGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
ATGGGATGCATATACTATCCATCAATGTGA
Found at i:18358820 original size:12 final size:12
Alignment explanation
Indices: 18358803--18358856 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
18358793 TTAAAAAAAA
18358803 ATTTGTTTGTTT
1 ATTTGTTTGTTT
18358815 ATTTGTTTGTTT
1 ATTTGTTTGTTT
* *
18358827 GTTTGTCTTTTTT
1 ATTTGT-TTGTTT
*
18358840 CTTT-TTT-TTT
1 ATTTGTTTGTTT
18358850 ATTTGTT
1 ATTTGTT
18358857 AATGCTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 6 0.17
11 4 0.11
12 18 0.50
13 8 0.22
ACGTcount: A:0.06, C:0.04, G:0.13, T:0.78
Consensus pattern (12 bp):
ATTTGTTTGTTT
Found at i:18362267 original size:25 final size:25
Alignment explanation
Indices: 18362230--18362278 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
18362220 GCTAGTAACT
*
18362230 TTTTCTTCCTTTTCCTTTGGCAACC
1 TTTTCTTCCTTTTCCTTTAGCAACC
*
18362255 TTTTCTTCTTTTTCCTTTAGCAAC
1 TTTTCTTCCTTTTCCTTTAGCAAC
18362279 TCCTCCTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.10, C:0.29, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTTCTTCCTTTTCCTTTAGCAACC
Found at i:18362428 original size:25 final size:25
Alignment explanation
Indices: 18362400--18362466 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
18362390 TTTTGCTAGT
18362400 AACTTTTTCTTCCTTTTCCTTTC-GC
1 AACTTTTTCTTCCTTTTCC-TTCAGC
*
18362425 AACTTTTTCTTCTTTTTCCTTCAGC
1 AACTTTTTCTTCCTTTTCCTTCAGC
**
18362450 AACTCCTTC-TCCTTTTC
1 AACTTTTTCTTCCTTTTC
18362467 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 10 0.27
25 27 0.73
ACGTcount: A:0.10, C:0.33, G:0.03, T:0.54
Consensus pattern (25 bp):
AACTTTTTCTTCCTTTTCCTTCAGC
Found at i:18362516 original size:174 final size:172
Alignment explanation
Indices: 18362203--18362564 Score: 536
Period size: 174 Copynumber: 2.1 Consensus size: 172
18362193 GGTTTCTACT
* *
18362203 TCTTCTTACTTTCTTTTGCTAGTAACTTTTTCTTCCTTTTCCTTTGGCAACCTTTTCTTCTTTTT
1 TCTTCTTTCTTTCTTTTGCTAGTAACTTTTTCTTCCTTTTCCTTTCGCAACCTTTTCTTCTTTTT
* * *
18362268 CCTTTAGCAACTCCTCCTCCTTTTCTTTTTCTTTTCTTTTCCTCCTTTTCCTTTTCTATTCGGTT
66 CCTTCAGCAACTCCTCCTCCTTTTCTTTTTCTTTTCTCTTCCTCCTTTTCCTTCTCTATTCGGTT
* *
18362333 TCCCTTTTTTTTTTTTTGTTTAGTAACTTCTCCT-TTGTGTTTGGC
131 TCCC----TTTTTTTTGGTTTAGCAACTTCTCCTCTTGTGTTTGGC
*
18362378 T-TTCTTTCTTTCTTTTGCTAGTAACTTTTTCTTCCTTTTCCTTTCGCAACTTTTTCTTCTTTTT
1 TCTTCTTTCTTTCTTTTGCTAGTAACTTTTTCTTCCTTTTCCTTTCGCAACCTTTTCTTCTTTTT
* * *
18362442 CCTTCAGCAACTCCTTCTCCTTTTCTTTTT-TTTT-TCTTCCTCTTTTTCCTTCTCTATTTGGTT
66 CCTTCAGCAACTCCTCCTCCTTTTCTTTTTCTTTTCTCTTCCTCCTTTTCCTTCTCTATTCGGTT
18362505 TCCCTCTTTTTTTTGGTTTAGCAACTTCTCCTCTTGTGTTTGGC
131 T-CC-CTTTTTTTTGGTTTAGCAACTTCTCCTCTTGTGTTTGGC
18362549 TCTT-TTTCTTTCTTTT
1 TCTTCTTTCTTTCTTTT
18362565 TTCTTCCAGA
Statistics
Matches: 172, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
170 24 0.14
171 24 0.14
172 28 0.16
173 6 0.03
174 89 0.52
175 1 0.01
ACGTcount: A:0.07, C:0.26, G:0.07, T:0.60
Consensus pattern (172 bp):
TCTTCTTTCTTTCTTTTGCTAGTAACTTTTTCTTCCTTTTCCTTTCGCAACCTTTTCTTCTTTTT
CCTTCAGCAACTCCTCCTCCTTTTCTTTTTCTTTTCTCTTCCTCCTTTTCCTTCTCTATTCGGTT
TCCCTTTTTTTTGGTTTAGCAACTTCTCCTCTTGTGTTTGGC
Found at i:18376026 original size:18 final size:17
Alignment explanation
Indices: 18375999--18376040 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
18375989 ACAAAAAAGC
*
18375999 AAAAAAAAAAGTGCAAA
1 AAAAAAAAAAGAGCAAA
*
18376016 AAAATAAAAAAGAGGAAA
1 AAAA-AAAAAAGAGCAAA
18376034 AAAAAAA
1 AAAAAAA
18376041 CTTAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAGAGCAAA
Found at i:18376893 original size:32 final size:33
Alignment explanation
Indices: 18376857--18376919 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
18376847 TTTGCATGAC
*
18376857 TAATATTATATTTACATGA-TAATTTATTTGCT
1 TAATATTATATTTACATGATTAATATATTTGCT
* *
18376889 TAATATTTTATTTGCATGATTAATATATTTG
1 TAATATTATATTTACATGATTAATATATTTG
18376920 TCTGATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (33 bp):
TAATATTATATTTACATGATTAATATATTTGCT
Found at i:18376911 original size:20 final size:20
Alignment explanation
Indices: 18376846--18376914 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 20
18376836 TTTTGCATGA
* *
18376846 ATTTGCATGACTAATATTAT
1 ATTTGCATGATTAATATTTT
*
18376866 ATTTACATGA-T-A-A-TTT
1 ATTTGCATGATTAATATTTT
18376882 ATTTGC----TTAATATTTT
1 ATTTGCATGATTAATATTTT
18376898 ATTTGCATGATTAATAT
1 ATTTGCATGATTAATAT
18376915 ATTTGTCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 1 0.03
16 16 0.42
17 1 0.03
18 1 0.03
19 1 0.03
20 16 0.42
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTTGCATGATTAATATTTT
Found at i:18376974 original size:20 final size:20
Alignment explanation
Indices: 18376896--18376979 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
18376886 GCTTAATATT
*
18376896 TTATTTGCATGATTA--ATA
1 TTATTTGCATGATTATTAAA
18376914 -TATTTGTC-TGATTTATTAAA
1 TTATTTG-CATGA-TTATTAAA
* * *
18376934 ATATTTGCATAACTATTAAA
1 TTATTTGCATGATTATTAAA
*
18376954 TTATTTGCATGATTATCAAA
1 TTATTTGCATGATTATTAAA
18376974 TTATTT
1 TTATTT
18376980 ATTTGTGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
17 9 0.17
18 4 0.08
20 32 0.60
21 8 0.15
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50
Consensus pattern (20 bp):
TTATTTGCATGATTATTAAA
Found at i:18377046 original size:41 final size:41
Alignment explanation
Indices: 18376989--18377226 Score: 237
Period size: 41 Copynumber: 5.7 Consensus size: 41
18376979 TATTTGTGTC
* ** *
18376989 ATTGCATGATTCTATATTTCCTTGCATGTTTTAAATTGCTA
1 ATTGCATGATTATATATTTAATTGCATGTTTTAAATTGTTA
* * * *
18377030 ATTGCATGATAATATATATATATATTTGCATG-ATTATATTGATA
1 ATTGCATGAT--TATATAT-T-TAATTGCATGTTTTAAATTGTTA
* * * * *
18377074 ATTGCATGATAATATATATATTTGCATGTTTTATATTTTTTA
1 ATTGCATGATTATATATTTAATTGCATGTTTTA-AATTGTTA
* *
18377116 ATTGCATGATTATATATTTAATTGCATGATTTATATAT-TTA
1 ATTGCATGATTATATATTTAATTGCATGTTTTAAAT-TGTTA
* * *
18377157 AATGCATGATCATATATTTAATTGCATGTTTTACATTGTTA
1 ATTGCATGATTATATATTTAATTGCATGTTTTAAATTGTTA
*
18377198 ATTGCATGATTATATATTTAATTACATGT
1 ATTGCATGATTATATATTTAATTGCATGT
18377227 CAATTTTGTA
Statistics
Matches: 163, Mismatches: 26, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
40 11 0.07
41 78 0.48
42 40 0.25
43 6 0.04
44 20 0.12
45 8 0.05
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (41 bp):
ATTGCATGATTATATATTTAATTGCATGTTTTAAATTGTTA
Found at i:18377063 original size:24 final size:22
Alignment explanation
Indices: 18377028--18377184 Score: 120
Period size: 20 Copynumber: 7.5 Consensus size: 22
18377018 TTTAAATTGC
18377028 TAATTGCATGATAATATATATA
1 TAATTGCATGATAATATATATA
18377050 TATATTTGCATGAT--TATAT-TGA
1 TA-A-TTGCATGATAATATATAT-A
18377072 TAATTGCATGATAATATATATA
1 TAATTGCATGATAATATATATA
** * *
18377094 T--TTGCATG-TTTTATATTTTT
1 TAATTGCATGATAATATA-TATA
*
18377114 TAATTGCATGAT--TATATATT
1 TAATTGCATGATAATATATATA
* *
18377134 TAATTGCATGAT-TTATATATT
1 TAATTGCATGATAATATATATA
* *
18377155 TAAATGCATGATCATATAT-T-
1 TAATTGCATGATAATATATATA
18377175 TAATTGCATG
1 TAATTGCATG
18377185 TTTTACATTG
Statistics
Matches: 115, Mismatches: 8, Indels: 26
0.77 0.05 0.17
Matches are distributed among these distances:
19 5 0.04
20 43 0.37
21 26 0.23
22 29 0.25
23 3 0.03
24 9 0.08
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (22 bp):
TAATTGCATGATAATATATATA
Found at i:18377078 original size:20 final size:19
Alignment explanation
Indices: 18377055--18377225 Score: 144
Period size: 20 Copynumber: 8.4 Consensus size: 19
18377045 ATATATATAT
*
18377055 TTGCATGATTATATTGATAA
1 TTGCATGATTATATT-TTAA
* * *
18377075 TTGCATGATAATATATATAT
1 TTGCATGATTATAT-TTTAA
*
18377095 TTGCATGTTTTATATTTTTTAA
1 TTGCATG-ATTATA--TTTTAA
18377117 TTGCATGATTATATATTTAA
1 TTGCATGATTATAT-TTTAA
18377137 TTGCATGATTTATATATTTAA
1 TTGCATGA-TTATAT-TTTAA
* *
18377158 ATGCATGATCATATATTTAA
1 TTGCATGATTATAT-TTTAA
* *
18377178 TTGCATGTTTTACATTGTTAA
1 TTGCATG-ATTATATT-TTAA
18377199 TTGCATGATTATATATTTAA
1 TTGCATGATTATAT-TTTAA
*
18377219 TTACATG
1 TTGCATG
18377226 TCAATTTTGT
Statistics
Matches: 126, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 69 0.55
21 45 0.36
22 10 0.08
23 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (19 bp):
TTGCATGATTATATTTTAA
Found at i:18377129 original size:62 final size:60
Alignment explanation
Indices: 18377045--18377214 Score: 180
Period size: 62 Copynumber: 2.8 Consensus size: 60
18377035 ATGATAATAT
* * * * ** * *
18377045 ATATATATATTTGCATGATTATATTGATAATTGCATGATAATATATATATTTGCATGTTTT
1 ATATATTTAATTGCATGATTATATTGTTAATTGCATGATTATATATATAAATGCATG-ATC
* *
18377106 ATATTTTTTAATTGCATGATTATATAT-TTAATTGCATGATTTATATATTTAAATGCATGATC
1 ATA-TATTTAATTGCATGATTATAT-TGTTAATTGCATGA-TTATATATATAAATGCATGATC
* *
18377168 ATATATTTAATTGCATGTTTTACATTGTTAATTGCATGATTATATAT
1 ATATATTTAATTGCATG-ATTATATTGTTAATTGCATGATTATATAT
18377215 TTAATTACAT
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
61 25 0.27
62 50 0.55
63 16 0.18
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.50
Consensus pattern (60 bp):
ATATATTTAATTGCATGATTATATTGTTAATTGCATGATTATATATATAAATGCATGATC
Found at i:18377308 original size:32 final size:32
Alignment explanation
Indices: 18377232--18377297 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
18377222 CATGTCAATT
* *
18377232 TTGTATGATTATTAATTTATTTGTTTATGTGA
1 TTGTATGATTATTAATATATTTGTTTATATGA
18377264 TTGTATGATTATTAATATATTTGTTT-TCATGA
1 TTGTATGATTATTAATATATTTGTTTAT-ATGA
18377296 TT
1 TT
18377298 TTATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.59
Consensus pattern (32 bp):
TTGTATGATTATTAATATATTTGTTTATATGA
Found at i:18378561 original size:13 final size:13
Alignment explanation
Indices: 18378505--18378566 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
18378495 AAATTTGTGT
18378505 TATTCCTTGTATA
1 TATTCCTTGTATA
*
18378518 TATT--TT-TACA
1 TATTCCTTGTATA
18378528 TATTAACCTT-TATA
1 TATT--CCTTGTATA
*
18378542 TTGTTCCTTGTATA
1 -TATTCCTTGTATA
18378556 TATTCCTTGTA
1 TATTCCTTGTA
18378567 CATGTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
13 18 0.46
14 9 0.23
15 3 0.08
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (13 bp):
TATTCCTTGTATA
Found at i:18384899 original size:16 final size:17
Alignment explanation
Indices: 18384860--18384978 Score: 71
Period size: 16 Copynumber: 6.6 Consensus size: 17
18384850 TTTTGCATGA
18384860 ATTTGCATGACTAATATAT
1 ATTTGCATGACTAAT-T-T
18384879 ATTTGCATGA-TAATTT
1 ATTTGCATGACTAATTT
* * *
18384895 ATTTGC-TTAATATTTT
1 ATTTGCATGACTAATTT
* *
18384911 ATTTGCATGATTAATAT
1 ATTTGCATGACTAATTT
* * *
18384928 ATTTGTCTTATTTATTAATAT
1 ATTTG-C--A-TGACTAATTT
18384949 ATTTGCATGACTATTAATTT
1 ATTTGCATGAC---TAATTT
18384969 ATTTGCATGA
1 ATTTGCATGA
18384979 TTATCAATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.02
16 18 0.22
17 14 0.17
18 6 0.07
19 10 0.12
20 17 0.21
21 14 0.17
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (17 bp):
ATTTGCATGACTAATTT
Found at i:18384924 original size:20 final size:19
Alignment explanation
Indices: 18384860--18385280 Score: 73
Period size: 20 Copynumber: 22.5 Consensus size: 19
18384850 TTTTGCATGA
* *
18384860 ATTTGCATGACTAATATAT
1 ATTTGCATGATTAATATTT
18384879 ATTTGCATGA-T-A-ATTT
1 ATTTGCATGATTAATATTT
18384895 ATTTGC----TTAATATTTT
1 ATTTGCATGATTAATA-TTT
18384911 ATTTGCATGATTAATA--T
1 ATTTGCATGATTAATATTT
*
18384928 ATTTGTCTTATTTATTAATA--T
1 ATTTG-C--A-TGATTAATATTT
* *
18384949 ATTTGCATGACTATTAATTT
1 ATTTGCATGATTAAT-ATTT
18384969 ATTTGCATGATT-ATCAATTT
1 ATTTGCATGATTAAT--ATTT
* * *
18384989 ATTT--AT--TT-GT-GTG
1 ATTTGCATGATTAATATTT
* *
18385002 A-TTACATGATTATATGTTT
1 ATTTGCATGATTA-ATATTT
* * *
18385021 ACTTGCATGTTTTATATTGTT
1 ATTTGCATGATTAATA-T-TT
* *
18385042 AATTGCATGA-TAATATAT
1 ATTTGCATGATTAATATTT
18385060 ATTTGCATGATT-ATATTGTT
1 ATTTGCATGATTAATA-T-TT
*
18385080 AATTGCATGA-TAATA--T
1 ATTTGCATGATTAATATTT
*
18385096 A--T--AT-A-T-ATATAT
1 ATTTGCATGATTAATATTT
* *
18385108 ATTTGCATGTTTTATATTTTT
1 ATTTGCATG-ATTA-ATATTT
* *
18385129 AATTGCATGATTGTATATTT
1 ATTTGCATGATT-AATATTT
*
18385149 AATTGCATGATTTATATATTT
1 ATTTGCATGA-TTA-ATATTT
* *
18385170 AATTGCATGATCACATATTT
1 ATTTGCATGATTA-ATATTT
* *
18385190 AATTGCATGTTTTACAT-TGTT
1 ATTTGCATG-ATTA-ATAT-TT
*
18385211 AATTGCATGATTAGATATTT
1 ATTTGCATGATTA-ATATTT
* *
18385231 AGTGGCAT-ATTTTACAT-TGTT
1 ATTTGCATGA--TTA-ATAT-TT
*
18385252 AATTGCATGATTATATATTT
1 ATTTGCATGATTA-ATATTT
*
18385272 AATTGCATG
1 ATTTGCATG
18385281 TCTATTTGAA
Statistics
Matches: 306, Mismatches: 44, Indels: 103
0.68 0.10 0.23
Matches are distributed among these distances:
10 3 0.01
11 2 0.01
12 6 0.02
13 3 0.01
14 5 0.02
15 1 0.00
16 27 0.09
17 12 0.04
18 20 0.07
19 21 0.07
20 120 0.39
21 85 0.28
22 1 0.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.51
Consensus pattern (19 bp):
ATTTGCATGATTAATATTT
Found at i:18384954 original size:38 final size:34
Alignment explanation
Indices: 18384874--18384958 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 34
18384864 GCATGACTAA
*
18384874 TATATATTTGCATGATAATTTATTTGCTTAATAT
1 TATATATTTGCATGATAATATATTTGCTTAATAT
*
18384908 T-T-TATTTGCATGATTAATATATTTGTCTTATTTAT
1 TATATATTTGCATGA-TAATATATTTG-CTTA-ATAT
18384943 TAATATATTTGCATGA
1 T-ATATATTTGCATGA
18384959 CTATTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 11 0.26
33 11 0.26
34 5 0.12
35 4 0.09
37 1 0.02
38 11 0.26
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (34 bp):
TATATATTTGCATGATAATATATTTGCTTAATAT
Found at i:18385035 original size:21 final size:21
Alignment explanation
Indices: 18385023--18385088 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 21
18385013 ATATGTTTAC
18385023 TTGCATGTTTTATATTGTTAA
1 TTGCATGTTTTATATTGTTAA
* * * *
18385044 TTGCATG-ATAATA-T-ATAT
1 TTGCATGTTTTATATTGTTAA
*
18385062 TTGCATG-ATTATATTGTTAA
1 TTGCATGTTTTATATTGTTAA
18385082 TTGCATG
1 TTGCATG
18385089 ATAATATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 14 0.39
19 2 0.06
20 13 0.36
21 7 0.19
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (21 bp):
TTGCATGTTTTATATTGTTAA
Found at i:18385051 original size:41 final size:41
Alignment explanation
Indices: 18385006--18385281 Score: 299
Period size: 41 Copynumber: 6.6 Consensus size: 41
18384996 TGTGTGATTA
* *
18385006 CATGATTATATGTTTACTTGCATGTTTTATATTGTTAATTG
1 CATGATTATATATTTAATTGCATGTTTTATATTGTTAATTG
* * *
18385047 CATGA-TA-ATATATATTTGCATG-ATTATATTGTTAATTG
1 CATGATTATATATTTAATTGCATGTTTTATATTGTTAATTG
*
18385085 CATGATAATATATATATATATATATTTGCATGTTTTATATTTTTAATTG
1 CATG---AT-TATATAT-T-TA-A-TTGCATGTTTTATATTGTTAATTG
* *
18385134 CATGATTGTATATTTAATTGCATGATTTATATAT-TTAATTG
1 CATGATTATATATTTAATTGCATGTTTTATAT-TGTTAATTG
* * *
18385175 CATGATCACATATTTAATTGCATGTTTTACATTGTTAATTG
1 CATGATTATATATTTAATTGCATGTTTTATATTGTTAATTG
* * * * *
18385216 CATGATTAGATATTTAGTGGCATATTTTACATTGTTAATTG
1 CATGATTATATATTTAATTGCATGTTTTATATTGTTAATTG
18385257 CATGATTATATATTTAATTGCATGT
1 CATGATTATATATTTAATTGCATGT
18385282 CTATTTGAAT
Statistics
Matches: 198, Mismatches: 24, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
38 19 0.10
39 12 0.06
40 3 0.02
41 118 0.60
42 2 0.01
43 4 0.02
44 5 0.03
45 6 0.03
46 4 0.02
48 7 0.04
49 18 0.09
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.50
Consensus pattern (41 bp):
CATGATTATATATTTAATTGCATGTTTTATATTGTTAATTG
Found at i:18385067 original size:18 final size:18
Alignment explanation
Indices: 18385044--18385099 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
18385034 ATATTGTTAA
18385044 TTGCATGATAATATATAT
1 TTGCATGATAATATATAT
* * *
18385062 TTGCATGATTATATTGTTAA
1 TTGCATGATAATA-T-ATAT
18385082 TTGCATGATAATATATAT
1 TTGCATGATAATATATAT
18385100 ATATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 14 0.47
19 2 0.07
20 14 0.47
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (18 bp):
TTGCATGATAATATATAT
Found at i:18385362 original size:32 final size:32
Alignment explanation
Indices: 18385290--18385351 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
18385280 GTCTATTTGA
* **
18385290 ATGATTATTAATTTATTTATTTGTGTGATTAT
1 ATGATTATTAATATATTTATTTGCATGATTAT
18385322 ATGATTATTAATATATTTATTTGCATGATT
1 ATGATTATTAATATATTTATTTGCATGATT
18385352 TTATATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (32 bp):
ATGATTATTAATATATTTATTTGCATGATTAT
Found at i:18385376 original size:19 final size:19
Alignment explanation
Indices: 18385334--18385382 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18385324 GATTATTAAT
* *
18385334 ATATTTATTTGCATGATTTT
1 ATATTTA-TTGCATGATATG
18385354 ATATTTATTGCATGATATG
1 ATATTTATTGCATGATATG
18385373 ATATTCTATT
1 ATATT-TATT
18385383 AATTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (19 bp):
ATATTTATTGCATGATATG
Found at i:18389715 original size:66 final size:67
Alignment explanation
Indices: 18389654--18389782 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 67
18389644 ATAATTAATT
*
18389654 TTTTCAGGCATTCTTTACCTTTTCATTTTC-TTCATTTTAAAAAATAATA-TTATATATTAATTG
1 TTTT-AGGCATTCTTTACCTTTTCATTTTCTTTCATTTT-AAAAATAATATTTATATATTAATTA
18389717 TGTC
64 TGTC
** * * *
18389721 TTTTTTGCTTTCTTTACCTTTTCATTTTCTTTGATTTTAAAAATAATATTTATCTATTAATT
1 TTTTAGGCATTCTTTACCTTTTCATTTTCTTTCATTTTAAAAATAATATTTATATATTAATT
18389783 GTGATAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
66 32 0.58
67 23 0.42
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (67 bp):
TTTTAGGCATTCTTTACCTTTTCATTTTCTTTCATTTTAAAAATAATATTTATATATTAATTATG
TC
Found at i:18390367 original size:402 final size:406
Alignment explanation
Indices: 18389755--18390513 Score: 859
Period size: 402 Copynumber: 1.9 Consensus size: 406
18389745 TTTTCTTTGA
*
18389755 TTTTAAAAATAATATTTATCTATTAATTGTGATAATTAATTATGTATTTTTTTATCTTTTTTATT
1 TTTTAAAAATAATATTTATCTATTAATTGTGATAATTAATTATGTATTTTTTTATCTTTTTCATT
* * *
18389820 TCTTTAGTTTTAAAAATAATATTTATCTATTAATTGTAATCATATGTTATACCTTATGGGTTTTC
66 TCTTTAATTTTAAAAATAATATTTATCTATTAATTATAATAATATGTTATACCTTATGGGTTTTC
* *
18389885 TTATCTTTTCATTTTTATAATATTGAAGAAAATATTCACATATTTAAAATTAGATTAATTATAAT
131 TTATCTTTTCATTTTTATAATATTGAAGAAAATATTCACATATTTAAAATTAAATTAATCATAAT
* * * * *
18389950 CACGGATAATG-TTTTT-AGGTTTAATTTACATTTTTATTTTTTGA-TTT-TAGAATAATGTGTA
196 CACGGATAATGTTTTTTGAGCTTT-ATTTACATTTTCATTTTTTGATTTTATAAAATAATATCTA
* *
18390011 TTTATTAATTATGATAATTGA-T-T-GTGCTTTT-TTTT-TTATCTTTTGA-TTTTCACTATTTA
260 TTTATTAATTATGATAATTGACTGTAGTGCTTTTATTTTCTTACCTTTTGATTTTTCACCATTTA
*
18390070 AAAAAGATATATATTAAATTGATTGTGTATTACTTCTTCTTCTTTTTTTTTTTTTTTTTGCCTTT
325 AAAAAGATATATATTAAATTAATTGTGTATTACTTCTTCTTCTTTTTTTTTTTTTTTTTGCCTTT
18390135 TGATTTTACCTTTTCAT
390 TGATTTTACCTTTTCAT
* * * * *
18390152 TTTTTAAACTAATATTTATCTATTAATTTTGATAATTTATTATTTATTATTTATT-TCTACCTTT
1 TTTTAAAAATAATATTTATCTATTAATTGTGATAATTAATTATGTATT-TTT-TTATCT---TTT
* * ** *
18390216 TCATTT-TTCTAATATTTAAAAATAATATTTATTTATTAATTATAATAAT-TGATTGTGTCTTTT
61 TCATTTCTT-TAAT-TTTAAAAATAATATTTATCTATTAATTATAATAATATG-TTATACCTTAT
* * * * **
18390279 GGG-TTTGTTGTCTTTT-AGTTTTTTATAAT-TTTAA-AAATAGTATTTATTTATTTAAAATTAA
123 GGGTTTTCTTATCTTTTCA--TTTTTATAATATTGAAGAAA-A-TATTCACATATTTAAAATTAA
* ** ** * * *
18390340 ATTACTCATAATCATTGATTGTGTTTTTTGAGCTTTATTTGCCTTTTCATTTTTTTATTTTAATA
184 ATTAATCATAATCACGGATAATGTTTTTTGAGCTTTATTTACATTTTCATTTTTTGATTTT-ATA
* * * **
18390405 AAATAATATCTATTTCTTAATTGTGATAATTGACTGTATTTTTTTTATTTTCCTTACCTTTTGAT
248 AAATAATATCTATTTATTAATTATGATAATTGACTGTAGTGCTTTTATTTT-CTTACCTTTTGAT
* *
18390470 TTTTCACCATTTTAAAAAGATATATATTATATTAATTGTGTATT
312 TTTTCACCATTTAAAAAAGATATATATTAAATTAATTGTGTATT
18390514 GCTTTCTTTG
Statistics
Matches: 293, Mismatches: 45, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
397 43 0.15
398 6 0.02
399 2 0.01
400 6 0.02
401 29 0.10
402 86 0.29
403 22 0.08
404 8 0.03
406 30 0.10
407 1 0.00
408 1 0.00
409 5 0.02
410 4 0.01
412 10 0.03
413 40 0.14
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (406 bp):
TTTTAAAAATAATATTTATCTATTAATTGTGATAATTAATTATGTATTTTTTTATCTTTTTCATT
TCTTTAATTTTAAAAATAATATTTATCTATTAATTATAATAATATGTTATACCTTATGGGTTTTC
TTATCTTTTCATTTTTATAATATTGAAGAAAATATTCACATATTTAAAATTAAATTAATCATAAT
CACGGATAATGTTTTTTGAGCTTTATTTACATTTTCATTTTTTGATTTTATAAAATAATATCTAT
TTATTAATTATGATAATTGACTGTAGTGCTTTTATTTTCTTACCTTTTGATTTTTCACCATTTAA
AAAAGATATATATTAAATTAATTGTGTATTACTTCTTCTTCTTTTTTTTTTTTTTTTTGCCTTTT
GATTTTACCTTTTCAT
Found at i:18415850 original size:2 final size:2
Alignment explanation
Indices: 18415843--18415891 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
18415833 AGCAAAGCCT
18415843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18415885 TA TA TA T
1 TA TA TA T
18415892 CTACTACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18415923 original size:2 final size:2
Alignment explanation
Indices: 18415916--18415949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18415906 AGCAAAGCCT
18415916 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
18415950 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18415954 original size:2 final size:2
Alignment explanation
Indices: 18415949--18415975 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18415939 ATATATATAT
18415949 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
18415976 ATTTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18416330 original size:138 final size:138
Alignment explanation
Indices: 18416173--18416446 Score: 458
Period size: 138 Copynumber: 2.0 Consensus size: 138
18416163 TATTGATAAG
* **
18416173 TTTTAAATATGGCCATGGTCTAGCAAATGTATTAGTATATTGACTGTCCATCACATCAACATGTT
1 TTTTAAATATGGCCATGGTCTAGCAAATGTAGTAGTATATTGACCATCCATCACATCAACATGTT
* *
18416238 TAATTTTTTTAATATAATCCAATTGACGAATAGGATAATTGATATGATAGGTTAATAATCATCTT
66 TAATTGTTTTAATATAATCCAATTGACGAATAGGATAATGGATATGATAGGTTAATAATCATCTT
18416303 ATCTCAAA
131 ATCTCAAA
* * *
18416311 TTTTAAATATTGTCATGGTCTAGCAAATGTAGTAGTATATTGACCATCCATCACATCAATATGTT
1 TTTTAAATATGGCCATGGTCTAGCAAATGTAGTAGTATATTGACCATCCATCACATCAACATGTT
* *
18416376 TAATTGTTTTAATATAATCCAATTGATGTATAGGATAATGGATATGATAGGTTAATAATCATCTT
66 TAATTGTTTTAATATAATCCAATTGACGAATAGGATAATGGATATGATAGGTTAATAATCATCTT
18416441 ATCTCA
131 ATCTCA
18416447 TGTTTAATTT
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 126 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (138 bp):
TTTTAAATATGGCCATGGTCTAGCAAATGTAGTAGTATATTGACCATCCATCACATCAACATGTT
TAATTGTTTTAATATAATCCAATTGACGAATAGGATAATGGATATGATAGGTTAATAATCATCTT
ATCTCAAA
Found at i:18419814 original size:31 final size:31
Alignment explanation
Indices: 18419791--18419894 Score: 106
Period size: 31 Copynumber: 3.3 Consensus size: 31
18419781 ATAAAATATG
18419791 TATAAACAATAATGTAATGAAATAATAAATA
1 TATAAACAATAATGTAATGAAATAATAAATA
* * *
18419822 TATAAACAATTAA--CAATCACATATAA-AATATG
1 TATAAACAA-TAATGTAATGA-A-ATAATAA-ATA
**
18419854 TATAAACTGTAATGTAATGAAATAATAAATA
1 TATAAACAATAATGTAATGAAATAATAAATA
18419885 TATAAACAAT
1 TATAAACAAT
18419895 TGACGAAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
30 4 0.07
31 29 0.52
32 19 0.34
33 4 0.07
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.30
Consensus pattern (31 bp):
TATAAACAATAATGTAATGAAATAATAAATA
Found at i:18419836 original size:63 final size:63
Alignment explanation
Indices: 18419769--18419895 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
18419759 TTAAAACACA
18419769 TAACAATCACAAATAAAATATGTATAAACAATAATGTAATGAAATAATAAATATATAAACAAT
1 TAACAATCACAAATAAAATATGTATAAACAATAATGTAATGAAATAATAAATATATAAACAAT
* **
18419832 TAACAATCACATATAAAATATGTATAAACTGTAATGTAATGAAATAATAAATATATAAACAAT
1 TAACAATCACAAATAAAATATGTATAAACAATAATGTAATGAAATAATAAATATATAAACAAT
18419895 T
1 T
18419896 GACGAAACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (63 bp):
TAACAATCACAAATAAAATATGTATAAACAATAATGTAATGAAATAATAAATATATAAACAAT
Found at i:18421465 original size:14 final size:16
Alignment explanation
Indices: 18421434--18421475 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
18421424 GGAAGAGAAA
18421434 AGAAGGGGAAAGAGAG
1 AGAAGGGGAAAGAGAG
18421450 AGAAGGGGAAAGAGAG
1 AGAAGGGGAAAGAGAG
18421466 AGAAGGGGAA
1 AGAAGGGGAA
18421476 TGGGAATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
AGAAGGGGAAAGAGAG
Found at i:18422300 original size:28 final size:27
Alignment explanation
Indices: 18422269--18422321 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
18422259 CCAAATGGTG
18422269 AAATAATTAGATA-TATTTTTCAACAAAA
1 AAATAATTA-A-ACTATTTTTCAACAAAA
*
18422297 AAATAATTAAACTTTTTTTCAACAA
1 AAATAATTAAACTATTTTTCAACAA
18422322 CGGAGCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 13 0.57
28 9 0.39
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATAATTAAACTATTTTTCAACAAAA
Found at i:18427387 original size:11 final size:11
Alignment explanation
Indices: 18427367--18427412 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
18427357 GAGTCTTAAA
18427367 TAAG-AATCTT
1 TAAGAAATCTT
18427377 TAAGAAATCTT
1 TAAGAAATCTT
18427388 TAAATGAGAATCTT
1 T-AA-GA-AATCTT
18427402 TAAGAAATCTT
1 TAAGAAATCTT
18427413 CAAATGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.12
11 13 0.41
12 4 0.12
13 4 0.12
14 7 0.22
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (11 bp):
TAAGAAATCTT
Found at i:18427397 original size:25 final size:24
Alignment explanation
Indices: 18427360--18427796 Score: 403
Period size: 25 Copynumber: 18.6 Consensus size: 24
18427350 AATCTTTGAG
*
18427360 TCTTAAATAAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
18427384 TCTTTAAATGAGAATCTTTAAGAAA
1 TC-TTAAATGAGAATCTTTAAGAAA
18427409 TCTTCAAATGAGAATCTTT---AAA
1 TCTT-AAATGAGAATCTTTAAGAAA
**
18427431 TCTTAAACAAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
* *
18427455 TCTTCAAATGAGAATATTT---TAA
1 TCTT-AAATGAGAATCTTTAAGAAA
*
18427477 TCTTAAATGAGAATCTTTAAAAAA
1 TCTTAAATGAGAATCTTTAAGAAA
*
18427501 TCTTTAAATAAGAATCTTTAAG---
1 TC-TTAAATGAGAATCTTTAAGAAA
*
18427523 TCTTAAATGAGAATCTTTAAAAAAA
1 TCTTAAATGAGAATCTTT-AAGAAA
* *
18427548 TCCTCAAATGAGAATCTTT--G-AG
1 T-CTTAAATGAGAATCTTTAAGAAA
18427570 TCTTAAATGAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
* ***
18427594 TCTTCAAATAAGAATCTTTAAGGCGC
1 TCTT-AAATGAGAATCTTTAA-GAAA
* * *
18427620 CCTTAAATGAGGATCTTT--G-AG
1 TCTTAAATGAGAATCTTTAAGAAA
*
18427641 TCTTAAATGAGAATTTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
*
18427665 TCCTCAAATGAGAATCTTTAAGAAA
1 T-CTTAAATGAGAATCTTTAAGAAA
*
18427690 TCTTCAAATGAGAATCTTT--G-AG
1 TCTT-AAATGAGAATCTTTAAGAAA
18427712 TCTTAAATGAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
* *
18427736 TTCTCAAATGAGAATCTTT--G-AG
1 -TCTTAAATGAGAATCTTTAAGAAA
*
18427758 TCTTAAATAAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTTAAGAAA
*
18427782 TCCTCAAATGAGAAT
1 T-CTTAAATGAGAAT
18427797 ATTTGAATTT
Statistics
Matches: 337, Mismatches: 43, Indels: 65
0.76 0.10 0.15
Matches are distributed among these distances:
21 101 0.30
22 26 0.08
23 6 0.02
24 27 0.08
25 157 0.47
26 20 0.06
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (24 bp):
TCTTAAATGAGAATCTTTAAGAAA
Found at i:18427419 original size:71 final size:71
Alignment explanation
Indices: 18427336--18427754 Score: 498
Period size: 71 Copynumber: 5.9 Consensus size: 71
18427326 TAAAATTGTG
* * *
18427336 AATCCTCAAATGATAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTTAAATGAGAATCT
1 AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATGAGAATCT
18427401 TTAAGA
66 TTAAGA
* * * *
18427407 AATCTTCAAATGAGAATCTTTAAATCTTAAACAAGAATCTTTAAGAAATCTTCAAATGAGAATAT
1 AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATGAGAATCT
*
18427472 TT---T
66 TTAAGA
* *
18427475 AATCTT-AAATGAGAATCTTTAAAAAATCTTTAAATAAGAATCTTTAAG---TCTT-AAATGAGA
1 AATCTTCAAATGAGAATCTTT---GAGTC-TTAAATAAGAATCTTTAAGAAATCTTCAAATGAGA
*
18427535 ATCTTTAAAAA
62 ATCTTT-AAGA
* * *
18427546 AATCCTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATAAGAATCT
1 AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATGAGAATCT
*
18427611 TTAAGGC
66 TTAA-GA
*** * * * *
18427618 GCCCTT-AAATGAGGATCTTTGAGTCTTAAATGAGAATTTTTAAGAAATCCTCAAATGAGAATCT
1 AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATGAGAATCT
18427682 TTAAGA
66 TTAAGA
*
18427688 AATCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAAT-TCTCAAATGAGAATC
1 AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCT-TCAAATGAGAATC
18427752 TTT
65 TTT
18427755 GAGTCTTAAA
Statistics
Matches: 299, Mismatches: 33, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
67 27 0.09
68 28 0.09
69 3 0.01
70 9 0.03
71 203 0.68
72 29 0.10
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (71 bp):
AATCTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATGAGAATCT
TTAAGA
Found at i:18427707 original size:14 final size:14
Alignment explanation
Indices: 18427663--18427707 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18427653 ATTTTTAAGA
*
18427663 AATCCTCAAATGAG
1 AATCTTCAAATGAG
*
18427677 AATCTT-TAA-GA-
1 AATCTTCAAATGAG
18427688 AATCTTCAAATGAG
1 AATCTTCAAATGAG
18427702 AATCTT
1 AATCTT
18427708 TGAGTCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (14 bp):
AATCTTCAAATGAG
Found at i:18427727 original size:210 final size:208
Alignment explanation
Indices: 18427336--18427732 Score: 530
Period size: 210 Copynumber: 1.9 Consensus size: 208
18427326 TAAAATTGTG
* * *
18427336 AATCCTCAAATGATAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTTAAATGAGAATCT
1 AATCCTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATAAGAATCT
* *
18427401 TTAAGAAATCTTCAAATGAGAATCTTTAAATCTTAAACAAGAATCTTTAAGAAATCTTCAAATGA
66 TTAAGAAACCTTCAAATGAGAATCTTTAAATCTTAAACAAGAATCTTTAAGAAATCCTCAAATGA
*
18427466 GAATATTTTAATCTTAAATGAGAATCTTTAAAAAATCTTTAAATAAGAATCTTTAAGTCTTAAAT
131 GAATATTTAAATCTTAAATGAGAATCTTT--AAAATCTTTAAATAAGAATCTTTAAGTCTTAAAT
18427531 GAGAATCTTTAAAAA
194 GAGAATCTTTAAAAA
*
18427546 AATCCTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATAAGAATCT
1 AATCCTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATAAGAATCT
*** * * * ** *
18427611 TTAAGGCGCCCTT-AAATGAGGATCTTTGAGTCTTAAATGAGAATTTTTAAGAAATCCTCAAATG
66 TTAA-GAAACCTTCAAATGAGAATCTTTAAATCTTAAACAAGAATCTTTAAGAAATCCTCAAATG
* * * *
18427675 AGAATCTTTAAGAAATCTTCAAATGAGAATCTTT-GAGTC-TTAAATGAGAATCTTTAAG
130 AGAATATTT---AAATCTT-AAATGAGAATCTTTAAAATCTTTAAATAAGAATCTTTAAG
18427733 AAATTCTCAA
Statistics
Matches: 162, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
210 135 0.83
211 7 0.04
213 6 0.04
214 14 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (208 bp):
AATCCTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTAAGAAATCTTCAAATAAGAATCT
TTAAGAAACCTTCAAATGAGAATCTTTAAATCTTAAACAAGAATCTTTAAGAAATCCTCAAATGA
GAATATTTAAATCTTAAATGAGAATCTTTAAAATCTTTAAATAAGAATCTTTAAGTCTTAAATGA
GAATCTTTAAAAA
Found at i:18427802 original size:46 final size:46
Alignment explanation
Indices: 18427387--18427802 Score: 491
Period size: 46 Copynumber: 8.9 Consensus size: 46
18427377 TAAGAAATCT
* *
18427387 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTAAATC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
** * * *
18427433 TTAAACAAGAATCTTTAAGAAATCTTCAAATGAGAATATTTTAATC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
* * * *
18427479 TTAAATGAGAATCTTTAAAAAATCTTTAAATAAGAATCTTTAAGTC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
* *
18427525 TTAAATGAGAATCTTTAAAAAAATCCTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTT-AAGAAATCTTCAAATGAGAATCTTTGAGTC
* * *
18427572 TTAAATGAGAATCTTTAAGAAATCTTCAAATAAGAATCTTTAAGGCGCCC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTT---GAG-TC
* * * *
18427622 TTAAATGAGGATCTTT--G-AGTCTT-AAATGAGAATTTTTAAGAAATCC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTT--G-AGT-C
*
18427668 TCAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
18427714 TTAAATGAGAATCTTTAAGAAAT-TCTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGAAATCT-TCAAATGAGAATCTTTGAGTC
* * *
18427760 TTAAATAAGAATCTTTAAGAAATCCTCAAATGAGAATATTTGA
1 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGA
18427803 ATTTCAAATA
Statistics
Matches: 319, Mismatches: 38, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
45 3 0.01
46 228 0.71
47 49 0.15
48 3 0.01
49 7 0.02
50 29 0.09
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (46 bp):
TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTGAGTC
Found at i:18427811 original size:21 final size:22
Alignment explanation
Indices: 18427334--18427844 Score: 298
Period size: 25 Copynumber: 22.1 Consensus size: 22
18427324 GATAAAATTG
* *
18427334 TGAATCCTCAAATGATAATCTT
1 TGAATCTTCAAATGAGAATCTT
* *
18427356 TGAGTCTT-AAATAAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
*
18427377 TAAGAAATCTTTAAATGAGAATCTT
1 T--G-AATCTTCAAATGAGAATCTT
18427402 TAAGAAATCTTCAAATGAGAATCTT
1 T--G-AATCTTCAAATGAGAATCTT
* **
18427427 TAAATCTT-AAACAAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
*
18427448 TAAGAAATCTTCAAATGAGAATATT
1 T--G-AATCTTCAAATGAGAATCTT
*
18427473 TTAATCTT-AAATGAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
* * *
18427494 TAAAAAATCTTTAAATAAGAATCTT
1 T---GAATCTTCAAATGAGAATCTT
18427519 T-AAGTCTT-AAATGAGAATCTT
1 TGAA-TCTTCAAATGAGAATCTT
* *
18427540 TAAAAAAATCCTCAAATGAGAATCTT
1 T----GAATCTTCAAATGAGAATCTT
*
18427566 TGAGTCTT-AAATGAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
*
18427587 TAAGAAATCTTCAAATAAGAATCTT
1 T--G-AATCTTCAAATGAGAATCTT
* *
18427612 T-AAGGCGCCCTT-AAATGAGGATCTT
1 TGAA-----TCTTCAAATGAGAATCTT
* *
18427637 TGAGTCTT-AAATGAGAATTTT
1 TGAATCTTCAAATGAGAATCTT
*
18427658 TAAGAAATCCTCAAATGAGAATCTT
1 T--G-AATCTTCAAATGAGAATCTT
18427683 TAAGAAATCTTCAAATGAGAATCTT
1 T--G-AATCTTCAAATGAGAATCTT
*
18427708 TGAGTCTT-AAATGAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
18427729 TAAGAAAT-TCTCAAATGAGAATCTT
1 T--G-AATCT-TCAAATGAGAATCTT
* *
18427754 TGAGTCTT-AAATAAGAATCTT
1 TGAATCTTCAAATGAGAATCTT
* *
18427775 TAAGAAATCCTCAAATGAGAATATT
1 T--G-AATCTTCAAATGAGAATCTT
*
18427800 TGAAT-TTCAAAT-ATGAATATT
1 TGAATCTTCAAATGA-GAATCTT
18427821 TG-AT-TGTCAAATGAGAATCTT
1 TGAATCT-TCAAATGAGAATCTT
18427842 TGA
1 TGA
18427845 GATGTGAAAC
Statistics
Matches: 396, Mismatches: 46, Indels: 94
0.74 0.09 0.18
Matches are distributed among these distances:
20 4 0.01
21 139 0.35
22 38 0.10
23 10 0.03
24 33 0.08
25 152 0.38
26 20 0.05
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
TGAATCTTCAAATGAGAATCTT
Found at i:18427915 original size:42 final size:43
Alignment explanation
Indices: 18427869--18427952 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
18427859 AAGTTCATCG
* * *
18427869 AATGTGAATCTTC-AAACT-AGAATGAAAAGTTTTGAACTTTTA
1 AATGTGAATCTCCAAAACTCA-AATGAAAAGCTTTAAACTTTTA
*
18427911 AATGTGAATCTCCAAAATTCAAATGAAAAGCTTTAAACTTTT
1 AATGTGAATCTCCAAAACTCAAATGAAAAGCTTTAAACTTTT
18427953 TAGGTACGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 12 0.33
43 23 0.64
44 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (43 bp):
AATGTGAATCTCCAAAACTCAAATGAAAAGCTTTAAACTTTTA
Found at i:18428066 original size:23 final size:22
Alignment explanation
Indices: 18428014--18428071 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
18428004 TAAATGTTGG
* * *
18428014 ATATGAGTCTTGCAATTTGCAA
1 ATATGAATCTTGAAATTTACAA
**
18428036 ATGCGAATCTTGAAATCTTACAA
1 ATATGAATCTTGAAAT-TTACAA
18428059 ATATGAATTCTTG
1 ATATGAA-TCTTG
18428072 CATATATGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 12 0.44
23 10 0.37
24 5 0.19
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
ATATGAATCTTGAAATTTACAA
Found at i:18428313 original size:40 final size:40
Alignment explanation
Indices: 18428260--18428351 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
18428250 GATTGTCAAT
* *
18428260 GAGCCTTTTATTTTTTAAAGTTGTTGAGACTTTGATTAGAG
1 GAGCC-TTTATTTTTCAAAGTTGTTGAGACTCTGATTAGAG
* *
18428301 GAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAG
1 GAGCCTTTATTTTTCAAAGTTGTTGAGACTCTGATTAGAG
18428341 GAG-CTTTATTT
1 GAGCCTTTATTT
18428352 ATTTTCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
39 8 0.17
40 34 0.72
41 5 0.11
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (40 bp):
GAGCCTTTATTTTTCAAAGTTGTTGAGACTCTGATTAGAG
Found at i:18428637 original size:4 final size:4
Alignment explanation
Indices: 18428628--18428652 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18428618 TTTATATTGA
18428628 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
18428653 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:18432000 original size:22 final size:22
Alignment explanation
Indices: 18431949--18432006 Score: 93
Period size: 21 Copynumber: 2.7 Consensus size: 22
18431939 ACCCGACCTA
18431949 AAATTAATAAAATATTATTTTTT
1 AAATT-ATAAAATATTATTTTTT
18431972 AAA-TATAAAATATTATTTTTT
1 AAATTATAAAATATTATTTTTT
18431993 AAATTAT-AAATATT
1 AAATTATAAAATATT
18432007 TAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 27 0.79
22 4 0.12
23 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTATAAAATATTATTTTTT
Found at i:18432012 original size:8 final size:8
Alignment explanation
Indices: 18431992--18432032 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
18431982 TATTATTTTT
18431992 TAAAT-TA
1 TAAATATA
*
18431999 TAAATATT
1 TAAATATA
18432007 TAAATATA
1 TAAATATA
*
18432015 TAATTATA
1 TAAATATA
18432023 TAAATATA
1 TAAATATA
18432031 TA
1 TA
18432033 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TAAATATA
Found at i:18432026 original size:16 final size:16
Alignment explanation
Indices: 18431974--18432032 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
18431964 TATTTTTTAA
*
18431974 ATATAAA-ATATTATT
1 ATATAAATATATAATT
* * *
18431989 TTTTAAAT-TATAAAT
1 ATATAAATATATAATT
*
18432004 ATTTAAATATATAATT
1 ATATAAATATATAATT
18432020 ATATAAATATATA
1 ATATAAATATATA
18432033 TAAATAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 17 0.49
16 18 0.51
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAAATATATAATT
Found at i:18439476 original size:20 final size:20
Alignment explanation
Indices: 18439453--18439494 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
18439443 ATACAAATAG
*
18439453 ATTAACCATGCAAGTATAAT
1 ATTAACCATGCAAATATAAT
*
18439473 ATTAATCATGCAAATATAAT
1 ATTAACCATGCAAATATAAT
18439493 AT
1 AT
18439495 AATCATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (20 bp):
ATTAACCATGCAAATATAAT
Found at i:18439618 original size:23 final size:25
Alignment explanation
Indices: 18439592--18439637 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18439582 AAATCACACA
*
18439592 AATAAATA-T-ATAGTCATGCAAAT
1 AATAAATATTAATAATCATGCAAAT
18439615 AATAAATATTAATAATCATGCAA
1 AATAAATATTAATAATCATGCAA
18439638 TTATATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 1 0.05
25 11 0.55
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (25 bp):
AATAAATATTAATAATCATGCAAAT
Found at i:18440923 original size:13 final size:13
Alignment explanation
Indices: 18440905--18440986 Score: 109
Period size: 13 Copynumber: 6.6 Consensus size: 13
18440895 TTGACTCAAG
18440905 AAATTAAAAATCA
1 AAATTAAAAATCA
18440918 AAATTAAAAATCA
1 AAATTAAAAATCA
18440931 AAATTAAAAATCA
1 AAATTAAAAATCA
*
18440944 AAA-TCAAAATCA
1 AAATTAAAAATCA
*
18440956 AAATT-AAAATTA
1 AAATTAAAAATCA
18440968 AAA--AAAAATCA
1 AAATTAAAAATCA
*
18440979 AATTTAAA
1 AAATTAAA
18440987 TTTAAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.13
12 20 0.33
13 33 0.54
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATTAAAAATCA
Found at i:18440926 original size:6 final size:6
Alignment explanation
Indices: 18440905--18440992 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
18440895 TTGACTCAAG
* * * * *
18440905 AAATTAA AAATCA AAATTAA AAATCA AAATTAA AAATCA AAATCA AAATCA
1 AAATT-A AAATTA AAATT-A AAATTA AAATT-A AAATTA AAATTA AAATTA
* * * *
18440956 AAATTA AAATTA AAA-AA AAATCA AATTTA AATTTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AA
18440993 TTTTAGGATT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
5 4 0.06
6 50 0.74
7 14 0.21
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (6 bp):
AAATTA
Found at i:18442542 original size:5 final size:5
Alignment explanation
Indices: 18442514--18442571 Score: 73
Period size: 5 Copynumber: 11.4 Consensus size: 5
18442504 AAATAATAGA
*
18442514 TATTT GTATTT T-TTT AACTTT TATTT TATTT TATTT TATTT TATTT TATTT
1 TATTT -TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TATTT TATTT
*
18442565 TCTTT TA
1 TATTT TA
18442572 CTAAATATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
4 3 0.07
5 34 0.74
6 9 0.20
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:18443021 original size:22 final size:21
Alignment explanation
Indices: 18442996--18443044 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
18442986 ATAATAATAA
18442996 TAATAAAAATAA-ATTGATAAAT
1 TAATAAAAATAACA-TGA-AAAT
* *
18443018 TAATAGAATTAACATGAAAAT
1 TAATAAAAATAACATGAAAAT
18443039 TAATAA
1 TAATAA
18443045 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 13 0.57
23 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (21 bp):
TAATAAAAATAACATGAAAAT
Found at i:18455222 original size:22 final size:19
Alignment explanation
Indices: 18455184--18455233 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
18455174 TTATTTATTC
*
18455184 TAAAAAAAAATCGAATAGCT
1 TAAAAAAAAATCAAATAG-T
18455204 TAAAAAAAATAGTCAAATAG-
1 TAAAAAAAA-A-TCAAATAGT
18455224 TAAAAAAAAA
1 TAAAAAAAAA
18455234 AAGAGACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 1 0.04
22 7 0.26
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (19 bp):
TAAAAAAAAATCAAATAGT
Found at i:18456067 original size:48 final size:47
Alignment explanation
Indices: 18455979--18456137 Score: 151
Period size: 48 Copynumber: 3.3 Consensus size: 47
18455969 TTTTATTATC
* * *
18455979 TATTCTTTTTAATAATTTTTCTATTTTTTAAGGTATCACTCCCTTACT
1 TATTCCTTTTAATAATTTTT-TATTTTTTAAGGAAACACTCCCTTACT
*
18456027 TATTCCTTTTAATAATTCTTTTATTTTTT-AGAGAAACACTCCTATTA-T
1 TATTCCTTTTAATAATT-TTTTATTTTTTAAG-GAAACACTCC-CTTACT
* ** * ** *
18456075 CATTTATTTTTATTAATTTTCTTATTTTTTAAGGAAACACTTTCTTACC
1 TA-TTCCTTTTAATAATTTT-TTATTTTTTAAGGAAACACTCCCTTACT
18456124 TATTCCTTTTAATA
1 TATTCCTTTTAATA
18456138 GTTCCTCTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
47 2 0.02
48 48 0.55
49 36 0.41
50 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (47 bp):
TATTCCTTTTAATAATTTTTTATTTTTTAAGGAAACACTCCCTTACT
Found at i:18456073 original size:97 final size:97
Alignment explanation
Indices: 18455984--18456163 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 97
18455974 TTATCTATTC
* * * * *
18455984 TTTTTAATAATTTT-TCTATTTTTTAAGGTATCACTCCCTTACTTATTCCTTTTAATAATTCTTT
1 TTTTTAATAATTTTCT-TATTTTTTAAGGAAACACTCCCTTACCTATTCCTTTTAATAATTCCTC
*
18456048 TATTTTTTAGAGAAACACTCCTATTATCATTTA
65 TATGTTTTAGAGAAACACTCCTATTATCATTTA
* ** *
18456081 TTTTTATTAATTTTCTTATTTTTTAAGGAAACACTTTCTTACCTATTCCTTTTAATAGTTCCTCT
1 TTTTTAATAATTTTCTTATTTTTTAAGGAAACACTCCCTTACCTATTCCTTTTAATAATTCCTCT
*
18456146 ATGTTTTAGGGAAACACT
66 ATGTTTTAGAGAAACACT
18456164 TTTACTGCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 70 0.99
98 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (97 bp):
TTTTTAATAATTTTCTTATTTTTTAAGGAAACACTCCCTTACCTATTCCTTTTAATAATTCCTCT
ATGTTTTAGAGAAACACTCCTATTATCATTTA
Found at i:18465525 original size:34 final size:34
Alignment explanation
Indices: 18465487--18465583 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 34
18465477 AAAAATTTGT
*
18465487 AAAAAAAAAAAGAAGACAAAGAAAAAAGTTATGA
1 AAAAAAAAAAAGAAGACAAAGAAAAAAGTGATGA
* * *
18465521 AAAAAAAATAA-AA-ACAAAAGCAATAAAGTGGTGA
1 AAAAAAAAAAAGAAGAC-AAAG-AAAAAAGTGATGA
18465555 AAAAGCAAATAAAAGAAGA-AAAGAAAAAA
1 AAAA--AAA-AAAAGAAGACAAAGAAAAAA
18465584 ATATAGGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
32 2 0.04
33 6 0.12
34 24 0.48
36 8 0.16
37 7 0.14
38 2 0.04
39 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.08
Consensus pattern (34 bp):
AAAAAAAAAAAGAAGACAAAGAAAAAAGTGATGA
Found at i:18468426 original size:17 final size:18
Alignment explanation
Indices: 18468393--18468427 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18468383 ATAAATTATG
*
18468393 TTAAAAAAGAAAGCAAAA
1 TTAAAAAAGAAACCAAAA
18468411 TTAAAAAA-AAACCAAAA
1 TTAAAAAAGAAACCAAAA
18468428 CTTCCTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (18 bp):
TTAAAAAAGAAACCAAAA
Found at i:18470738 original size:96 final size:97
Alignment explanation
Indices: 18470630--18470882 Score: 336
Period size: 97 Copynumber: 2.6 Consensus size: 97
18470620 TTAACTCAAG
* *
18470630 ATTTAAATCCTCCAATAGTTTAGTAGGATTG-AAAATTTTTATTTTTCATAAAAATTTATTAAGT
1 ATTTAAATCCTCCAATAGTTTGGTAAGATTGAAAAATTTTTATTTTTCATAAAAATTTATTAAGT
*
18470694 -CCCTCAATAGTTTGGT-GAAACTTAATTTAGAA
66 CCCCT-AATAGTTTGGTAG-AACCTAATTTAGAA
** *
18470726 ATTTAAATCCTCCAATAGTTTGGTAAGATTGAAAAAAATTTATTTTTCATAAAAATTCATTAAGT
1 ATTTAAATCCTCCAATAGTTTGGTAAGATTGAAAAATTTTTATTTTTCATAAAAATTTATTAAGT
*
18470791 CCCCTAATAGTTTGGTAGCACCTAATTTAGAA
66 CCCCTAATAGTTTGGTAGAACCTAATTTAGAA
* * * * * *
18470823 ATTTAAATCCTCTAATAGTTTGGTATGCTTGAAAAATTATT-TTTTT-ATGAAATTTTATTA
1 ATTTAAATCCTCCAATAGTTTGGTAAGATTGAAAAATTTTTATTTTTCATAAAAATTTATTA
18470883 TGAAATCCTC
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
95 11 0.08
96 34 0.25
97 88 0.64
98 5 0.04
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (97 bp):
ATTTAAATCCTCCAATAGTTTGGTAAGATTGAAAAATTTTTATTTTTCATAAAAATTTATTAAGT
CCCCTAATAGTTTGGTAGAACCTAATTTAGAA
Found at i:18471029 original size:9 final size:9
Alignment explanation
Indices: 18471015--18471066 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
18471005 AAGAATCAAT
18471015 TAAAATAAA
1 TAAAATAAA
18471024 TAAAATTTAAA
1 TAAAA--TAAA
*
18471035 TCAAATAAA
1 TAAAATAAA
**
18471044 TTGAATAAA
1 TAAAATAAA
18471053 TAAAATAAA
1 TAAAATAAA
18471062 TAAAA
1 TAAAA
18471067 AATTTCACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 28 0.78
11 8 0.22
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
TAAAATAAA
Found at i:18472050 original size:20 final size:20
Alignment explanation
Indices: 18472027--18472064 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18472017 AATATAGCTA
18472027 AAGATAAACAACAAATAAAC
1 AAGATAAACAACAAATAAAC
*
18472047 AAGATAAACAATAAATAA
1 AAGATAAACAACAAATAA
18472065 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.11, G:0.05, T:0.13
Consensus pattern (20 bp):
AAGATAAACAACAAATAAAC
Found at i:18476379 original size:21 final size:21
Alignment explanation
Indices: 18476355--18476402 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
18476345 TTCAATGTAC
18476355 TTCAAGAGCAGATGCAATCA-T
1 TTCAAGAGCAGATGCAAT-ATT
* * *
18476376 TTCAGGGGCAGATGTAATATT
1 TTCAAGAGCAGATGCAATATT
18476397 TTCAAG
1 TTCAAG
18476403 GGTAGTTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (21 bp):
TTCAAGAGCAGATGCAATATT
Found at i:18477168 original size:124 final size:124
Alignment explanation
Indices: 18476957--18477190 Score: 405
Period size: 124 Copynumber: 1.9 Consensus size: 124
18476947 AGCTGAAGTA
*
18476957 TGGTTTGATAGGTATGTCATGTAACAAGGCAAAGTAACTTGGCAAGAGTTTTCCACTAATTTATG
1 TGGTTTGATAGGTATGTCATGCAACAAGGCAAAGTAACTTGGCAAGAGTTTTCCACTAATTTATG
* *
18477022 CCATAGGTTTTGTGATCGAACCTATTTAGATATAGTGGAGGAATTAAAAAGCTAAAATG
66 CCATAGGTTTTATGATCAAACCTATTTAGATATAGTGGAGGAATTAAAAAGCTAAAATG
** * *
18477081 TGGTTTGATAGGTATGTCATGCAATGAGGCAGAGTAACTTGGCAAGAGTTTTCCACTGATTTATG
1 TGGTTTGATAGGTATGTCATGCAACAAGGCAAAGTAACTTGGCAAGAGTTTTCCACTAATTTATG
18477146 CCATAGGTTTTATGATCAAACCTATTTAGATATAGTGGAGGAATT
66 CCATAGGTTTTATGATCAAACCTATTTAGATATAGTGGAGGAATT
18477191 TAACAAACTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 103 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (124 bp):
TGGTTTGATAGGTATGTCATGCAACAAGGCAAAGTAACTTGGCAAGAGTTTTCCACTAATTTATG
CCATAGGTTTTATGATCAAACCTATTTAGATATAGTGGAGGAATTAAAAAGCTAAAATG
Found at i:18480417 original size:17 final size:17
Alignment explanation
Indices: 18480395--18480428 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18480385 CAAGCCACTC
*
18480395 ATCACATGCTCAAACTT
1 ATCACATGCCCAAACTT
18480412 ATCACATGCCCAAACTT
1 ATCACATGCCCAAACTT
18480429 TATTTCTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26
Consensus pattern (17 bp):
ATCACATGCCCAAACTT
Found at i:18484713 original size:8 final size:8
Alignment explanation
Indices: 18484697--18484737 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
18484687 TGCAATCTAT
*
18484697 GCATGCAA
1 GCATACAA
18484705 GCATACAA
1 GCATACAA
18484713 GCATACAA
1 GCATACAA
18484721 GCATACAA
1 GCATACAA
18484729 GCATACAA
1 GCATACAA
18484737 G
1 G
18484738 ATAGTAGTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.12
Consensus pattern (8 bp):
GCATACAA
Found at i:18493848 original size:14 final size:16
Alignment explanation
Indices: 18493818--18493862 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
18493808 CATCCGGGTA
18493818 GAGAGAGAAAGAGAGG
1 GAGAGAGAAAGAGAGG
18493834 GAGAG-GAAAGA-AGG
1 GAGAGAGAAAGAGAGG
* *
18493848 GTGA-AGAGAGAGAGG
1 GAGAGAGAAAGAGAGG
18493863 AAAGAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (16 bp):
GAGAGAGAAAGAGAGG
Found at i:18494211 original size:6 final size:6
Alignment explanation
Indices: 18494200--18494225 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18494190 TTCCTTATTT
18494200 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
18494226 AATTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:18494470 original size:58 final size:59
Alignment explanation
Indices: 18494350--18494477 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 59
18494340 AAATATTTCT
* *
18494350 AATTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGACAATAAA
1 AATTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA
* *
18494409 AATTTTTAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAAT-AA
1 AATTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAA
18494467 AATTTCTAAAA
1 AATTTCTAAAA
18494478 TAAAAATTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 17 0.27
59 46 0.73
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (59 bp):
AATTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA
Found at i:18498133 original size:13 final size:13
Alignment explanation
Indices: 18498111--18498170 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
18498101 AAAAGGTCTC
*
18498111 AAAGATAGAAAGA
1 AAAGAAAGAAAGA
18498124 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
*
18498137 AAAGCAAAACAAAGA
1 AAAG--AAAGAAAGA
18498152 AAA-AAGAGAAA-A
1 AAAGAA-AGAAAGA
18498164 AAA-AAAG
1 AAAGAAAG
18498171 GAAATGAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.05
12 8 0.20
13 20 0.49
15 11 0.27
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:18498164 original size:19 final size:19
Alignment explanation
Indices: 18498110--18498164 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
18498100 TAAAAGGTCT
*
18498110 CAAAGATAG-AAAG-AAAA
1 CAAAGAAAGAAAAGAAAAA
* *
18498127 GAAAGAAAGAAAAGCAAAA
1 CAAAGAAAGAAAAGAAAAA
18498146 CAAAGAAA-AAAGAGAAAAA
1 CAAAGAAAGAAA-AGAAAAA
18498165 AAAAAGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 17 0.55
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02
Consensus pattern (19 bp):
CAAAGAAAGAAAAGAAAAA
Found at i:18498168 original size:23 final size:23
Alignment explanation
Indices: 18498124--18498169 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
18498114 GATAGAAAGA
**
18498124 AAAGAAAGAAAGAAAAGCAAAAC
1 AAAGAAAGAAAGAAAAAAAAAAC
*
18498147 AAAGAAAAAAGAGAAAAAAAAAA
1 AAAGAAAGAA-AGAAAAAAAAAA
18498170 GGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAGAAAGAAAGAAAAAAAAAAC
Found at i:18498568 original size:18 final size:17
Alignment explanation
Indices: 18498542--18498598 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 17
18498532 AAAAAAGATG
18498542 AAAAAGGAAAAGAGAAA
1 AAAAAGGAAAAGAGAAA
18498559 AAAAAGGGAAAATGGATGAAA
1 AAAAA-GGAAAA--GA-GAAA
*
18498580 AAAAAGAAAAAGAGAAA
1 AAAAAGGAAAAGAGAAA
18498597 AA
1 AA
18498599 TGAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 11 0.31
18 8 0.23
20 7 0.20
21 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (17 bp):
AAAAAGGAAAAGAGAAA
Found at i:18498597 original size:45 final size:46
Alignment explanation
Indices: 18498524--18498617 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
18498514 AGATATCAAC
* *
18498524 AATGGATGAAAAAAGATGAAAAAGGAAAAGA-GAAAAAA-AAGGGAA
1 AATGGATGAAAAAAGAAGAAAAAGGAAAA-ATGAAAAAATAAGAGAA
18498569 AATGGATGAAAAAA-AAGAAAAAGAGAAAAATGAAAAAATAAGAGAA
1 AATGGATGAAAAAAGAAGAAAAAG-GAAAAATGAAAAAATAAGAGAA
18498615 AAT
1 AAT
18498618 AAAAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
44 9 0.20
45 26 0.59
46 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (46 bp):
AATGGATGAAAAAAGAAGAAAAAGGAAAAATGAAAAAATAAGAGAA
Found at i:18498605 original size:25 final size:25
Alignment explanation
Indices: 18498533--18498616 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
18498523 CAATGGATGA
* *
18498533 AAAAAGATGAAAAAGGAAAAGAGAAA-
1 AAAAAGA-GAAAAATGAAAA-AAAAAG
*
18498559 AAAAAG-GGAAAATGGATGAAAAAAAAG
1 AAAAAGAGAAAAAT-GA--AAAAAAAAG
*
18498586 AAAAAGAGAAAAATGAAAAAATAAG
1 AAAAAGAGAAAAATGAAAAAAAAAG
18498611 AGAAAA
1 A-AAAA
18498617 TAAAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
24 5 0.11
25 11 0.23
26 14 0.30
27 11 0.23
28 6 0.13
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAAAGAGAAAAATGAAAAAAAAAG
Found at i:18498616 original size:18 final size:18
Alignment explanation
Indices: 18498581--18498648 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
18498571 TGGATGAAAA
18498581 AAAAGAAAAAGAGAAAAATG
1 AAAA-AAAAAGAG-AAAATG
* *
18498601 AAAAAATAAGAGAAAATAA
1 AAAAAAAAAGAGAAAAT-G
18498620 AAAAAAAAAGATGAAAA-G
1 AAAAAAAAAGA-GAAAATG
*
18498638 AAAAAAGAAGA
1 AAAAAAAAAGA
18498649 CTCAAATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 15 0.37
19 17 0.41
20 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAGAGAAAATG
Found at i:18498627 original size:37 final size:35
Alignment explanation
Indices: 18498577--18498648 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 35
18498567 AAAATGGATG
* *
18498577 AAAAAAAAGAAAAAGAGAAAAATGAAAAAATAAGAGA
1 AAAAAAAAAAAAAAGAG-AAAA-GAAAAAAGAAGAGA
18498614 AAATAAAAAAAAAAAGATGAAAAGAAAAAAGAAGA
1 AAA-AAAAAAAAAAAGA-GAAAAGAAAAAAGAAGA
18498649 CTCAAATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 14 0.45
38 16 0.52
39 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (35 bp):
AAAAAAAAAAAAAAGAGAAAAGAAAAAAGAAGAGA
Found at i:18498637 original size:46 final size:45
Alignment explanation
Indices: 18498532--18498646 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
18498522 ACAATGGATG
* **
18498532 AAAAAAGATGAAAA-AGGAAAAGAGAAAAAAAAGGGAAAATGGATGAA
1 AAAAAAGATGAAAAGA-GAAAA-AGAAAAAAAAGAGAAAAT-GAAAAA
18498579 AAAAAAGA--AAAAGAGAAAAATGAAAAAATAAGAGAAAAT-AAAAA
1 AAAAAAGATGAAAAGAGAAAAA-GAAAAAA-AAGAGAAAATGAAAAA
18498623 AAAAAAGATGAAAAGA-AAAAAGAA
1 AAAAAAGATGAAAAGAGAAAAAGAA
18498647 GACTCAAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
44 15 0.25
45 21 0.35
46 16 0.27
47 8 0.13
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (45 bp):
AAAAAAGATGAAAAGAGAAAAAGAAAAAAAAGAGAAAATGAAAAA
Found at i:18499790 original size:46 final size:46
Alignment explanation
Indices: 18499749--18499890 Score: 166
Period size: 46 Copynumber: 3.2 Consensus size: 46
18499739 TATCTTAATT
* * *
18499749 TCTTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTCGAG
1 TCTTAAATGAAAATCTTTAAGAAATCCTCAAATGAGAATCTTCAAG
**
18499795 TCTTAAATGAAAATCTTTAAGAAATCCTCAAATGAGAATCTTTGAG
1 TCTTAAATGAAAATCTTTAAGAAATCCTCAAATGAGAATCTTCAAG
* * * **
18499841 TGTCAAATGAAAATCTTT--G-AAT-TTCAAATGAGAATCTTTGAG
1 TCTTAAATGAAAATCTTTAAGAAATCCTCAAATGAGAATCTTCAAG
18499883 TCTTAAAT
1 TCTTAAAT
18499891 AATAATTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 25 0.28
43 3 0.03
44 1 0.01
46 59 0.67
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (46 bp):
TCTTAAATGAAAATCTTTAAGAAATCCTCAAATGAGAATCTTCAAG
Found at i:18499791 original size:14 final size:13
Alignment explanation
Indices: 18499749--18499790 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
18499739 TATCTTAATT
18499749 TCTTAAATGAGAA
1 TCTTAAATGAGAA
*
18499762 TCTTTAA-GA-AA
1 TCTTAAATGAGAA
18499773 TCTTCAAATGAGAA
1 TCTT-AAATGAGAA
18499787 TCTT
1 TCTT
18499791 CGAGTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 8 0.33
14 6 0.25
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (13 bp):
TCTTAAATGAGAA
Found at i:18499802 original size:21 final size:21
Alignment explanation
Indices: 18499749--18499890 Score: 115
Period size: 21 Copynumber: 6.4 Consensus size: 21
18499739 TATCTTAATT
18499749 TCTTAAATGAGAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTT--G-AA
* *
18499773 TCTTCAAATGAGAATCTTCGAG
1 TCTT-AAATGAGAATCTTTGAA
*
18499795 TCTTAAATGAAAATCTTTAAGAAA
1 TCTTAAATGAGAATCTTT--G-AA
* *
18499819 TCCTCAAATGAGAATCTTTGAG
1 T-CTTAAATGAGAATCTTTGAA
* * *
18499841 TGTCAAATGAAAATCTTTGAA
1 TCTTAAATGAGAATCTTTGAA
*
18499862 T-TTCAAATGAGAATCTTTGAG
1 TCTT-AAATGAGAATCTTTGAA
18499883 TCTTAAAT
1 TCTTAAAT
18499891 AATAATTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.01
21 50 0.52
22 9 0.09
23 3 0.03
24 6 0.06
25 28 0.29
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
TCTTAAATGAGAATCTTTGAA
Found at i:18499954 original size:20 final size:20
Alignment explanation
Indices: 18499926--18499978 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
18499916 AAATTTATCG
*
18499926 AATGTGAATCTTCAAATTCA
1 AATGAGAATCTTCAAATTCA
* *
18499946 AATGAGAATCTTTGAATTTCA
1 AATGAGAATC-TTCAAATTCA
*
18499967 AATGAAAATCTT
1 AATGAGAATCTT
18499979 TGAGATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
AATGAGAATCTTCAAATTCA
Found at i:18499968 original size:21 final size:21
Alignment explanation
Indices: 18499942--18499981 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18499932 AATCTTCAAA
*
18499942 TTCAAATGAGAATCTTTGAAT
1 TTCAAATGAAAATCTTTGAAT
18499963 TTCAAATGAAAATCTTTGA
1 TTCAAATGAAAATCTTTGA
18499982 GATGTGAAAC
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:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCAAATGAAAATCTTTGAAT
Found at i:18500483 original size:44 final size:43
Alignment explanation
Indices: 18500433--18500569 Score: 193
Period size: 44 Copynumber: 3.1 Consensus size: 43
18500423 CGAGAAGCCT
18500433 TTTATTTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTG
1 TTTATTTTTTCAAAGTTGTTGAGCCTCT-ATTAGAGGAGCTTTG
* *
18500477 TTTATTTTTCTCAAAGTTGTTGAGCCTCTAATTAGAGGAGTTTTA
1 TTTATTTTT-TCAAAGTTGTTGAGCCTCT-ATTAGAGGAGCTTTG
* **
18500522 TTTATTTTTCCAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTG
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTA-TTAGAGGAGCTTTG
18500566 TTTA
1 TTTA
18500570 CTTGTTAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
43 1 0.01
44 41 0.49
45 41 0.49
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (43 bp):
TTTATTTTTTCAAAGTTGTTGAGCCTCTATTAGAGGAGCTTTG
Found at i:18500500 original size:45 final size:44
Alignment explanation
Indices: 18500433--18500569 Score: 197
Period size: 45 Copynumber: 3.1 Consensus size: 44
18500423 CGAGAAGCCT
18500433 TTTATTTTT-TCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTG
1 TTTATTTTTCTCAAAGTTGTTGAGCCTCT-ATTAGAGGAGCTTTG
* *
18500477 TTTATTTTTCTCAAAGTTGTTGAGCCTCTAATTAGAGGAGTTTTA
1 TTTATTTTTCTCAAAGTTGTTGAGCCTCT-ATTAGAGGAGCTTTG
**
18500522 TTTATTTTTC-CAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTG
1 TTTATTTTTCTCAAAGTTGTTGAGCCTCTA-TTAGAGGAGCTTTG
18500566 TTTA
1 TTTA
18500570 CTTGTTAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
43 1 0.01
44 41 0.49
45 42 0.50
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (44 bp):
TTTATTTTTCTCAAAGTTGTTGAGCCTCTATTAGAGGAGCTTTG
Found at i:18500840 original size:17 final size:17
Alignment explanation
Indices: 18500818--18500859 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
18500808 TATTTTATTC
* *
18500818 TTATTTTTTTATTTGTG
1 TTATTTTATTATTTATG
*
18500835 TTATTTTATTATTTATT
1 TTATTTTATTATTTATG
18500852 TTATTTTA
1 TTATTTTA
18500860 GGACATTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTATTTTATTATTTATG
Found at i:18501236 original size:12 final size:12
Alignment explanation
Indices: 18501221--18501251 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
18501211 AAATAGAAAA
18501221 GAAAATTTTTTG
1 GAAAATTTTTTG
18501233 G-AAATTTTTTG
1 GAAAATTTTTTG
18501244 GAAAATTT
1 GAAAATTT
18501252 CTAGATTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
GAAAATTTTTTG
Found at i:18501841 original size:4 final size:4
Alignment explanation
Indices: 18501832--18501858 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18501822 TAATTTTAAT
18501832 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
18501859 TTGTCAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:18502085 original size:137 final size:128
Alignment explanation
Indices: 18501892--18502200 Score: 333
Period size: 137 Copynumber: 2.3 Consensus size: 128
18501882 AATTTCCAAA
** *
18501892 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATC-ATTTTTCCTTAGAAATAAATTTTCTAAAA-A
1 AAAAAA-ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTCTAAAATA
* *
18501955 ATATTTCCAATTTCTAAAAAATATTTTTGA-AGAAAAGTTGAAAGTATTAATTTT-TATTGATAA
65 A-A-----AATTT-TAAAAAACA-TTTTGAGA-AAAAGTTGAAAGTATCAATTTTCT-TTGA-AA
*
18502018 CAAAAAATTTT
119 -AAAAAATTTC
*
18502029 AAAAAACATTTTTTAGGAAAAGTTGAAAGTATCAATTTTT-CTTAAAAATAAATTTTCTAAAATA
1 AAAAAA-ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTCTAAAATA
* * **
18502093 AAAATTTTCAAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAATTAAAATTTC
65 AAAATTTTAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAAAAAAATTTC
18502157 AAAAAAATATGTTTAAGGAAAAGTTGAAAGTATCAA-TTTTCCTT
1 AAAAAAAT-T-TTTAAGGAAAAGTTGAAAGTATCAATTTTTCCTT
18502201 GTATAAAAGA
Statistics
Matches: 153, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
127 2 0.01
128 18 0.12
129 29 0.19
130 31 0.20
131 8 0.05
132 5 0.03
137 52 0.34
138 8 0.05
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (128 bp):
AAAAAAATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTCTAAAATAA
AAATTTTAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAAAAAAATTTC
Found at i:18502086 original size:16 final size:16
Alignment explanation
Indices: 18502065--18502105 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18502055 AAGTATCAAT
*
18502065 TTTTCTTAAAA-ATAAA
1 TTTTC-TAAAATAAAAA
18502081 TTTTCTAAAATAAAAA
1 TTTTCTAAAATAAAAA
18502097 TTTTC-AAAA
1 TTTTCTAAAA
18502106 GCATTTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTCTAAAATAAAAA
Found at i:18506153 original size:21 final size:21
Alignment explanation
Indices: 18506129--18506173 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
18506119 AATTAATTCC
*
18506129 TTTCC-TTCCTTTATTTTTTCT
1 TTTCCTTTCCTTT-CTTTTTCT
*
18506150 TTTCCTTTTCTTTCTTTTTCT
1 TTTCCTTTCCTTTCTTTTTCT
18506171 TTT
1 TTT
18506174 TTTGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCCTTTCCTTTCTTTTTCT
Found at i:18506242 original size:46 final size:46
Alignment explanation
Indices: 18506163--18506268 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 46
18506153 CCTTTTCTTT
* * * * *
18506163 CTTTTTCTTTTTTTGAAATAAGAAATAAATCAAATTTATAACAAAA
1 CTTTTTTTTTTTTTCAAACAAAAAATAAATCAAATTTAAAACAAAA
*
18506209 -TTTTTTTTTTTTTCAAACAAAAAGATAAGTCAAATTTAAAACAAAA
1 CTTTTTTTTTTTTTCAAACAAAAA-ATAAATCAAATTTAAAACAAAA
* *
18506255 CATTTTTTATTTTT
1 CTTTTTTTTTTTTT
18506269 GGAACAAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 19 0.38
46 20 0.40
47 11 0.22
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (46 bp):
CTTTTTTTTTTTTTCAAACAAAAAATAAATCAAATTTAAAACAAAA
Found at i:18506708 original size:19 final size:20
Alignment explanation
Indices: 18506680--18506721 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
18506670 TTAGGTTAGA
*
18506680 GTTAGAGTTTTAGGTTTTGG
1 GTTAGAGTTTTAGGGTTTGG
18506700 GTTAG-GTTTTAGGGTTTGG
1 GTTAGAGTTTTAGGGTTTGG
18506719 GTT
1 GTT
18506722 TATGGCTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (20 bp):
GTTAGAGTTTTAGGGTTTGG
Found at i:18506737 original size:6 final size:6
Alignment explanation
Indices: 18506667--18506758 Score: 53
Period size: 6 Copynumber: 14.3 Consensus size: 6
18506657 GGGCGTTTGG
* * *
18506667 GGTTTA GG-TTA GAG-TTA GAGTTTTA GGTTTT GGGTTA GGTTTTA GGGTTTG
1 GGTTTA GGTTTA G-GTTTA G-G-TTTA GGTTTA GGTTTA GG-TTTA -GGTTTA
* *
18506718 GGTTTA TGGCTTA GGTTTA GAGTTTA AGTTTA GGGTTTA GG
1 GGTTTA -GGTTTA GGTTTA G-GTTTA GGTTTA -GGTTTA GG
18506759 GCTTGGGTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 36 0.53
7 22 0.32
8 6 0.09
ACGTcount: A:0.17, C:0.01, G:0.36, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:18506762 original size:33 final size:33
Alignment explanation
Indices: 18506713--18506789 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
18506703 AGGTTTTAGG
* *
18506713 GTTT-GGGTTTATGGCTTAGGTTTA-GAGTTTAA
1 GTTTAGGGTTTAGGGCTTAGGTTTATGA-TTCAA
*
18506745 GTTTAGGGTTTAGGGCTTGGGTTTATGATTCAA
1 GTTTAGGGTTTAGGGCTTAGGTTTATGATTCAA
18506778 GATTTAGGGTTT
1 G-TTTAGGGTTT
18506790 TTGATTTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 4 0.10
33 23 0.59
34 12 0.31
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.45
Consensus pattern (33 bp):
GTTTAGGGTTTAGGGCTTAGGTTTATGATTCAA
Found at i:18506795 original size:14 final size:14
Alignment explanation
Indices: 18506778--18506840 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 14
18506768 TATGATTCAA
*
18506778 GATTTAGGGTTTTT
1 GATTTAGGGTTTTG
*
18506792 GATTTAGGGTTTGG
1 GATTTAGGGTTTTG
* *
18506806 GGTTTAGGGTTTAG
1 GATTTAGGGTTTTG
*
18506820 GTTTTAGGGTTTT-
1 GATTTAGGGTTTTG
18506833 GATTTAGG
1 GATTTAGG
18506841 ATTTCGATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
13 7 0.17
14 35 0.83
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (14 bp):
GATTTAGGGTTTTG
Found at i:18506808 original size:21 final size:21
Alignment explanation
Indices: 18506753--18506840 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 21
18506743 AAGTTTAGGG
*
18506753 TTTAGGGCTT-GGGTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
* * * *
18506773 TTCAAGATTTAGGGTTTTTGA
1 TTTAGGGTTTAGGGTTTATGA
* * *
18506794 TTTAGGGTTTGGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTATGA
*
18506815 TTTAGGTTTTAGGGTTT-TGA
1 TTTAGGGTTTAGGGTTTATGA
18506835 TTTAGG
1 TTTAGG
18506841 ATTTCGATTT
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 13 0.25
21 38 0.75
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATGA
Found at i:18506838 original size:13 final size:13
Alignment explanation
Indices: 18506778--18506850 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 13
18506768 TATGATTCAA
*
18506778 GATTTAGGGTTTTT
1 GATTTAGGG-TTTG
18506792 GATTTAGGGTTTGG
1 GATTTAGGGTTT-G
*
18506806 GGTTTAGGGTTTAG
1 GATTTAGGGTTT-G
* *
18506820 GTTTTAGGGTTTT
1 GATTTAGGGTTTG
* *
18506833 GATTTAGGATTTC
1 GATTTAGGGTTTG
18506846 GATTT
1 GATTT
18506851 GAAATCTCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
13 18 0.36
14 32 0.64
ACGTcount: A:0.15, C:0.01, G:0.33, T:0.51
Consensus pattern (13 bp):
GATTTAGGGTTTG
Found at i:18506844 original size:7 final size:7
Alignment explanation
Indices: 18506688--18506831 Score: 93
Period size: 7 Copynumber: 21.4 Consensus size: 7
18506678 GAGTTAGAGT
18506688 TTTA-GG
1 TTTAGGG
*
18506694 TTTTGGG
1 TTTAGGG
*
18506701 -TTAGGT
1 TTTAGGG
18506707 TTTAGGG
1 TTTAGGG
18506714 TTT-GGG
1 TTTAGGG
*
18506720 TTTATGG
1 TTTAGGG
*
18506727 CTTA-GG
1 TTTAGGG
*
18506733 TTTAGAG
1 TTTAGGG
*
18506740 TTTA-AG
1 TTTAGGG
18506746 TTTAGGG
1 TTTAGGG
18506753 TTTAGGG
1 TTTAGGG
*
18506760 CTT-GGG
1 TTTAGGG
* *
18506766 TTTATGA
1 TTTAGGG
* * *
18506773 TTCAAGA
1 TTTAGGG
18506780 TTTAGGG
1 TTTAGGG
** *
18506787 TTTTTGA
1 TTTAGGG
18506794 TTTAGGG
1 TTTAGGG
*
18506801 TTTGGGG
1 TTTAGGG
18506808 TTTAGGG
1 TTTAGGG
*
18506815 TTTAGGT
1 TTTAGGG
18506822 TTTAGGG
1 TTTAGGG
18506829 TTT
1 TTT
18506832 TGATTTAGGA
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
6 29 0.28
7 75 0.72
ACGTcount: A:0.15, C:0.02, G:0.35, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:18511123 original size:13 final size:13
Alignment explanation
Indices: 18511105--18511147 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
18511095 GGCCTTTCTT
18511105 AGTTTATATATAA
1 AGTTTATATATAA
*
18511118 AGTTTA-ATCT-A
1 AGTTTATATATAA
18511129 AGTTTATATATAA
1 AGTTTATATATAA
18511142 AGTTTA
1 AGTTTA
18511148 ATCTATCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 6 0.23
13 13 0.50
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (13 bp):
AGTTTATATATAA
Found at i:18511133 original size:24 final size:24
Alignment explanation
Indices: 18511105--18511152 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
18511095 GGCCTTTCTT
18511105 AGTTTATATATAAAGTTTAATCTA
1 AGTTTATATATAAAGTTTAATCTA
18511129 AGTTTATATATAAAGTTTAATCTA
1 AGTTTATATATAAAGTTTAATCTA
18511153 TCACTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
AGTTTATATATAAAGTTTAATCTA
Found at i:18512262 original size:18 final size:18
Alignment explanation
Indices: 18512241--18512385 Score: 140
Period size: 18 Copynumber: 8.1 Consensus size: 18
18512231 ATTTTACTTT
18512241 TAAATAATATTATATTAA
1 TAAATAATATTATATTAA
18512259 TAAATAATATTATATTAA
1 TAAATAATATTATATTAA
*
18512277 TAGATAATA-TACTATTAA
1 TAAATAATATTA-TATTAA
18512295 T--AT-A-A-TATATTAA
1 TAAATAATATTATATTAA
18512308 TAAATAATATTATATTAA
1 TAAATAATATTATATTAA
18512326 TAAATAATATTTAATATATTAA
1 TAAATAATA--T--TATATTAA
* * *
18512348 TAAAATAATATAAAAATAA
1 T-AAATAATATTATATTAA
* *
18512367 TAAATAATTTTATTTTAA
1 TAAATAATATTATATTAA
18512385 T
1 T
18512386 TATATTTATA
Statistics
Matches: 107, Mismatches: 9, Indels: 22
0.78 0.07 0.16
Matches are distributed among these distances:
13 7 0.07
14 3 0.03
15 3 0.03
16 3 0.03
17 3 0.03
18 63 0.59
19 6 0.06
20 1 0.01
21 1 0.01
22 9 0.08
23 8 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
TAAATAATATTATATTAA
Found at i:18512367 original size:67 final size:67
Alignment explanation
Indices: 18512241--18512368 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 67
18512231 ATTTTACTTT
* * * *
18512241 TAAATAATATTATATTAATAAATAATATTATATTAATAGATAATATACTATTAATATAATATATT
1 TAAATAATATTATATTAATAAATAATATTATATTAATAGATAAAATAATATAAAAATAATATATT
18512306 AA
66 AA
*
18512308 TAAATAATATTATATTAATAAATAATATT-TAATATATTA-ATAAAATAATATAAAAATAATA
1 TAAATAATATTATATTAATAAATAATATTAT-AT-TAATAGATAAAATAATATAAAAATAATA
18512369 AATAATTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
66 1 0.02
67 49 0.91
68 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (67 bp):
TAAATAATATTATATTAATAAATAATATTATATTAATAGATAAAATAATATAAAAATAATATATT
AA
Done.