Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 86 of 106
Found at i:17251667 original size:31 final size:29
Alignment explanation
Indices: 17251611--17251668 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
17251601 TATAAACAGT
* *
17251611 ATTTTATTAAATTAATATATTAAATTATA
1 ATTTTATTAAAATAATAAATTAAATTATA
17251640 ATTTTATTAATAATATATAAATTAAATTA
1 ATTTTATTAA-AATA-ATAAATTAAATTA
17251669 AATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 3 0.12
31 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTATTAAAATAATAAATTAAATTATA
Found at i:17251676 original size:25 final size:27
Alignment explanation
Indices: 17251618--17251680 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
17251608 AGTATTTTAT
**
17251618 TAAATTAATATATTAAATTATAATTTTA
1 TAAA-TAATATATTAAATTATAATTAAA
*
17251646 TTAATAATATA-TAAATTA-AATTAAA
1 TAAATAATATATTAAATTATAATTAAA
17251671 TAAATAATAT
1 TAAATAATAT
17251681 TATATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 14 0.45
26 7 0.23
27 7 0.23
28 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATAATATATTAAATTATAATTAAA
Found at i:17254188 original size:28 final size:29
Alignment explanation
Indices: 17254121--17254188 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
17254111 ATAGTTCTTG
17254121 AATTATAATAAAATATTTAATATAATAATTA
1 AATTAT-A-AAAATATTTAATATAATAATTA
* *
17254152 AATTCTAAAAAT-TTTAATATAATATTTA
1 AATTATAAAAATATTTAATATAATAATTA
*
17254180 CATTATAAA
1 AATTATAAA
17254189 TTTATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 22 0.67
29 5 0.15
30 1 0.03
31 5 0.15
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTATAAAAATATTTAATATAATAATTA
Found at i:17254692 original size:14 final size:15
Alignment explanation
Indices: 17254673--17254701 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17254663 ATGATTGTTT
17254673 TTATTT-AAATATAA
1 TTATTTAAAATATAA
17254687 TTATTTAAAATATAA
1 TTATTTAAAATATAA
17254702 ATAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTTAAAATATAA
Found at i:17254717 original size:21 final size:21
Alignment explanation
Indices: 17254678--17254717 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17254668 TGTTTTTATT
* * *
17254678 TAAATATAATTATTTAAAATA
1 TAAATAAAATTAATAAAAATA
17254699 TAAATAAAATTAATAAAAA
1 TAAATAAAATTAATAAAAA
17254718 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAAATTAATAAAAATA
Found at i:17255682 original size:14 final size:14
Alignment explanation
Indices: 17255663--17255693 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17255653 TAGACTTGTA
17255663 TTTTTTTTAATTTT
1 TTTTTTTTAATTTT
17255677 TTTTTTTTAATTTT
1 TTTTTTTTAATTTT
17255691 TTT
1 TTT
17255694 ACCTATACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTAATTTT
Found at i:17255751 original size:55 final size:55
Alignment explanation
Indices: 17255682--17255800 Score: 166
Period size: 55 Copynumber: 2.2 Consensus size: 55
17255672 ATTTTTTTTT
* *
17255682 TTTAATTTTTTTACCTATACCGACTATTAGAGACTGTCAATATAGAATTATATGC
1 TTTAATTTTCTTACCTATACCGACGATTAGAGACTGTCAATATAGAATTATATGC
* ** * * *
17255737 TTTAATTTTCTTACCTTTATTGACGATTAGAGATTGTCAATATAGACTTATATGT
1 TTTAATTTTCTTACCTATACCGACGATTAGAGACTGTCAATATAGAATTATATGC
17255792 TTTAATTTT
1 TTTAATTTT
17255801 TTTATTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (55 bp):
TTTAATTTTCTTACCTATACCGACGATTAGAGACTGTCAATATAGAATTATATGC
Found at i:17255928 original size:24 final size:24
Alignment explanation
Indices: 17255896--17255942 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17255886 TTTTTTTAAA
* *
17255896 AATTATATTTTTAATTATTAATATT
1 AATTATATTTATAATCA-TAATATT
17255921 AATT-TATTTATAATCATAATAT
1 AATTATATTTATAATCATAATAT
17255943 GATATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATATTTATAATCATAATATT
Found at i:17256098 original size:15 final size:15
Alignment explanation
Indices: 17256078--17256113 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17256068 TATCAAGTCT
*
17256078 GATAAAACAAACATC
1 GATAAAACAAACATA
17256093 GATAAAACAAACATA
1 GATAAAACAAACATA
17256108 GATAAA
1 GATAAA
17256114 GAGTTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.14, G:0.08, T:0.14
Consensus pattern (15 bp):
GATAAAACAAACATA
Found at i:17263845 original size:99 final size:99
Alignment explanation
Indices: 17263667--17263855 Score: 270
Period size: 99 Copynumber: 1.9 Consensus size: 99
17263657 TTTTTTGCTT
* * * *
17263667 AAAATACCTTCAATAATCTCCTTCAATTTTATAGAAGCGACATTTTCTATCAAAAACACATTCAA
1 AAAACACCTTCAATAATCCCCTTCAATTTTATAAAAGAGACATTTTCTATCAAAAACACATTCAA
17263732 TAATCCCTAATCATTTTTTTTGGATTATTGGCCA
66 TAATCCCTAATCATTTTTTTTGGATTATTGGCCA
* * * * *
17263766 AAAACACCTTCAATAATCCCCTTCAATTTTTTAAAAGAGACATTTTTTGTCAAAAACACCTTTAA
1 AAAACACCTTCAATAATCCCCTTCAATTTTATAAAAGAGACATTTTCTATCAAAAACACATTCAA
* **
17263831 TAATTCCTTTTCATTTTTTTTGGAT
66 TAATCCCTAATCATTTTTTTTGGAT
17263856 CATTCAAGGC
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (99 bp):
AAAACACCTTCAATAATCCCCTTCAATTTTATAAAAGAGACATTTTCTATCAAAAACACATTCAA
TAATCCCTAATCATTTTTTTTGGATTATTGGCCA
Found at i:17264202 original size:234 final size:233
Alignment explanation
Indices: 17263806--17264226 Score: 542
Period size: 233 Copynumber: 1.8 Consensus size: 233
17263796 TTAAAAGAGA
* * * **
17263806 CATTTTTTGTCAAAAACACCTTTAATAATTCCTTTTCATTTTTTTTGGATCATTCAAGGCATTTT
1 CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGGATCATTCAAGGCATTTT
* * * * * *
17263871 TTATGATAAAATACCTTGAATAATCCATTGGGTTAGTCAAGGCATTTATGGCCTAAATTGTCTTG
66 TTATGATAAAACACCTTGAATAATCCATTAGGTTAGTCAAGGCATTTATGGCCAAAAATGCCTTA
* * * * * *
17263936 AATAATCTCCTTTAGGCGTTTATAAAGAGATTATTGAAGGACGTTTTTGGCC-AAAAACGCCTTT
131 AATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGG-CATTTTTGCCCTAAAAACGCCTTT
17264000 AATAATTTTGTCCAATTTTTTAGAGGGGATTATTCAAGG
195 AATAATTTTGTCCAATTTTTTAGAGGGGATTATTCAAGG
* *
17264039 CATTTTTTGTCGAAAACGCCTTCAATAATCCCCTCCCATTTTTTTTGGAATCATTCAAAGG-A-T
1 CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGG-ATCATTC-AAGGCATT
* * * * * *
17264102 TTTTGTGATAAAACGCTTTGAATAATCCTTTAAGGTTAGTTAAGGCGTTTATGGCCAAAAATGCC
64 TTTTATGATAAAACACCTTGAATAATCCATT-AGGTTAGTCAAGGCATTTATGGCCAAAAATGCC
* *
17264167 TTAAATAATCACCTTCAAGCATTTATGAGGAGATTATTGAAGGCATTTTTGCCCTAAAAA
128 TTAAATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGGCATTTTTGCCCTAAAAA
17264227 TTCCTTGAAT
Statistics
Matches: 157, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
233 77 0.49
234 76 0.48
235 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (233 bp):
CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGGATCATTCAAGGCATTTT
TTATGATAAAACACCTTGAATAATCCATTAGGTTAGTCAAGGCATTTATGGCCAAAAATGCCTTA
AATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGGCATTTTTGCCCTAAAAACGCCTTTA
ATAATTTTGTCCAATTTTTTAGAGGGGATTATTCAAGG
Found at i:17264275 original size:234 final size:233
Alignment explanation
Indices: 17263806--17264301 Score: 525
Period size: 234 Copynumber: 2.1 Consensus size: 233
17263796 TTAAAAGAGA
* * * **
17263806 CATTTTTTGTCAAAAACACCTTTAATAATTCCTTTTCATTTTTTTTGGATCATTCAAGGCATTTT
1 CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGGATCATTCAAGGCATTTT
* * * * * *
17263871 TTATGATAAAATACCTTGAATAATCCATTGGGTTAGTCAAGGCATTTATGGCCTAAATTGTCTTG
66 TTATGATAAAACACCTTGAATAATCCATTAGGTTAGTCAAGGCATTTATGGCCAAAAATGCCTTA
* * * * * * *
17263936 AATAATCTCCTTTAGGCGTTTATAAAGAGATTATTGAAGGACGTTTTTGGCCAAAAACGCCTTTA
131 AATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGGACATTTTTGCCCAAAAACGCCTTGA
* ** * * * *
17264001 ATAATTTTGTCCAATTTTTTAGAGGGGATTATTCAAGG
196 ATAATTCTAACAAAATATTGAGAGGGGATTATTCAAGG
* *
17264039 CATTTTTTGTCGAAAACGCCTTCAATAATCCCCTCCCATTTTTTTTGGAATCATTCAAAGG-A-T
1 CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGG-ATCATTC-AAGGCATT
* * * * * *
17264102 TTTTGTGATAAAACGCTTTGAATAATCCTTTAAGGTTAGTTAAGGCGTTTATGGCCAAAAATGCC
64 TTTTATGATAAAACACCTTGAATAATCCATT-AGGTTAGTCAAGGCATTTATGGCCAAAAATGCC
* * **
17264167 TTAAATAATCACCTTCAAGCATTTATGAGGAGATTATTGAAGG-CATTTTTGCCCTAAAAATTCC
128 TTAAATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGGACATTTTTGCCC-AAAAACGCC
*
17264231 TTGAATAATCTCTAACAAAATATTGA-ATGGGG-TTATTGAAGG
192 TTGAATAAT-TCTAACAAAATATTGAGA-GGGGATTATTCAAGG
* * * *
17264273 CATTTCTAGCCAAAAACACCTTGAATAAT
1 CATTTTTTGTCAAAAACACCTTCAATAAT
17264302 TTTTGGATTA
Statistics
Matches: 213, Mismatches: 44, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
233 77 0.36
234 119 0.56
235 17 0.08
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (233 bp):
CATTTTTTGTCAAAAACACCTTCAATAATCCCCTCCCATTTTTTTTGGATCATTCAAGGCATTTT
TTATGATAAAACACCTTGAATAATCCATTAGGTTAGTCAAGGCATTTATGGCCAAAAATGCCTTA
AATAATCACCTTCAAGCATTTATAAAGAGATTATTGAAGGACATTTTTGCCCAAAAACGCCTTGA
ATAATTCTAACAAAATATTGAGAGGGGATTATTCAAGG
Found at i:17269096 original size:26 final size:30
Alignment explanation
Indices: 17269031--17269098 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 30
17269021 TTGAAACCAA
17269031 ATTAATATAATATTTAAATTTAAAAAATTT
1 ATTAATATAATATTTAAATTTAAAAAATTT
* * *
17269061 -TTAGTCTAATATTT-AA-TT-ATAAATTT
1 ATTAATATAATATTTAAATTTAAAAAATTT
17269087 ATTAAT-TAATAT
1 ATTAATATAATAT
17269099 AATGCTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 2 0.06
29 12 0.36
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATTAATATAATATTTAAATTTAAAAAATTT
Found at i:17273030 original size:153 final size:154
Alignment explanation
Indices: 17272809--17273111 Score: 362
Period size: 154 Copynumber: 2.0 Consensus size: 154
17272799 CCTTTTATAT
* * * *
17272809 TTTAGGGTTTAGGATTAGTATTTTTATAAAAGGATTATTTAAGCCGTTTCTATACATATACACCT
1 TTTAGGGTTTAAGATTAATATTTTTATAAAAGGATTATTTAAGCAGTTTCTATACATAAACACCT
* * * * * *
17272874 TAAATAATCCTTTTATA-AAAATATAAATGGATTATTTAAGGTATTTCTGTATAGAAAATGGCTT
66 TAAACAATACTTTTATATAAAATATAAATAGATTATTTAAAGCATTTCTGTATAGAAAATGCCTT
17272938 AAATAATCT-TTTTATATTTTAGGA
131 AAATAAT-TATTTTATATTTTAGGA
* * * *
17272962 TTTAGGGTTTAAGATTAATATTTTTATAAAA-GATTATTTAAAGTATTTATGTATAGA-AAACAC
1 TTTAGGGTTTAAGATTAATATTTTTATAAAAGGATTATTT-AAGCAGTT-TCTATACATAAACAC
* **** * *
17273025 CTTAAACAATATTTTTATATTTTTTATAAATAGATTATTTAAAGCATTTTTGTATATAAAATGCC
64 CTTAAACAATACTTTTATATAAAATATAAATAGATTATTTAAAGCATTTCTGTATAGAAAATGCC
17273090 TTAAATAATTATTTTATATTTT
129 TTAAATAATTATTTTATATTTT
17273112 TATAAAAGTA
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
152 8 0.06
153 56 0.45
154 61 0.49
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.46
Consensus pattern (154 bp):
TTTAGGGTTTAAGATTAATATTTTTATAAAAGGATTATTTAAGCAGTTTCTATACATAAACACCT
TAAACAATACTTTTATATAAAATATAAATAGATTATTTAAAGCATTTCTGTATAGAAAATGCCTT
AAATAATTATTTTATATTTTAGGA
Found at i:17273066 original size:64 final size:61
Alignment explanation
Indices: 17272979--17273237 Score: 299
Period size: 63 Copynumber: 4.1 Consensus size: 61
17272969 TTTAAGATTA
* * * *
17272979 ATATTTTTATAAAAGATTATTTAA-AGTATTTATGTATAGAAAACACCTTAAACAATATTTTT
1 ATATTTTTATAAAAGATTATTTAAGA-CATTTTTGTATAGAAAATACCTTAAATAAT-TTTTT
* *
17273041 ATATTTTTTATAAATAGATTATTTAA-AGCATTTTTGTATATAAAATGCCTTAAATAATTATTTT
1 ATA-TTTTTATAAA-AGATTATTTAAGA-CATTTTTGTATAGAAAATACCTTAAATAATT-TTTT
*
17273105 ATATTTTTATAAAAGTATTATTTAAGACATTTTTTGTACAG-AAATACCTTAAATAATCTTTTT
1 ATATTTTTATAAAAG-ATTATTTAAGACA-TTTTTGTATAGAAAATACCTTAAATAAT-TTTTT
* * * *
17273168 ATATTTTTATAACTAGATTATTTAAGATATTTTTGTATAAAAAATGCCTTAAATAATTTTTGT
1 ATATTTTTATAA-AAGATTATTTAAGACATTTTTGTATAGAAAATACCTTAAATAATTTTT-T
17273231 ATATTTT
1 ATATTTT
17273238 AGGATTTAGG
Statistics
Matches: 173, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
62 18 0.10
63 98 0.57
64 57 0.33
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATTTTTATAAAAGATTATTTAAGACATTTTTGTATAGAAAATACCTTAAATAATTTTTT
Found at i:17273115 original size:126 final size:126
Alignment explanation
Indices: 17272979--17273237 Score: 357
Period size: 126 Copynumber: 2.1 Consensus size: 126
17272969 TTTAAGATTA
* *
17272979 ATATTTTTATAAAAG-ATTATTTAA-A-GTATTTATGTATAGAAAACACCTTAAACAATATTTTT
1 ATATTTTTATAAAAGTATTATTTAAGACAT-TTTATGTACAG-AAACACCTTAAACAATATTTTT
*
17273041 ATATTTTTTATAAATAGATTATTTAA-AGCATTTTTGTATATAAAATGCCTTAAATAATTATTT-
64 ATA-TTTTTATAAATAGATTATTTAAGA-CATTTTTGTATAAAAAATGCCTTAAATAATT-TTTG
17273104 T
126 T
* * * *
17273105 ATATTTTTATAAAAGTATTATTTAAGACATTTTTTGTACAGAAATACCTTAAATAATCTTTTTAT
1 ATATTTTTATAAAAGTATTATTTAAGACATTTTATGTACAGAAACACCTTAAACAATATTTTTAT
* *
17273170 ATTTTTATAACTAGATTATTTAAGATATTTTTGTATAAAAAATGCCTTAAATAATTTTTGT
66 ATTTTTATAAATAGATTATTTAAGACATTTTTGTATAAAAAATGCCTTAAATAATTTTTGT
17273231 ATATTTT
1 ATATTTT
17273238 AGGATTTAGG
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
125 3 0.03
126 73 0.61
127 32 0.27
128 10 0.08
129 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (126 bp):
ATATTTTTATAAAAGTATTATTTAAGACATTTTATGTACAGAAACACCTTAAACAATATTTTTAT
ATTTTTATAAATAGATTATTTAAGACATTTTTGTATAAAAAATGCCTTAAATAATTTTTGT
Found at i:17273453 original size:69 final size:68
Alignment explanation
Indices: 17273336--17273466 Score: 167
Period size: 69 Copynumber: 1.9 Consensus size: 68
17273326 GATCTATAAT
*
17273336 ATAAAAAAATTATTCAAGGCATTTTTATATAGAAAACATCTTAAATAATC-TTTTAATAAATATA
1 ATAAAAAAATAATTCAAGGCATTTTTATATAGAAAACATCTTAAATAATCATTTT-ATAAATATA
17273400 AAAA
65 AAAA
* * ** *
17273404 ATAAAAATAATAATTTAAGGTATTTTCTATATAG-AAATGTCTTGAATAATCATTTTATAAATA
1 ATAAAAA-AATAATTCAAGGCATTTT-TATATAGAAAACATCTTAAATAATCATTTTATAAATA
17273467 AATTAAAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 7 0.13
69 36 0.67
70 11 0.20
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (68 bp):
ATAAAAAAATAATTCAAGGCATTTTTATATAGAAAACATCTTAAATAATCATTTTATAAATATAA
AAA
Found at i:17273560 original size:12 final size:13
Alignment explanation
Indices: 17273530--17273560 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17273520 ATTAATTGAT
17273530 ATTTTTTCTAACA
1 ATTTTTTCTAACA
*
17273543 ATTTTTTCTATCA
1 ATTTTTTCTAACA
17273556 ATTTT
1 ATTTT
17273561 GTTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTTTTCTAACA
Found at i:17274906 original size:29 final size:29
Alignment explanation
Indices: 17274867--17274922 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
17274857 TAATGAAATC
* * *
17274867 TTTAATCTAATATTTAAATTTTAAAATTT
1 TTTAATATAATATTTAAACTATAAAATTT
17274896 TTTAATATAATATTTAAACTATAAAAT
1 TTTAATATAATATTTAAACTATAAAAT
17274923 CATATCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAATATAATATTTAAACTATAAAATTT
Found at i:17275427 original size:124 final size:124
Alignment explanation
Indices: 17275200--17275437 Score: 356
Period size: 124 Copynumber: 1.9 Consensus size: 124
17275190 AGAATAACAG
* * * * *
17275200 TCTTCTTTATATTCATATCCCTTTGAATTAGATACAAATTAAATATAATATAAAATATTTATCAT
1 TCTTCTTTATATTCATATCACTTTCAATTAGATAAAAACTAAATATAATATAAAATAATTATCAT
* *
17275265 ACTATTTTATTTATTATATTATATACATAAAAAAATTTAAATTTATTAAATAAATATAA
66 ACTATTTTATCTATTATACTATATACATAAAAAAATTTAAATTTATTAAATAAATATAA
*
17275324 TCTTCTTTATATTCATTTCACTTTCAATTAGATAAAAACTAAATATAATATAAAATAATTATCAT
1 TCTTCTTTATATTCATATCACTTTCAATTAGATAAAAACTAAATATAATATAAAATAATTATCAT
17275389 ACT-TATTTATCTATTAT-CT-TATACATAAAAAATTATTTAAATTTATTAA
66 ACTAT-TTTATCTATTATACTATATACATAAAAAA--ATTTAAATTTATTAA
17275438 CTAATATGAT
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
122 13 0.13
123 2 0.02
124 88 0.85
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.45
Consensus pattern (124 bp):
TCTTCTTTATATTCATATCACTTTCAATTAGATAAAAACTAAATATAATATAAAATAATTATCAT
ACTATTTTATCTATTATACTATATACATAAAAAAATTTAAATTTATTAAATAAATATAA
Found at i:17276620 original size:191 final size:192
Alignment explanation
Indices: 17276396--17276756 Score: 436
Period size: 191 Copynumber: 1.9 Consensus size: 192
17276386 AATAAGTATT
*
17276396 AATTATCCAATGATGGAATTTATAGAAATTTCAAATGATAAATTTT-TACA-AAAT-TCTTAGGT
1 AATTATCCAATAATGGAATTTATAGAAATTTCAAATGATAAATTTTCTA-ATAAATCTC-TAGGT
* * * * * * * *
17276458 GAAAAATTTTATTTAAATTTGTCCCAAATTG-AGGAATAATTTAGAT-AAAGTTTCAATAACAAT
64 G-AAAACTTTATTTAAATTTATCCCAAATGGTA-AAAGAATTTAAATGAAA-TTTCAAGAAAAAT
17276521 AATTA--ATATTTATTTTCATTAAAAAAAAGAA-AAAAATAAAAAAACATTTGGTTGAAAATATG
126 AATTATCATA-TTATTTTCATTAAAAAAAA-AAGAAAAATAAAAAAACATTTGGTTGAAAATATG
17276583 TGAC
189 TGAC
*
17276587 AATTATCCAATAAT-GAGATTCT-TAGAAATTTCAAATGGTAAATTTTCTAATAAATCTCTAGGT
1 AATTATCCAATAATGGA-ATT-TATAGAAATTTCAAATGATAAATTTTCTAATAAATCTCTAGGT
* *
17276650 GAGAACTTTCTTTAAATTTATCCCAAATGGTAAAAGAATTTAAATGAAATTTCAAGAAAAATAAT
64 GAAAACTTTATTTAAATTTATCCCAAATGGTAAAAGAATTTAAATGAAATTTCAAGAAAAATAAT
* * *
17276715 TGTCATATTATTTTCTTTAAAAAAAAAAGAGAAATAAAAAAA
129 TATCATATTATTTTCATTAAAAAAAAAAGAAAAATAAAAAAA
17276757 TTTTCTAAAT
Statistics
Matches: 145, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
190 2 0.01
191 91 0.63
192 47 0.32
193 5 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (192 bp):
AATTATCCAATAATGGAATTTATAGAAATTTCAAATGATAAATTTTCTAATAAATCTCTAGGTGA
AAACTTTATTTAAATTTATCCCAAATGGTAAAAGAATTTAAATGAAATTTCAAGAAAAATAATTA
TCATATTATTTTCATTAAAAAAAAAAGAAAAATAAAAAAACATTTGGTTGAAAATATGTGAC
Found at i:17276857 original size:120 final size:121
Alignment explanation
Indices: 17276744--17276961 Score: 289
Period size: 121 Copynumber: 1.8 Consensus size: 121
17276734 AAAAAAAAAG
* * *
17276744 AGAAATAAA-AAAATTTTCTAAATAGGCCCAAATTGTGAAAAATTTAGAAATTCCAAAAAAGAAA
1 AGAAATAAATAAAA-TTTATAAATAGGCCCAAATTATGAAAAATTTAAAAATT-CAAAAAAGAAA
17276808 ATATTTCTAAATTGA-CCCAAATAGTGAAA-AATTTAGAAATCCAACAAAAATAAATAA
64 ATATTT-TAAATTGAGCCCAAATAGTGAAATAATTTAGAAATCCAACAAAAATAAATAA
* * * * * *
17276865 ATAAATAAATAGAATTTATAAATAGGCCTAAATTATGGAAATTTTAAAAATTTAAAAAAGAAAAT
1 AGAAATAAATAAAATTTATAAATAGGCCCAAATTATGAAAAATTTAAAAATTCAAAAAAGAAAAT
* *
17276930 ATTTTTAATTTAGCCCAAATAGTGAAATAATT
66 ATTTTAAATTGAGCCCAAATAGTGAAATAATT
17276962 AAATATATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
119 6 0.07
120 30 0.36
121 44 0.53
122 3 0.04
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (121 bp):
AGAAATAAATAAAATTTATAAATAGGCCCAAATTATGAAAAATTTAAAAATTCAAAAAAGAAAAT
ATTTTAAATTGAGCCCAAATAGTGAAATAATTTAGAAATCCAACAAAAATAAATAA
Found at i:17276863 original size:53 final size:52
Alignment explanation
Indices: 17276750--17276863 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
17276740 AAAGAGAAAT
* *
17276750 AAAAAAAT-TTTCTAAATAGGCCCAAATTGTGAAAAATTTAGAAATTCCAAA
1 AAAAAAATATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAAA
*
17276801 AAAGAAAATATTTCTAAATTGACCCAAATAGTGAAAAATTTAGAAA-TCCAACA
1 AAA-AAAATATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAA-A
17276854 AAAATAAATA
1 AAAA-AAATA
17276864 AATAAATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
51 3 0.05
52 11 0.20
53 42 0.75
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.25
Consensus pattern (52 bp):
AAAAAAATATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAAA
Found at i:17280912 original size:13 final size:14
Alignment explanation
Indices: 17280895--17280976 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 14
17280885 AATGGATGAA
17280895 AAAAATGAGAAAA-G
1 AAAAA-GAGAAAATG
17280909 AAAAAGAGAAAATG
1 AAAAAGAGAAAATG
*
17280923 AAAAAAAATGAAAAATG
1 -AAAAAGA-G-AAAATG
17280940 AAAATA-ATGAAAAT-
1 AAAA-AGA-GAAAATG
17280954 -AAAAGAGAAAAT-
1 AAAAAGAGAAAATG
17280966 AAAAA-AGAAAA
1 AAAAAGAGAAAA
17280977 AAATAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
12 13 0.22
13 15 0.25
14 6 0.10
15 11 0.18
16 8 0.13
17 7 0.12
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAAAGAGAAAATG
Found at i:17280921 original size:21 final size:20
Alignment explanation
Indices: 17280904--17281002 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 20
17280894 AAAAAATGAG
17280904 AAAAGAAAAAGAGAAAATGAAAA
1 AAAAGAAAAAGAGAAAAT---AA
*
17280927 AAAATGAAAAA-TGAAAATAA
1 AAAA-GAAAAAGAGAAAATAA
*
17280947 TGAAAA-TAAAAGAGAAAATAA
1 --AAAAGAAAAAGAGAAAATAA
* * *
17280968 AAAAGAAAAAAATAAAA-AT
1 AAAAGAAAAAGAGAAAATAA
17280987 AAAAGAAAAAGA-AAAA
1 AAAAGAAAAAGAGAAAA
17281003 AACTCAAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
18 4 0.06
19 16 0.25
20 15 0.24
21 8 0.13
22 4 0.06
23 10 0.16
24 6 0.10
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAAGAGAAAATAA
Found at i:17280965 original size:12 final size:12
Alignment explanation
Indices: 17280948--17281001 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
17280938 TGAAAATAAT
17280948 GAAAATAAAAGA
1 GAAAATAAAAGA
*
17280960 GAAAATAAAAAA
1 GAAAATAAAAGA
*
17280972 G-AAA-AAAATA
1 GAAAATAAAAGA
17280982 -AAAATAAAAGA
1 GAAAATAAAAGA
*
17280993 -AAAAGAAAA
1 GAAAATAAAA
17281002 AAACTCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.22
11 16 0.44
12 12 0.33
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (12 bp):
GAAAATAAAAGA
Found at i:17280969 original size:26 final size:25
Alignment explanation
Indices: 17280904--17280990 Score: 82
Period size: 26 Copynumber: 3.7 Consensus size: 25
17280894 AAAAAATGAG
*
17280904 AAAA-GAAAAA-GAGAAAATGAAAA
1 AAAATGAAAAATGAAAAAATGAAAA
17280927 AAAATGAAAAATGAAAATAATGAAAA
1 AAAATGAAAAATGAAAA-AATGAAAA
17280953 TAAAA-GAGAAAAT-AAAAAA-G-AAA
1 -AAAATGA-AAAATGAAAAAATGAAAA
17280976 AAAAT-AAAAAT-AAAA
1 AAAATGAAAAATGAAAA
17280991 GAAAAAGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
21 9 0.16
22 5 0.09
23 7 0.12
24 7 0.12
25 6 0.11
26 14 0.25
27 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (25 bp):
AAAATGAAAAATGAAAAAATGAAAA
Found at i:17280970 original size:27 final size:26
Alignment explanation
Indices: 17280919--17281004 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
17280909 AAAAAGAGAA
*
17280919 AATGAAAAAAAATGAAAAATGAAAAT
1 AATGAAAAAAAATGAAAAATAAAAAT
17280945 AATGAAAATAAAA-GAGAAAAT-AAAA-
1 AATGAAAA-AAAATGA-AAAATAAAAAT
*
17280970 AA-G-AAAAAAAT-AAAAATAAAAGAA
1 AATGAAAAAAAATGAAAAATAAAA-AT
*
17280994 AAAGAAAAAAA
1 AATGAAAAAAA
17281005 CTCAAATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
21 5 0.10
22 8 0.15
23 4 0.08
24 3 0.06
25 3 0.06
26 20 0.38
27 9 0.17
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (26 bp):
AATGAAAAAAAATGAAAAATAAAAAT
Found at i:17280978 original size:14 final size:15
Alignment explanation
Indices: 17280892--17280985 Score: 57
Period size: 16 Copynumber: 5.9 Consensus size: 15
17280882 ACTAATGGAT
*
17280892 GAAAAAAATGAGAAAA
1 GAAAAAAAT-AAAAAA
* * *
17280908 GAAAAAGA-GAAAAT
1 GAAAAAAATAAAAAA
*
17280922 GAAAAAAAATGAAAAAT
1 G-AAAAAAAT-AAAAAA
*
17280939 GAAAATAATGAAAATAA
1 GAAAAAAAT-AAAA-AA
17280956 -AAGAGAAAATAAAAAA
1 GAA-A-AAAATAAAAAA
17280972 GAAAAAAATAAAAA
1 GAAAAAAATAAAAA
17280986 TAAAAGAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
14 4 0.06
15 16 0.26
16 24 0.39
17 14 0.23
18 4 0.06
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
GAAAAAAATAAAAAA
Found at i:17282285 original size:22 final size:22
Alignment explanation
Indices: 17282260--17282304 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17282250 AATTCTCAAA
17282260 TGAGAATCTTTGAGTTTTTAAG
1 TGAGAATCTTTGAGTTTTTAAG
17282282 TGAGAATCTTTGAGTTTTTAAG
1 TGAGAATCTTTGAGTTTTTAAG
17282304 T
1 T
17282305 TCTCAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (22 bp):
TGAGAATCTTTGAGTTTTTAAG
Found at i:17282354 original size:25 final size:24
Alignment explanation
Indices: 17282326--17282390 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
17282316 AGTCTTTGAA
*
17282326 TTTCAAATGAAAATCTTTATGACGT
1 TTTCAAATGAGAATCTTTATGA-GT
*
17282351 TTTCAAATGAGAA-CCTT-TGAGT
1 TTTCAAATGAGAATCTTTATGAGT
17282373 TTT-AAATGAGAATCTTTA
1 TTTCAAATGAGAATCTTTA
17282391 AGAAGAACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 9 0.26
22 8 0.23
23 3 0.09
24 3 0.09
25 12 0.34
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (24 bp):
TTTCAAATGAGAATCTTTATGAGT
Found at i:17282380 original size:21 final size:22
Alignment explanation
Indices: 17282326--17282389 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
17282316 AGTCTTTGAA
* *
17282326 TTTCAAATGAAAATCTTTATGACGT
1 TTTCAAATGAGAA-CCTT-TGA-GT
17282351 TTTCAAATGAGAACCTTTGAGT
1 TTTCAAATGAGAACCTTTGAGT
*
17282373 TTT-AAATGAGAATCTTT
1 TTTCAAATGAGAACCTTT
17282390 AAGAAGAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 13 0.36
22 5 0.14
23 3 0.08
24 3 0.08
25 12 0.33
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TTTCAAATGAGAACCTTTGAGT
Found at i:17282403 original size:46 final size:47
Alignment explanation
Indices: 17282252--17282423 Score: 152
Period size: 46 Copynumber: 3.6 Consensus size: 47
17282242 GGTTTGTAAA
* * *
17282252 TTCTCAAATGAGAATCTTTGAGTTTTTAAGTGAGAATCTTTGAGTTTTTAAG
1 TTCTCAAATGAGAATCTTTGAGATTTTAAATGAGAATCTTTAAG-----AAG
* * * *
17282304 TTCTCAAATGA-AAGTCTTTGA-ATTTCAAATGAAAATCTTTATGACG
1 TTCTCAAATGAGAA-TCTTTGAGATTTTAAATGAGAATCTTTAAGAAG
* *
17282350 TTTTCAAATGAGAACCTTTGAG-TTTTAAATGAGAATCTTTAAGAAG
1 TTCTCAAATGAGAATCTTTGAGATTTTAAATGAGAATCTTTAAGAAG
** * *
17282396 AACTCAAATAAGAATATTTGAGATTTTA
1 TTCTCAAATGAGAATCTTTGAGATTTTA
17282424 GATGTGAAAC
Statistics
Matches: 97, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
46 54 0.56
47 7 0.07
51 18 0.19
52 18 0.19
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (47 bp):
TTCTCAAATGAGAATCTTTGAGATTTTAAATGAGAATCTTTAAGAAG
Found at i:17282994 original size:41 final size:41
Alignment explanation
Indices: 17282866--17283199 Score: 343
Period size: 41 Copynumber: 8.2 Consensus size: 41
17282856 ATCAATGAGT
* * *
17282866 TTTTATTTTTTAAAAGTTGTTGTACCTC-GGTTCAGAGGAGCC
1 TTTTA-TTTTTCAAAGTTGTTGTGCCTCTGCTT-AGAGGAGCC
* * * * * *
17282908 TTTTATTTTTTAAAATCGTTATGCCTTTG-TTAGAGAAGCC
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
* * * * *
17282948 TTTTATTTTTCAAAGTTGTTATGTCTTTGTTTAGAGGAGAC
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
* * *
17282989 TTTTATTTTTCAAAGTTGTTGTGCCTCTACTTAAAAGAGCC
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
* * *
17283030 TTTTATTTTTCAAAGTTGTTGTACCTCTGCCTAGAGGAGCA
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
** *
17283071 TTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAGGAGCC
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
* *** * * *
17283112 TTTTATTTTTCAAAGTTGTTGTACCTCAATTTAAATGAGCT
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
*
17283153 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAAGAG--
1 TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
17283192 TTTTATTT
1 TTTTATTT
17283200 ATTGTTTTCA
Statistics
Matches: 247, Mismatches: 43, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
39 8 0.03
40 33 0.13
41 200 0.81
42 6 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (41 bp):
TTTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGCC
Found at i:17283086 original size:123 final size:122
Alignment explanation
Indices: 17282866--17283199 Score: 386
Period size: 123 Copynumber: 2.7 Consensus size: 122
17282856 ATCAATGAGT
* ** * * * * * *
17282866 TTTTATTTTTTAAAAGTTGTTGTACCTC-GGTTCAGAGGAGCCTTTTATTTTTTAAAATCGTTAT
1 TTTTA-TTTTTCAAAGTTGTTGTACCTCAACTT-AAAAGAGCCTTTTATTTTTCAAAGTTGTTGT
* * * * * *
17282930 GCCTTTG-TTAGAGAAGCCTTTTATTTTTCAAAGTTGTTATGTCTTTGTTTAGAGGAGAC
64 GCCTCTGCTTAGAGGAG-CTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGAC
* * *
17282989 TTTTATTTTTCAAAGTTGTTGTGCCTCTACTTAAAAGAGCCTTTTATTTTTCAAAGTTGTTGTAC
1 TTTTATTTTTCAAAGTTGTTGTACCTCAACTTAAAAGAGCCTTTTATTTTTCAAAGTTGTTGTGC
* * *
17283054 CTCTGCCTAGAGGAGCATTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAGGAGCC
66 CTCTGCTTAGAGGAGC-TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGAC
* * *
17283112 TTTTATTTTTCAAAGTTGTTGTACCTCAATTTAAATGAGCTTTTTATTTTTCAAAGTTGTTGTGC
1 TTTTATTTTTCAAAGTTGTTGTACCTCAACTTAAAAGAGCCTTTTATTTTTCAAAGTTGTTGTGC
*
17283177 CTCTGCTTAGAAGAG-TTTTATTT
66 CTCTGCTTAGAGGAGCTTTTATTT
17283200 ATTGTTTTCA
Statistics
Matches: 180, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
121 8 0.04
122 51 0.28
123 121 0.67
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (122 bp):
TTTTATTTTTCAAAGTTGTTGTACCTCAACTTAAAAGAGCCTTTTATTTTTCAAAGTTGTTGTGC
CTCTGCTTAGAGGAGCTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGAC
Found at i:17283224 original size:45 final size:44
Alignment explanation
Indices: 17283072--17283302 Score: 158
Period size: 45 Copynumber: 5.4 Consensus size: 44
17283062 AGAGGAGCAT
** * *
17283072 TTTA-TTTTTCAAAGTTGTTGTGCCTCTATTTA-AAGGAGC-CT-
1 TTTATTTTTTCAAAGTTACTGAGCCTCTATTTAGAA-GAGCTTTA
** *
17283113 TTTA-TTTTTCAAAGTTGTTGTA-CCTCAATTTA-AATGAGC-TT-
1 TTTATTTTTTCAAAGTTACTG-AGCCTCTATTTAGAA-GAGCTTTA
** * ** *
17283154 TTTA-TTTTTCAAAGTTGTTGTGCCTCTGCTTAGAAGAGTTTTA
1 TTTATTTTTTCAAAGTTACTGAGCCTCTATTTAGAAGAGCTTTA
* *
17283197 TTTATTGTTTTCAAAGTTACTGAGCCTCTATTTAGAGGAGCTTGA
1 TTTATT-TTTTCAAAGTTACTGAGCCTCTATTTAGAAGAGCTTTA
* * * * *
17283242 TTTATTTTTTCCAAAATCATTGAGCCTCTATTTAGAGGAGCTTTG
1 TTTATTTTTT-CAAAGTTACTGAGCCTCTATTTAGAAGAGCTTTA
*
17283287 TTTACTTTTTCAAAGT
1 TTTATTTTTTCAAAGT
17283303 CGTGAAGCCT
Statistics
Matches: 158, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
41 66 0.42
42 4 0.03
43 4 0.03
44 10 0.06
45 74 0.47
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTTACTGAGCCTCTATTTAGAAGAGCTTTA
Found at i:17284708 original size:191 final size:192
Alignment explanation
Indices: 17284365--17284722 Score: 460
Period size: 191 Copynumber: 1.9 Consensus size: 192
17284355 AATAAGTATT
* * *
17284365 AATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTTTAGGTGAG
1 AATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATCTCTAGATGAG
* * * * * * *
17284430 AAATTTTATTTAAATTTGTCTCAAATTGTGGAACAATTTACATAAAGTTTCAATAACAATAATTA
66 AAATTTTATTTAAATTTATCCCAAATTGTAGAACAATTTAAATAAAATTTCAAGAAAAATAATTA
*
17284495 ATATTTATTTTCAATCAAAAAAAAGAAA-AATAAAATAAAATTTTGGTTGAAAATATGTGAC
131 ATATTTATTTTCAATCAAAAAAAAGAAATAAAAAAATAAAATTTTGGTTGAAAATATGTGAC
*
17284556 AATTATCCAATGATGAGATTCT-TAGAAATTTCAAATGGTAAATTTTT-TAATAAATCTCTAGAT
1 AATTATCCAATGATGAAATT-TATAGAAATTTCAAATGGTAAATTTTTAT-A-AAATCTCTAGAT
* *
17284619 GAGAAA-TTTCTTTAAATTTATCCCAAA-TGATAGAAGAATTTAAATAAAATTTCAAGAAAAATA
63 GAGAAATTTTATTTAAATTTATCCCAAATTG-TAGAACAATTTAAATAAAATTTCAAGAAAAATA
* * *
17284682 ATT-GTCATATTATTTTC-TTTAAAAAAAAGAAATAAAAAAAT
127 ATTAAT-AT-TTATTTTCAATCAAAAAAAAGAAATAAAAAAAT
17284723 TTCTAAATGG
Statistics
Matches: 143, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
190 4 0.03
191 108 0.76
192 31 0.22
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (192 bp):
AATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATCTCTAGATGAG
AAATTTTATTTAAATTTATCCCAAATTGTAGAACAATTTAAATAAAATTTCAAGAAAAATAATTA
ATATTTATTTTCAATCAAAAAAAAGAAATAAAAAAATAAAATTTTGGTTGAAAATATGTGAC
Found at i:17284785 original size:62 final size:61
Alignment explanation
Indices: 17284702--17284834 Score: 178
Period size: 63 Copynumber: 2.2 Consensus size: 61
17284692 TATTTTCTTT
* ** *
17284702 AAAAAAAAGAAATAAAAAAA-TTTCTAAATGGGCCCAAATGGTGAAAAATTTAGAAATCCA
1 AAAAAAAATAAATAAAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAGAAATCCA
* * *
17284762 ACAAAATAAATAAATAAAGAAATTTTTTAAATAAGCCCAAATGGTAAAAAATTTAGAAATTCA
1 A-AAAA-AAATAAATAAAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAGAAATCCA
17284825 AAAAAAAATA
1 AAAAAAAATA
17284835 TTTCTAATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 1 0.02
61 9 0.14
62 17 0.27
63 36 0.57
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (61 bp):
AAAAAAAATAAATAAAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAGAAATCCA
Found at i:17286409 original size:23 final size:21
Alignment explanation
Indices: 17286382--17286438 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 21
17286372 TTTAAGTAAA
17286382 AAAAATCAAAAAAATGAAAATG
1 AAAAA-CAAAAAAATGAAAATG
*
17286404 ACAAAAACAAAAAAATGAGAATG
1 --AAAAACAAAAAAATGAAAATG
17286427 AAAAACAAAAAA
1 AAAAACAAAAAA
17286439 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.38
23 15 0.47
24 5 0.16
ACGTcount: A:0.75, C:0.07, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAACAAAAAAATGAAAATG
Found at i:17288772 original size:17 final size:16
Alignment explanation
Indices: 17288750--17288805 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
17288740 TCATTTTTAA
*
17288750 AATTATTATATTAATTT
1 AATTATTA-AATAATTT
17288767 AATTATTGAAATAATTT
1 AATTATT-AAATAATTT
*
17288784 TATTATTAAAATAATTT
1 AATTATT-AAATAATTT
*
17288801 TATTA
1 AATTA
17288806 CTCGAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
17 34 0.97
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTATTAAATAATTT
Found at i:17291998 original size:19 final size:19
Alignment explanation
Indices: 17291976--17292022 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
17291966 TTATGGTGGG
*
17291976 AGATACATTTTGTGGTAAA
1 AGATACATTTTGAGGTAAA
* *
17291995 AGATATA-TTTGAGGTGAA
1 AGATACATTTTGAGGTAAA
17292013 AGATACATTT
1 AGATACATTT
17292023 GTGATGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (19 bp):
AGATACATTTTGAGGTAAA
Found at i:17295622 original size:22 final size:22
Alignment explanation
Indices: 17295597--17295638 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
17295587 ATGACAAAAG
17295597 AAATTATTAAATT-ATAAATATA
1 AAATTA-TAAATTAATAAATATA
17295619 AAATTATAAATTAATAAATA
1 AAATTATAAATTAATAAATA
17295639 ACGAAACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTATAAATTAATAAATATA
Found at i:17303370 original size:203 final size:199
Alignment explanation
Indices: 17302984--17303757 Score: 730
Period size: 203 Copynumber: 3.8 Consensus size: 199
17302974 CAAATACTGC
* * * * * * *
17302984 GACAATAAAATAAAACGTCACCCTATGTTTTTTTTTTGTGACATTAGTTTTCATCAGTTATTTAT
1 GACAATAAAATCAAACATCACCTTATATTTATTTTTTATGACATTAGTTTTCATCAGCTATTTAT
* * * * * *
17303049 GAAAAAAAAAAGTCATTGAAA-GCTATATTCATCACAAAAAAAATAAGAAAATCTGATATATTAG
66 --AAAAAAAATGTCATT-AAAGGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAG
* * * * ** * ** *
17303113 TGACGAAAGGTAAATGGTCACAGTATTAGCGACAAAATTATCATCACCAATAATTGTAAGATAAT
128 TGACAAAAGGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAGATAAT
*
17303178 GTCTACTGT
193 -TCAAC-GT
* * * *
17303187 GACAATAAAATCAAACATCACCTTATATGTTAATTTTTATGACGTTAGTTTTCGTCAGCAATTTA
1 GACAATAAAATCAAACATCACCTTATAT-TTATTTTTTATGACATTAGTTTTCATCAGCTATTTA
* * * *
17303252 TAAACAAAAACGTCATTAAAGGATATGATCGTCACAAAATAAATAATAAAATCTGATATTTTAGT
65 TAAA-AAAAATGTCATTAAAGGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAGT
* * * *
17303317 GACAAAAGGTAAATCGTCACAATATTGGTAACACAATTATTGTCACGAATAATTATAAAATAATA
129 GACAAAAGGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAGATAAT-
*
17303382 TCAAACAT
193 TC-AACGT
* ** * ** *
17303390 AACAATAAAATCAAATGTCACCTTATATTT-TTTTTATATGACATTAATTTTTGTCAGTTATTTA
1 GACAATAAAATCAAACATCACCTTATATTTATTTTT-TATGACATTAGTTTTCATCAGCTATTTA
* * * * * * * *
17303454 TAAGGAAGAATGTCATTAAAAGTTATAATCGTTACAAAATAAATGATAAAATCTTACATATTAAT
65 TAA-AAAAAATGTCATTAAAGGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAGT
* * * **
17303519 GACGAAAA-GTAAATCGTCATAGTATTGGTAATATAATTATTGTCACAAATGGTTGTAAGA-ACA
129 GAC-AAAAGGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAGATA-A
*
17303582 TTAAACGT
192 TTCAACGT
* * * *
17303590 GACAATAAAATCAAACATCACATTATGCTTTATTTTTTTGTGACATTAGTTTTCATTAGCTATTT
1 GACAATAAAATCAAACATCACCTTAT-ATTTA-TTTTTTATGACATTAGTTTTCATCAGCTATTT
* * * * *
17303655 AT-GAAAAAATGTCATTAAAGGTTATAATCGTCATAAGATAAATGATTAAATCTGATATATTAGT
64 ATAAAAAAAATGTCATTAAAGGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAGT
** * * *
17303719 GATGAAAGATAAATCATCACAATATTGGTGACATAATTA
129 GACAAAAGGTAAATCGTCACAATATTGGTAACATAATTA
17303758 ATGTTTTCAA
Statistics
Matches: 463, Mismatches: 96, Indels: 27
0.79 0.16 0.05
Matches are distributed among these distances:
199 3 0.01
200 104 0.22
201 9 0.02
202 154 0.33
203 161 0.35
204 32 0.07
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (199 bp):
GACAATAAAATCAAACATCACCTTATATTTATTTTTTATGACATTAGTTTTCATCAGCTATTTAT
AAAAAAAATGTCATTAAAGGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAGTGA
CAAAAGGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAGATAATTCA
ACGT
Found at i:17303402 original size:18 final size:17
Alignment explanation
Indices: 17303371--17303404 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17303361 ACGAATAATT
*
17303371 ATAAAATAATATCAAAC
1 ATAAAATAAAATCAAAC
17303388 ATAACAATAAAATCAAA
1 ATAA-AATAAAATCAAA
17303405 TGTCACCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAAATAAAATCAAAC
Found at i:17303533 original size:202 final size:202
Alignment explanation
Indices: 17302984--17303757 Score: 726
Period size: 202 Copynumber: 3.8 Consensus size: 202
17302974 CAAATACTGC
* * * * * *
17302984 GACAATAAAATAAAACGTCACCCTATGTTT-TTTTTTTGTGACATTAGTTTTCATCAGTTATTTA
1 GACAATAAAATCAAACATCACCTTATATTTATTTTTTTATGACATTAGTTTTCATCAGCTATTTA
* * * * * * *
17303048 TGAAAAAAAAAAGTCATTGAAAGCTATATTCATCACAAAAAAAATAAGAAAATCTGATATATTAG
66 TG-AAAAAAAATGTCATTAAAAGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAG
* * * * ** * ** * *
17303113 TGACGAAAGGTAAATGGTCACAGTATTAGCGACAAAATTATCATCACCAATAATTGTAAGATAAT
130 TGACGAAAAGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAAATAAT
*
17303178 GTC-TACTGT
195 -TCAAAC-GT
* * * *
17303187 GACAATAAAATCAAACATCACCTTATATGTTA-ATTTTTATGACGTTAGTTTTCGTCAGCAATTT
1 GACAATAAAATCAAACATCACCTTATAT-TTATTTTTTTATGACATTAGTTTTCATCAGCTATTT
* * * * *
17303251 AT-AAACAAAAACGTCATTAAAGGATATGATCGTCACAAAATAAATAATAAAATCTGATATTTTA
65 ATGAAA-AAAAATGTCATTAAAAGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTA
* * *
17303315 GTGAC-AAAAGGTAAATCGTCACAATATTGGTAACACAATTATTGTCACGAATAATTATAAAATA
129 GTGACGAAAA-GTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAAATA
*
17303379 ATATCAAACAT
193 AT-TCAAACGT
* ** * * ** *
17303390 AACAATAAAATCAAATGTCACCTTATATTT-TTTTTATATGACATTAATTTTTGTCAGTTATTTA
1 GACAATAAAATCAAACATCACCTTATATTTATTTTTTTATGACATTAGTTTTCATCAGCTATTTA
* * * * * * *
17303454 T-AAGGAAGAATGTCATTAAAAGTTATAATCGTTACAAAATAAATGATAAAATCTTACATATTAA
66 TGAA-AAAAAATGTCATTAAAAGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAG
* * * ** *
17303518 TGACGAAAAGTAAATCGTCATAGTATTGGTAATATAATTATTGTCACAAATGGTTGTAAGAA-CA
130 TGACGAAAAGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAA-AATAA
17303582 TT-AAACGT
194 TTCAAACGT
* * * *
17303590 GACAATAAAATCAAACATCACATTATGCTTTATTTTTTTGTGACATTAGTTTTCATTAGCTATTT
1 GACAATAAAATCAAACATCACCTTAT-ATTTATTTTTTTATGACATTAGTTTTCATCAGCTATTT
* * * * *
17303655 ATG--AAAAAATGTCATTAAAGGTTATAATCGTCATAAGATAAATGATTAAATCTGATATATTAG
65 ATGAAAAAAAATGTCATTAAAAGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAG
* * *
17303718 TGATG-AAAGATAAATCATCACAATATTGGTGACATAATTA
130 TGACGAAAAG-TAAATCGTCACAATATTGGTAACATAATTA
17303758 ATGTTTTCAA
Statistics
Matches: 463, Mismatches: 95, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
199 4 0.01
200 106 0.23
201 4 0.01
202 161 0.35
203 156 0.34
204 32 0.07
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (202 bp):
GACAATAAAATCAAACATCACCTTATATTTATTTTTTTATGACATTAGTTTTCATCAGCTATTTA
TGAAAAAAAATGTCATTAAAAGTTATAATCGTCACAAAATAAATAATAAAATCTGATATATTAGT
GACGAAAAGTAAATCGTCACAATATTGGTAACATAATTATTGTCACAAATAATTGTAAAATAATT
CAAACGT
Found at i:17314643 original size:16 final size:16
Alignment explanation
Indices: 17314622--17314652 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17314612 AAAGCAGAAC
17314622 AAAATAGAAACCAAAA
1 AAAATAGAAACCAAAA
*
17314638 AAAATAGAAATCAAA
1 AAAATAGAAACCAAA
17314653 CTTCTATTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAGAAACCAAAA
Found at i:17316719 original size:237 final size:234
Alignment explanation
Indices: 17316250--17317441 Score: 1425
Period size: 235 Copynumber: 5.1 Consensus size: 234
17316240 AAAATCCCAT
* * *
17316250 CAAATTAATTTGGA-GGTAAAAGTTTGTCACATTTATATTATCATCATATAACACCA-A-A-T--
1 CAAATAAATTT-GACGGTAAAA-TTTGTGACATTTATATTATCGTCATATAACACCATACATTGA
* ** * * **
17316309 -GTGACGAAATTATAATGTCATTAATAGTTAAGTAAAATACTCAATTTGTGACAAAAATTAATAA
64 CGTAACGAAATTGCAATGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAA
* * * ** *
17316373 CGTCACCTAAAATTTATAAAAAAAAAAAAATTCATCATAGATAAAATTTTAAATTGGTGACAAAA
129 CGTCACCTAAAATCTAT----CAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAA
** * *
17316438 TTATAACGTCACCTAATATAAAAAAATGTCATAAAAAATTTTTTCAT
190 TTATAATATCACCTAAAAT-AAAAAATGTCATAAAAAA-TTTTTCAC
* *
17316485 TAAATAAATTTGACGGTAAAAGTTTGTGACATTTA-AGTTATCGTCATATAACACCATATATTGA
1 CAAATAAATTTGACGGTAAAA-TTTGTGACATTTATA-TTATCGTCATATAACACCATACATTGA
* * * *
17316549 CGTGACAAAATTGCAATGTCATTAATAGTTAACTAAAGTATTCAATTTATGACAAAAATTAATAA
64 CGTAACGAAATTGCAATGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAA
* *
17316614 CATCACCTAAAATCTATCAGAAAAAATTTGTCACAGATAAAATTTTAAATTAGTGACAAAATTAT
129 CGTCACCTAAAATCTATCAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAATTAT
** * *
17316679 AACGTCGA-TTAAAATAAAAAATGTCACAAAAAATTTTTTTCAC
194 AATATC-ACCTAAAATAAAAAATGTCATAAAAAA--TTTTTCAC
* ** * * * * * * *
17316722 CAAATAAAATTGACAATAAAAATTTATGACAATTATATTATCGTCATATAATACCATAAAATAAA
1 CAAATAAATTTGACGGT-AAAATTTGTGACATTTATATTATCGTCATATAACACCATACATTGAC
* * * * *
17316787 GATAACGAAATTGTAATGTCATTAATAGTTAACTGAAGTGTTCTATTTGTGATAAAAATTTATAA
65 G-TAACGAAATTGCAATGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAA
* * * *
17316852 CGTCACCTAAAATCTATTAGAAAAATTTTGTCACATATAAAATTTTAAATTAGTGACAAAATT-T
129 CGTCACCTAAAATCTATCAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAATTAT
* *
17316916 AAATATCACCTAAAATAAAAAATGTCATAAAAAAATTCTCAC
194 -AATATCACCTAAAATAAAAAATGTCATAAAAAATTTTTCAC
** * *
17316958 CAAATAAATTTGGTGGTAAAATTTGTGACATTTATATTATCGTCATATACCACCATACATTGACA
1 CAAATAAATTTGACGGTAAAATTTGTGACATTTATATTATCGTCATATAACACCATACATTGACG
* * * * *
17317023 TAATGAAATTGCAATGTTTATTAATAGTTAACTAAAGTGTTCCATTTGTGATAAAAATTGATAAC
66 TAACGAAATTGCAATG-TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAAC
* *
17317088 GTCACCTAAAATCTATTAGAAAAAATTTGTCATAGATAGAATTTTAAATTAGTGACAAAATT-TA
130 GTCACCTAAAATCTATCAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAATTAT-
* *
17317152 AATATCACCTAAAATAAAAAATGTCATAAAAAAATTCTCAC
194 AATATCACCTAAAATAAAAAATGTCATAAAAAATTTTTCAC
** * *
17317193 CAAATAAATTTGGTGGTAAAATTTGTGACATTTATATTATCGTCATATACCACCATACATTGACA
1 CAAATAAATTTGACGGTAAAATTTGTGACATTTATATTATCGTCATATAACACCATACATTGACG
* * *
17317258 TAATGAAATTGCAATGTTTATTAATAGTTAACTAAAGTGTTCAATTTATGACAAAAATTAATAAC
66 TAACGAAATTGCAATG-TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAAC
* * *
17317323 GTCACCTAAAATCTATCAGAAAAAATTTGTCATAGAGAAAATTTTAAATTGGTGATAAAATTATA
130 GTCACCTAAAATCTATCAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAATTATA
*
17317388 ATATCACCTAAAATAAAAAAATGTCACAAAAATATTTTTCAC
195 ATATCACCTAAAAT-AAAAAATGTCATAAAAA-ATTTTTCAC
17317430 CAAATAAATTTG
1 CAAATAAATTTG
17317442 GTTGTAAAAT
Statistics
Matches: 849, Mismatches: 89, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
234 17 0.02
235 429 0.51
236 53 0.06
237 131 0.15
238 147 0.17
241 72 0.08
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (234 bp):
CAAATAAATTTGACGGTAAAATTTGTGACATTTATATTATCGTCATATAACACCATACATTGACG
TAACGAAATTGCAATGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAACG
TCACCTAAAATCTATCAGAAAAAATTTGTCATAGATAAAATTTTAAATTAGTGACAAAATTATAA
TATCACCTAAAATAAAAAATGTCATAAAAAATTTTTCAC
Found at i:17318756 original size:2 final size:2
Alignment explanation
Indices: 17318749--17318788 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17318739 TTTGGATTCC
17318749 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17318789 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17318793 original size:2 final size:2
Alignment explanation
Indices: 17318788--17318825 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
17318778 TCTCTCTCTC
*
17318788 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17318826 GTTAGCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:17330367 original size:33 final size:33
Alignment explanation
Indices: 17330330--17330400 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
17330320 TTTTATCTTG
*
17330330 GCATTTCTC-TTCTTAAATGCTAGTCCTTCTAAA
1 GCATTTCTCGTT-TTAAATGCTAATCCTTCTAAA
*
17330363 GCATTTCTCGTTTTAGATGCTAATCCTTCTAAA
1 GCATTTCTCGTTTTAAATGCTAATCCTTCTAAA
17330396 GCATT
1 GCATT
17330401 GGGAGGCGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (33 bp):
GCATTTCTCGTTTTAAATGCTAATCCTTCTAAA
Found at i:17330725 original size:2 final size:2
Alignment explanation
Indices: 17330718--17330742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17330708 TATGTGTTTG
17330718 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17330743 TTAAAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17331473 original size:2 final size:2
Alignment explanation
Indices: 17331468--17331503 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17331458 AAGAAGGTAC
17331468 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17331504 TTTAATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17335553 original size:34 final size:34
Alignment explanation
Indices: 17335464--17335543 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 34
17335454 AAAAAATTTA
* *
17335464 TTTTTATTTAAATTA-ACTTTTTTAAATTTTTGGAAT
1 TTTTTATTT-TATTAGA-TTTTTAAAATTTTT-GAAT
*
17335500 TTTTTATTTTATTAGATTTTTAAAATTTTT-ATT
1 TTTTTATTTTATTAGATTTTTAAAATTTTTGAAT
17335533 TTTTTAATTTT
1 TTTTT-ATTTT
17335544 CATATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
33 7 0.18
34 5 0.13
35 17 0.44
36 10 0.26
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.68
Consensus pattern (34 bp):
TTTTTATTTTATTAGATTTTTAAAATTTTTGAAT
Found at i:17336374 original size:13 final size:13
Alignment explanation
Indices: 17336356--17336385 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17336346 GTTAGTGGGA
17336356 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
17336369 AAAAAAACAAAAC
1 AAAAAAAAAAAAC
17336382 AAAA
1 AAAA
17336386 CATGTACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:17336940 original size:2 final size:2
Alignment explanation
Indices: 17336923--17336967 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
17336913 TTCCCAATTC
* * * *
17336923 AT AT AT AC AT AC AT AT AT AT AT AT AC AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17336965 AT A
1 AT A
17336968 AATTATTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:17336946 original size:18 final size:18
Alignment explanation
Indices: 17336923--17336965 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17336913 TTCCCAATTC
17336923 ATATATACATACATATAT
1 ATATATACATACATATAT
* *
17336941 ATATATACATATATATGT
1 ATATATACATACATATAT
17336959 ATATATA
1 ATATATA
17336966 TAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATATACATACATATAT
Found at i:17336961 original size:14 final size:14
Alignment explanation
Indices: 17336923--17336967 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
17336913 TTCCCAATTC
*
17336923 ATATATACATACAT
1 ATATATATATACAT
17336937 ATATATATATACAT
1 ATATATATATACAT
* *
17336951 ATATATGTATATAT
1 ATATATATATACAT
17336965 ATA
1 ATA
17336968 AATTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:17342186 original size:21 final size:21
Alignment explanation
Indices: 17342160--17342203 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17342150 TACTTAAGTT
17342160 TACTATATTTTAAACAAAAGA
1 TACTATATTTTAAACAAAAGA
*
17342181 TACTATATTTTAAATAAAAGA
1 TACTATATTTTAAACAAAAGA
17342202 TA
1 TA
17342204 ATAATAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
TACTATATTTTAAACAAAAGA
Found at i:17343756 original size:373 final size:371
Alignment explanation
Indices: 17343254--17345133 Score: 2136
Period size: 373 Copynumber: 5.1 Consensus size: 371
17343244 TATTATAGGA
17343254 AAATGCCTTCAATAATTTTTGTTTAAAAATTTTTGAGATTATTAAATG-AGT-TTTCTAGTGAAA
1 AAATGCCTTCAATAATTTTT-TTTAAAAATTTTTGAGATTATTAAA-GCA-TCTTT-TAGTGAAA
* * * * * * *
17343317 AATACCTTTAATATTTCACTACTCAAATTTTAAAACGGTTAGTAAAGGCATTTATTCTAAAAAAA
62 AATGCCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCT-AGAAAA
** * * * * *
17343382 ATGTCTTCACTATTTCCTTTTAATTTATGTACATAATTATTAAAGGTATTTTTTTAGAATAAATG
126 ATACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACG
* * * *
17343447 CCTTCAATAATTTTCTTTTCAAAATTTTTGAGATTATTAAAGATGTCTTCTAGTGAAAAACACAT
191 CCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGTGTCTTCTAATGAAAAACACCT
* * * * * ***
17343512 TCAATATTTCACTACTCAAATTTAAATATGGTTAGCAAATGCATTTATTCTAGAAAAACGTCTTC
255 TCAATATTTCACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTC
* * *
17343577 AATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAAC
320 AATAATTCTTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
*
17343629 AAACGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGCCATCTTTTAGT-AAAAAT
1 AAATGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAG-CATCTTTTAGTGAAAAAT
* ** ** ** *
17343693 ACCTTCAATATACCAGCACTCAAATTTTAAGACAGTTAGTGAAGGCATTTTATT-TCAAAAAAAT
65 GCCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCA-TTTATTCT-AGAAAAAT
* * * * *
17343757 ACCTTCAATAATTTCTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAACAAACACC
128 ACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACGCC
* ** * *
17343822 TTCAATAACTTTTTTTAAAAAATTTTT-AGGATTATTAAAGGCATTTTCTAATGAAAAATACCTT
193 TTCAATAA-TTTTTTTTAAAAATTTTTGA-GATTATTAAAGGTGTCTTCTAATGAAAAACACCTT
* * * ** *
17343886 CAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAAGTTGTTTATTCTAAAAAAATACCTTCA
256 CAATATTTCACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTCA
* * * *
17343951 CTAATTCATTTTAGTTTATGTACATAATTATT-ACAGGTATTTTTTGAGAAC
321 ATAATTCTTTTTAATTTTTGTACATAATTATTGA-AGGTATTTTTTGAGAAC
* * * *
17344002 AAATGCCTTCAATAATTTCTTTTTAAAAATTTTTAAGATTATTAAAAGCTTCTTATAATGAAAAA
1 AAATGCCTTCAATAATTT-TTTTTAAAAATTTTTGAGATTATT-AAAGCATCTTTTAGTGAAAAA
* * * * * *
17344067 CGCCTTCAATATTTTATTACTCAAATTTTAAAATGGTTAATAAAGGCATTTATTCTAGAAAAATA
64 TGCCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAGAAAAATA
* * * *
17344132 CCTTCATTAATTCTTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTATAACAAATGCCT
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACGCCT
** *
17344197 TCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTCTAATGAAAAACACCTTTA
194 TCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGTGTCTTCTAATGAAAAACACCTTCA
* * * *
17344262 ATA-TACTAGTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCCACAAAAATACCTTCAA
258 ATATTTC-ACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTCAA
*
17344326 TAATT-TTTTTAATTTTTGTACATAATTATTGAAGGCT-TTTTTTTAGAAC
322 TAATTCTTTTTAATTTTTGTACATAATTATTGAAGG-TATTTTTTGAGAAC
* * *
17344375 AAATGCCTTTAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAAGCATCTTCTAGTAAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATT-AAAGCATCTTTTAGTGAAAAA
* * *
17344440 TGCCTTCAATATTTCAATACTCAAATTTTAAGATAGTTAGTGAAAGCATTTGTTCTAGAAAAATA
64 TGCCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAGAAAAATA
* * * * *
17344505 CATTCACTAATTCCTTTTAGTTTATGTACATAATTATTGCAGGCATTTTTTGAGAACAAACACCT
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACGCCT
* *
17344570 TCAATAATTTTTTTTTAAAAATTTTT-AGGATTATTAAAGGTGTTTTCTAATGAAAAATACCTTC
194 TCAATAA-TTTTTTTTAAAAATTTTTGA-GATTATTAAAGGTGTCTTCTAATGAAAAACACCTTC
* *** * * * *
17344634 AATATTTCACTACTCAAATTTTGAGACAATTAGTGAAGGTGTTTATTCTAGAAAAATGCCTTCAT
257 AATATTTCACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTCAA
17344699 TAATT-TCTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
322 TAATTCT-TTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
* * *
17344749 AAATGCCTTCAATAATTTTCTTTTAAAAATTTTTTAGATTATTAAAGGTATTTTTTAGTGAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAA-GCATCTTTTAGTGAAAAA
* * * ** * *
17344814 TGGCTTCAATATTTCAATATTAAAATTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGGAAAACA
64 TGCCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAGAAAAATA
* * * *
17344879 CCTTCACTAATTCCTTTTAGTTTATGTTCATATTTATTGAAGGCATCTTTTTAGAACAAACGCCT
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACGCCT
* * * *
17344944 TCAA-AA--ATTTTT----A-----G-GATTATTAAAGGTGTTTTCTAGTGAAAAACACATTCAA
194 TCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGGTGTCTTCTAATGAAAAACACCTTCAA
* * * * * * * * **
17344996 TACTCCACTACTCAAAATTTGAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCCCTA
259 TATTTCACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTCAATA
* * **
17345061 ATTCTTTTTAATTTTTGTACATAATTAGTGAAGGTAATTTTCTGCTAA-
324 ATTCTTTTTAATTTTTGTACATAATTATTGAAGGT-ATTTTTTGAGAAC
* *
17345109 AAATACCTTCAATCATTTTTGTTTA
1 AAATGCCTTCAATAATTTTT-TTTA
17345134 GAATTATCAA
Statistics
Matches: 1299, Mismatches: 179, Indels: 69
0.84 0.12 0.04
Matches are distributed among these distances:
359 1 0.00
360 140 0.11
361 10 0.01
366 1 0.00
370 5 0.00
372 4 0.00
373 595 0.46
374 473 0.36
375 70 0.05
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (371 bp):
AAATGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGCATCTTTTAGTGAAAAATG
CCTTCAATATTTCAATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAGAAAAATACC
TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAACGCCTTC
AATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGGTGTCTTCTAATGAAAAACACCTTCAATA
TTTCACTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCTAGAAAAATACCTTCAATAAT
TCTTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
Found at i:17343775 original size:187 final size:185
Alignment explanation
Indices: 17343254--17344955 Score: 1907
Period size: 187 Copynumber: 9.1 Consensus size: 185
17343244 TATTATAGGA
*
17343254 AAATGCCTTCAATAATTTTTGTTTAAAAATTTTTGAGATTATTAAATG-AGT-TTTCTAGTGAAA
1 AAATGCCTTCAATAATTTTT-TTTAAAAATTTTTGAGATTATTAAAGGCA-TCTTT-TAGTGAAA
* * * *
17343317 AATACCTTTAATATTTCACTACTCAAATTTTAAAACGGTTAGTAAAGGCATTTATTCTAAAAAAA
63 AATACCTTCAATATTTCA-TACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCT-AAAAAA
** * * *
17343382 ATGTCTTCACTATTTCCTTTTAATTTATGTACATAATTATTAAAGGTATTTTTTTAGAAT
126 ATACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
* *** *
17343442 AAATGCCTTCAATAATTTTCTTTTCAAAATTTTTGAGATTATTAAAGATGTCTTCTAGTGAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAA
* * * * ** * * **
17343507 CACATTCAATATTTCACTACTCAAATTTAAATATGGTTAGCAAATGCATTTATTCTAGAAAAACG
65 TACCTTCAATATTTCA-TACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAATA
* * * *
17343572 TCTTCAATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAAC
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
* *
17343629 AAACGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGCCATCTTTTAGT-AAAAAT
1 AAATGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAAT
** * **
17343693 ACCTTCAATATACCAGCACTCAAATTTTAAGACAGTTAGTGAAGGCATTTTATT-TCAAAAAAAT
66 ACCTTCAATATTTCA-TACTCAAATTTTAAGATGGTTAGTGAAGGCA-TTTATTCT-AAAAAAAT
* * *
17343757 ACCTTCAATAATTTCTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAAC
128 ACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
** * *
17343815 AAACACCTTCAATAACTTTTTTTAAAAAATTTTT-AGGATTATTAAAGGCAT-TTTCTAATGAAA
1 AAATGCCTTCAATAA-TTTTTTTTAAAAATTTTTGA-GATTATTAAAGGCATCTTT-TAGTGAAA
* ***
17343878 AATACCTTCAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAAGTTGTTTATTCTAAAAAAA
63 AATACCTTCAATATTTC-ATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAA
* * *
17343943 TACCTTCACTAATTCATTTTAGTTTATGTACATAATTATT-ACAGGTATTTTTTGAGAAC
127 TACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGA-AGGTATTTTTTTAGAAC
* * * * *
17344002 AAATGCCTTCAATAATTTCTTTTTAAAAATTTTTAAGATTATTAAAAGCTTCTTATAATGAAAAA
1 AAATGCCTTCAATAATTT-TTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAA
** * * * * *
17344067 CGCCTTCAATATTTTATTACTCAAATTTTAAAATGGTTAATAAAGGCATTTATTCTAGAAAAATA
65 TACCTTCAATATTTCA-TACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAATA
* * * *
17344132 CCTTCATTAATTCTTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTATAAC
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
* *
17344189 AAATGCCTTCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTCTAATGAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAA
* * * * * * *
17344254 CACCTTTAATA-TACTAGTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCCACAAAAAT
65 TACCTTCAATATTTC-A-TACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAAT
* * *
17344318 ACCTTCAATAATT-TTTTTAATTTTTGTACATAATTATTGAAGGCT-TTTTTTTAGAAC
128 ACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGG-TATTTTTTTAGAAC
* * * *
17344375 AAATGCCTTTAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAAGCATCTTCTAGTAAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAA
* * * * *
17344440 TGCCTTCAATATTTCAATACTCAAATTTTAAGATAGTTAGTGAAAGCATTTGTTCTAGAAAAATA
65 TACCTTCAATATTTC-ATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAATA
* * * * *
17344505 CATTCACTAATTCCTTTTAGTTTATGTACATAATTATTGCAGGCATTTTTTGAGAAC
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
** ** *
17344562 AAACACCTTCAATAATTTTTTTTTAAAAATTTTT-AGGATTATTAAAGGTGT-TTTCTAATGAAA
1 AAATGCCTTCAATAA-TTTTTTTTAAAAATTTTTGA-GATTATTAAAGGCATCTTT-TAGTGAAA
* *** ** *
17344625 AATACCTTCAATATTTCACTACTCAAATTTTGAGACAATTAGTGAAGGTGTTTATTCTAGAAAAA
63 AATACCTTCAATATTTCA-TACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAA
* * * * *
17344690 TGCCTTCATTAATTTCTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
127 TACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
* * *
17344749 AAATGCCTTCAATAATTTTCTTTTAAAAATTTTTTAGATTATTAAAGGTATTTTTTAGTGAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAA
** * * ** ** *
17344814 TGGCTTCAATATTTCAATATTAAAATTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGGAAAACA
65 TACCTTCAATATTTC-ATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAATA
* * * * *
17344879 CCTTCACTAATTCCTTTTAGTTTATGTTCATATTTATTGAAGGCATCTTTTTAGAAC
129 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
* *
17344936 AAACGCCTTCAAAAATTTTT
1 AAATGCCTTCAATAATTTTT
17344956 AGGATTATTA
Statistics
Matches: 1302, Mismatches: 181, Indels: 64
0.84 0.12 0.04
Matches are distributed among these distances:
185 41 0.03
186 292 0.22
187 805 0.62
188 160 0.12
189 4 0.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (185 bp):
AAATGCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAAT
ACCTTCAATATTTCATACTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTCTAAAAAAATACC
TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAAC
Found at i:17344338 original size:560 final size:557
Alignment explanation
Indices: 17343258--17344955 Score: 2235
Period size: 560 Copynumber: 3.0 Consensus size: 557
17343248 ATAGGAAAAT
*
17343258 GCCTTCAATAATTTTTGTTTAAAAATTTTTGAGATTATTAAATG-AGTTTTCTAGTGAAAAATAC
1 GCCTTCAATAATTTTT-TTTAAAAATTTTTGAGATTATTAAAAGCA-TTTTCTAGTGAAAAATAC
* * * * **
17343322 CTTTAATATTTCACTACTCAAATTTTAAAACGGTTAGTAAAGGCATTTATTCTAAAAAAAATGTC
64 CTTCAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAA-GCATTTATTCT-AAAAAAATACC
* * * * *
17343387 TTCACTATTTCCTTTTAATTTATGTACATAATTATTAAAGGTATTTTTTTAGAATAAATGCCTTC
127 TTCACTAATTCCTTTTAGTTTATGTACATAATTATTACAGGTATTTTTTGAGAACAAATGCCTTC
* * * *
17343452 AATAATTTTCTTTTCAAAATTTTTGAGATTATTAAAGATGTCTTCTAGTGAAAAACACATTCAAT
192 AATAATTTT-TTTTAAAAATTTTTAAGATTATTAAAGATGTCTTCTAATGAAAAACACCTTCAAT
* * * * *
17343517 ATTTCACTACTCAAA-TTTAAATATGGTTAGCAAATGCATTTATTCTAGAAAAACGTCTTCAATA
256 ATTTCACTACTCAAATTTTAAA-ATGGTTAGTAAAGGCATTTATTCTAGAAAAATGCCTTCATTA
*
17343581 ATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAACGCCTTCAATAATT
320 ATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAATGCCTTCAATAATT
* *
17343646 TT-TTTTAAAAATTTTTGAGATTATTAAAGCCATCTTTTAGT-AAAAATACCTTCAATATACCAG
385 TTCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAATACCTTCAATATACTAG
* ** * *
17343709 CACTCAAATTTTAAGACAGTTAGTGAAGGCATTTTATTTCAAAAAAATACCTTCAATAATTTCTT
450 TACTCAAATTTTAAGATGGTTAGTGAAGGC-GTTTATTCCAAAAAAATACCTTCAATAATTT-TT
17343774 TTAATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAACAAAC
513 TTAATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAACAAAC
* * * *
17343819 ACCTTCAATAACTTTTTTTAAAAAATTTTT-AGGATTATTAAAGGCATTTTCTAATGAAAAATAC
1 GCCTTCAATAA-TTTTTTTTAAAAATTTTTGA-GATTATTAAAAGCATTTTCTAGTGAAAAATAC
**
17343883 CTTCAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAAGTTGTTTATTCTAAAAAAATACCT
64 CTTCAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAAG-CATTTATTCTAAAAAAATACCT
*
17343948 TCACTAATTCATTTTAGTTTATGTACATAATTATTACAGGTATTTTTTGAGAACAAATGCCTTCA
128 TCACTAATTCCTTTTAGTTTATGTACATAATTATTACAGGTATTTTTTGAGAACAAATGCCTTCA
* * *
17344013 ATAATTTCTTTTTAAAAATTTTTAAGATTATTAAAAGCT-TCTTATAATGAAAAACGCCTTCAAT
193 ATAATTT-TTTTTAAAAATTTTTAAGATTATT-AAAGATGTCTTCTAATGAAAAACACCTTCAAT
* * * *
17344077 ATTTTATTACTCAAATTTTAAAATGGTTAATAAAGGCATTTATTCTAGAAAAATACCTTCATTAA
256 ATTTCACTACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATGCCTTCATTAA
*
17344142 TTCTTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTATAACAAATGCCTTCAATAATTT
321 TTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAATGCCTTCAATAATTT
* * * *
17344207 TCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTCTAATGAAAAACACCTTTAATATACTAGT
386 TCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAATACCTTCAATATACTAGT
* *
17344272 ACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCCACAAAAATACCTTCAATAATTTTTTTA
451 ACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCCAAAAAAATACCTTCAATAATTTTTTTA
*
17344337 ATTTTTGTACATAATTATTGAAGGCT-TTTTTTTAGAACAAAT
516 ATTTTTGTACATAATTATTGAAGG-TATTTTTTTAGAACAAAC
* * * *
17344379 GCCTTTAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAAGCATCTTCTAGTAAAAAATGCC
1 GCCTTCAATAATTTT-TTTTAAAAATTTTTGAGATTATTAAAAGCATTTTCTAGTGAAAAATACC
** * * *
17344444 TTCAATATTTCAATACTCAAATTTTAAGATAGTTAGTGAAAGCATTTGTTCTAGAAAAATACATT
65 TTCAATATTTCAATACTCAAATTTTAAGACGGTTAGTG-AAGCATTTATTCTAAAAAAATACCTT
* * **
17344509 CACTAATTCCTTTTAGTTTATGTACATAATTATTGCAGGCATTTTTTGAGAACAAACACCTTCAA
129 CACTAATTCCTTTTAGTTTATGTACATAATTATTACAGGTATTTTTTGAGAACAAATGCCTTCAA
* * * *
17344574 TAATTTTTTTTTAAAAATTTTTAGGATTATTAAAGGTGTTTTCTAATGAAAAATACCTTCAATAT
194 TAA-TTTTTTTTAAAAATTTTTAAGATTATTAAAGATGTCTTCTAATGAAAAACACCTTCAATAT
* * *** * **
17344639 TTCACTACTCAAATTTTGAGACAATTAGTGAAGGTGTTTATTCTAGAAAAATGCCTTCATTAATT
258 TTCACTACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATGCCTTCATTAATT
* * *
17344704 -TCTTTTAATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAACAAATGCCTTCAATAATTTT
323 CT-TTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAATGCCTTCAATAATTTT
* * * ** * *
17344768 CTTTTAAAAATTTTTTAGATTATTAAAGGTATTTTTTAGTGAAAAATGGCTTCAATAT-TTCAAT
387 CTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAATACCTTCAATATACT-AGT
* * * * ** * * *
17344832 ATTAAAATTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGGAAAACACCTTCACTAATTCCTTTT
451 ACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCCAAAAAAATACCTTCAATAATT-TTTTT
* * * * * *
17344897 AGTTTATGTTCATATTTATTGAAGGCATCTTTTTAGAACAAAC
515 AATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAACAAAC
*
17344940 GCCTTCAAAAATTTTT
1 GCCTTCAATAATTTTT
17344956 AGGATTATTA
Statistics
Matches: 996, Mismatches: 122, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
559 11 0.01
560 703 0.71
561 231 0.23
562 51 0.05
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (557 bp):
GCCTTCAATAATTTTTTTTAAAAATTTTTGAGATTATTAAAAGCATTTTCTAGTGAAAAATACCT
TCAATATTTCAATACTCAAATTTTAAGACGGTTAGTGAAGCATTTATTCTAAAAAAATACCTTCA
CTAATTCCTTTTAGTTTATGTACATAATTATTACAGGTATTTTTTGAGAACAAATGCCTTCAATA
ATTTTTTTTAAAAATTTTTAAGATTATTAAAGATGTCTTCTAATGAAAAACACCTTCAATATTTC
ACTACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATGCCTTCATTAATTCTT
TTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAATGCCTTCAATAATTTTCTTT
TAAAAATTTTTGAGATTATTAAAGGCATCTTTTAGTGAAAAATACCTTCAATATACTAGTACTCA
AATTTTAAGATGGTTAGTGAAGGCGTTTATTCCAAAAAAATACCTTCAATAATTTTTTTAATTTT
TGTACATAATTATTGAAGGTATTTTTTTAGAACAAAC
Found at i:17344621 original size:747 final size:744
Alignment explanation
Indices: 17343254--17345101 Score: 2340
Period size: 747 Copynumber: 2.5 Consensus size: 744
17343244 TATTATAGGA
* *
17343254 AAATGCCTTCAATAATTTTTGTTTAAAAATTTTTGAGATTATTAAATGAGTTTTCTAGTGAAAAA
1 AAATGCCTTCAATAATTTTT-TTTAAAAATTTTTAAGATTATTAAA--AGTTTTATAGTGAAAAA
* * * * *
17343319 TACCTTTAATATTTCACTACTCAAATTTTAAAACGGTTAGTAAAGGCATTTATTCTAAAAAAAAT
63 TGCCTTCAATATTTCAATACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCT-AGAAAAAT
** * * * *
17343384 GTCTTCACTATTTCCTTTTAATTTATGTACATAATTATTAAAGGTATTTTTTTAGAATAAATGCC
127 ACCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAATGCC
* ** *
17343449 TTCAATAATTTTCTTTTCAAAATTTTTGAGATTATTAAAGATGTCTTCTAGTGAAAAACACATTC
192 TTCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGACATCTTCTAATGAAAAACACATTC
* * * * * **
17343514 AATATTTCACTACTCAAATTTAAATATGGTTAGCAAATGCATTTATTCTAGAAAAACGTCTTCAA
257 AATATCTCACTACTCAAATTTAAAGATGGTTAGCAAAGGCATTTATTCCACAAAAACACCTTCAA
*
17343579 TAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTATAACAAACGCCTTCAATAA
322 TAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAACAAACGCCTTCAATAA
* *
17343644 TTTTTTTTAAAAATTTTTGAGATTATTAAAGCCATCTTTTAGTAAAAATACCTTCAATATACCAG
387 TTTTTTTTAAAAATTTTTGAGATTATTAAAGCCATCTTCTAGTAAAAATACCTTCAATATACCAA
* * * *
17343709 CACTCAAATTTTAAGACAGTTAGTGAAGGCATTTTATTTCAAAAAAATACCTTCAATAATTTCTT
452 CACTCAAATTTTAAGACAGTTAGTGAAAGCATTTTATCTCAAAAAAATACATTCAATAATTCCTT
* * *
17343774 TTAATTTTTGTACATAATTATTGAAGGTATTTTTTTAGAACAAACACCTTCAATAACTTTTTTTA
517 TTAATTTATGTACATAATTATTGAAGGCATTTTTTGAGAACAAACACCTTCAATAACTTTTTTTA
17343839 AAAAATTTTTAGGATTATTAAAGGCATTTTCTAATGAAAAATACCTTCAATATTTCAATACTCAA
582 AAAAATTTTTAGGATTATTAAAGGCATTTTCTAATGAAAAATACCTTCAATATTTCAATACTCAA
** * *
17343904 ATTTTAAGACGGTTAGTGAAGTTGTTTATTCTAAAAAAATACCTTCACTAA-TTCATTTTAGTTT
647 ATTTTAAGACAATTAGTGAAGGTGTTTATTCTAAAAAAATACCTTCACTAATTTC-TTTTAATTT
17343968 ATGTACATAATTATT-ACAGGTATTTTTTGAGAAC
711 ATGTACATAATTATTGA-AGGTATTTTTTGAGAAC
*
17344002 AAATGCCTTCAATAATTTCTTTTTAAAAATTTTTAAGATTATTAAAAGCTTCTTATAATGAAAAA
1 AAATGCCTTCAATAATTT-TTTTTAAAAATTTTTAAGATTATTAAAAG-TT-TTATAGTGAAAAA
* * * *
17344067 CGCCTTCAATATTTTATTACTCAAATTTTAAAATGGTTAATAAAGGCATTTATTCTAGAAAAATA
63 TGCCTTCAATATTTCAATACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATA
* * *
17344132 CCTTCATTAATTCTTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTATAACAAATGCCT
128 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAATGCCT
* * *
17344197 TCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGGCATCTTCTAATGAAAAACACCTTTA
193 TCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGACATCTTCTAATGAAAAACACATTCA
* * * * *
17344262 ATATACT-AGTACTCAAATTTTAAGATGGTTAGTAAAGGCGTTTATTCCACAAAAATACCTTCAA
258 ATAT-CTCACTACTCAAATTTAAAGATGGTTAGCAAAGGCATTTATTCCACAAAAACACCTTCAA
* * *
17344326 TAATT-TTTTTAATTTTTGTACATAATTATTGAAGGCT-TTTTTTTAGAACAAATGCCTTTAATA
322 TAATTCTTTTTAATTTATGTACATAATTATTGAAGG-TATTTTTTTAGAACAAACGCCTTCAATA
* *
17344389 ATTTTCTTTTAAAAATTTTTGAGATTATTAAAAG-CATCTTCTAGTAAAAAATGCCTTCAATATT
386 ATTTT-TTTTAAAAATTTTTGAGATTATT-AAAGCCATCTTCTAGT-AAAAATACCTTCAATATA
* * * * *
17344453 TCAATACTCAAATTTTAAGATAGTTAGTGAAAGCATTTGT-TCT-AGAAAAATACATTCACTAAT
448 CCAACACTCAAATTTTAAGACAGTTAGTGAAAGCATTT-TATCTCAAAAAAATACATTCAATAAT
* * *
17344516 TCCTTTTAGTTTATGTACATAATTATTGCAGGCATTTTTTGAGAACAAACACCTTCAATAATTTT
512 TCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTGAGAACAAACACCTTCAATAACTTT
* ** *
17344581 TTTTTAAAAATTTTTAGGATTATTAAAGGTGTTTTCTAATGAAAAATACCTTCAATATTTCACTA
577 TTTTAAAAAATTTTTAGGATTATTAAAGGCATTTTCTAATGAAAAATACCTTCAATATTTCAATA
* * * *
17344646 CTCAAATTTTGAGACAATTAGTGAAGGTGTTTATTCTAGAAAAATGCCTTCATTAATTTCTTTTA
642 CTCAAATTTTAAGACAATTAGTGAAGGTGTTTATTCTAAAAAAATACCTTCACTAATTTCTTTTA
*
17344711 ATTTTTGTACATAATTATTGAAGGTATTTTTTGAGAAC
707 ATTTATGTACATAATTATTGAAGGTATTTTTTGAGAAC
* * *
17344749 AAATGCCTTCAATAATTTTCTTTTAAAAATTTTTTAGATTATTAAAGGTATTTTTTAGTGAAAAA
1 AAATGCCTTCAATAATTTT-TTTTAAAAATTTTTAAGATTATTAAAAG--TTTTATAGTGAAAAA
* * * * * ** * *
17344814 TGGCTTCAATATTTCAATATTAAAATTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGGAAAACA
63 TGCCTTCAATATTTCAATACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATA
* * * * *
17344879 CCTTCACTAATTCCTTTTAGTTTATGTTCATATTTATTGAAGGCATCTTTTTAGAACAAACGCCT
128 CCTTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAATGCCT
* *** * *
17344944 TCAA-AA--AT-TTTT----A-----G-GATTATTAAAGGTGTTTTCTAGTGAAAAACACATTCA
193 TCAATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGACATCTTCTAATGAAAAACACATTCA
* *** * * * * *
17344995 ATA-CTCCACTACTCAAAATTT-GAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCC
258 ATATCT-CACTACTC-AAATTTAAAGATGGTTAGCAAAGGCATTTATTCCACAAAAACACCTTCA
* * * *
17345058 CTAATTCTTTTTAATTTTTGTACATAATTAGTGAAGGTAATTTT
321 ATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTT
17345102 CTGCTAAAAA
Statistics
Matches: 962, Mismatches: 120, Indels: 50
0.85 0.11 0.04
Matches are distributed among these distances:
731 2 0.00
733 80 0.08
734 40 0.04
739 1 0.00
743 4 0.00
744 1 0.00
746 62 0.06
747 605 0.63
748 164 0.17
749 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (744 bp):
AAATGCCTTCAATAATTTTTTTTAAAAATTTTTAAGATTATTAAAAGTTTTATAGTGAAAAATGC
CTTCAATATTTCAATACTCAAATTTTAAAATGGTTAGTAAAGGCATTTATTCTAGAAAAATACCT
TCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGCATTTTTTTAGAACAAATGCCTTCA
ATAATTTTCTTTTAAAAATTTTTGAGATTATTAAAGACATCTTCTAATGAAAAACACATTCAATA
TCTCACTACTCAAATTTAAAGATGGTTAGCAAAGGCATTTATTCCACAAAAACACCTTCAATAAT
TCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAACAAACGCCTTCAATAATTTT
TTTTAAAAATTTTTGAGATTATTAAAGCCATCTTCTAGTAAAAATACCTTCAATATACCAACACT
CAAATTTTAAGACAGTTAGTGAAAGCATTTTATCTCAAAAAAATACATTCAATAATTCCTTTTAA
TTTATGTACATAATTATTGAAGGCATTTTTTGAGAACAAACACCTTCAATAACTTTTTTTAAAAA
ATTTTTAGGATTATTAAAGGCATTTTCTAATGAAAAATACCTTCAATATTTCAATACTCAAATTT
TAAGACAATTAGTGAAGGTGTTTATTCTAAAAAAATACCTTCACTAATTTCTTTTAATTTATGTA
CATAATTATTGAAGGTATTTTTTGAGAAC
Found at i:17344790 original size:62 final size:60
Alignment explanation
Indices: 17344537--17344824 Score: 181
Period size: 62 Copynumber: 4.6 Consensus size: 60
17344527 TATGTACATA
* * ** *
17344537 ATTATTGCAGGCATTTTTTGAGAACAAACACCTTCAATAATTTTTTTTTAAAAATTTTTAGG
1 ATTATTGAAGGTATTTTTTGAGAA-AAATGCCTTCAATAATTTTCTTTT-AAAATTTTTAGG
* * * * * * ** * * *
17344599 ATTATTAAAGGTGTTTTCTAATGAAAAATACCTTCAAT-ATTTCACTACTCAAATTTTGAGACA
1 ATTATTGAAGGTATTTTTTGA-GAAAAATGCCTTCAATAATTT-TCTTTTAAAATTTTTAG--G
* * * * **
17344662 ATTAGTGAAGGTGTTTATTCT-AGAAAAATGCCTTCATTAA-TTTCTTTT-AATTTTTGTACATA
1 ATTATTGAAGGTATTT-TT-TGAGAAAAATGCCTTCAATAATTTTCTTTTAAAATTTT-T--AGG
17344724 ATTATTGAAGGTATTTTTTGAGAACAAATGCCTTCAATAATTTTCTTTTAAAAATTTTTTA-G
1 ATTATTGAAGGTATTTTTTGAGAA-AAATGCCTTCAATAATTTTCTTTT-AAAA-TTTTTAGG
* * *
17344786 ATTATTAAAGGTATTTTTTAGTGAAAAATGGCTTCAATA
1 ATTATTGAAGGTATTTTTT-GAGAAAAATGCCTTCAATA
17344825 TTTCAATATT
Statistics
Matches: 176, Mismatches: 33, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
60 1 0.01
61 25 0.14
62 92 0.52
63 46 0.26
64 4 0.02
65 4 0.02
66 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (60 bp):
ATTATTGAAGGTATTTTTTGAGAAAAATGCCTTCAATAATTTTCTTTTAAAATTTTTAGG
Found at i:17345064 original size:173 final size:173
Alignment explanation
Indices: 17344773--17345094 Score: 416
Period size: 173 Copynumber: 1.9 Consensus size: 173
17344763 ATTTTCTTTT
* ** * * *
17344773 AAAAATTTTTTAGATTATTAAAGGTATTTTTTAGTGAAAAATGGCTTCAATATTTCAATATTAAA
1 AAAAATTTTTTAGATTATTAAAGGTATTTTCTAGTGAAAAATCACTTCAATACTCCAATATCAAA
* * * * *
17344838 ATTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGGAAAACACCTTCACTAATTCCTTTTAGTTTA
66 ATTTTAAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCACTAATTCCTTTTAATTTA
* * *
17344903 TGTTCATATTTATTGAAGGCATCTTTTTAGAACAAACGCCTTC
131 TGTACATAATTAGTGAAGGCATCTTTTTAGAACAAACGCCTTC
* *
17344946 AAAAA-TTTTTAGGATTATTAAAGGTGTTTTCTAGTGAAAAA-CACATTCAATACTCCACTACTC
1 AAAAATTTTTTA-GATTATTAAAGGTATTTTCTAGTGAAAAATCAC-TTCAATACTCCAATA-TC
* * *
17345009 AAAA-TTTGAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCCCTAATTCTTTTTAAT
63 AAAATTTTAAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCACTAATTCCTTTTAAT
*
17345073 TTTTGTACATAATTAGTGAAGG
128 TTATGTACATAATTAGTGAAGG
17345095 TAATTTTCTG
Statistics
Matches: 126, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
172 7 0.06
173 114 0.90
174 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (173 bp):
AAAAATTTTTTAGATTATTAAAGGTATTTTCTAGTGAAAAATCACTTCAATACTCCAATATCAAA
ATTTTAAGATGGTTAATGAAGGCGTTTATTCTAGAAAAACACATTCACTAATTCCTTTTAATTTA
TGTACATAATTAGTGAAGGCATCTTTTTAGAACAAACGCCTTC
Found at i:17345761 original size:12 final size:12
Alignment explanation
Indices: 17345746--17345826 Score: 54
Period size: 12 Copynumber: 6.6 Consensus size: 12
17345736 ATCATATGCC
17345746 GAATGGTTTGCT
1 GAATGGTTTGCT
**
17345758 GAATGGTATTTTT
1 GAATGGT-TTGCT
17345771 GAATGGTTTGCT
1 GAATGGTTTGCT
* * *
17345783 AAAGGGTGTGTCT
1 GAATGGTTTG-CT
****
17345796 GAACACATTGCT
1 GAATGGTTTGCT
*
17345808 GATTGGTTTGCT
1 GAATGGTTTGCT
17345820 GAATGGT
1 GAATGGT
17345827 GTTTCTGTAC
Statistics
Matches: 48, Mismatches: 19, Indels: 4
0.68 0.27 0.06
Matches are distributed among these distances:
12 32 0.67
13 16 0.33
ACGTcount: A:0.21, C:0.09, G:0.31, T:0.40
Consensus pattern (12 bp):
GAATGGTTTGCT
Found at i:17345798 original size:25 final size:25
Alignment explanation
Indices: 17345746--17345798 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
17345736 ATCATATGCC
* * * *
17345746 GAATGGTTTGCTGAATGGTATTTTT
1 GAATGGTTTGCTAAAGGGTATGTCT
*
17345771 GAATGGTTTGCTAAAGGGTGTGTCT
1 GAATGGTTTGCTAAAGGGTATGTCT
17345796 GAA
1 GAA
17345799 CACATTGCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.06, G:0.32, T:0.40
Consensus pattern (25 bp):
GAATGGTTTGCTAAAGGGTATGTCT
Found at i:17349056 original size:35 final size:35
Alignment explanation
Indices: 17349004--17349072 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
17348994 TATATAAACC
* * * *
17349004 AAATGTTTTCTGGGCATAAATATACAATTGACTTT
1 AAATGTTTTATGAGCATAAACATACAACTGACTTT
*
17349039 AAATGTTTTATGAGCATAAACCTACAACTGACTT
1 AAATGTTTTATGAGCATAAACATACAACTGACTT
17349073 GACATATACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (35 bp):
AAATGTTTTATGAGCATAAACATACAACTGACTTT
Found at i:17349685 original size:305 final size:302
Alignment explanation
Indices: 17349267--17350025 Score: 786
Period size: 305 Copynumber: 2.5 Consensus size: 302
17349257 TTTCAAATAA
* * ***
17349267 TTTGTATGGATTATTGAAGGTATTTTTGACAAAAATTACCTTCAATAATGTCTGTTAAAAATTTA
1 TTTGTAT-GATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAAT-CCAACTAAAAATTTA
*
17349332 TTGATTGGATTATTGAAGGCGCTTTCA-CCAAAAAATGCCTTTAAGAATCCATTTCATATTTTTT
64 TTGATT-GATTATTGAA-G-GCTTTCAGCC-AAAAATGCCTTCAAGAATCCATTTCATATTTTTT
*
17349396 CTATAGATTATTAAAGG-CATATTTAGC-A-AGAAAACACCTTGAATTATCCCTAAAAAAATGTT
125 CTAT-GATTATTAAAGGACAT-TTT-GCTACAGAAAACACCTTGAATAATCCCTAAAAAAATGTT
* * * ** * *
17349458 ATTAAAGGCATTTTTTAT-CAAAACT-GCCTTCAATAATTTTATCCA-AAAATTTATTGTGTGGA
187 ATTAAAGGCATTTTTTATAAAAAAATCACCTTCAATAATCCTAT-CATAAAATTTATCGTGTGAA
* * * * *
17349520 ATATTAAAGGCATTTTTG-GCTAAAAACGCCTTTAAGAATCCATT-TCAACTTT
251 ATATTAAAAGC-GTTTTGAGCCAAAAACACCTTCAAGAATCCATTAT-AACTTT
* * * * *
17349572 TTTGTATAGATTATTGATGGTATTTTTTAAAAAAATTACCGTCAATAATACCAACTAAAAACTAA
1 TTTGTAT-GATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAAT-CCAACTAAAAATTTA
* *
17349637 TTGAATTGATTATTGAATGTGCTTTCAGCCAAAAATGCCTTCAAGAATCCGTTTCATATTTTTCC
64 TTG-ATTGATTATTGAA-G-GCTTTCAGCCAAAAATGCCTTCAAGAATCCATTTCATATTTTTTC
* * * * * *
17349702 TATGAATTATT-AAGGACGTTTTTCTACCGAAAATACCTTGAATAATCCTTAATAAAATGTTATT
126 TATG-ATTATTAAAGGACATTTTGCTACAGAAAACACCTTGAATAATCCCTAAAAAAATGTTATT
* * *
17349766 GAAGGCGTTTTTTATAAAAAAATCACCTTCAATAATCCTATCATTCAAATTTATCGTGTGAAATA
190 AAAGGCATTTTTTATAAAAAAATCACCTTCAATAATCCTATCA-TAAAATTTATCGTGTGAAATA
*
17349831 TTAAAAGCGTTTTGAGCCAAAAACACCTTCGAGAATCCATTATAACTTT
254 TTAAAAGCGTTTTGAGCCAAAAACACCTTCAAGAATCCATTATAACTTT
* * * *
17349880 TGTGTATGAATTATTGAAGGCATTTTTGAAAAAAACTACCTTTAATAATCCAAACTAAAAATTTA
1 TTTGTATG-ATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATCC-AACTAAAAATTTA
* ** *
17349945 TTGATTGAATTATTGAAGGCAAGTTT-GGCCAAAAACACATTCAAGAAT-CAGTTTCATATTTTT
64 TTGATTG-ATTATTGAAGGC---TTTCAGCCAAAAATGCCTTCAAGAATCCA-TTTCATATTTTT
*
17350008 TCTGTGGATTATTAAAGG
124 TCTAT-GATTATTAAAGG
17350026 TGTTTCTCTA
Statistics
Matches: 377, Mismatches: 56, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
303 1 0.00
304 9 0.02
305 162 0.43
306 14 0.04
307 28 0.07
308 154 0.41
309 9 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (302 bp):
TTTGTATGATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATCCAACTAAAAATTTATT
GATTGATTATTGAAGGCTTTCAGCCAAAAATGCCTTCAAGAATCCATTTCATATTTTTTCTATGA
TTATTAAAGGACATTTTGCTACAGAAAACACCTTGAATAATCCCTAAAAAAATGTTATTAAAGGC
ATTTTTTATAAAAAAATCACCTTCAATAATCCTATCATAAAATTTATCGTGTGAAATATTAAAAG
CGTTTTGAGCCAAAAACACCTTCAAGAATCCATTATAACTTT
Found at i:17349978 original size:308 final size:301
Alignment explanation
Indices: 17349269--17350022 Score: 781
Period size: 308 Copynumber: 2.5 Consensus size: 301
17349259 TCAAATAATT
* * ** ***
17349269 TGTATGGATTATTGAAGGTATTTTTGACAAAAATTACCTTCAATAATGTCTGTTAAAAATTTATT
1 TGTATGAATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATACCAACTAAAAATTTATT
* *
17349334 GATTGGATTATTGAAGGCGCTTTCA-CCAAAAAATGCCTTTAAGAATCCATTTCATATTTTTTCT
66 GATT-GATTATTGAAGGCG-TTT-AGCC-AAAAATGCCTTCAAGAATCCGTTTCATATTTTTTCT
*
17349398 AT-AGATTATTAAAGGCATATTTAGCAAGAAAACACCTTGAATTATCCCTAAAAAAATGTTATTA
127 ATGA-ATTATT-AAGGCATATTTAGCAAGAAAACACCTTGAATAATCCCTAAAAAAATGTTATTA
* * * ** * *
17349462 AAGGCATTTTTTATCAAAACTGCCTTCAATAATTTTATCCAAAAATTTATTGTGTGGAATATTAA
190 AAGGCATTTTTTATAAAAAATACCTTCAATAATCCTATCCAAAAATTTATCGTGTGAAATATTAA
* * * * * *
17349527 AGGCATTTTTGGCTAAAAACGCCTTTAAGAATCCATTTCAACTTTTT
255 AAGCAGTTTTGGCCAAAAACACCTTCAAGAATCCATTTCAACTTTTG
* * * * *
17349574 TGTAT-AGATTATTGATGGTATTTTTTAAAAAAATTACCGTCAATAATACCAACTAAAAACTAAT
1 TGTATGA-ATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATACCAACTAAAAATTTAT
*
17349638 TGAATTGATTATTGAATGTGC-TTTCAGCCAAAAATGCCTTCAAGAATCCGTTTCATATTTTTCC
65 TG-ATTGATTATTGAA-G-GCGTTT-AGCCAAAAATGCCTTCAAGAATCCGTTTCATATTTTTTC
* * * * * *
17349702 TATGAATTATTAAGGACGT-TTT-TCTACCGAAAATACCTTGAATAATCCTTAATAAAATGTTAT
126 TATGAATTATTAAGG-CATATTTAGC-A-AGAAAACACCTTGAATAATCCCTAAAAAAATGTTAT
* * *
17349765 TGAAGGCGTTTTTTATAAAAAAATCACCTTCAATAATCCTAT-CATTCAAATTTATCGTGTGAAA
188 TAAAGGCATTTTTTAT-AAAAAAT-ACCTTCAATAATCCTATCCA--AAAATTTATCGTGTGAAA
*
17349829 TATTAAAAGC-GTTTTGAGCCAAAAACACCTTCGAGAATCCATTAT-AACTTTTG
249 TATTAAAAGCAGTTTTG-GCCAAAAACACCTTCAAGAATCCATT-TCAACTTTTG
* * *
17349882 TGTATGAATTATTGAAGGCATTTTTGAAAAAAACTACCTTTAATAAT-CCAAACTAAAAATTTAT
1 TGTATGAATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATACC-AACTAAAAATTTAT
* ** * *
17349946 TGATTGAATTATTGAAGGCAAGTTTGGCCAAAAACACATTCAAGAATCAGTTTCATATTTTTTCT
65 TGATTG-ATTATTGAAGGC--GTTTAGCCAAAAATGCCTTCAAGAATCCGTTTCATATTTTTTCT
* *
17350011 GTGGATTATTAA
127 ATGAATTATTAA
17350023 AGGTGTTTCT
Statistics
Matches: 373, Mismatches: 55, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
303 1 0.00
304 8 0.02
305 156 0.42
306 16 0.04
307 28 0.08
308 159 0.43
309 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (301 bp):
TGTATGAATTATTGAAGGTATTTTTGAAAAAAATTACCTTCAATAATACCAACTAAAAATTTATT
GATTGATTATTGAAGGCGTTTAGCCAAAAATGCCTTCAAGAATCCGTTTCATATTTTTTCTATGA
ATTATTAAGGCATATTTAGCAAGAAAACACCTTGAATAATCCCTAAAAAAATGTTATTAAAGGCA
TTTTTTATAAAAAATACCTTCAATAATCCTATCCAAAAATTTATCGTGTGAAATATTAAAAGCAG
TTTTGGCCAAAAACACCTTCAAGAATCCATTTCAACTTTTG
Found at i:17351155 original size:2 final size:2
Alignment explanation
Indices: 17351148--17351189 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17351138 GTCATCTGCA
17351148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17351190 TCTGAACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17352562 original size:2 final size:2
Alignment explanation
Indices: 17352555--17352598 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
17352545 TTCTTGTTTT
17352555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17352596 TA T
1 TA T
17352599 GCGAGAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17356200 original size:6 final size:6
Alignment explanation
Indices: 17356184--17356231 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
17356174 CAATCTTCAA
* *
17356184 AAAAAC TAAAAAC AAAAAC GAAAAAC ACAAAAT GAAAAC AAAAAC AAA
1 AAAAAC -AAAAAC AAAAAC -AAAAAC A-AAAAC AAAAAC AAAAAC AAA
17356232 CCACCCCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 19 0.54
7 16 0.46
ACGTcount: A:0.77, C:0.15, G:0.04, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:17356202 original size:13 final size:13
Alignment explanation
Indices: 17356184--17356228 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
17356174 CAATCTTCAA
17356184 AAAAACTAAAAAC
1 AAAAACTAAAAAC
*
17356197 AAAAACGAAAAAC
1 AAAAACTAAAAAC
*
17356210 ACAAAA-TGAAAAC
1 A-AAAACTAAAAAC
17356223 AAAAAC
1 AAAAAC
17356229 AAACCACCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 19 0.70
14 4 0.15
ACGTcount: A:0.76, C:0.16, G:0.04, T:0.04
Consensus pattern (13 bp):
AAAAACTAAAAAC
Found at i:17356498 original size:42 final size:42
Alignment explanation
Indices: 17356443--17356530 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
17356433 AGAATGCACC
* *
17356443 AAAACATTTGTATAAGGTTTCTAAATATAAAATGTTTTATAT
1 AAAACATTCGTATAAGGTTTCTAAATATAAAACGTTTTATAT
*
17356485 AAAACGTTCGTATAAGGTTTCTAAATATAAAACGTTTTATAT
1 AAAACATTCGTATAAGGTTTCTAAATATAAAACGTTTTATAT
17356527 AAAA
1 AAAA
17356531 TTTACAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (42 bp):
AAAACATTCGTATAAGGTTTCTAAATATAAAACGTTTTATAT
Found at i:17358449 original size:24 final size:26
Alignment explanation
Indices: 17358421--17358475 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
17358411 GATGTATCTC
17358421 ATATTGAGTAAAA-AAATCACTTAT-
1 ATATTGAGTAAAATAAATCACTTATG
** *
17358445 ATATTGTTTAAAATAAATTACTTATG
1 ATATTGAGTAAAATAAATCACTTATG
17358471 ATATT
1 ATATT
17358476 TAAGTAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 11 0.42
25 10 0.38
26 5 0.19
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (26 bp):
ATATTGAGTAAAATAAATCACTTATG
Found at i:17361798 original size:24 final size:24
Alignment explanation
Indices: 17361764--17361810 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17361754 ATAGATATTC
*
17361764 AAAGTTATTCTCTAGTTAAAACTT
1 AAAGTTATTCTCTAGCTAAAACTT
*
17361788 AAAGTTTTTCTCTAGCTAAAACT
1 AAAGTTATTCTCTAGCTAAAACT
17361811 AGAGCTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (24 bp):
AAAGTTATTCTCTAGCTAAAACTT
Found at i:17367663 original size:5 final size:5
Alignment explanation
Indices: 17367653--17367685 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
17367643 TGCTTTGGTA
17367653 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
17367686 TATCCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:17370769 original size:3 final size:3
Alignment explanation
Indices: 17370761--17370800 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
17370751 CAGTAATACC
17370761 CTT CTT CTT CTTT CTTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT C-TT C-TT CTT CTT CTT CTT CTT CTT CTT CT
17370801 CTCTAACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:17376642 original size:16 final size:18
Alignment explanation
Indices: 17376621--17376653 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17376611 TTTTTTATAA
17376621 TTTTAA-TTA-TAAAATG
1 TTTTAAGTTATTAAAATG
17376637 TTTTAAGTTATTAAAAT
1 TTTTAAGTTATTAAAAT
17376654 TATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTTAAGTTATTAAAATG
Found at i:17377352 original size:31 final size:31
Alignment explanation
Indices: 17377308--17377381 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
17377298 ATATTTAAAA
*
17377308 AAATAAATGTATAATTTACACTATAAATTTTC
1 AAAT-AATATATAATTTACACTATAAATTTTC
* * *
17377340 AAGTAATATATAATTTGCATTATAAATTTTC
1 AAATAATATATAATTTACACTATAAATTTTC
*
17377371 AAATTATATAT
1 AAATAATATAT
17377382 TATATTAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (31 bp):
AAATAATATATAATTTACACTATAAATTTTC
Found at i:17383125 original size:38 final size:38
Alignment explanation
Indices: 17383083--17383157 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
17383073 TTCTAACAAT
17383083 TTTCTATTTACTCTATAGTCTATATGCACCTCATCCTC
1 TTTCTATTTACTCTATAGTCTATATGCACCTCATCCTC
17383121 TTTCTATTTACTCTATAGTCTATATGCACCTCATCCT
1 TTTCTATTTACTCTATAGTCTATATGCACCTCATCCT
17383158 TTGTTTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTCTATTTACTCTATAGTCTATATGCACCTCATCCTC
Found at i:17389087 original size:4 final size:4
Alignment explanation
Indices: 17389078--17389114 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
17389068 ACTGCATTGG
17389078 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
17389115 GTTCCATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:17396191 original size:39 final size:39
Alignment explanation
Indices: 17396135--17396209 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
17396125 AATGTTAGCT
17396135 TAAACAAGAAATATTTTCTACTTTATTATATATAAGCAG
1 TAAACAAGAAATATTTTCTACTTTATTATATATAAGCAG
* *
17396174 TAAAGAAGAAATATTTTCTACTTTATTGTATATAAG
1 TAAACAAGAAATATTTTCTACTTTATTATATATAAG
17396210 TAGAAATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (39 bp):
TAAACAAGAAATATTTTCTACTTTATTATATATAAGCAG
Found at i:17397422 original size:14 final size:14
Alignment explanation
Indices: 17397403--17397431 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17397393 AAAAATTACT
17397403 TACTATAAAAAAAA
1 TACTATAAAAAAAA
17397417 TACTATAAAAAAAA
1 TACTATAAAAAAAA
17397431 T
1 T
17397432 GATAATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
TACTATAAAAAAAA
Found at i:17418291 original size:2 final size:2
Alignment explanation
Indices: 17418284--17418324 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17418274 CGAATTACCC
17418284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17418325 CACAGTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17419876 original size:105 final size:105
Alignment explanation
Indices: 17419693--17419897 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 105
17419683 TTGAATACTT
* * *
17419693 ATAAATTTCATTTCTACGGATGATATATATCCTGTAGATAGCGTGAAAAAAATAATTTCTTTTCA
1 ATAAATTTCATTTCTACGGATGATATATATCATATAGATAGCGTGAAAAAAATAAGTTCTTTTCA
* * *
17419758 ATATGTTTATCTCTCTCCTCTTTGGTGTTAATGTCCTACA
66 AGATGTTTATCTCTCTCCTCCTTGATGTTAATGTCCTACA
* *
17419798 ATAAATTTCATTTCTACGGATGATATATATCATATAGATAGCGTGAATAAAATCAGTTCTTTTCA
1 ATAAATTTCATTTCTACGGATGATATATATCATATAGATAGCGTGAAAAAAATAAGTTCTTTTCA
* *
17419863 AGGTGTTTGTCTCTCTCCTCCTTGATGTTAATGTC
66 AGATGTTTATCTCTCTCCTCCTTGATGTTAATGTC
17419898 TTAGAATTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (105 bp):
ATAAATTTCATTTCTACGGATGATATATATCATATAGATAGCGTGAAAAAAATAAGTTCTTTTCA
AGATGTTTATCTCTCTCCTCCTTGATGTTAATGTCCTACA
Found at i:17425795 original size:3 final size:3
Alignment explanation
Indices: 17425789--17425823 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17425779 ATATTTTTTT
17425789 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17425824 GAGGATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17429682 original size:27 final size:27
Alignment explanation
Indices: 17429639--17429716 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
17429629 GATAAAAAAA
*
17429639 TTTTAAAGATAAATAAATTATTTAAT-T
1 TTTTAAA-TTAAATAAATTATTTAATAT
*
17429666 TTTTAAATTAAATTAAAATATTTAATAT
1 TTTTAAATTAAA-TAAATTATTTAATAT
* *
17429694 TTAATAATTTAAAATAAATTATT
1 TT-TTAAATT-AAATAAATTATT
17429717 ATAAATCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 4 0.10
27 19 0.45
28 3 0.07
29 13 0.31
30 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TTTTAAATTAAATAAATTATTTAATAT
Found at i:17432950 original size:14 final size:13
Alignment explanation
Indices: 17432929--17432971 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
17432919 TCTTTGAGAT
17432929 TTTTTAATATAAA
1 TTTTTAATATAAA
17432942 TTATTTAAT-TAAA
1 TT-TTTAATATAAA
*
17432955 ATTTTAATATATAA
1 TTTTTAATATA-AA
17432969 TTT
1 TTT
17432972 AAATAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.24
13 9 0.36
14 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAATATAAA
Found at i:17432962 original size:12 final size:13
Alignment explanation
Indices: 17432930--17432976 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
17432920 CTTTGAGATT
*
17432930 TTTTAATATAAAT
1 TTTTAATATAAAA
17432943 TATTTAAT-TAAAA
1 T-TTTAATATAAAA
*
17432956 TTTTAATATATAA
1 TTTTAATATAAAA
*
17432969 TTTAAATA
1 TTTTAATA
17432977 AACAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 6 0.21
13 17 0.59
14 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTAATATAAAA
Found at i:17432978 original size:24 final size:25
Alignment explanation
Indices: 17432930--17432978 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
17432920 CTTTGAGATT
* *
17432930 TTTTAATATAAATTATTTAATTAAAA
1 TTTTAATAT-AATAATTTAAATAAAA
17432956 TTTTAATAT-ATAATTTAAATAAA
1 TTTTAATATAATAATTTAAATAAA
17432979 CAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTAATATAATAATTTAAATAAAA
Found at i:17433334 original size:13 final size:13
Alignment explanation
Indices: 17433307--17433351 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
17433297 AGTCTTTGAG
17433307 AATTTTTAATATA
1 AATTTTTAATATA
17433320 AATTATTTAAT-TA
1 AATT-TTTAATATA
*
17433333 AATGTTTAATATA
1 AATTTTTAATATA
17433346 TAATTT
1 -AATTT
17433352 AAATCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.22
13 11 0.41
14 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
AATTTTTAATATA
Found at i:17435662 original size:14 final size:13
Alignment explanation
Indices: 17435630--17435662 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17435620 ACGTAACATT
17435630 AAAAAA-GAAAAA
1 AAAAAAGGAAAAA
17435642 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
17435655 AAACAAAG
1 AAA-AAAG
17435663 AGACAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 9 0.47
14 4 0.21
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGGAAAAA
Found at i:17438601 original size:2 final size:2
Alignment explanation
Indices: 17438594--17438622 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17438584 TTGGACAGTC
17438594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17438623 ACCCTAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17439382 original size:23 final size:24
Alignment explanation
Indices: 17439352--17439407 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 24
17439342 ACCCCTCTTT
*
17439352 TTTTTTTTTTCACAA-AAAAT-GA
1 TTTTTTTTTTAACAAGAAAATAGA
*
17439374 -GTTTTTTTTAACAAGAAAATAGA
1 TTTTTTTTTTAACAAGAAAATAGA
17439397 TTTTTTTTTTA
1 TTTTTTTTTTA
17439408 TTTATTGCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 12 0.43
22 5 0.18
23 2 0.07
24 9 0.32
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTTTTTTTTAACAAGAAAATAGA
Found at i:17440936 original size:14 final size:15
Alignment explanation
Indices: 17440913--17440945 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17440903 ACTCTACAAT
*
17440913 AAAAACAGAAAAA-A
1 AAAAAAAGAAAAAGA
17440927 AAAAAAAGAAAAAGA
1 AAAAAAAGAAAAAGA
17440942 AAAA
1 AAAA
17440946 GAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAGA
Found at i:17447831 original size:2 final size:2
Alignment explanation
Indices: 17447824--17447864 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17447814 AAATAAGCAT
17447824 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG A
17447865 TAAAGCATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17453215 original size:2 final size:2
Alignment explanation
Indices: 17453210--17453247 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17453200 AAGATGGAGC
17453210 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17453248 AATGGTTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17456006 original size:15 final size:15
Alignment explanation
Indices: 17455986--17456015 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17455976 CATTGTTGTA
17455986 TGTGCATGTTTGTCT
1 TGTGCATGTTTGTCT
17456001 TGTGCATGTTTGTCT
1 TGTGCATGTTTGTCT
17456016 GACTATCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.53
Consensus pattern (15 bp):
TGTGCATGTTTGTCT
Found at i:17456059 original size:22 final size:22
Alignment explanation
Indices: 17456031--17456081 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
17456021 TCTCTCTAGA
17456031 CATGCATGTATGGATGCACATG
1 CATGCATGTATGGATGCACATG
17456053 CATGCATGTATGGATGCACATG
1 CATGCATGTATGGATGCACATG
17456075 CATGCAT
1 CATGCAT
17456082 AGTTTACACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (22 bp):
CATGCATGTATGGATGCACATG
Found at i:17475746 original size:2 final size:2
Alignment explanation
Indices: 17475739--17475766 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17475729 ACCAGGAGAA
17475739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17475767 GAATTTCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17477579 original size:25 final size:25
Alignment explanation
Indices: 17477546--17477598 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
17477536 GAAATATACT
17477546 AAAAAAGGAGGTAGTCACGTTGGTA
1 AAAAAAGGAGGTAGTCACGTTGGTA
17477571 AAAAAAGGAGGTAGTCACGTTGGTA
1 AAAAAAGGAGGTAGTCACGTTGGTA
17477596 AAA
1 AAA
17477599 GAAAATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.30, T:0.19
Consensus pattern (25 bp):
AAAAAAGGAGGTAGTCACGTTGGTA
Found at i:17495332 original size:26 final size:26
Alignment explanation
Indices: 17495297--17495352 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
17495287 AAACAGTAAT
* *
17495297 AAAATTTATTATAGTTACAATTAAAA
1 AAAAATTATTATAATTACAATTAAAA
* **
17495323 AAAAATTATTGTAATTATGATTAAAA
1 AAAAATTATTATAATTACAATTAAAA
17495349 AAAA
1 AAAA
17495353 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (26 bp):
AAAAATTATTATAATTACAATTAAAA
Found at i:17499212 original size:105 final size:105
Alignment explanation
Indices: 17499030--17499240 Score: 404
Period size: 105 Copynumber: 2.0 Consensus size: 105
17499020 ATTTTGGTCC
*
17499030 TGTGGATAGACTTGGCTTGACAGGGACATCAAGCATTAAAGGTGGGGAGATTGTAACGCCCCCAA
1 TGTGGATAGACTCGGCTTGACAGGGACATCAAGCATTAAAGGTGGGGAGATTGTAACGCCCCCAA
17499095 TCCCACATCAGGAGGATGTGTGGATAAGGAATGATATATA
66 TCCCACATCAGGAGGATGTGTGGATAAGGAATGATATATA
17499135 TGTGGATAGACTCGGCTTGACAGGGACATCAAGCATTAAAGGTGGGGAGATTGTAACGCCCCCAA
1 TGTGGATAGACTCGGCTTGACAGGGACATCAAGCATTAAAGGTGGGGAGATTGTAACGCCCCCAA
*
17499200 TCCCACATCAGGATGATGTGTGGATAAGGAATGATATATA
66 TCCCACATCAGGAGGATGTGTGGATAAGGAATGATATATA
17499240 T
1 T
17499241 ATAGAGACTT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (105 bp):
TGTGGATAGACTCGGCTTGACAGGGACATCAAGCATTAAAGGTGGGGAGATTGTAACGCCCCCAA
TCCCACATCAGGAGGATGTGTGGATAAGGAATGATATATA
Found at i:17505233 original size:5 final size:5
Alignment explanation
Indices: 17505225--17505258 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17505215 TCTAGTTATT
* *
17505225 CTTTC CTTTC TTTTC CTTTC CTTTA CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
17505259 TAATTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (5 bp):
CTTTC
Found at i:17512996 original size:2 final size:2
Alignment explanation
Indices: 17512989--17513015 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17512979 GCAACAACAG
17512989 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
17513016 CTTTGTAAAG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:17513725 original size:27 final size:27
Alignment explanation
Indices: 17513695--17513750 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
17513685 TAGTCAGGGC
*
17513695 ATCGATCAATCATATTTTAATGTTAGG
1 ATCGATCAAACATATTTTAATGTTAGG
*
17513722 ATCGATCAAACATATTTTATTGTTAGG
1 ATCGATCAAACATATTTTAATGTTAGG
17513749 AT
1 AT
17513751 AATCTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (27 bp):
ATCGATCAAACATATTTTAATGTTAGG
Found at i:17515226 original size:2 final size:2
Alignment explanation
Indices: 17515219--17515246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17515209 TAGCATACCA
17515219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17515247 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17516601 original size:12 final size:12
Alignment explanation
Indices: 17516584--17516609 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17516574 GGACTTGATA
17516584 GACATAGGAAAG
1 GACATAGGAAAG
17516596 GACATAGGAAAG
1 GACATAGGAAAG
17516608 GA
1 GA
17516610 AAAAGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.35, T:0.08
Consensus pattern (12 bp):
GACATAGGAAAG
Found at i:17522636 original size:23 final size:22
Alignment explanation
Indices: 17522609--17522659 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
17522599 TTAATATAAA
*
17522609 AATTAAAATAAAAAAATATTTTT
1 AATTAAAA-AAAAAAATATTTAT
* *
17522632 AATTATAACAAAAAATATTTAT
1 AATTAAAAAAAAAAATATTTAT
17522654 -ATTAAA
1 AATTAAA
17522660 TTTTATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTAAAAAAAAAAATATTTAT
Found at i:17530358 original size:2 final size:2
Alignment explanation
Indices: 17530353--17530384 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17530343 ACACACACAC
17530353 AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17530385 TTGTATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17531771 original size:2 final size:2
Alignment explanation
Indices: 17531764--17531815 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
17531754 TCAAAACGTT
17531764 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17531806 AG AG AG AG AG
1 AG AG AG AG AG
17531816 TTGCTTTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17535969 original size:17 final size:17
Alignment explanation
Indices: 17535947--17535980 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17535937 CTAACTGCTA
17535947 ACGTTATCGACTATGGG
1 ACGTTATCGACTATGGG
17535964 ACGTTATCGACTATGGG
1 ACGTTATCGACTATGGG
17535981 GTTAAGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (17 bp):
ACGTTATCGACTATGGG
Found at i:17541431 original size:126 final size:128
Alignment explanation
Indices: 17541206--17541470 Score: 281
Period size: 126 Copynumber: 2.1 Consensus size: 128
17541196 ACACATATCG
* *
17541206 CATTAAAA-TTTCTTTTTCGAATTATTTAAAACATTTTTTATTAAAAACACTTTGAATAATTATT
1 CATTAAAATTTTCTTTTTCGAATTATTTAAAACATTTTTTATTAAAAACACTTTAAATAATCATT
* * *
17541270 TCATAAAAATTTAAAATAAAATTATTGAAAATA-TTTTTGATAAAAAATATCTTTAATAA-TTT
66 TCATAAAAATTTAAAAGAAAATTATTGAAAATATTTTTTG-TAAAAAATACCTTAAATAACTTT
*** ** *
17541332 CATTAAAATTTTC-TTTT-GAGATTATTTAAGGTATTTTTGT-TTAAAAATGCTTTAAATAATCC
1 CATTAAAATTTTCTTTTTCGA-ATTATTTAAAACATTTTT-TATTAAAAACACTTTAAATAATCA
* * * * ** *
17541394 TTTCATAAAAATTTATAAGGAGATTATTTAAGGTATTTTTTGTTAAAAATACCTTAAATAACTTT
64 TTTCATAAAAATTTAAAAGAAAATTATTGAAAATATTTTTTGTAAAAAATACCTTAAATAACTTT
* *
17541459 TATTAAATTTTT
1 CATTAAAATTTT
17541471 TATAAGAAAT
Statistics
Matches: 114, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
125 2 0.02
126 88 0.77
127 24 0.21
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (128 bp):
CATTAAAATTTTCTTTTTCGAATTATTTAAAACATTTTTTATTAAAAACACTTTAAATAATCATT
TCATAAAAATTTAAAAGAAAATTATTGAAAATATTTTTTGTAAAAAATACCTTAAATAACTTT
Found at i:17541473 original size:64 final size:63
Alignment explanation
Indices: 17541349--17541494 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 63
17541339 ATTTTCTTTT
* *
17541349 GAGATTATTTAAGGTA-TTTTTGTTTAAAAATGCTTTAAATAATCCTTTCATAAAAATTTATAA
1 GAGATTATTTAAGGTATTTTTTGTTTAAAAATACCTTAAATAA-CCTTTCATAAAAATTTATAA
* **
17541412 GGAGATTATTTAAGGTATTTTTTG-TTAAAAATACCTTAAATAA-CTTTTATTAAATTTTTTATA
1 -GAGATTATTTAAGGTATTTTTTGTTTAAAAATACCTTAAATAACCTTTCA-TAAA-AATTTATA
17541475 A
63 A
* *
17541476 GAAATTATTTAAGGCATTT
1 GAGATTATTTAAGGTATTT
17541495 CTTGACAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
62 5 0.07
63 21 0.29
64 40 0.56
65 6 0.08
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (63 bp):
GAGATTATTTAAGGTATTTTTTGTTTAAAAATACCTTAAATAACCTTTCATAAAAATTTATAA
Found at i:17557049 original size:36 final size:34
Alignment explanation
Indices: 17556997--17557081 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 34
17556987 AAAAAATAAT
* * *
17556997 TTAATAAAATTTTAATAAAAAATCTAAATTGATATA
1 TTAAAAAAAATTTAATAAAAAATCT-AA-TAATATA
**
17557033 TTAAAAAAAATTTAATATGAAATCTAATAATATA
1 TTAAAAAAAATTTAATAAAAAATCTAATAATATA
17557067 -TAAAAAAATATTTAA
1 TTAAAAAAA-ATTTAA
17557082 AATATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
33 8 0.19
34 12 0.28
35 2 0.05
36 21 0.49
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (34 bp):
TTAAAAAAAATTTAATAAAAAATCTAATAATATA
Found at i:17557229 original size:14 final size:15
Alignment explanation
Indices: 17557210--17557247 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
17557200 ATAATAAAAT
17557210 TTTTTAATTT-ATTA
1 TTTTTAATTTAATTA
17557224 TTTTTAATTTAATTA
1 TTTTTAATTTAATTA
17557239 TTTTTAATT
1 TTTTTAATT
17557248 AAAAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATTTAATTA
Found at i:17557254 original size:22 final size:22
Alignment explanation
Indices: 17557229--17557274 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
17557219 TATTATTTTT
* *
17557229 AATTTAATTATTTTTAATTAAA
1 AATTTAATAAATTTTAATTAAA
* *
17557251 AATTTCATAAATTTTACTTAAA
1 AATTTAATAAATTTTAATTAAA
17557273 AA
1 AA
17557275 AACTTTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTAATAAATTTTAATTAAA
Found at i:17557717 original size:16 final size:14
Alignment explanation
Indices: 17557688--17557734 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
17557678 AAAAATTTAT
17557688 AAAAAAAA-TATTA
1 AAAAAAAATTATTA
17557701 AAAAAATAGATTATTA
1 AAAAAA-A-ATTATTA
*
17557717 ATAAAAAATTA-TA
1 AAAAAAAATTATTA
17557730 AAAAA
1 AAAAA
17557735 GAGATTTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 12 0.41
14 5 0.17
15 2 0.07
16 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAAAAAATTATTA
Found at i:17560020 original size:36 final size:36
Alignment explanation
Indices: 17559973--17560043 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
17559963 TCTCAGATAA
*
17559973 TACAATAATTGGATCATTATAGCATACTCAACAATG
1 TACAATAATTGGATCATTATAACATACTCAACAATG
*
17560009 TACAATAATTGGATCATTATAACATACTGAACAAT
1 TACAATAATTGGATCATTATAACATACTCAACAAT
17560044 AATTGATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (36 bp):
TACAATAATTGGATCATTATAACATACTCAACAATG
Done.