Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 92 of 160
Found at i:17488959 original size:85 final size:87
Alignment explanation
Indices: 17488800--17488971 Score: 224
Period size: 85 Copynumber: 2.0 Consensus size: 87
17488790 TTCCTTGAAA
* *
17488800 ATAAAATTGTAAAAAAAACGTTTTTAAGGAAGAGTTAAAAGTATCAAATTTCCTTGAAAATAAAA
1 ATAAAATTGTAAAAAAAACATTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTGAAAATAAAA
17488865 TTTTCAAAAAAGCATTTTTGAG
66 TTTTCAAAAAAGCATTTTTGAG
* * * * *
17488887 ATAAAATT-TTAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATC-AATTTTCTTGAAAATAAAG
1 ATAAAATTGTAAAAAAAACATTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTGAAAATAAA-
* * *
17488950 A-TTTGAAAAAGGGATTTTTGAG
65 ATTTTCAAAAAAGCATTTTTGAG
17488972 GAAAAGTTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 35 0.47
86 31 0.42
87 8 0.11
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (87 bp):
ATAAAATTGTAAAAAAAACATTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTGAAAATAAAA
TTTTCAAAAAAGCATTTTTGAG
Found at i:17488968 original size:58 final size:58
Alignment explanation
Indices: 17488887--17489066 Score: 254
Period size: 61 Copynumber: 3.1 Consensus size: 58
17488877 CATTTTTGAG
*
17488887 ATAAAATTTTAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC-TTGAAA
1 ATAAAATTTAAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAA
* * * * *
17488944 ATAAAGATTTGAAAAAGGGATTTTTGAGGAAAAGTTAAAAGTATCAATATTCTTTGAAA
1 ATAAA-ATTTAAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAA
*
17489003 ATAAAATTTTCAAAAAAAAGCATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAA
1 ATAAAA-TTT--AAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAA
17489064 ATA
1 ATA
17489067 GAAACGTCAA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 5 0.05
58 42 0.39
59 14 0.13
61 46 0.43
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (58 bp):
ATAAAATTTAAAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAA
Found at i:17489013 original size:144 final size:145
Alignment explanation
Indices: 17488753--17489029 Score: 402
Period size: 144 Copynumber: 1.9 Consensus size: 145
17488743 AATTTAAAAG
* *
17488753 AAAAAACATTTTTTAGGAAAAGTTGAAGGTATCAATTTTCCTTGAAAATAAAATTGTAAAAAAAA
1 AAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTGTAAAAAAAA
*
17488818 CGTTTTTAAGGAAGAGTTAAAAGTATCAAATTTCCTTGAAAATAAAATTTTC-AAAAAAGCATTT
66 CGTTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTGAAAATAAAATTTTCAAAAAAAGCATTT
17488882 TTGAGATAAAATTTT
131 TTGAGATAAAATTTT
*
17488897 AAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTTGAAAATAAAGATT-T-GAAAA
1 AAAAAA-CATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA-ATTGTAAAAAA
** * *
17488959 AGGGATTTTTGAGGAAAAGTTAAAAGTATC-AATATTCTTTGAAAATAAAATTTTCAAAAAAAAG
64 AACG-TTTTTAAGGAAAAGTTAAAAGTATCAAAT-TTCCTTGAAAATAAAATTTTC-AAAAAAAG
17489023 CATTTTT
126 CATTTTT
17489030 AAGGAAAAGT
Statistics
Matches: 119, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
143 9 0.08
144 62 0.52
145 34 0.29
146 14 0.12
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.34
Consensus pattern (145 bp):
AAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTGTAAAAAAAA
CGTTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTGAAAATAAAATTTTCAAAAAAAGCATTT
TTGAGATAAAATTTT
Found at i:17499823 original size:18 final size:18
Alignment explanation
Indices: 17499800--17499836 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17499790 AGAAACATTG
*
17499800 GTATGAAAATTTGCTGAT
1 GTATGAAAATTTGATGAT
17499818 GTATGAAAATTTGATGAT
1 GTATGAAAATTTGATGAT
17499836 G
1 G
17499837 CTTTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (18 bp):
GTATGAAAATTTGATGAT
Found at i:17500467 original size:21 final size:20
Alignment explanation
Indices: 17500443--17500493 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
17500433 AAAAGAGATT
17500443 GATCCCCTCA-CATAGAGGATC
1 GATCCCCTCAGCA-AG-GGATC
* *
17500464 GATCACCTAAGGCAAGGGATC
1 GATCCCCTCA-GCAAGGGATC
17500485 GATCCCCTC
1 GATCCCCTC
17500494 TTAAAGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 20 0.83
22 2 0.08
23 2 0.08
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (20 bp):
GATCCCCTCAGCAAGGGATC
Found at i:17503652 original size:13 final size:13
Alignment explanation
Indices: 17503634--17503666 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
17503624 CTTCTCAATG
17503634 TCTTTATATATGT
1 TCTTTATATATGT
17503647 TCTTTATATATGT
1 TCTTTATATATGT
17503660 T-TTTATA
1 TCTTTATA
17503667 CATTCACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (13 bp):
TCTTTATATATGT
Found at i:17505045 original size:159 final size:160
Alignment explanation
Indices: 17504831--17505765 Score: 827
Period size: 161 Copynumber: 5.8 Consensus size: 160
17504821 TCTGTTTACA
* * * * * * * * **
17504831 ACTTTTTATGCCGTTAAAAGGTAAAAATACAAATTTACAGTTATTATTTTGTTTTAATAGTTTTA
1 ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
* * * *
17504896 ATAGTTTCAATACATGATATTAAACTTATCCAAATTATTGAACTTAGTTTTCACGGTTGATATGT
66 ATAGCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGGTTTTCACAGTTGATATGT
* *
17504961 ATG-AAAGTTGTTGTTTACGTCTATTTAGG
131 GTGAAAAGTTGTTGTTTACCTCTATTTAGG
* * * * *
17504990 ACTTTTTGTGCCATTAATAGGTAAAAATACAAATTTGTTGTTATTGTTCTATTTTAACAGTTTGC
1 ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
* * * ** * * *
17505055 ATAGCTCCAATACATGATGTTAAACTTGTCGGAATAATTGAACTTGGTATCCACAGTTGATATGT
66 ATAGCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGGTTTTCACAGTTGATATGT
* **** *
17505120 GTGAAAAAGCTAACATTTACATCTATTTAGG
131 GTG-AAAAGTTGTTGTTTACCTCTATTTAGG
** * * * * *
17505151 ACTTTTTATGATATTAAAAGG-CAAAATGCAAATTTGATATTATTGTTCT-GTTTAACAATTTGG
1 ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
* * *
17505214 ATAGCTTCAATACATGATATTAAACTTGTCCAAATGATT--TCTT-GATTTCTA-ATGTTGATAT
66 ATAGCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGGTTTTC-ACA-GTTGATAT
* **
17505275 GTGTGAAAATTTTGTTGTTTATGTCTATTTAGG
129 GTGTGAAAA-GTTGTTGTTTACCTCTATTTAGG
* * * * *
17505308 ACTATTTT-TGTCATTTAAAGGCAAAAATACAAATTTGTTGTTATTATTCTATTTTAACAATTTG
1 ACT-TTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTG
* * *** *
17505372 GA-AGGCTTCAATACATTATATTAAACTTTTTTGAATGATTGAACTTGGCTTTT-TCAGTTGATA
65 GATA-GCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGG-TTTTCACAGTTGATA
* **
17505435 TATGTGAAAAAGTTGTTAG-TTACCTCCGTTTAGG
128 TGTGTG-AAAAGTTGTT-GTTTACCTCTATTTAGG
* * * ** * *
17505469 ATTTTTTTTACTGTTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAATAGTTTGG
1 ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
* * * *** * *
17505534 ATAACTTCAATACATGATATTAAATTTTTTTGAATGATTGAACTTGGTTTTCATAGTTGATATAT
66 ATAGCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGGTTTTCACAGTTGATATGT
** *
17505599 GTGAAAAAGCCGTTGTTTACCTCTATTTATG
131 GTG-AAAAGTTGTTGTTTACCTCTATTTAGG
* *** * * * *
17505630 ACTTTTTTTGTTGTTAAAAGGTAAAAATACAAAGTCGCTATTATTGTTCTGTTTTAACAATTTGG
1 ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
* * * *
17505695 ATGGCTTCAATATATGATATTAAACTTGA-CCAAATGATTGAATTTAG-TTTC-CATGATTGATA
66 ATAGCTTCAATACATGATATTAAACTT-ATCCAAATGATTGAACTTGGTTTTCACA-G-TTGATA
17505757 TGTGTGAAA
128 TGTGTGAAA
17505766 GGCTAAAATG
Statistics
Matches: 630, Mismatches: 123, Indels: 45
0.79 0.15 0.06
Matches are distributed among these distances:
156 8 0.01
157 45 0.07
158 28 0.04
159 200 0.32
160 41 0.07
161 297 0.47
162 8 0.01
163 3 0.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (160 bp):
ACTTTTTATGCCATTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAACAATTTGG
ATAGCTTCAATACATGATATTAAACTTATCCAAATGATTGAACTTGGTTTTCACAGTTGATATGT
GTGAAAAGTTGTTGTTTACCTCTATTTAGG
Found at i:17505336 original size:318 final size:319
Alignment explanation
Indices: 17504844--17505722 Score: 873
Period size: 318 Copynumber: 2.7 Consensus size: 319
17504834 TTTTATGCCG
* * * * * ** *
17504844 TTAAAAGGTAAAAATACAAATTT-ACAGTTATTATT-TTGTTTTAATAGTTTTAATAGTTTCAAT
1 TTAAAAGGTAAAAATACAAATTTGATA-TTATTGTTCTAG-TTTAACAATTTGGATAGCTTCAAT
* * ** *
17504907 ACATGATATTAAACTTATCCAAATTATTGAACTTAGTTTTC-ACGGTTGATATGTATG-AAAGTT
64 ACATGATATTAAACTTATCCAAATGATT-AACTT-GATTTCTAATGTTGATATGTGTGAAAAGTT
*
17504970 GTTGTTTACGTCTATTTAGGACTTTTTGTGCCA-TTAATAGGTAAAAATACAAATTTGTTGTTAT
127 GTTGTTTACGTCTATTTAGGACTTTTT-TGTCATTTAA-AGGTAAAAATACAAATTTGTTGTTAT
* * * *
17505034 TGTTCTATTTTAACAGTTTGCATAGCTCCAATACATGATGTTAAACTTGTCGGAATAATTGAACT
190 TGTTCTATTTTAACAATTTGGATAGCTTCAATACATGATATTAAACTTGTCGGAATAATTGAACT
* * *
17505099 TGG-TATCCACAGTTGATATGTGTGAAAAAGCTAACATTTACATCTATTTAGGACTTTTTATGA-
255 TGGCT-TCCACAGTTGATATATGTGAAAAAGCTAACAGTTACATCCATTTAGGA-TTTTTATGAC
17505162 TA
318 TA
* *
17505164 TTAAAAGG-CAAAATGCAAATTTGATATTATTGTTCT-GTTTAACAATTTGGATAGCTTCAATAC
1 TTAAAAGGTAAAAATACAAATTTGATATTATTGTTCTAGTTTAACAATTTGGATAGCTTCAATAC
* * *
17505227 ATGATATTAAACTTGTCCAAATGATT-TCTTGATTTCTAATGTTGATATGTGTGAAAATTTTGTT
66 ATGATATTAAACTTATCCAAATGATTAACTTGATTTCTAATGTTGATATGTGTGAAAA-GTTGTT
* * *
17505291 GTTTATGTCTATTTAGGACTATTTTTGTCATTTAAAGGCAAAAATACAAATTTGTTGTTATTATT
130 GTTTACGTCTATTTAGGACT-TTTTTGTCATTTAAAGGTAAAAATACAAATTTGTTGTTATTGTT
* * ** *
17505356 CTATTTTAACAATTTGGA-AGGCTTCAATACATTATATTAAACTTTTTTGAATGATTGAACTTGG
194 CTATTTTAACAATTTGGATA-GCTTCAATACATGATATTAAACTTGTCGGAATAATTGAACTTGG
*** * *** * * * * *
17505420 CTTTTTCAGTTGATATATGTGAAAAAGTTGTTAGTTACCTCCGTTTAGGATTTTTTTTACTG
258 CTTCCACAGTTGATATATGTGAAAAAGCTAACAGTTACATCCATTTAGGATTTTTATGACTA
* * * * * *
17505482 TTAAAAGGTAAAAATACAAATTTGCTGTTATTGTTCTATTTTAATAGTTTGGATAACTTCAATAC
1 TTAAAAGGTAAAAATACAAATTTGATATTATTGTTCTAGTTTAACAATTTGGATAGCTTCAATAC
* * *** * * * **
17505547 ATGATATTAAATTTTTTTGAATGATTGAACTTGGTTT-TCATAGTTGATATATGTGAAAAAGCCG
66 ATGATATTAAACTTATCCAAATGATT-AACTTGATTTCTAAT-GTTGATATGTGTG-AAAAGTTG
* * ** * * * * *
17505611 TTGTTTACCTCTATTTATGACTTTTTTTGTTGTTAAAAGGTAAAAATACAAAGTCGCTATTATTG
128 TTGTTTACGTCTATTTAGGAC-TTTTTTGTCATTTAAAGGTAAAAATACAAATTTGTTGTTATTG
* * *
17505676 TTCTGTTTTAACAATTTGGATGGCTTCAATATATGATATTAAACTTG
192 TTCTATTTTAACAATTTGGATAGCTTCAATACATGATATTAAACTTG
17505723 ACCAAATGAT
Statistics
Matches: 459, Mismatches: 82, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
315 5 0.01
316 16 0.03
317 11 0.02
318 199 0.43
319 53 0.12
320 55 0.12
321 3 0.01
322 112 0.24
323 5 0.01
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (319 bp):
TTAAAAGGTAAAAATACAAATTTGATATTATTGTTCTAGTTTAACAATTTGGATAGCTTCAATAC
ATGATATTAAACTTATCCAAATGATTAACTTGATTTCTAATGTTGATATGTGTGAAAAGTTGTTG
TTTACGTCTATTTAGGACTTTTTTGTCATTTAAAGGTAAAAATACAAATTTGTTGTTATTGTTCT
ATTTTAACAATTTGGATAGCTTCAATACATGATATTAAACTTGTCGGAATAATTGAACTTGGCTT
CCACAGTTGATATATGTGAAAAAGCTAACAGTTACATCCATTTAGGATTTTTATGACTA
Found at i:17507228 original size:32 final size:34
Alignment explanation
Indices: 17507184--17507291 Score: 109
Period size: 34 Copynumber: 3.2 Consensus size: 34
17507174 ATGTTTTATG
*
17507184 ATACAAATGTCACTAAATT-A-G-TGATTTTTTTT
1 ATACAAACGTCACTAAATTAACGAT-ATTTTTTTT
17507216 ATACAAACGTCACTAAATTAACGATATTTTTTTT
1 ATACAAACGTCACTAAATTAACGATATTTTTTTT
* * * *
17507250 ATACAAA--TACTACTAAATTAGCGGTATTTTTCTA
1 ATACAAACGT-C-ACTAAATTAACGATATTTTTTTT
17507284 ATACAAAC
1 ATACAAAC
17507292 ACTATCAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
32 19 0.29
33 2 0.03
34 43 0.66
35 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (34 bp):
ATACAAACGTCACTAAATTAACGATATTTTTTTT
Found at i:17507302 original size:34 final size:34
Alignment explanation
Indices: 17507195--17507304 Score: 102
Period size: 34 Copynumber: 3.3 Consensus size: 34
17507185 TACAAATGTC
* * *
17507195 ACTAAATTAGTGAT-TTTTT-TTATACAAAC-GT
1 ACTAAATTAGCGATATTTTTCTAATACAAACACT
* * * *
17507226 CACTAAATTAACGATATTTTTTTTATACAAATACT
1 -ACTAAATTAGCGATATTTTTCTAATACAAACACT
*
17507261 ACTAAATTAGCGGTATTTTTCTAATACAAACACT
1 ACTAAATTAGCGATATTTTTCTAATACAAACACT
17507295 A-TCAAATTAG
1 ACT-AAATTAG
17507305 TGGCATTTCT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 12 0.18
33 6 0.09
34 46 0.71
35 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (34 bp):
ACTAAATTAGCGATATTTTTCTAATACAAACACT
Found at i:17507947 original size:34 final size:34
Alignment explanation
Indices: 17507900--17507975 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
17507890 TAGGAGATAA
* *
17507900 TGAATAGTGCTAAGTTAGAATAGTATC-AACTTAG
1 TGAATAGTACTAAGTCAGAATAGTATCGAA-TTAG
*
17507934 TGAATAGTACTAAGTCAGCATAGTATCGAATTAG
1 TGAATAGTACTAAGTCAGAATAGTATCGAATTAG
*
17507968 TAAATAGT
1 TGAATAGT
17507976 GATAAAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (34 bp):
TGAATAGTACTAAGTCAGAATAGTATCGAATTAG
Found at i:17513766 original size:135 final size:132
Alignment explanation
Indices: 17513492--17513768 Score: 308
Period size: 132 Copynumber: 2.1 Consensus size: 132
17513482 TTGTAAAGAT
* * ** *
17513492 AATTTTTAGTTGTTATAAATATTATAAAAAATTTTGTAATAATTTTTTTATTGTTGTACAAAAAT
1 AATTTTTA-TTGTTATAAATATGATAAAAAATTTTGTAACAATTTTTTTATCATTGTACAAAAAC
* * *
17513557 ATTAAAAAAATAAATTAAATAATAATATTTAAAAATCGTTTCAAATAAAACAAGTTTTCACAACA
65 ATTAAAAAAATAAATTAAAAAATAATATTTAAAAATCGTTGCAAATAAAACAAATTTTCACAACA
17513622 ATA
130 ATA
* * * *
17513625 ACTTTTTATTGTTATAAATATGATAATAAATTTTGTAACAA-TTTTTTGTCATTGTA-TAAAACA
1 AATTTTTATTGTTATAAATATGATAAAAAATTTTGTAACAATTTTTTTATCATTGTACAAAAACA
* * * * *
17513688 TTAAGAAAATAAATTGAATAAAATAATGATATTGAAAATTTGTTGCAAATACAACAAATTTT-AG
66 TTAAAAAAATAAATT-AA-AAAATAAT-AT-TT-AAAAATCGTTGCAAATAAAACAAATTTTCAC
*
17513752 AATTAATA
126 AA-CAATA
17513760 AATTTTTAT
1 AATTTTTAT
17513769 CGTTGTATAA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
130 19 0.16
131 14 0.12
132 37 0.31
133 9 0.08
134 5 0.04
135 35 0.29
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (132 bp):
AATTTTTATTGTTATAAATATGATAAAAAATTTTGTAACAATTTTTTTATCATTGTACAAAAACA
TTAAAAAAATAAATTAAAAAATAATATTTAAAAATCGTTGCAAATAAAACAAATTTTCACAACAA
TA
Found at i:17514110 original size:267 final size:263
Alignment explanation
Indices: 17513771--17514380 Score: 731
Period size: 267 Copynumber: 2.3 Consensus size: 263
17513761 ATTTTTATCG
* ** * * *
17513771 TTGTATAAAATATTTACAAAAATAAATTAAGTAACCATATTTAAAAATTGTTTCGAATAAAATAA
1 TTGTATAAAA-A-TTA-AAAAATAAATTAAGCAATGATATTTAAAAATTATTACAAATAAAATAA
* * * * * *
17513836 ATTTTCACAACAATAATTTTTTATCATTATAAATATGATAAAATTTTTTATAACAATTTTTTTGT
63 GTTTTCACAACAATAATTTTTTATCATTACAAATATGATAAAAATTTTCAAAACAACTTTTTTGT
* *
17513901 TGTTATATAAAATATTAAAAAAAATAAATAAATTAAGCAACGACATTAAAAAAATCATTGTAAAT
128 TGTTATATAAAATATT---AAAAATAAATAAATTAAGCAAAGACATT-AAAAAATCATTGCAAAT
* * * *
17513966 AAAAGAA-TTTTTCACAACAATAA-ATTTTTATTGTTACAAATATGATAAAAACTTTTGTAACAA
189 AAAACAAGTTTTT-ACAACAATAATA-TTTTATAGTTACAAACATGATAAAAACTTGTGTAACAA
17514029 C-TTTTTTGCCA
252 CTTTTTTTGCCA
*
17514040 TTGTATAAAACATTAAAAAATAAATTAAGCAATGATATTTAAAAATTATTGCAAATAAAATAAGT
1 TTGTATAAAA-ATTAAAAAATAAATTAAGCAATGATATTTAAAAATTATTACAAATAAAATAAGT
* ** *
17514105 TTTCACAATAATAATTTTTTATTGTTACAAATATGATAAAAATTTTCAAAATAACTTTTTTGTTG
65 TTTCACAACAATAATTTTTTATCATTACAAATATGATAAAAATTTTCAAAACAACTTTTTTGTTG
* * * **
17514170 TTGTATAAATTATTAAAAATAAATAAATTAAGCAAAGACATTGAAAAATTGTTGCAAATAAAACA
130 TTATATAAAATATTAAAAATAAATAAATTAAGCAAAGACATTAAAAAATCATTGCAAATAAAACA
** * * *
17514235 AGTTTTTGTAATAATAATATTTTATAGTTACAAACATGATAAATACTTGTGTAATAACTTTTTTT
195 AGTTTTTACAACAATAATATTTTATAGTTACAAACATGATAAAAACTTGTGTAACAACTTTTTTT
*
17514300 GTCA
260 GCCA
* ** * * *
17514304 TTGTATAAAATTGTAAAAAATAGTTTAAACAATGAAATTGAAAAATTATTACAAATAAAATAAGT
1 TTGTATAAAAAT-TAAAAAATAAATTAAGCAATGATATTTAAAAATTATTACAAATAAAATAAGT
*
17514369 TTTCTCAACAAT
65 TTTCACAACAAT
17514381 TTTTTATTGT
Statistics
Matches: 294, Mismatches: 43, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
263 61 0.21
264 108 0.37
267 111 0.38
268 3 0.01
269 11 0.04
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (263 bp):
TTGTATAAAAATTAAAAAATAAATTAAGCAATGATATTTAAAAATTATTACAAATAAAATAAGTT
TTCACAACAATAATTTTTTATCATTACAAATATGATAAAAATTTTCAAAACAACTTTTTTGTTGT
TATATAAAATATTAAAAATAAATAAATTAAGCAAAGACATTAAAAAATCATTGCAAATAAAACAA
GTTTTTACAACAATAATATTTTATAGTTACAAACATGATAAAAACTTGTGTAACAACTTTTTTTG
CCA
Found at i:17514133 original size:130 final size:130
Alignment explanation
Indices: 17513762--17514380 Score: 567
Period size: 130 Copynumber: 4.7 Consensus size: 130
17513752 AATTAATAAA
* * * * * * * * *
17513762 TTTTTATCGTTGTATAAAATATTTACAAAAATAAATTAAGTAACCATATTTAAAAATTGTTTCGA
1 TTTTTGTCATTGTATAAAATA-TTA-AAAAATAAATTAAGCAACGACATTGAAAAATTATTGCAA
* ** * **
17513827 ATAAAATAAATTTTCACAACAATAATTTTTTATCATTATAAATATGATAAAATTTTTTATAACAA
64 ATAAAATAAGTTTTCACAACAATAATTTTTTATTGTTACAAATATGATAAAAACTTTTATAACAA
*
17513892 TT
129 CT
** * * *
17513894 TTTTTGTTGTTATATAAAATATTAAAAAAAATAAATAAATTAAGCAACGACATTAAAAAAATCAT
1 TTTTTGTCATTGTATAAAATATT-----AAA-AAATAAATTAAGCAACGACATT-GAAAAATTAT
* * * * *
17513959 TGTAAATAAAAGAATTTTTCACAACAATAAATTTTTATTGTTACAAATATGATAAAAACTTTTGT
59 TGCAAATAAAATAAGTTTTCACAACAATAATTTTTTATTGTTACAAATATGATAAAAACTTTTAT
17514024 AACAACT
124 AACAACT
* * * * *
17514031 TTTTTGCCATTGTATAAAACATTAAAAAATAAATTAAGCAATGATATTTAAAAATTATTGCAAAT
1 TTTTTGTCATTGTATAAAATATTAAAAAATAAATTAAGCAACGACATTGAAAAATTATTGCAAAT
* * *
17514096 AAAATAAGTTTTCACAATAATAATTTTTTATTGTTACAAATATGATAAAAA-TTTTCAAAATAAC
66 AAAATAAGTTTTCACAACAATAATTTTTTATTGTTACAAATATGATAAAAACTTTT-ATAACAAC
17514160 T
130 T
** * * *
17514161 TTTTTGTTGTTGTATAAATTATTAAAAATAAATAAATTAAGCAAAGACATTGAAAAATTGTTGCA
1 TTTTTGTCATTGTATAAAATATT--AAA-AAATAAATTAAGCAACGACATTGAAAAATTATTGCA
* *** * * * * * * * *
17514226 AATAAAACAAGTTTTTGTAATAATAATATTTTATAGTTACAAACATGATAAATACTTGTGTAATA
63 AATAAAATAAGTTTTCACAACAATAATTTTTTATTGTTACAAATATGATAAAAACTTTTATAACA
17514291 ACTT
128 AC-T
** * * * *
17514295 TTTTTGTCATTGTATAAAAT-TGTAAAAAATAGTTTAAACAATGAAATTGAAAAATTATTACAAA
1 TTTTTGTCATTGTATAAAATAT-TAAAAAATAAATTAAGCAACGACATTGAAAAATTATTGCAAA
*
17514359 TAAAATAAGTTTTCTCAACAAT
65 TAAAATAAGTTTTCACAACAAT
17514381 TTTTTATTGT
Statistics
Matches: 399, Mismatches: 74, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
129 4 0.01
130 85 0.21
131 70 0.18
132 27 0.07
133 85 0.21
134 22 0.06
135 2 0.01
136 20 0.05
137 84 0.21
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (130 bp):
TTTTTGTCATTGTATAAAATATTAAAAAATAAATTAAGCAACGACATTGAAAAATTATTGCAAAT
AAAATAAGTTTTCACAACAATAATTTTTTATTGTTACAAATATGATAAAAACTTTTATAACAACT
Found at i:17520354 original size:38 final size:36
Alignment explanation
Indices: 17520309--17520382 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 36
17520299 AAACAAGAAA
* *
17520309 TAAATCAAATTTGAAACAAAACTTCTTTTCTTTTTTTT
1 TAAATCAAATTTAAAACAAAACTT-TATT-TTTTTTTT
17520347 TAAATCAAATTTAAAACAAAACTTTATTTTTTTTTT
1 TAAATCAAATTTAAAACAAAACTTTATTTTTTTTTT
17520383 GGATCAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 8 0.24
37 3 0.09
38 23 0.68
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (36 bp):
TAAATCAAATTTAAAACAAAACTTTATTTTTTTTTT
Found at i:17520606 original size:13 final size:13
Alignment explanation
Indices: 17520588--17520621 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17520578 TATTATTTTA
17520588 TTTTAAAAC-AATT
1 TTTTAAAACTAA-T
17520601 TTTTAAAACTAAT
1 TTTTAAAACTAAT
17520614 TTTTAAAA
1 TTTTAAAA
17520622 ATAAATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.90
14 2 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTAAAACTAAT
Found at i:17520849 original size:13 final size:13
Alignment explanation
Indices: 17520832--17520954 Score: 62
Period size: 13 Copynumber: 9.6 Consensus size: 13
17520822 AAAGTTTAAA
17520832 GTTAGGG-TTAGG
1 GTTAGGGTTTAGG
17520844 GTTTA--GTTTAGG
1 G-TTAGGGTTTAGG
*
17520856 GTTAGGGTTTCA-T
1 GTTAGGGTTT-AGG
*
17520869 GATAGGGTTTAGG
1 GTTAGGGTTTAGG
* *
17520882 TTTAGGG-TTAGTC
1 GTTAGGGTTTAG-G
* * *
17520895 TTTA-GATTTAAG
1 GTTAGGGTTTAGG
* *
17520907 GTTAGGGTATAAG
1 GTTAGGGTTTAGG
17520920 GTTAGGGTTTAGG
1 GTTAGGGTTTAGG
*
17520933 GTTTA-GATTTAGG
1 G-TTAGGGTTTAGG
17520946 GTTTAGGGT
1 G-TTAGGGT
17520955 AAAAGTTTAG
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
11 4 0.05
12 16 0.19
13 58 0.69
14 6 0.07
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (13 bp):
GTTAGGGTTTAGG
Found at i:17520933 original size:20 final size:20
Alignment explanation
Indices: 17520908--17520965 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
17520898 AGATTTAAGG
*
17520908 TTAGGGTATAAGGTTAGGGT
1 TTAGGGTATAAGTTTAGGGT
*
17520928 TTAGGGT-TTAGATTTAGGGT
1 TTAGGGTATAAG-TTTAGGGT
*
17520948 TTAGGGTAAAAGTTTAGG
1 TTAGGGTATAAGTTTAGG
17520966 TTTGGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 27 0.84
21 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (20 bp):
TTAGGGTATAAGTTTAGGGT
Found at i:17521065 original size:41 final size:40
Alignment explanation
Indices: 17521000--17521082 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 40
17520990 AAGGTAAGGT
** *
17521000 TTGGGATTTAGAGTTTTTGATTTAAAATTTTGATTTAGGGG
1 TTGGGATTTAGAGTTTAGGATTTAAAATTTGGATTT-GGGG
* * **
17521041 TTGGGATTTAGGGTTTAGGGTTTAAGGTTTGGATTTGGGG
1 TTGGGATTTAGAGTTTAGGATTTAAAATTTGGATTTGGGG
17521081 TT
1 TT
17521083 TTGATTTTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
40 6 0.17
41 29 0.83
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (40 bp):
TTGGGATTTAGAGTTTAGGATTTAAAATTTGGATTTGGGG
Found at i:17521096 original size:27 final size:27
Alignment explanation
Indices: 17521027--17521107 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
17521017 TGATTTAAAA
* * *
17521027 TTTTGATTTAGGGGTTGGGATTTAGGG
1 TTTTGATTTTGGGGTTTGGATTTGGGG
* ** **
17521054 TTTAGGGTTTAAGGTTTGGATTTGGGG
1 TTTTGATTTTGGGGTTTGGATTTGGGG
*
17521081 TTTTGATTTTGGGGTTTCGATTTGGGG
1 TTTTGATTTTGGGGTTTGGATTTGGGG
17521108 CTTACAAAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.12, C:0.01, G:0.40, T:0.47
Consensus pattern (27 bp):
TTTTGATTTTGGGGTTTGGATTTGGGG
Found at i:17521097 original size:14 final size:13
Alignment explanation
Indices: 17521066--17521107 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17521056 TAGGGTTTAA
*
17521066 GGTTTGGATTTGG
1 GGTTTCGATTTGG
*
17521079 GGTTTTGATTTTGG
1 GGTTTCGA-TTTGG
17521093 GGTTTCGATTTGG
1 GGTTTCGATTTGG
17521106 GG
1 GG
17521108 CTTACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.07, C:0.02, G:0.43, T:0.48
Consensus pattern (13 bp):
GGTTTCGATTTGG
Found at i:17521610 original size:13 final size:12
Alignment explanation
Indices: 17521575--17521915 Score: 119
Period size: 11 Copynumber: 27.8 Consensus size: 12
17521565 AATATTGTAT
17521575 TATAATATATTAA
1 TATAATATA-TAA
* *
17521588 CA-AATAATATTA
1 TATAAT-ATATAA
17521600 TATGAATATATAA
1 TAT-AATATATAA
*
17521613 TATACTAT-TAA
1 TATAATATATAA
17521624 TATAATATATTAA
1 TATAATATA-TAA
17521637 TA-AATAATATAA
1 TATAAT-ATATAA
*
17521649 -ATAAT-TAATAT
1 TATAATAT-ATAA
17521660 TATAATATATTAA
1 TATAATATA-TAA
17521673 TAAATAATATTATAA
1 T--ATAATA-TATAA
**
17521688 -ATAA-ATATTT
1 TATAATATATAA
17521698 TAATAATATATTAA
1 T-ATAATATA-TAA
*
17521712 TATTAATAAATAA
1 TA-TAATATATAA
17521725 TA-AATCATATTAA
1 TATAAT-ATA-TAA
17521738 TA-AATA-ATAA
1 TATAATATATAA
*
17521748 TATTATAT-TAA
1 TATAATATATAA
*
17521759 T-GAATAATATAA
1 TATAAT-ATATAA
17521771 TATTAAATATTATTAA
1 TA-T-AATA-TA-TAA
*
17521787 TTTAAT-TAATAA
1 TATAATAT-ATAA
*
17521799 -ATATTATAATAA
1 TATAATAT-ATAA
*
17521811 TATATTA-ATAA
1 TATAATATATAA
* * *
17521822 AATAATATGTTA
1 TATAATATATAA
*
17521834 T-TAATAAATAA
1 TATAATATATAA
*
17521845 TATACTAT-TAA
1 TATAATATATAA
17521856 TATAATATAATAA
1 TATAATAT-ATAA
*
17521869 CA-AATATTATTAA
1 TATAATA-TA-TAA
17521882 TTAATAATATATTAA
1 -T-ATAATATA-TAA
*
17521897 TATATTA-ATAA
1 TATAATATATAA
17521908 -ATAATATA
1 TATAATATA
17521916 AAGAATAATA
Statistics
Matches: 249, Mismatches: 36, Indels: 88
0.67 0.10 0.24
Matches are distributed among these distances:
10 16 0.06
11 62 0.25
12 62 0.25
13 61 0.24
14 16 0.06
15 22 0.09
16 10 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (12 bp):
TATAATATATAA
Found at i:17521628 original size:16 final size:16
Alignment explanation
Indices: 17521607--17521864 Score: 124
Period size: 16 Copynumber: 15.6 Consensus size: 16
17521597 TTATATGAAT
*
17521607 ATATAATATACTATTA
1 ATATAATATATTATTA
*
17521623 ATATAATATATTAATA
1 ATATAATATATTATTA
*
17521639 A-ATAATATAAATAATTA
1 ATATAATAT--ATTATTA
*
17521656 ATATTATA-ATATATTA
1 ATATAATATAT-TATTA
*
17521672 ATA-AATAATATTATAA
1 ATATAAT-ATATTATTA
* *
17521688 ATA-AATATTTTAATA
1 ATATAATATATTATTA
* *
17521703 ATATATTAATATTAATA
1 ATATAAT-ATATTATTA
*
17521720 A-ATAATAAATCATATTA
1 ATATAATATAT--TATTA
17521737 ATAAATAATAATATTATATTA
1 AT--ATAAT-ATA-T-TATTA
*
17521758 ATGAATAATATAATATTA
1 AT--ATAATATATTATTA
17521776 A-AT-AT-TATTAATTTA
1 ATATAATATATT-A-TTA
*
17521791 AT-TAATA-AATATT-
1 ATATAATATATTATTA
*
17521804 ATAATAATATATTAATA
1 AT-ATAATATATTATTA
* *
17521821 AAATAATATGTTATTA
1 ATATAATATATTATTA
*
17521837 ATAAATAATATACTATTA
1 AT--ATAATATATTATTA
17521855 ATATAATATA
1 ATATAATATA
17521865 ATAACAAATA
Statistics
Matches: 187, Mismatches: 29, Indels: 52
0.70 0.11 0.19
Matches are distributed among these distances:
13 5 0.03
14 5 0.03
15 36 0.19
16 68 0.36
17 23 0.12
18 25 0.13
20 8 0.04
21 16 0.09
22 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
ATATAATATATTATTA
Found at i:17521634 original size:36 final size:34
Alignment explanation
Indices: 17521579--17521864 Score: 158
Period size: 32 Copynumber: 8.5 Consensus size: 34
17521569 TTGTATTATA
*
17521579 ATATATTAACA-AATAATATTATATGAATATATAAT
1 ATATATTAATATAAT-ATATTATAT-AATATATAAT
17521614 ATACTATTAATATAATATATTA-ATAAATAATATAA-
1 ATA-TATTAATATAATATATTATAT-AAT-ATATAAT
* *
17521649 ATA-ATTAATAT--TATAATATATTAATAAATAAT
1 ATATATTAATATAATATATTATA-TAATATATAAT
* *
17521681 AT-TATAAATA-AATATTTTA-ATAATATATTAAT
1 ATATATTAATATAATATATTATATAATATA-TAAT
* * * *
17521713 AT-TAATAA-ATAATAAATCATATTAATAAATAAT
1 ATATATTAATATAATATATTATA-TAATATATAAT
*
17521746 A-ATATT-ATATTAATGA-ATAATATAATAT-TAA-
1 ATATATTAATA-TAAT-ATATTATATAATATATAAT
* * * *
17521777 ATATTATTAATTTAAT-TAATAAATATTATAATAAT
1 ATA-TATTAATATAATATATTATATAATAT-ATAAT
* * * *
17521812 ATATTAATAAAATAATATGTTAT-TAATAAATAAT
1 ATA-TATTAATATAATATATTATATAATATATAAT
17521846 ATACTATTAATATAATATA
1 ATA-TATTAATATAATATA
17521865 ATAACAAATA
Statistics
Matches: 192, Mismatches: 34, Indels: 51
0.69 0.12 0.18
Matches are distributed among these distances:
31 19 0.10
32 42 0.22
33 37 0.19
34 40 0.21
35 29 0.15
36 22 0.11
37 3 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
ATATATTAATATAATATATTATATAATATATAAT
Found at i:17521671 original size:49 final size:47
Alignment explanation
Indices: 17521541--17521897 Score: 182
Period size: 49 Copynumber: 7.4 Consensus size: 47
17521531 AATTTTACTT
* * *
17521541 ATAAATAATATTAT-ATTAATA-AATAATAT-TGTATTATAATATATTA
1 ATAAATAATATAATAATTAATATTATAATATAT-TAATA-AATATATTA
* * *
17521587 ACAAATAATATTAT-ATGAATA-TATAATATACTATTAATATAATATATTA
1 ATAAATAATATAATAATTAATATTAT-A-ATA-TATTAATA-AATATATTA
17521636 ATAAATAATATAAATAATTAATATTATAATATATTAATAAATAATATT-
1 ATAAATAATAT-AATAATTAATATTATAATATATTAATAAAT-ATATTA
* * *
17521684 ATAAATAAATATTTTAATAATATATTAATATTAATA-AATAATAAATCATATTA
1 ATAAAT-AATA---TAATAAT-TAATATTA-TAATATATTAATAAAT-ATATTA
* * *
17521737 ATAAATAATAATATTATATTAATGA--ATAATATAATATTAAATATTATTA
1 ATAAATAAT-ATAATA-ATTAAT-ATTATAATATATTAATAAATA-TATTA
* * * * *
17521786 AT--TTAAT-TAATAAATATTATAATAATATATTAATAAAATAATATGTT
1 ATAAATAATATAATAATTAATATTATAATATATTAAT-AAAT-ATAT-TA
* * * * * *
17521833 ATTAATAA-ATAATATACTATTAATATAATATAATAACAAATATTATTA
1 ATAAATAATATAATA-ATTAATATTATAATATATTAATAAATA-TATTA
* *
17521881 ATTAATAATATATTAAT
1 ATAAATAATATAATAAT
17521898 ATATTAATAA
Statistics
Matches: 250, Mismatches: 30, Indels: 60
0.74 0.09 0.18
Matches are distributed among these distances:
43 1 0.00
44 4 0.02
45 15 0.06
46 28 0.11
47 9 0.04
48 29 0.12
49 79 0.32
50 30 0.12
51 16 0.06
52 27 0.11
53 12 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (47 bp):
ATAAATAATATAATAATTAATATTATAATATATTAATAAATATATTA
Found at i:17521746 original size:101 final size:105
Alignment explanation
Indices: 17521541--17521820 Score: 263
Period size: 107 Copynumber: 2.8 Consensus size: 105
17521531 AATTTTACTT
* ** * *
17521541 ATAAATAAT-AT-TATATTAATAAATAATATTGTATTATA-AT-AT-A-TTAACAAAT-AATATT
1 ATAAATAATAATATATATTAATGAATAATATAATATTAAATATAATAATTTAATAAATAAATATT
* *
17521599 AT-ATGAATATA-TAATA-TACT-ATTAATATAATATATTA
66 ATAAT-AATATATTAATATTAATAAATAATATAATATATTA
* * *
17521636 ATAAATAAT-ATA-A-A-TAATTAATATTATAATATATTAATA-AATAATATT-ATAAATAAATA
1 ATAAATAATAATATATATTAATGAATAATATAATAT-TAAATATAATAAT-TTAATAAATAAATA
*
17521695 TTTTAATAATATATTAATATTAATAAATAATA-AATCATATTA
64 TTATAATAATATATTAATATTAATAAATAATATAAT-ATATTA
* *
17521737 ATAAATAATAATATTATATTAATGAATAATATAATATTAAATATTATTAATTTAATTAATAAATA
1 ATAAATAATAATA-TATATTAATGAATAATATAATATTAAATA-TAATAATTTAATAAATAAATA
17521802 TTATAATAATATATTAATA
64 TTATAATAATATATTAATA
17521821 AAATAATATG
Statistics
Matches: 148, Mismatches: 16, Indels: 30
0.76 0.08 0.15
Matches are distributed among these distances:
93 14 0.09
94 3 0.02
95 15 0.10
96 1 0.01
97 5 0.03
98 15 0.10
99 7 0.05
100 6 0.04
101 21 0.14
102 3 0.02
104 1 0.01
105 6 0.04
106 18 0.12
107 33 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (105 bp):
ATAAATAATAATATATATTAATGAATAATATAATATTAAATATAATAATTTAATAAATAAATATT
ATAATAATATATTAATATTAATAAATAATATAATATATTA
Found at i:17521821 original size:23 final size:23
Alignment explanation
Indices: 17521594--17521916 Score: 131
Period size: 23 Copynumber: 13.8 Consensus size: 23
17521584 TTAACAAATA
*
17521594 ATATTATATGAATA-TATAAT-AT
1 ATATTA-ATAAATATTATAATAAT
17521616 ACTATTAATATAATA-TATTAATAAAT
1 A-TATTAATA-AATATTA-TAAT-AAT
* * * *
17521642 AATATAAATAATTAATATTATAAT
1 -ATATTAATAAATATTATAATAAT
17521666 ATATTAATAAATAATATTATAAATAAAT
1 ATATTAAT--A-AATATTAT-AAT-AAT
* *
17521694 ATTTTAATAATATATTAATATTAAT
1 ATATTAATAA-ATATT-ATAATAAT
*
17521719 A-AATAATAAATCA-TATTAATAA-
1 ATATTAATAAAT-ATTA-TAATAAT
* *
17521741 ATAATAATATTATATTAATGAATAAT
1 ATATTAATA-AATATT-AT-AATAAT
* *
17521767 ATAATATTAAATATTAT--TAAT
1 ATATTAATAAATATTATAATAAT
*
17521788 TTAATTAATAAATATTATAATAAT
1 AT-ATTAATAAATATTATAATAAT
* *
17521812 ATATTAATAAA-ATAAT-AT-GT
1 ATATTAATAAATATTATAATAAT
17521832 -TATTAATAAATA--AT-AT-A-
1 ATATTAATAAATATTATAATAAT
* * *
17521849 CTATTAATATAATATAATAACAAAT
1 ATATTAATA-AATATTATAA-TAAT
* * *
17521874 ATTATTAATTAATAATATATTAAT
1 A-TATTAATAAATATTATAATAAT
*
17521898 ATATTAATAAATAATATAA
1 ATATTAATAAATATTATAA
17521917 AGAATAATAA
Statistics
Matches: 234, Mismatches: 32, Indels: 69
0.70 0.10 0.21
Matches are distributed among these distances:
18 12 0.05
19 14 0.06
20 2 0.01
21 9 0.04
22 23 0.10
23 59 0.25
24 30 0.13
25 30 0.13
26 40 0.17
27 5 0.02
28 10 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATATTAATAAATATTATAATAAT
Found at i:17522013 original size:17 final size:17
Alignment explanation
Indices: 17521945--17522042 Score: 76
Period size: 18 Copynumber: 5.6 Consensus size: 17
17521935 ATTTTAAGTA
17521945 TTTTT-ATATTAAAATAAT
1 TTTTTAATATT-AAAT-AT
*
17521963 ATTTTAATATTAAATAT
1 TTTTTAATATTAAATAT
* *
17521980 TATTATTAAAATATAATTAT
1 T-TT-TTAATAT-TAAATAT
17522000 TTTTTAATATT-AATA-
1 TTTTTAATATTAAATAT
* * *
17522015 ATTTTAATAATAAATAA
1 TTTTTAATATTAAATAT
17522032 TTTTTAATATT
1 TTTTTAATATT
17522043 TTACTAGTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
15 9 0.14
16 7 0.11
17 12 0.19
18 16 0.25
19 13 0.20
20 7 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTTAATATTAAATAT
Found at i:17522038 original size:32 final size:34
Alignment explanation
Indices: 17521956--17522042 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 34
17521946 TTTTATATTA
17521956 AAATAATATTTTAATATTAAATATTATTATTAAAAT
1 AAATAAT-TTTTAATATTAAATA-TATTATTAAAAT
*
17521992 ATAATTATTTTTTAATATT-AATA-ATT-TTAATAAT
1 A-AA-TAATTTTTAATATTAAATATATTATTAA-AAT
17522026 AAATAATTTTTAATATT
1 AAATAATTTTTAATATT
17522043 TTACTAGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
32 13 0.28
33 6 0.13
34 7 0.15
36 5 0.11
37 12 0.26
38 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
AAATAATTTTTAATATTAAATATATTATTAAAAT
Found at i:17524604 original size:49 final size:49
Alignment explanation
Indices: 17524444--17524782 Score: 357
Period size: 49 Copynumber: 7.0 Consensus size: 49
17524434 TTTGAGAAGA
* *
17524444 GCTCCTATAAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAAG
1 GCTCCTATCAACATAGGCAAGTAAC-TTTAAAAATCAATTCTGAAAAAGG
* * **
17524494 GCTCCTTTCAACATAGGTAA-TGAACTTT-AAAATCAATTCT-AAAAAAA
1 GCTCCTATCAACATAGGCAAGT-AACTTTAAAAATCAATTCTGAAAAAGG
* *
17524541 GCTCCTATCAACATAGGCAAGTAACTTCAAAAATCAATTTTGAAAAAGG
1 GCTCCTATCAACATAGGCAAGTAACTTTAAAAATCAATTCTGAAAAAGG
* * ** *
17524590 GCTCATATCAACATAAGCAACAAACTTT-AAAATCAATT-TCAAAAAGG
1 GCTCCTATCAACATAGGCAAGTAACTTTAAAAATCAATTCTGAAAAAGG
* *
17524637 GCTTCTATCAACATAAGCAAGTAACTTTAAAAAATCAATTCTGAAAAAGG
1 GCTCCTATCAACATAGGCAAGTAACTTT-AAAAATCAATTCTGAAAAAGG
* * * * * * * **
17524687 GTTCCTATTAATATAGGTAAGGAACTTTAAAAGTCAATTTTGAAAAATA
1 GCTCCTATCAACATAGGCAAGTAACTTTAAAAATCAATTCTGAAAAAGG
* * *
17524736 GCTCCTATCAACATAGACAA-TGAACTTTAAAAATTAATTCTAAAAAA
1 GCTCCTATCAACATAGGCAAGT-AACTTTAAAAATCAATTCTGAAAAA
17524783 AGGGTTGATC
Statistics
Matches: 239, Mismatches: 42, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
47 61 0.26
48 34 0.14
49 95 0.40
50 49 0.21
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (49 bp):
GCTCCTATCAACATAGGCAAGTAACTTTAAAAATCAATTCTGAAAAAGG
Found at i:17524616 original size:96 final size:97
Alignment explanation
Indices: 17524443--17524782 Score: 400
Period size: 96 Copynumber: 3.5 Consensus size: 97
17524433 TTTTGAGAAG
* * *
17524443 AGCTCCTATAAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAAGGCTCCTTTCAACAT
1 AGCTCCTATCAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAGGGCTCCTATCAACAT
*
17524508 AGGTAATGAACTTTAAAATCAA-TTCTAAAAAA
66 AGGTAACGAACTTTAAAATCAATTTC-AAAAAA
* * *
17524540 AGCTCCTATCAACATAGGCAAGTAAC-TTCAAAAATCAATTTTGAAAAAGGGCTCATATCAACAT
1 AGCTCCTATCAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAGGGCTCCTATCAACAT
* * * *
17524604 AAGCAACAAACTTTAAAATCAATTTCAAAAAG
66 AGGTAACGAACTTTAAAATCAATTTCAAAAAA
* * * * * * *
17524636 GGCTTCTATCAACATAAGCAAGTAACTTTAAAAAATCAATTCTGAAAAAGGGTTCCTATTAATAT
1 AGCTCCTATCAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAGGGCTCCTATCAACAT
* * *
17524701 AGGTAAGGAACTTTAAAAGTCAATTTTGAAAAAT
66 AGGTAACGAACTTTAAAA-TCAA-TTTCAAAAAA
* * *
17524735 AGCTCCTATCAACATAGACAA-TGAAC-TTTAAAAATTAATTCTAAAAAA
1 AGCTCCTATCAACATAGGCAAGT-AACTTTTAAAAATCAATTCTGAAAAA
17524783 AGGGTTGATC
Statistics
Matches: 205, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
96 79 0.39
97 74 0.36
98 24 0.12
99 28 0.14
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (97 bp):
AGCTCCTATCAACATAGGCAAGTAACTTTTAAAAATCAATTCTGAAAAAGGGCTCCTATCAACAT
AGGTAACGAACTTTAAAATCAATTTCAAAAAA
Found at i:17526039 original size:16 final size:16
Alignment explanation
Indices: 17526020--17526095 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
17526010 CAATCGGATC
17526020 CTTTTTTTTTTGTTTT
1 CTTTTTTTTTTGTTTT
*
17526036 CTTTTTCTTTTGTTTT
1 CTTTTTTTTTTGTTTT
*
17526052 CTTTTTTATTTTTTGTTT
1 CTTTTTT-TTTTGT-TTT
* * *
17526070 ATTCTTTTTTT-CTTT
1 CTTTTTTTTTTGTTTT
17526085 CTTTTATTTTT
1 CTTTT-TTTTT
17526096 AAGCATAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
15 6 0.12
16 26 0.53
17 9 0.18
18 8 0.16
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (16 bp):
CTTTTTTTTTTGTTTT
Found at i:17526075 original size:31 final size:29
Alignment explanation
Indices: 17526020--17526095 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 29
17526010 CAATCGGATC
*
17526020 CTTTTTTTTTTGTTTTCTTTTTCTTTTGTTT
1 CTTTTTTTATT-TTTTCTTTTTCTTTT-TTT
*
17526051 -TCTTTTTTATTTTTTGTTTATTCTTTTTTT
1 CT-TTTTTTATTTTTTCTTT-TTCTTTTTTT
17526081 CTTTCTTTTATTTTT
1 CTTT-TTTTATTTTT
17526096 AAGCATAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (29 bp):
CTTTTTTTATTTTTTCTTTTTCTTTTTTT
Found at i:17536997 original size:24 final size:23
Alignment explanation
Indices: 17536935--17537079 Score: 71
Period size: 23 Copynumber: 6.6 Consensus size: 23
17536925 CCAATTGGCT
*
17536935 TTTATTTTTATTATTTGTCTATT
1 TTTATTTTTATTATTTATCTATT
* *
17536958 TATTA-ATATATATATTT-T-TATT
1 T-TTATTTTTAT-TATTTATCTATT
17536980 TTTA---TT-TT-TTTATCTATT
1 TTTATTTTTATTATTTATCTATT
** **
17536998 AATATTTTTATTATTTATCTGCT
1 TTTATTTTTATTATTTATCTATT
17537021 TTTATTTTTTATTA-TTAT-TATT
1 TTTA-TTTTTATTATTTATCTATT
* *
17537043 ATCTATTTCTT-TTATTTATCTAAT
1 -TTTATTT-TTATTATTTATCTATT
*
17537067 TAT-TTTTTATTAT
1 TTTATTTTTATTAT
17537080 CATTAATATA
Statistics
Matches: 93, Mismatches: 14, Indels: 31
0.67 0.10 0.22
Matches are distributed among these distances:
16 3 0.03
17 2 0.02
18 7 0.08
19 1 0.01
21 7 0.08
22 22 0.24
23 31 0.33
24 20 0.22
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (23 bp):
TTTATTTTTATTATTTATCTATT
Found at i:17537014 original size:23 final size:23
Alignment explanation
Indices: 17536976--17537079 Score: 76
Period size: 23 Copynumber: 4.5 Consensus size: 23
17536966 TATATATTTT
*
17536976 TATTTTTATTTTTTTATCT-ATTAA
1 TATTTTTA-TTATTTATCTAATT-A
** *
17537000 TATTTTTATTATTTATCTGCTTT
1 TATTTTTATTATTTATCTAATTA
17537023 TATTTTTTATTA-TTAT-T-ATTA
1 TA-TTTTTATTATTTATCTAATTA
17537044 TCTATTTCTT-TTATTTATCTAATTA
1 --TATTT-TTATTATTTATCTAATTA
17537069 T-TTTTTATTAT
1 TATTTTTATTAT
17537080 CATTAATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
21 4 0.06
22 14 0.21
23 24 0.36
24 20 0.30
25 4 0.06
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (23 bp):
TATTTTTATTATTTATCTAATTA
Found at i:17537063 original size:46 final size:43
Alignment explanation
Indices: 17536994--17537092 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 43
17536984 TTTTTTTATC
17536994 TATTAATATTTTTATTATTTATCTGCTTTTATTTTTTATTATTAT
1 TATTAATATTTTTATTATTTATCT--TTTTATTTTTTATTATTAT
* ** *
17537039 TATTATCTATTTCTT-TTATTTATCTAATTATTTTTTATTATCAT
1 TATTA-ATATTT-TTATTATTTATCTTTTTATTTTTTATTATTAT
*
17537083 TAAT-ATATTT
1 TATTAATATTT
17537093 ATCTTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
42 5 0.11
44 19 0.41
45 5 0.11
46 15 0.33
47 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (43 bp):
TATTAATATTTTTATTATTTATCTTTTTATTTTTTATTATTAT
Found at i:17537480 original size:19 final size:19
Alignment explanation
Indices: 17537458--17537494 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17537448 AATCCGACAA
17537458 AATTTTTC-ATCGAATTTTG
1 AATTTTTCGA-CGAATTTTG
17537477 AATTTTTCGACGAATTTT
1 AATTTTTCGACGAATTTT
17537495 TTGGCTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (19 bp):
AATTTTTCGACGAATTTTG
Found at i:17544595 original size:34 final size:33
Alignment explanation
Indices: 17544525--17544613 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 33
17544515 AGATATCAAC
*
17544525 AATGGATGAAAGATGAGAAAAAAAAAGAAAAGAA
1 AATGG-TGAAAGATGAAAAAAAAAAAGAAAAGAA
*
17544559 AATGGTGAAAGGTGAAAAAAAGAAAATGAAAA-AA
1 AATGGTGAAAGATGAAAAAAA-AAAA-GAAAAGAA
17544593 AATGG-GAAA-ATGAAAAAAAAA
1 AATGGTGAAAGATGAAAAAAAAA
17544614 GAAAAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.04
32 9 0.18
33 18 0.36
34 16 0.32
35 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.10
Consensus pattern (33 bp):
AATGGTGAAAGATGAAAAAAAAAAAGAAAAGAA
Found at i:17544620 original size:18 final size:16
Alignment explanation
Indices: 17544573--17544618 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
17544563 GTGAAAGGTG
17544573 AAAAAAAGAAAATGAA
1 AAAAAAAGAAAATGAA
*
17544589 AAAAAATGGGAAAATGAA
1 AAAAAA--AGAAAATGAA
17544607 AAAAAAAGAAAA
1 AAAAAAAGAAAA
17544619 AAAAAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (16 bp):
AAAAAAAGAAAATGAA
Found at i:17545813 original size:22 final size:22
Alignment explanation
Indices: 17545788--17545846 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
17545778 GAATATTTTG
* *
17545788 ATGAGAATTTTTTAGAATTC-AA
1 ATGAGAATATTTGAG-ATTCAAA
*
17545810 ATGAGAATATTTGAGTTTCAAA
1 ATGAGAATATTTGAGATTCAAA
*
17545832 ATGAGAATCTTTGAG
1 ATGAGAATATTTGAG
17545847 GAGTGAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (22 bp):
ATGAGAATATTTGAGATTCAAA
Found at i:17546069 original size:80 final size:80
Alignment explanation
Indices: 17545971--17546193 Score: 243
Period size: 80 Copynumber: 2.7 Consensus size: 80
17545961 TAGAAGAGCA
*
17545971 ATTTACTTTTCAAGGTCATGGAGCCTCTGTTTAGAGGAGC-ATTTATTTTT-AAAGTCATGGTGC
1 ATTTA-TTTTCAAGGTCATGGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCATGGAG-
* * * * *
17546034 TTTTGCTTAGAGAATTT
64 GTCTGATTAGAGAAGTC
* * * * * *
17546051 ATTTATTTTCCAAAGTCATTGAGCCTCTGATTAAAGGAGCTATTTATTTTTCAAAGTCGTTGAGG
1 ATTTATTTT-CAAGGTCATGGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCATGGAGG
*
17546116 TCTGATTAGAGGAGTC
65 TCTGATTAGAGAAGTC
* *
17546132 ATTTATTTTCAAGGTCGTGGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTTCAAAGTCAT
1 ATTTATTTTCAAGGTCATGGAGCCTCTGTTTAGAGGAGC--TATTTA-TTTTTCAAAGTCAT
17546194 AGAGCCTCTA
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
79 4 0.03
80 56 0.48
81 30 0.26
82 14 0.12
83 13 0.11
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (80 bp):
ATTTATTTTCAAGGTCATGGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCATGGAGGT
CTGATTAGAGAAGTC
Found at i:17546136 original size:40 final size:41
Alignment explanation
Indices: 17545960--17546215 Score: 182
Period size: 41 Copynumber: 6.3 Consensus size: 41
17545950 GAATTTCTAT
* * * * * * *
17545960 TTAGAAGAGCAATTTACTTTTCAAGGTCATGGAGCCTCTGT
1 TTAGAGGAGCTATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* * * * * *
17546001 TTAGAGGAGC-ATTTATTTTT-AAAGTCATGGTGCTTTTGC
1 TTAGAGGAGCTATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* ** * *
17546040 TTAGAGAATTTATTTATTTTCCAAAGTCATTGAGCCTCTGA
1 TTAGAGGAGCTATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* *
17546081 TTAAAGGAGCTATTTATTTTTCAAAGTCGTTGAG-GTCTGA
1 TTAGAGGAGCTATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* * *
17546121 TTAGAGGAG-TCATTTA-TTTTCAAGGTCGTGGAGCCTCTGT
1 TTAGAGGAGCT-ATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* * *
17546161 TTAGAGGAGCTTTGTTTATTTTTTCAAAGTCATAGAGCCTCT-A
1 TTAGAGGAGC--TATTTA-TTTTTCAAAGTCGTTGAGCCTCTGA
*
17546204 CTTATAGGAGCT
1 -TTAGAGGAGCT
17546216 TTGATAAAAA
Statistics
Matches: 171, Mismatches: 34, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
39 37 0.22
40 49 0.29
41 51 0.30
42 5 0.03
43 1 0.01
44 28 0.16
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (41 bp):
TTAGAGGAGCTATTTATTTTTCAAAGTCGTTGAGCCTCTGA
Found at i:17546438 original size:6 final size:6
Alignment explanation
Indices: 17546427--17546463 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
17546417 CCCAATTGGC
17546427 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
17546464 ATTTGTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:17546503 original size:16 final size:15
Alignment explanation
Indices: 17546430--17546513 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 15
17546420 AATTGGCTTT
17546430 TATTTTTATT-TT--
1 TATTTTTATTATTAA
17546442 TATTTTTATT-TT--
1 TATTTTTATTATTAA
**
17546454 TATTTTTATTATTTG
1 TATTTTTATTATTAA
* * *
17546469 TCTATTTATTAATATA
1 TATTTTTATTATTA-A
17546485 TATTTTTATCTATTAA
1 TATTTTTAT-TATTAA
17546501 TATTTTTATTATT
1 TATTTTTATTATT
17546514 TATCTACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
12 22 0.37
13 2 0.03
15 14 0.24
16 17 0.29
17 4 0.07
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.71
Consensus pattern (15 bp):
TATTTTTATTATTAA
Found at i:17546510 original size:22 final size:22
Alignment explanation
Indices: 17546436--17546577 Score: 77
Period size: 22 Copynumber: 6.6 Consensus size: 22
17546426 CTTTTATTTT
* *
17546436 TATTTTTATTTTTAT-TTTTAT
1 TATTTTTATTTTTATCTATTAA
* * *
17546457 TTTTATTATTTGTCTATTTATTAA
1 TATTTTTATTT-T-TATCTATTAA
*
17546481 TA-TA-TATTTTTATCTATTAA
1 TATTTTTATTTTTATCTATTAA
17546501 TATTTTTATTATTTATCTACTT--
1 TATTTTTATT-TTTATCTA-TTAA
* *
17546523 TTTTTTTATTATTTATCTA--AT
1 TATTTTTATT-TTTATCTATTAA
*
17546544 TA-TTTT-TTGTTATCTATTAA
1 TATTTTTATTTTTATCTATTAA
*
17546564 TATATTTATCTTTT
1 TATTTTTAT-TTTT
17546578 TTATTTTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 26
0.71 0.10 0.20
Matches are distributed among these distances:
18 7 0.07
19 2 0.02
20 18 0.19
21 15 0.16
22 29 0.31
23 16 0.17
24 7 0.07
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (22 bp):
TATTTTTATTTTTATCTATTAA
Found at i:17546572 original size:26 final size:25
Alignment explanation
Indices: 17546521--17546582 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
17546511 ATTTATCTAC
* * *
17546521 TTTTTTTTTATTATTTATCTAATTA
1 TTTTTTGTTATTATTAATATAATTA
*
17546546 TTTTTTGTTATCTATTAATATATTTA
1 TTTTTTGTTAT-TATTAATATAATTA
*
17546572 TCTTTT-TTATT
1 TTTTTTGTTATT
17546583 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 14 0.45
26 16 0.52
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTTTGTTATTATTAATATAATTA
Found at i:17546942 original size:19 final size:19
Alignment explanation
Indices: 17546906--17546942 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17546896 AATCCGACGA
*
17546906 AATTTTTCGACGAATTTTG
1 AATTTTTCGAAGAATTTTG
*
17546925 AATTTTTCGAAGAGTTTT
1 AATTTTTCGAAGAATTTT
17546943 TCAGCCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (19 bp):
AATTTTTCGAAGAATTTTG
Found at i:17547334 original size:9 final size:9
Alignment explanation
Indices: 17547322--17547371 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
17547312 TTTTGGTATT
17547322 TTTTATTTA
1 TTTTATTTA
17547331 TTTTATTTA
1 TTTTATTTA
* *
17547340 ATTTATTTG
1 TTTTATTTA
* *
17547349 TTTTACTTG
1 TTTTATTTA
17547358 TTTT-TTTA
1 TTTTATTTA
17547366 TTTTAT
1 TTTTAT
17547372 CAAAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 6 0.18
9 28 0.82
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:17548904 original size:25 final size:25
Alignment explanation
Indices: 17548876--17548978 Score: 113
Period size: 25 Copynumber: 4.2 Consensus size: 25
17548866 AATATATAAT
17548876 AAATGACATAATTAAAATATGCATG
1 AAATGACATAATTAAAATATGCATG
* * **
17548901 AAATAACATAACTAAAATATGTGTG
1 AAATGACATAATTAAAATATGCATG
* *
17548926 AAGTG--A-AATTGACAATATGCATG
1 AAATGACATAATT-AAAATATGCATG
*
17548949 AAATGACATAATTAACATATGCATG
1 AAATGACATAATTAAAATATGCATG
17548974 AAATG
1 AAATG
17548979 TAAAGCACAT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
22 3 0.05
23 14 0.23
25 40 0.66
26 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATGACATAATTAAAATATGCATG
Found at i:17549598 original size:21 final size:20
Alignment explanation
Indices: 17549572--17549616 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
17549562 AAATTAATTC
17549572 TTTTT-CTTCTTTTCTTTCTTT
1 TTTTTCCTT-TTTTCTTT-TTT
17549593 TTTTTCCTTTTTTCTTTTTT
1 TTTTTCCTTTTTTCTTTTTT
17549613 TTTT
1 TTTT
17549617 GAAACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 13 0.57
22 3 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCCTTTTTTCTTTTTT
Found at i:17549612 original size:9 final size:9
Alignment explanation
Indices: 17549569--17549614 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
17549559 TTAAAATTAA
*
17549569 TTCTTTTTC
1 TTCTTTTTT
*
17549578 TTCTTTTCT
1 TTCTTTTTT
17549587 TTCTTTTTT
1 TTCTTTTTT
*
17549596 TTC-CTTTT
1 TTCTTTTTT
17549604 TTCTTTTTT
1 TTCTTTTTT
17549613 TT
1 TT
17549615 TTGAAACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:17550083 original size:6 final size:6
Alignment explanation
Indices: 17550072--17550205 Score: 88
Period size: 6 Copynumber: 21.0 Consensus size: 6
17550062 TTGGAGTCTA
* * * * * *
17550072 GGTTAG GGTTAG GGTTTAG GTTTAG GTTTTG GGTTTAG GTTTAG GTTTTG
1 GGTTAG GGTTAG GG-TTAG GGTTAG GGTTAG GG-TTAG GGTTAG GGTTAG
* * * * *
17550122 GGTTTAG GGTTAG GGTTTAA GTTTAG GGTTAG GTTTAG AGTTTAAG GTTTAG
1 GG-TTAG GGTTAG GG-TTAG GGTTAG GGTTAG GGTTAG -GGTT-AG GGTTAG
*
17550174 GGTTAG GGTTTAG GTTTAG GGCTTAG GGTTAG
1 GGTTAG GG-TTAG GGTTAG GG-TTAG GGTTAG
17550206 AGTTTGGATT
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
6 65 0.62
7 37 0.36
8 2 0.02
ACGTcount: A:0.16, C:0.01, G:0.40, T:0.43
Consensus pattern (6 bp):
GGTTAG
Found at i:17550105 original size:19 final size:19
Alignment explanation
Indices: 17550070--17550203 Score: 146
Period size: 19 Copynumber: 7.0 Consensus size: 19
17550060 GTTTGGAGTC
17550070 TAGG-TTAGGGTTAGGGTT
1 TAGGTTTAGGGTTAGGGTT
* *
17550088 TAGGTTTAGGTTTTGGGTT
1 TAGGTTTAGGGTTAGGGTT
* *
17550107 TAGGTTTAGGTTTTGGGTT
1 TAGGTTTAGGGTTAGGGTT
* *
17550126 TAGGGTTAGGGTTTA-AGTT
1 TAGGTTTAGGG-TTAGGGTT
* * *
17550145 TAGGGTTAGGTTTAGAGTT
1 TAGGTTTAGGGTTAGGGTT
17550164 TAAGGTTTAGGGTTAGGGTT
1 T-AGGTTTAGGGTTAGGGTT
17550184 TAGGTTTAGGGCTTAGGGTT
1 TAGGTTTAGGG-TTAGGGTT
17550204 AGAGTTTGGA
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
18 7 0.07
19 68 0.67
20 26 0.26
ACGTcount: A:0.16, C:0.01, G:0.39, T:0.44
Consensus pattern (19 bp):
TAGGTTTAGGGTTAGGGTT
Found at i:17550217 original size:26 final size:25
Alignment explanation
Indices: 17550144--17550229 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
17550134 GGGTTTAAGT
* *
17550144 TTAGGGTTAGGTTTAGAGTTTAAGGT
1 TTAGGGTTAGGTTTGGA-TTTAAGGC
*
17550170 TTAGGGTTAGGGTTTAGG-TTTAGGGC
1 TTAGGGTTA-GGTTT-GGATTTAAGGC
*
17550196 TTAGGGTTAGAGTTTGGATTTAAGGT
1 TTAGGGTTAG-GTTTGGATTTAAGGC
*
17550222 TTAAGGTT
1 TTAGGGTT
17550230 TATATTTGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 3 0.06
26 41 0.82
27 5 0.10
28 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.42
Consensus pattern (25 bp):
TTAGGGTTAGGTTTGGATTTAAGGC
Found at i:17550263 original size:14 final size:14
Alignment explanation
Indices: 17550245--17550286 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
17550235 TTGGGATTTG
*
17550245 GGATTTAAGGTTTT
1 GGATTTAGGGTTTT
* *
17550259 TGATTTAGGGTTTA
1 GGATTTAGGGTTTT
17550273 GGATTTAGGGTTTT
1 GGATTTAGGGTTTT
17550287 AAATTGAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
GGATTTAGGGTTTT
Found at i:17550277 original size:28 final size:27
Alignment explanation
Indices: 17550211--17550286 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
17550201 GTTAGAGTTT
*
17550211 GGATTTAAGG-TTTAAGGTTTATATTTG
1 GGATTT-AGGATTTAAGGTTTTTATTTG
*
17550238 GGATTTGGGATTTAAGGTTTTTGATTTAG
1 GGATTTAGGATTTAAGGTTTTT-ATTT-G
*
17550267 GG-TTTAGGATTTAGGGTTTT
1 GGATTTAGGATTTAAGGTTTT
17550287 AAATTGAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.05
27 17 0.40
28 20 0.48
29 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (27 bp):
GGATTTAGGATTTAAGGTTTTTATTTG
Found at i:17550341 original size:20 final size:20
Alignment explanation
Indices: 17550298--17550342 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17550288 AATTGAGATT
* *
17550298 TTTGGGTTTGGGATTTAAGG
1 TTTGGATTTGGGATTTAAGC
17550318 TTTGGATTTGGGATTTCAA-C
1 TTTGGATTTGGGATTT-AAGC
17550338 TTTGG
1 TTTGG
17550343 GGTTTCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.47
Consensus pattern (20 bp):
TTTGGATTTGGGATTTAAGC
Found at i:17553538 original size:38 final size:38
Alignment explanation
Indices: 17553496--17553571 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
17553486 TCAATATAAA
17553496 TGTCAAGAATGCTAAACTAGATAAACCAAATTAATCTT
1 TGTCAAGAATGCTAAACTAGATAAACCAAATTAATCTT
17553534 TGTCAAGAATGCTAAACTAGATAAACCAAATTAATCTT
1 TGTCAAGAATGCTAAACTAGATAAACCAAATTAATCTT
17553572 ACTTGTGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (38 bp):
TGTCAAGAATGCTAAACTAGATAAACCAAATTAATCTT
Found at i:17558027 original size:20 final size:20
Alignment explanation
Indices: 17557976--17558031 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
17557966 GTCAACTTTG
*
17557976 GTCAAA-TCTAGTCAAATTTA
1 GTCAAACTC-AGTCAAAATTA
**
17557996 GTC-AACAAAGTCAAAATTA
1 GTCAAACTCAGTCAAAATTA
17558015 GTCAAACTCAGTCAAAA
1 GTCAAACTCAGTCAAAA
17558032 GTGGTCGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (20 bp):
GTCAAACTCAGTCAAAATTA
Found at i:17560375 original size:7 final size:7
Alignment explanation
Indices: 17560365--17560551 Score: 80
Period size: 7 Copynumber: 28.6 Consensus size: 7
17560355 CCCAAAAATG
*
17560365 AAACCTT
1 AAACCCT
*
17560372 AAACTCT
1 AAACCCT
17560379 AAACCCT
1 AAACCCT
17560386 AAACCCT
1 AAACCCT
*
17560393 -AACCAT
1 AAACCCT
17560399 AAACCCT
1 AAACCCT
17560406 AAACCCCT
1 AAA-CCCT
*
17560414 --ACACT
1 AAACCCT
*
17560419 AAATCCT
1 AAACCCT
*
17560426 -AATCCT
1 AAACCCT
* *
17560432 AAA-TCA
1 AAACCCT
*
17560438 AAAACC-
1 AAACCCT
*
17560444 AAACCAT
1 AAACCCT
* *
17560451 ACACCTT
1 AAACCCT
*
17560458 AAATTCC-
1 AAA-CCCT
17560465 AAACCCT
1 AAACCCT
*
17560472 TAACCCT
1 AAACCCT
17560479 -AACCCT
1 AAACCCT
17560485 -AACCCT
1 AAACCCT
17560491 -AACCCT
1 AAACCCT
17560497 -AACCC-
1 AAACCCT
17560502 AAACCCT
1 AAACCCT
*
17560509 AAA-TCT
1 AAACCCT
*
17560515 GAA-CCT
1 AAACCCT
*
17560521 TAACCCT
1 AAACCCT
*
17560528 AAACCTT
1 AAACCCT
*
17560535 AAATCCT
1 AAACCCT
17560542 -AACCCT
1 AAACCCT
17560548 AAAC
1 AAAC
17560552 AAATCCTAAA
Statistics
Matches: 138, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
5 3 0.02
6 63 0.46
7 67 0.49
8 5 0.04
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:17560483 original size:6 final size:6
Alignment explanation
Indices: 17560466--17560549 Score: 78
Period size: 6 Copynumber: 13.3 Consensus size: 6
17560456 TTAAATTCCA
* **
17560466 AACCCTT AACCCT AACCCT AACCCT AACCCT AACCCA AACCCT AAATCT
1 AACCC-T AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT
* * *
17560515 GAACCTT AACCCT AAACCTT AAATCCT AACCCT AA
1 -AACCCT AACCCT -AACCCT -AACCCT AACCCT AA
17560550 ACAAATCCTA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
6 45 0.71
7 18 0.29
ACGTcount: A:0.38, C:0.40, G:0.01, T:0.20
Consensus pattern (6 bp):
AACCCT
Found at i:17560550 original size:13 final size:13
Alignment explanation
Indices: 17560417--17560550 Score: 55
Period size: 13 Copynumber: 10.4 Consensus size: 13
17560407 AACCCCTACA
*
17560417 CTAAATCCTAATC
1 CTAAATCCTAACC
** *
17560430 CTAAATCAAAAAC
1 CTAAATCCTAACC
17560443 C-AAA-CCATACACC
1 CTAAATCC-TA-ACC
* *
17560456 TTAAATTCCAAACC
1 CTAAA-TCCTAACC
* *
17560470 CTTAACCCTAACC
1 CTAAATCCTAACC
*
17560483 CT-AACCCTAACC
1 CTAAATCCTAACC
* *
17560495 CT-AACCCAAACC
1 CTAAATCCTAACC
17560507 CTAAAT-CTGAA-C
1 CTAAATCCT-AACC
* *
17560519 CTTAACCCTAAACC
1 CTAAATCCT-AACC
*
17560533 TTAAATCCTAACC
1 CTAAATCCTAACC
17560546 CTAAA
1 CTAAA
17560551 CAAATCCTAA
Statistics
Matches: 90, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
11 1 0.01
12 33 0.37
13 37 0.41
14 16 0.18
15 1 0.01
16 2 0.02
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.21
Consensus pattern (13 bp):
CTAAATCCTAACC
Found at i:17560557 original size:17 final size:19
Alignment explanation
Indices: 17560366--17560579 Score: 91
Period size: 19 Copynumber: 11.1 Consensus size: 19
17560356 CCAAAAATGA
* *
17560366 AACCTTAAACTCTAAACCCT
1 AACCCTAAAC-CTAAATCCT
*
17560386 AAACCCT-AACCATAAACCCT
1 -AACCCTAAACC-TAAATCCT
*
17560406 AAACCCCTACA-CTAAATCCT
1 -AA-CCCTAAACCTAAATCCT
* * * * *
17560426 AATCCTAAATCAAAAACCA
1 AACCCTAAACCTAAATCCT
* * *
17560445 AACCATACACCTTAAATTCCA
1 AACCCTAAACC-TAAA-TCCT
* *
17560466 AACCCTTAACCCT-AACCCT
1 AACCC-TAAACCTAAATCCT
* * *
17560485 AACCCTAACCCT-AACCCA
1 AACCCTAAACCTAAATCCT
* *
17560503 AACCCTAAATCTGAA-CCTT
1 AACCCTAAACCTAAATCC-T
17560522 AACCCTAAACCTTAAATCCT
1 AACCCTAAACC-TAAATCCT
17560542 AACCCTAAA-C-AAATCCT
1 AACCCTAAACCTAAATCCT
* * *
17560559 AAACCTAAATCAAAATCCT
1 AACCCTAAACCTAAATCCT
17560578 AA
1 AA
17560580 ACTTAAATTG
Statistics
Matches: 154, Mismatches: 26, Indels: 28
0.74 0.12 0.13
Matches are distributed among these distances:
17 15 0.10
18 30 0.19
19 45 0.29
20 39 0.25
21 20 0.13
22 5 0.03
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.20
Consensus pattern (19 bp):
AACCCTAAACCTAAATCCT
Found at i:17560576 original size:19 final size:18
Alignment explanation
Indices: 17560535--17560587 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
17560525 CCTAAACCTT
*
17560535 AAATCCTAACCCTAAA-C
1 AAATCCTAAACCTAAATC
17560552 AAATCCTAAACCTAAATC
1 AAATCCTAAACCTAAATC
*
17560570 AAAATCCTAAACTTAAAT
1 -AAATCCTAAACCTAAAT
17560588 TGAAACCCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATCCTAAACCTAAATC
Found at i:17561853 original size:25 final size:24
Alignment explanation
Indices: 17561805--17561911 Score: 81
Period size: 25 Copynumber: 4.3 Consensus size: 24
17561795 CATTTCATGC
* * *
17561805 ATATTGTAATTATGTGATCCCATTA
1 ATATTGTAAATATGTCAT-TCATTA
*
17561830 ATATTGTAAATATGTCATATCATTC
1 ATATTGTAAATATGTCAT-TCATTA
* * **
17561855 ATATTTTAAGTATGTCATTTCATGC
1 ATATTGTAAATATGTCA-TTCATTA
*
17561880 ATATT-TAAATTATGTCATTTATTA
1 ATATTGTAAA-TATGTCATTCATTA
17561904 TATATTGT
1 -ATATTGT
17561912 TGTTCTTTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.11
25 57 0.86
26 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (24 bp):
ATATTGTAAATATGTCATTCATTA
Found at i:17568716 original size:22 final size:22
Alignment explanation
Indices: 17568673--17568717 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
17568663 TTTTAACATG
* *
17568673 CTTTTATTCTTGCTAAATATAT
1 CTTTGATTCTTGCCAAATATAT
17568695 CTTTGATTCTTTGCCAAA-ATAT
1 CTTTGATTC-TTGCCAAATATAT
17568717 C
1 C
17568718 CACTCATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (22 bp):
CTTTGATTCTTGCCAAATATAT
Found at i:17570891 original size:23 final size:24
Alignment explanation
Indices: 17570858--17570905 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
17570848 CTAATAATTC
17570858 AACTAAAGAACTAAAAGAAATAAG
1 AACTAAAGAACTAAAAGAAATAAG
17570882 AACT-AAGAACTAAAAGAAATAAG
1 AACTAAAGAACTAAAAGAAATAAG
17570905 A
1 A
17570906 GAAGTAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.12
Consensus pattern (24 bp):
AACTAAAGAACTAAAAGAAATAAG
Found at i:17578861 original size:17 final size:17
Alignment explanation
Indices: 17578839--17578871 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17578829 ATGTTCCTCC
17578839 TGCACTGTTGCATATGT
1 TGCACTGTTGCATATGT
17578856 TGCACTGTTGCATATG
1 TGCACTGTTGCATATG
17578872 AAGCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (17 bp):
TGCACTGTTGCATATGT
Found at i:17579293 original size:9 final size:9
Alignment explanation
Indices: 17579265--17579308 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
17579255 AGCAAACAAA
*
17579265 AAAACAAAAC
1 AAAA-AAAAT
17579275 AAAAAGAAAT
1 AAAAA-AAAT
17579285 AAAAAAAAT
1 AAAAAAAAT
17579294 AAAAAAAAT
1 AAAAAAAAT
17579303 GAAAAA
1 -AAAAA
17579309 TAAGAGGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 14 0.45
10 17 0.55
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.07
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:17579301 original size:23 final size:24
Alignment explanation
Indices: 17579262--17579306 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17579252 AAAAGCAAAC
17579262 AAAAAAACAAAACAAAAAGAAATA
1 AAAAAAACAAAACAAAAAGAAATA
* *
17579286 AAAAAAATAAAA-AAAATGAAA
1 AAAAAAACAAAACAAAAAGAAA
17579307 AATAAGAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.84, C:0.04, G:0.04, T:0.07
Consensus pattern (24 bp):
AAAAAAACAAAACAAAAAGAAATA
Found at i:17580912 original size:31 final size:31
Alignment explanation
Indices: 17580790--17580913 Score: 148
Period size: 31 Copynumber: 4.0 Consensus size: 31
17580780 AGTCTAGCTG
* *
17580790 GCAC-AAGGAGAATTAAGCCTAATTTAGTT-
1 GCACTAAGGAGAATTAAGCCCAATTTAATTA
* *
17580819 GACACTGAA-GAGAACTAAGCCCAATTTAATTG
1 G-CACT-AAGGAGAATTAAGCCCAATTTAATTA
*
17580851 GCACTAAGAAGAATTAAGCCCAATTTAATTA
1 GCACTAAGGAGAATTAAGCCCAATTTAATTA
17580882 GCACTAAGGAGAATTAAGCCCAGA-TTAATTA
1 GCACTAAGGAGAATTAAGCCCA-ATTTAATTA
17580913 G
1 G
17580914 TTCCAAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.01
30 5 0.06
31 72 0.88
32 4 0.05
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (31 bp):
GCACTAAGGAGAATTAAGCCCAATTTAATTA
Found at i:17581000 original size:48 final size:48
Alignment explanation
Indices: 17580925--17581154 Score: 176
Period size: 48 Copynumber: 4.7 Consensus size: 48
17580915 TCCAAAAATA
* *** * *
17580925 TTTTTTAAAGTTCATTGTTTATTTTCATAGGAGCCTCTCTAGAGAGAT
1 TTTTTTAAAGTTCGTTACCTATATTCATAGGAGCCTCTCTAGACAGAT
* * *
17580973 ATTTTTAAAGTTCGTTGCCTATATTCATAGGAGCC-CTTTTCAGACA-AT
1 TTTTTTAAAGTTCGTTACCTATATTCATAGGAGCCTC-TCT-AGACAGAT
* * ** * * * *
17581021 TTTTTTAAAATTCGTTACCTATTTTCATAAAAGCCCTTTCAAGATAAAAT
1 TTTTTTAAAGTTCGTTACCTATATTCATAGGAG-CCTCTCTAGA-CAGAT
* * * * * *
17581071 TTTTTTAAAGTTTGTTACCTATGTTTATATGAGCCTTTTCCAGACAGAT
1 TTTTTTAAAGTTCGTTACCTATATTCATAGGAGCC-TCTCTAGACAGAT
* *
17581120 TTTTTTAAAGTTCATTTCCTATATTCATAGGAGCC
1 TTTTTTAAAGTTCGTTACCTATATTCATAGGAGCC
17581155 CTTTTCAAAC
Statistics
Matches: 143, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.01
48 64 0.45
49 42 0.29
50 36 0.25
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (48 bp):
TTTTTTAAAGTTCGTTACCTATATTCATAGGAGCCTCTCTAGACAGAT
Found at i:17581122 original size:49 final size:48
Alignment explanation
Indices: 17580974--17581179 Score: 218
Period size: 48 Copynumber: 4.2 Consensus size: 48
17580964 TAGAGAGATA
*
17580974 TTTTTAAAGTTCGTTGCCTATATTCATAGGAGCCCTTTTCAGACAATT
1 TTTTTAAAGTTCGTTACCTATATTCATAGGAGCCCTTTTCAGACAATT
* * ** *
17581022 TTTTTAAAATTCGTTACCTATTTTCATAAAAGCCC-TTTCAAGATAAAATT
1 TTTTTAAAGTTCGTTACCTATATTCATAGGAGCCCTTTTC-AG--ACAATT
* * * *
17581072 TTTTTAAAGTTTGTTACCTATGTTTATATGAG-CCTTTTCCAGACAGATT
1 TTTTTAAAGTTCGTTACCTATATTCATAGGAGCCCTTTT-CAGACA-ATT
* * * **
17581121 TTTTTAAAGTTCATTTCCTATATTCATAGGAGCCCTTTTCAAACAAAA
1 TTTTTAAAGTTCGTTACCTATATTCATAGGAGCCCTTTTCAGACAATT
17581169 TTTTTAAAGTT
1 TTTTTAAAGTT
17581180 TGTTTCGAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
47 4 0.03
48 46 0.36
49 36 0.28
50 42 0.33
51 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (48 bp):
TTTTTAAAGTTCGTTACCTATATTCATAGGAGCCCTTTTCAGACAATT
Found at i:17581334 original size:47 final size:48
Alignment explanation
Indices: 17581283--17581409 Score: 125
Period size: 47 Copynumber: 2.7 Consensus size: 48
17581273 TATTTTCATT
* * ***
17581283 GGAGCTCTTTCCAGACAGATTTTTAAAATTTA-TTGCCTATATTAATA
1 GGAGCTCTTTCCAAACAGATTTTTAAAAGTTACCCACCTATATTAATA
* *
17581330 GGAGC-CTTTTCCAAATAGATTTTTTAAAGTTACCCACCTATATTAATA
1 GGAGCTC-TTTCCAAACAGATTTTTAAAAGTTACCCACCTATATTAATA
* * *
17581378 AGAGCCTTTTTCCAAACAAATTTTT-AAAGTTA
1 GGAG-CTCTTTCCAAACAGATTTTTAAAAGTTA
17581410 GTTGCTTACG
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
46 1 0.02
47 26 0.40
48 22 0.34
49 16 0.25
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (48 bp):
GGAGCTCTTTCCAAACAGATTTTTAAAAGTTACCCACCTATATTAATA
Found at i:17581354 original size:48 final size:49
Alignment explanation
Indices: 17581318--17581409 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 49
17581308 AAATTTATTG
* * *
17581318 CCTATATTAATAGGAGCC-TTTTCCAAATAGATTTTTTAAAGTTACCCA
1 CCTATATTAATAAGAGCCTTTTTCCAAACAAATTTTTTAAAGTTACCCA
17581366 CCTATATTAATAAGAGCCTTTTTCCAAACAAA-TTTTTAAAGTTA
1 CCTATATTAATAAGAGCCTTTTTCCAAACAAATTTTTTAAAGTTA
17581410 GTTGCTTACG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 29 0.73
49 11 0.28
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (49 bp):
CCTATATTAATAAGAGCCTTTTTCCAAACAAATTTTTTAAAGTTACCCA
Found at i:17581734 original size:28 final size:29
Alignment explanation
Indices: 17581702--17581758 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
17581692 CCAAATGCTT
*
17581702 TAAAGTCAACA-TTGGTCAAACTT-GTCAA
1 TAAAGTCAA-ATTTAGTCAAACTTAGTCAA
17581730 TAAAGTCAAATTTAGTCAAACTTAGTCAA
1 TAAAGTCAAATTTAGTCAAACTTAGTCAA
17581759 ATTTGGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 20 0.77
29 5 0.19
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (29 bp):
TAAAGTCAAATTTAGTCAAACTTAGTCAA
Found at i:17581748 original size:10 final size:10
Alignment explanation
Indices: 17581733--17581762 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17581723 TTGTCAATAA
17581733 AGTCAAATTT
1 AGTCAAATTT
*
17581743 AGTCAAACTT
1 AGTCAAATTT
17581753 AGTCAAATTT
1 AGTCAAATTT
17581763 GGTTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (10 bp):
AGTCAAATTT
Found at i:17581758 original size:20 final size:20
Alignment explanation
Indices: 17581733--17581772 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17581723 TTGTCAATAA
17581733 AGTCAAATTTAGTCAAACTT
1 AGTCAAATTTAGTCAAACTT
* *
17581753 AGTCAAATTTGGTTAAACTT
1 AGTCAAATTTAGTCAAACTT
17581773 GATAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
AGTCAAATTTAGTCAAACTT
Found at i:17586596 original size:11 final size:12
Alignment explanation
Indices: 17586564--17586596 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17586554 ACAAAGATGA
17586564 ATAAAAAAAACC
1 ATAAAAAAAACC
*
17586576 ATTAAAAAAA-C
1 ATAAAAAAAACC
17586587 ATAAAAAAAA
1 ATAAAAAAAA
17586597 AATAGATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (12 bp):
ATAAAAAAAACC
Found at i:17589749 original size:62 final size:62
Alignment explanation
Indices: 17589493--17589753 Score: 183
Period size: 62 Copynumber: 4.2 Consensus size: 62
17589483 GGTATTTTTG
* * *
17589493 GCCTTGAATAATCACCTCATAAAAAT-TGAAGGAGATTATTGAAGGCATTTTTTGCTAGAAAT
1 GCCTTGAATAATC-CCTCATAAAAATATGAAGGAGATTATTGAAGGCATTTTTAGCTAAAAAC
* ** * * * * *
17589555 GCCTTCAATAA-CCCT-ATTAAATTTTTTGTAA-GTGATTATTCAAAGCATTTTATAGGTAAAAA
1 GCCTTGAATAATCCCTCA-TAAA-AATATG-AAGGAGATTATTGAAGGCATTTT-TAGCTAAAAA
17589617 C
62 C
* * *** * ** * *
17589618 GCCTTGAATAATCCC-CAATAAAAAAAAGTTTTGAGATTATTAAAGGTGTTTTTGGCCAAAAAC
1 GCCTTGAATAATCCCTC-ATAAAAATATG-AAGGAGATTATTGAAGGCATTTTTAGCTAAAAAC
** * *
17589681 ATCTTGAATAATCACCTCATAAAAATATG-AGGGGATTATTGAAGGCATTTTTAGCTAGAAAC
1 GCCTTGAATAATC-CCTCATAAAAATATGAAGGAGATTATTGAAGGCATTTTTAGCTAAAAAC
17589743 GCCTTGAATAA
1 GCCTTGAATAA
17589754 CCTCTATTAA
Statistics
Matches: 147, Mismatches: 41, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
59 1 0.01
60 7 0.05
61 2 0.01
62 62 0.42
63 40 0.27
64 33 0.22
65 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (62 bp):
GCCTTGAATAATCCCTCATAAAAATATGAAGGAGATTATTGAAGGCATTTTTAGCTAAAAAC
Found at i:17589968 original size:62 final size:63
Alignment explanation
Indices: 17589804--17589972 Score: 191
Period size: 63 Copynumber: 2.7 Consensus size: 63
17589794 AATCACTGAG
* * ** * *
17589804 GATTATTAAAGGCGTTTTTGGCCAAAAACACCTTGAATAATCCCTTACAAAAAATTTATTAGA
1 GATTATTCAAGGCATTTTTGGCCAAAAATGCCTTGAATAATCCCCTACAAAAAATTTATTACA
* * * * *
17589867 GGTTATTCAAGGCATTTTCGGCTAAAATTGCCTTCAATAATCCCCT-CATAAAAATTT-TTACA
1 GATTATTCAAGGCATTTTTGGCCAAAAATGCCTTGAATAATCCCCTACA-AAAAATTTATTACA
* *
17589929 TATTGTTCAAGGCATTTTTGGCCAAAAATGCCTTGAATAA-CCCC
1 GATTATTCAAGGCATTTTTGGCCAAAAATGCCTTGAATAATCCCC
17589973 ATTCAATTTT
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
61 4 0.05
62 39 0.45
63 44 0.51
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (63 bp):
GATTATTCAAGGCATTTTTGGCCAAAAATGCCTTGAATAATCCCCTACAAAAAATTTATTACA
Found at i:17591075 original size:25 final size:27
Alignment explanation
Indices: 17591047--17591097 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
17591037 AGAAGAACTT
*
17591047 GAAAAAT-AGAG-GAAAAAAAGAAAGG
1 GAAAAATGAGAGAAAAAAAAAGAAAGG
*
17591072 GAAAAATGTGAGAAAAAAAAAGAAAG
1 GAAAAATGAGAGAAAAAAAAAGAAAG
17591098 AAAAAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (27 bp):
GAAAAATGAGAGAAAAAAAAAGAAAGG
Found at i:17592436 original size:13 final size:13
Alignment explanation
Indices: 17592418--17592649 Score: 91
Period size: 13 Copynumber: 17.7 Consensus size: 13
17592408 CTCAAACCCT
*
17592418 AAACCTTAAATCC
1 AAACCCTAAATCC
* * *
17592431 AAACCTTAGATCT
1 AAACCCTAAATCC
* *
17592444 TAATCCTAAATCC
1 AAACCCTAAATCC
*
17592457 AAACCCTAAACCC
1 AAACCCTAAATCC
17592470 TAAACCCTAAATCCC
1 -AAACCCTAAAT-CC
*
17592485 AAACCCTAAACCC
1 AAACCCTAAATCC
* * *
17592498 TAACCCCAAACCC
1 AAACCCTAAATCC
*
17592511 TAAA-CCGAAA-CC
1 -AAACCCTAAATCC
* *
17592523 TAAACCCTAACTCT
1 -AAACCCTAAATCC
*
17592537 AAACCTTAAAT-C
1 AAACCCTAAATCC
*
17592549 AAACCCTAAACCC
1 AAACCCTAAATCC
* *
17592562 TAACCC-CAA-CC
1 AAACCCTAAATCC
* *
17592573 TCAACCACTAAA-CATA
1 -AAACC-CTAAATC--C
*
17592589 AAACCCT-AACCC
1 AAACCCTAAATCC
17592601 TAAACCCTAAATCC
1 -AAACCCTAAATCC
** *
17592615 AAACTTTAAATCA
1 AAACCCTAAATCC
* *
17592628 AAACCTTAAATCT
1 AAACCCTAAATCC
*
17592641 TAACCCTAA
1 AAACCCTAA
17592650 GCTCTAACCT
Statistics
Matches: 166, Mismatches: 39, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
11 2 0.01
12 21 0.13
13 104 0.63
14 33 0.20
15 6 0.04
ACGTcount: A:0.44, C:0.36, G:0.01, T:0.19
Consensus pattern (13 bp):
AAACCCTAAATCC
Found at i:17592455 original size:7 final size:7
Alignment explanation
Indices: 17592448--17592611 Score: 129
Period size: 7 Copynumber: 24.9 Consensus size: 7
17592438 AGATCTTAAT
*
17592448 CCTAAAT
1 CCTAAAC
17592455 CC-AAAC
1 CCTAAAC
17592461 CCTAAAC
1 CCTAAAC
17592468 CCTAAAC
1 CCTAAAC
17592475 CCTAAATC
1 CCTAAA-C
17592483 CC-AAAC
1 CCTAAAC
17592489 CCTAAAC
1 CCTAAAC
17592496 CCT-AAC
1 CCTAAAC
*
17592502 CCCAAAC
1 CCTAAAC
17592509 CCTAAA-
1 CCTAAAC
*
17592515 CCGAAA-
1 CCTAAAC
17592521 CCTAAAC
1 CCTAAAC
17592528 CCT-AAC
1 CCTAAAC
*
17592534 TCTAAAC
1 CCTAAAC
*
17592541 CTTAAA-
1 CCTAAAC
*
17592547 TC-AAAC
1 CCTAAAC
17592553 CCTAAAC
1 CCTAAAC
17592560 CCT-AAC
1 CCTAAAC
*
17592566 CC-CAA-
1 CCTAAAC
*
17592571 CCTCAAC
1 CCTAAAC
17592578 CACTAAA-
1 C-CTAAAC
*
17592585 CATAAAAC
1 CCT-AAAC
17592593 CCT-AAC
1 CCTAAAC
17592599 CCTAAAC
1 CCTAAAC
17592606 CCTAAA
1 CCTAAA
17592612 TCCAAACTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 30
0.74 0.08 0.17
Matches are distributed among these distances:
5 5 0.04
6 46 0.36
7 68 0.53
8 9 0.07
ACGTcount: A:0.44, C:0.41, G:0.01, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:17594733 original size:96 final size:96
Alignment explanation
Indices: 17594564--17594754 Score: 292
Period size: 96 Copynumber: 2.0 Consensus size: 96
17594554 AGAATAGATA
* * * *
17594564 ATACATTATTTTGTTATGACTCCATTTATTGAAGTGTTCCCTATTTATTATTCAAAGTTTGATTG
1 ATACATAAGTTTGTTATGACTCCATTTATTGAAATGCTCCCTATTTATTATTCAAAGTTTGATTG
* *
17594629 GAGAATGTTTGTGATTCGCTAGATCAATGGG
66 GAGAATGTTTGTGATTAGCTAAATCAATGGG
* **
17594660 ATACATAAGTTTGTTATGACTCTATTTATTGAAATGCTCTTTATTTATTATTCAAAGTTTGATTG
1 ATACATAAGTTTGTTATGACTCCATTTATTGAAATGCTCCCTATTTATTATTCAAAGTTTGATTG
*
17594725 GAGCATGTTTGTGATTAGCTAAATCAATGG
66 GAGAATGTTTGTGATTAGCTAAATCAATGG
17594755 AAGTCATTGT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (96 bp):
ATACATAAGTTTGTTATGACTCCATTTATTGAAATGCTCCCTATTTATTATTCAAAGTTTGATTG
GAGAATGTTTGTGATTAGCTAAATCAATGGG
Found at i:17598531 original size:131 final size:130
Alignment explanation
Indices: 17598382--17598640 Score: 473
Period size: 131 Copynumber: 2.0 Consensus size: 130
17598372 TTCTCATTTT
*
17598382 CTTAAAATATTAATATTAAAAGTCTATGACAAATATTGATTTAAATTTAAATTTTATTTTAATTC
1 CTTAAAATATTAATATTAAAAGTCTATGACAAATATTGATTTAAATTTAAATTTTATGTTAATTC
*
17598447 AAATATATCTAAATCTATTTTTTAAAATTGGTAGATTGTTTATTAAAATTATCTTTATCTATAAT
66 AAATATATCTAAATCTA-TTTTTAAAACTGGTAGATTGTTTATTAAAATTATCTTTATCTATAAT
17598512 G
130 G
*
17598513 CTTAAAATATTAATATTAAAAGTCTATGATAAATATTGATTTAAATTTAAATTTTATGTTAATTC
1 CTTAAAATATTAATATTAAAAGTCTATGACAAATATTGATTTAAATTTAAATTTTATGTTAATTC
*
17598578 AGATATATCTAAATCTATTTTTAAAACTGGTAGATTGTTTATTAAAATTATCTTTATCTATAA
66 AAATATATCTAAATCTATTTTTAAAACTGGTAGATTGTTTATTAAAATTATCTTTATCTATAA
17598641 CTAATATATT
Statistics
Matches: 124, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
130 45 0.36
131 79 0.64
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (130 bp):
CTTAAAATATTAATATTAAAAGTCTATGACAAATATTGATTTAAATTTAAATTTTATGTTAATTC
AAATATATCTAAATCTATTTTTAAAACTGGTAGATTGTTTATTAAAATTATCTTTATCTATAATG
Found at i:17600284 original size:20 final size:19
Alignment explanation
Indices: 17600256--17600295 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
17600246 ATTGATTGTA
17600256 TTATAATTTTTGAAATTTTT
1 TTATAATTTTT-AAATTTTT
* *
17600276 TTATGATTTTTATATTTTT
1 TTATAATTTTTAAATTTTT
17600295 T
1 T
17600296 ATCTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTATAATTTTTAAATTTTT
Found at i:17600343 original size:9 final size:9
Alignment explanation
Indices: 17600272--17600344 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
17600262 TTTTTGAAAT
17600272 TTTTTTATGA
1 TTTTTTAT-A
17600282 -TTTTTATA
1 TTTTTTATA
*
17600290 TTTTTTATC
1 TTTTTTATA
*
17600299 TTTTATTATG
1 TTTT-TTATA
*
17600309 TAATTTTATCA
1 T-TTTTTAT-A
17600320 TTTCTTT-TA
1 TTT-TTTATA
17600329 TTTTTTATA
1 TTTTTTATA
17600338 TATTTTT
1 T-TTTTT
17600345 TTTGTAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 4 0.08
9 25 0.49
10 16 0.31
11 6 0.12
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTTTTATA
Found at i:17610497 original size:16 final size:16
Alignment explanation
Indices: 17610471--17610503 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17610461 TTATAATGGG
17610471 AAACAAAAAAGAACAAA
1 AAACAAAAAAGAA-AAA
17610488 AAAC-AAAAAGAAAAA
1 AAACAAAAAAGAAAAA
17610503 A
1 A
17610504 CAAAGAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
AAACAAAAAAGAAAAA
Found at i:17621263 original size:24 final size:23
Alignment explanation
Indices: 17621228--17621280 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
17621218 CAAAAATTGT
*
17621228 AAAAGTGAAAAAATGATAAACAAA
1 AAAAGTGAAAAAATGAGAAA-AAA
17621252 AAAAGTAGAAAAAATGAGAAAAAA
1 AAAAGT-GAAAAAATGAGAAAAAA
17621276 AAAAG
1 AAAAG
17621281 CTAACAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (23 bp):
AAAAGTGAAAAAATGAGAAAAAA
Found at i:17623564 original size:18 final size:17
Alignment explanation
Indices: 17623543--17623630 Score: 71
Period size: 15 Copynumber: 5.4 Consensus size: 17
17623533 TCACTTAATA
17623543 AAAATAACAAAATAAAAT
1 AAAATAA-AAAATAAAAT
17623561 AAAATAAAAAATAAAA-
1 AAAATAAAAAATAAAAT
*
17623577 AAAGCT-AAAAAT-AAA-
1 AAA-ATAAAAAATAAAAT
** **
17623592 AACTTAAAATGTAAAAT
1 AAAATAAAAAATAAAAT
17623609 -AAAT-AAAAATAAAAT
1 AAAATAAAAAATAAAAT
17623624 AAAATAA
1 AAAATAA
17623631 CTTACGATCG
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.02
15 18 0.33
16 18 0.33
17 11 0.20
18 7 0.13
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:17623627 original size:41 final size:39
Alignment explanation
Indices: 17623543--17623631 Score: 85
Period size: 43 Copynumber: 2.2 Consensus size: 39
17623533 TCACTTAATA
17623543 AAAATAACAAAATAAAATAAAATAAAAAATAAAAAAAGCTA
1 AAAATAACAAAATAAAATAAAATAAAAAATAAAAAAA--TA
* *
17623584 AAAATAA-AAACTTAAAATGTAAAATAAATAAA-AATAAAAT-
1 AAAATAACAAA-ATAAAA--TAAAATAAA-AAATAAAAAAATA
17623624 AAAATAAC
1 AAAATAAC
17623632 TTACGATCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
40 10 0.24
41 13 0.32
43 15 0.37
44 3 0.07
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.18
Consensus pattern (39 bp):
AAAATAACAAAATAAAATAAAATAAAAAATAAAAAAATA
Found at i:17623628 original size:16 final size:16
Alignment explanation
Indices: 17623551--17623630 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
17623541 TAAAAATAAC
17623551 AAAATAAAATAAAATAA
1 AAAATAAAATAAAAT-A
*
17623568 AAAATAAAA-AAAGCTA
1 AAAATAAAATAAA-ATA
**
17623584 AAAAT-AAA-AACTTA
1 AAAATAAAATAAAATA
*
17623598 AAATGTAAAAT-AAATA
1 AAA-ATAAAATAAAATA
17623614 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
17623630 A
1 A
17623631 CTTACGATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
14 5 0.10
15 12 0.24
16 24 0.47
17 10 0.20
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:17624050 original size:20 final size:20
Alignment explanation
Indices: 17624025--17624062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17624015 ATGTCAGTGA
* *
17624025 TTCAAACCTAACCTAAAAAC
1 TTCAAACCAAACCCAAAAAC
17624045 TTCAAACCAAACCCAAAA
1 TTCAAACCAAACCCAAAA
17624063 GTCTAACTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (20 bp):
TTCAAACCAAACCCAAAAAC
Found at i:17624457 original size:3 final size:3
Alignment explanation
Indices: 17624436--17624673 Score: 144
Period size: 3 Copynumber: 83.3 Consensus size: 3
17624426 AAGGAAAGAA
* * * *
17624436 AAT AAA AAT AAT AAA AAT AAT AAT AAT AGA- ATT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * * *
17624481 AAT AAT AAT ATT AGT AAT AAT AGT AAA AAT AA- AA- AAT AA- GAT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
17624526 -AT ACT -AT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
17624571 AAT GAT ATT AAT AAT AAT -AT AAT -AT AAT AAC GAT -AT AAT -GT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
17624614 CAT ACT -AT ACT -AT AAT AAT AGT AAT AACA AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
*
17624658 AAT AAA AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
17624674 CCCCAGATAG
Statistics
Matches: 176, Mismatches: 44, Indels: 30
0.70 0.18 0.12
Matches are distributed among these distances:
2 20 0.11
3 153 0.87
4 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17625149 original size:56 final size:56
Alignment explanation
Indices: 17625048--17625161 Score: 131
Period size: 56 Copynumber: 2.0 Consensus size: 56
17625038 GCAAGTCGAG
* * * * *
17625048 AAAATGATCTGGATTAAGTCAAGATCAAACAATAATGATTGAATCGTAAGTATGAA
1 AAAATGATCTAGATTAAGCCAAGATCAAACAATAAGGATTAAATCGTAACTATGAA
** * *
17625104 AAAATGATCTAGATTGAA-CCAAGATCAAATGATCAGGATTAAATCGTAACTTTGAA
1 AAAATGATCTAGATT-AAGCCAAGATCAAACAATAAGGATTAAATCGTAACTATGAA
17625160 AA
1 AA
17625162 GCTGACCTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
56 46 0.96
57 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (56 bp):
AAAATGATCTAGATTAAGCCAAGATCAAACAATAAGGATTAAATCGTAACTATGAA
Found at i:17626242 original size:94 final size:99
Alignment explanation
Indices: 17626058--17626248 Score: 232
Period size: 94 Copynumber: 2.0 Consensus size: 99
17626048 CCTATTCAGT
* * * **
17626058 TCAAGCCATCTTTTCGGGTTTTCAACTTGAACTCTTCTTTCTTTTATTTTTTAGCTTAAGCTGCC
1 TCAAGCCATCTTTTCGGGTTTTCAACTTGAACACTTCTTTCCTTTATTCTTTAGCTTAAGCCACC
*
17626123 CTTTTTTGGGTTTTCAACATAAACTT-TTTTTGGC
66 C-TTTTTGGATTTTCAACATAAACTTCTTTTTGGC
**
17626157 TCAAGCCATCATTTTTTGGTTTTCAACTT-AA-ACTT-TTTCCTTT-TTCTTTAGCTTAAGCCAC
1 TCAAGCCATC-TTTTCGGGTTTTCAACTTGAACACTTCTTTCCTTTATTCTTTAGCTTAAGCCAC
* *
17626218 CC-TTTTGGATTTTCAACTTGAACTTCTTTTT
65 CCTTTTTGGATTTTCAACATAAACTTCTTTTT
17626249 TATTTTTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
94 20 0.25
95 5 0.06
96 17 0.21
97 7 0.09
98 3 0.04
99 12 0.15
100 16 0.20
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (99 bp):
TCAAGCCATCTTTTCGGGTTTTCAACTTGAACACTTCTTTCCTTTATTCTTTAGCTTAAGCCACC
CTTTTTGGATTTTCAACATAAACTTCTTTTTGGC
Found at i:17639349 original size:30 final size:30
Alignment explanation
Indices: 17639255--17639349 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 30
17639245 AAAATTTTGT
* *
17639255 AAAATAAAATAAAAAAATAATAA-AAAAGCTA
1 AAAATAAAATCAAAAAATAA-AATAAAATC-A
*
17639286 AAAATAAAATCTTAAAATATAAAAT-AAAT-A
1 AAAATAAAATC--AAAAAATAAAATAAAATCA
17639316 AAAATAAAATCAAAAAATAAAATAAAATCA
1 AAAATAAAATCAAAAAATAAAATAAAATCA
17639346 AAAA
1 AAAA
17639350 AGAAAAACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
28 11 0.20
29 4 0.07
30 17 0.31
31 10 0.18
32 5 0.09
33 8 0.15
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (30 bp):
AAAATAAAATCAAAAAATAAAATAAAATCA
Found at i:17640163 original size:9 final size:9
Alignment explanation
Indices: 17640149--17640173 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17640139 AGAAGAAAGG
17640149 AAAAAAAAT
1 AAAAAAAAT
17640158 AAAAAAAAT
1 AAAAAAAAT
17640167 AAAAAAA
1 AAAAAAA
17640174 TAATAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:17640189 original size:3 final size:3
Alignment explanation
Indices: 17640183--17640380 Score: 77
Period size: 3 Copynumber: 70.0 Consensus size: 3
17640173 ATAATAGAAT
* * * * *
17640183 TAA TAA TAA TAG TAA TAA TAA TAT TAG TAA TAA TAG TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
17640230 -AA TAA -GA TCA T-A TAC T-A TACGA TTA TAA TAA TAA TAA T-G TAA
1 TAA TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA TAA TAA
17640272 T-A TAA T-A TAA TAA -ATA TAA T-A TAA T-A TAA TATA TAA T-A TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* * * * * *
17640313 CAA T-A TAA T-G TAA -CA TAC T-A TAA TAA TAG TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
17640357 TAA TAA AAA TCA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
17640381 AAATCAACCC
Statistics
Matches: 141, Mismatches: 35, Indels: 38
0.66 0.16 0.18
Matches are distributed among these distances:
2 25 0.18
3 110 0.78
4 4 0.03
5 2 0.01
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17640198 original size:12 final size:11
Alignment explanation
Indices: 17640183--17640380 Score: 85
Period size: 12 Copynumber: 17.5 Consensus size: 11
17640173 ATAATAGAAT
17640183 TAATAATAATA
1 TAATAATAATA
17640194 GTAATAATAATA
1 -TAATAATAATA
*
17640206 TTAGTAATAATA
1 -TAATAATAATA
*
17640218 GTAAAAATAA-A
1 -TAATAATAATA
* *
17640229 AAATAAGATCATA
1 TAAT-A-ATAATA
*
17640242 TACTATACGATTATAA
1 TA--ATA--ATAAT-A
*
17640258 TAATAATAATG
1 TAATAATAATA
17640269 TAAT-ATAATA
1 TAATAATAATA
17640279 TAAT-A-AATA
1 TAATAATAATA
17640288 TAAT-ATAATA
1 TAATAATAATA
17640298 TAAT-AT-ATA
1 TAATAATAATA
*
17640307 -ATATAACAATA
1 TA-ATAATAATA
* *
17640318 TAAT-GTAACA
1 TAATAATAATA
17640328 TACTATAATAATA
1 TA--ATAATAATA
17640341 GTAATAATAATA
1 -TAATAATAATA
17640353 CTAATAATAA-A
1 -TAATAATAATA
*
17640364 -AATCATAATA
1 TAATAATAATA
17640374 GTAATAA
1 -TAATAA
17640381 AAATCAACCC
Statistics
Matches: 145, Mismatches: 22, Indels: 38
0.71 0.11 0.19
Matches are distributed among these distances:
8 1 0.01
9 21 0.14
10 29 0.20
11 12 0.08
12 60 0.41
13 6 0.04
14 6 0.04
15 7 0.05
16 3 0.02
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (11 bp):
TAATAATAATA
Found at i:17640287 original size:14 final size:15
Alignment explanation
Indices: 17640257--17640304 Score: 71
Period size: 14 Copynumber: 3.2 Consensus size: 15
17640247 TACGATTATA
*
17640257 ATAATAATAATGTAAT
1 ATAAT-ATAATATAAT
17640273 ATAATATAATA-AAT
1 ATAATATAATATAAT
17640287 ATAATATAATATAAT
1 ATAATATAATATAAT
17640302 ATA
1 ATA
17640305 TAATATAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 14 0.47
15 11 0.37
16 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:17640312 original size:5 final size:5
Alignment explanation
Indices: 17640257--17640304 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
17640247 TACGATTATA
*
17640257 ATAAT AATAAT GTAAT ATAAT ATAAT A-AAT ATAAT ATAAT ATAAT ATA
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
17640305 TAATATAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
4 4 0.10
5 30 0.77
6 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:17652000 original size:24 final size:24
Alignment explanation
Indices: 17651972--17652038 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
17651962 ATATATCTTC
17651972 ATAATTTACATGTTAAATAAATAA
1 ATAATTTACATGTTAAATAAATAA
17651996 ATAATTTACATGTTAAATAAATAA
1 ATAATTTACATGTTAAATAAATAA
* *
17652020 ATAATTTATATGCTAAATA
1 ATAATTTACATGTTAAATA
17652039 TATTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAATTTACATGTTAAATAAATAA
Found at i:17652038 original size:16 final size:18
Alignment explanation
Indices: 17652017--17652050 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17652007 GTTAAATAAA
17652017 TAAATA-ATT-TATATGC
1 TAAATATATTATATATGC
17652033 TAAATATATTATATATGC
1 TAAATATATTATATATGC
17652051 CACATAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TAAATATATTATATATGC
Found at i:17652183 original size:20 final size:20
Alignment explanation
Indices: 17652158--17652206 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
17652148 CAAAAAAATA
* *
17652158 TTAAATAAACCATTTATATG
1 TTAAATAAACCATTAACATG
* **
17652178 TTAAATTAATTATTAACATG
1 TTAAATAAACCATTAACATG
17652198 TTAAATAAA
1 TTAAATAAA
17652207 TAAGTAAGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (20 bp):
TTAAATAAACCATTAACATG
Found at i:17653071 original size:20 final size:20
Alignment explanation
Indices: 17653033--17653071 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17653023 TAAATGTCCT
*
17653033 AAAGTCAAACTTGGCCAAAC
1 AAAGTCAAACTTGACCAAAC
*
17653053 AAAGTCAAACTTGATCAAA
1 AAAGTCAAACTTGACCAAA
17653072 ATTGGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.18
Consensus pattern (20 bp):
AAAGTCAAACTTGACCAAAC
Found at i:17654375 original size:62 final size:60
Alignment explanation
Indices: 17654187--17654394 Score: 185
Period size: 62 Copynumber: 3.5 Consensus size: 60
17654177 CTTAAATCTT
* ** * * *
17654187 AAAATATAAAAGGATTATTTAAGGTATTTTCTATATAAAAA-GCTTTAAATAATCATTTTATA
1 AAAATATAAAATGATTATTTAAGACATTTT-TATA-AAAAACACCTTAAATAAT-AATTTATA
* * *** ***
17654249 AAAATATAAAATGATTATTTAAGGCA-TTTTAT---ATACACCTTAAACCCTAAACCAT-
1 AAAATATAAAATGATTATTTAAGACATTTTTATAAAAAACACCTTAAATAATAATTTATA
* *
17654304 AAAATATAAAAAGATTATTTAAGACATTTTTATACAAAAACACCTTAAATAATTTATTTATA
1 AAAATATAAAATGATTATTTAAGACATTTTTATA-AAAAACACCTTAAATAA-TAATTTATA
17654366 AAAATATAAAATGATTATTTAAGACATTT
1 AAAATATAAAATGATTATTTAAGACATTT
17654395 CTTCATGCCA
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
55 24 0.21
56 11 0.10
57 7 0.06
60 14 0.12
61 7 0.06
62 52 0.45
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (60 bp):
AAAATATAAAATGATTATTTAAGACATTTTTATAAAAAACACCTTAAATAATAATTTATA
Found at i:17654432 original size:117 final size:115
Alignment explanation
Indices: 17654186--17654394 Score: 287
Period size: 117 Copynumber: 1.8 Consensus size: 115
17654176 CCTTAAATCT
* ** * * *
17654186 TAAAATATAAAAGGATTATTTAAGGTATTTTCTATATAAAAAGCTTTAAATAATCATTTTATAAA
1 TAAAATATAAAAAGATTATTTAAGACATTTTCTATACAAAAAACCTTAAATAATCATTTTATAAA
* *
17654251 AATATAAAATGATTATTTAAGGCATTTTATATACACCTTAAACCCTAAACCA
66 AATATAAAATGATTATTTAAGACATTTTATATA-ACC-TAAACCCTAAACAA
*
17654303 TAAAATATAAAAAGATTATTTAAGACATTTT-TATACAAAAACACCTTAAATAAT-TTATTTATA
1 TAAAATATAAAAAGATTATTTAAGACATTTTCTATACAAAAA-ACCTTAAATAATCAT-TTTATA
17654366 AAAATATAAAATGATTATTTAAGACATTT
64 AAAATATAAAATGATTATTTAAGACATTT
17654395 CTTCATGCCA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
116 10 0.12
117 72 0.88
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (115 bp):
TAAAATATAAAAAGATTATTTAAGACATTTTCTATACAAAAAACCTTAAATAATCATTTTATAAA
AATATAAAATGATTATTTAAGACATTTTATATAACCTAAACCCTAAACAA
Found at i:17655377 original size:74 final size:72
Alignment explanation
Indices: 17655246--17655383 Score: 163
Period size: 72 Copynumber: 1.9 Consensus size: 72
17655236 AGGCATAGCC
** * *
17655246 AATCAATCCCTTCCATGAGGGGGGATTTATTGGTTCATGTTTTCGAACCAATTTGCCTTTGAAAA
1 AATCAATCCCTTCCATGA-GGGGGATCGATTGGTTCATGTTTGCAAACCAATTTGCC-TTGAAAA
17655311 TCATGACCT
64 TCATGACCT
* *
17655320 AATCGATCCCTTCCATGA-GGGGATCGATTGGTTCAT-TTTGCAAAACCATTTCATGCCTTGAAA
1 AATCAATCCCTTCCATGAGGGGGATCGATTGGTTCATGTTTGC-AAACCAATT--TGCCTTGAAA
17655383 A
63 A
17655384 ACCACTACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
71 4 0.07
72 23 0.42
73 7 0.13
74 21 0.38
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (72 bp):
AATCAATCCCTTCCATGAGGGGGATCGATTGGTTCATGTTTGCAAACCAATTTGCCTTGAAAATC
ATGACCT
Found at i:17657072 original size:473 final size:468
Alignment explanation
Indices: 17656475--17657540 Score: 1234
Period size: 473 Copynumber: 2.3 Consensus size: 468
17656465 TTAGGTGACA
*
17656475 TTATTAATTTTTGTCACAAATTGAATACTTTGTTAACTATTAATGACATTGCAATTTTATCACAT
1 TTATTAATTTTTGTCACAAATTGAATACTTTGTTAACTATTAATGACATTACAATTTTATCACAT
* * ** *
17656540 TAATGTATGGTGTTATATGACAATAATATAAATGTCACAAACTTTTATCGTCGAATTTATTTGAT
66 CAATGTATGGTGTTATATGACAATAACATAAATGTCACAAACTTTTATCACCAAATTTATTTGAT
*
17656605 GAAAAATTTTTT-TGTA-ATGTTTTTTATTTTAAGTGACGTT-TAAATTTTGTCACAAATTTAAA
131 GAAAAATTTTTTATG-ACAT-TTTTTTATTTTAAGTGA-GTTAT-AATTTTATCACAAATTTAAA
* * *
17656667 ATTTTATCTGTGATAAA-TTTTTCTAATAGATTTTAGGTGACGTTATTAATTTTTGTCATAAA-T
192 ATTTTATCTGTGACAAATTTTTTCTAATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATT
* * * * * *
17656730 GTAACACTTTAGTTAACTATTAATGACATTACAATTTCATTACCTTTATTTTATGGTATTATATG
257 G-AACACTTTAGTTAACTATTAATAACATTACAATTTCATCACATTAATATT-TGATATTATATG
* *
17656795 ATGATAACATAAATGTCACAAAACTTTTACTATC-AATTTTATTTGGTGAAAAAATTTTTAGTGA
320 ACGATAACATAAATGTCAC-AAACTTTTAC-AGCTAATTTTATTTGGTGAAAAAATTTTTA-TGA
*
17656859 CTTTTTTATTTATTTTAAGTGATGTTATAA-ATGTCACTAATTTAAAATTTTATTTATGA-TAAA
382 C--ATTT-TTTATTTTAAGTGATGTTATAATATGTCACTAA-TTAAAATTTTATTTATGATTAAA
17656922 TG-TTTTTTGATAAATTTTAGGTCTG
443 TGTTTTTTTGATAAATTTTAGGTCTG
* * * * * **
17656947 TTATTAATTTTTGTCATAGATTGAATACTTTAGTTAACTATTAATTACATTATAATTTTGTCATG
1 TTATTAATTTTTGTCACAAATTGAATACTTT-GTTAACTATTAATGACATTACAATTTTATCACA
* *
17657012 TCAATGTATGGTGTTATATGACGATAACATAAATGTCATAAACTTTTATCACCAAATTTATTTGA
65 TCAATGTATGGTGTTATATGACAATAACATAAATGTCACAAACTTTTATCACCAAATTTATTTGA
** * * * *
17657077 TGGGAAATTTTTTATGACATTTTTTTATTTTATGTGAGTTATAATTTTATTACCAATTTAAATTT
130 TGAAAAATTTTTTATGACATTTTTTTATTTTAAGTGAGTTATAATTTTATCACAAATTTAAAATT
* * * *
17657142 TTATTTGTGACAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTTACAAATTGAA
195 TTATCTGTGACAAATTTTTTCTAATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAA
* * * * *
17657207 CACTTTGGTTAACTATTAATAACATTATAATTTCGTCACATTAATATTTGATTTTATATTACGAT
260 CACTTTAGTTAACTATTAATAACATTACAATTTCATCACATTAATATTTGATATTATATGACGAT
* *
17657272 AACATAAATGTCACAAACTTTTACCGCTAATTTTATTTGGTGAAAAATTTTTTATGACATTTTTT
325 AACATAAATGTCACAAACTTTTACAGCTAATTTTATTTGGTGAAAAAATTTTTATGACATTTTTT
* * *
17657337 ATTTTAGGTGATGTTATAATTTTGTCACTAATTAAAATTTTATTTGTGATT-AA-------TTG-
390 ATTTTAAGTGATGTTATAA-TATGTCACTAATTAAAATTTTATTTATGATTAAATGTTTTTTTGA
17657393 T---TTTT---T-TG
454 TAAATTTTAGGTCTG
* * * *
17657401 --ATAAATTTTTGTCACAAATTGAACACTTTAGTTAACTATTAATGACATCACAATTTCATCACA
1 TTATTAATTTTTGTCACAAATTGAATACTTT-GTTAACTATTAATGACATTACAATTTTATCACA
* * * * * * * *
17657464 TCAATATTTGGTGTTATATGACAACAACAAAAATGTGACAAACTTTTA-CTGCCAAATTAATTTA
65 TCAATGTATGGTGTTATATGACAATAACATAAATGTCACAAACTTTTATC-ACCAAATTTATTTG
*
17657528 ATGGAAAATTTTT
129 ATGAAAAATTTTT
17657541 GTAACATTTT
Statistics
Matches: 513, Mismatches: 70, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
451 1 0.00
452 116 0.23
454 2 0.00
455 1 0.00
458 4 0.01
461 1 0.00
462 3 0.01
467 21 0.04
468 22 0.04
469 10 0.02
470 5 0.01
471 35 0.07
472 90 0.18
473 196 0.38
474 6 0.01
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (468 bp):
TTATTAATTTTTGTCACAAATTGAATACTTTGTTAACTATTAATGACATTACAATTTTATCACAT
CAATGTATGGTGTTATATGACAATAACATAAATGTCACAAACTTTTATCACCAAATTTATTTGAT
GAAAAATTTTTTATGACATTTTTTTATTTTAAGTGAGTTATAATTTTATCACAAATTTAAAATTT
TATCTGTGACAAATTTTTTCTAATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAAC
ACTTTAGTTAACTATTAATAACATTACAATTTCATCACATTAATATTTGATATTATATGACGATA
ACATAAATGTCACAAACTTTTACAGCTAATTTTATTTGGTGAAAAAATTTTTATGACATTTTTTA
TTTTAAGTGATGTTATAATATGTCACTAATTAAAATTTTATTTATGATTAAATGTTTTTTTGATA
AATTTTAGGTCTG
Found at i:17657226 original size:235 final size:236
Alignment explanation
Indices: 17656440--17657540 Score: 1096
Period size: 235 Copynumber: 4.8 Consensus size: 236
17656430 TCACAAATAA
* * * * *
17656440 TGTGATGAGTTTTTTCTAATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAATACTT
1 TGTGATAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAACACTT
* * * *
17656505 T-GTTAACTATTAATGACATTGCAATTTTATCACATTAATGTATGGTGTTATATGACAATAATAT
66 TAGTTAACTATTAATGACATTACAATTTTGTCACATTAATGTATGGTGTTATATGACGATAACAT
** *
17656569 AAATGTCACAAACTTTTATCGTCGAATTTATTTGATGAAAAATTTTTT-TGTA-ATGTTTTTTAT
131 AAATGTCACAAACTTTTATCACCAAATTTATTTGATGAAAAATTTTTTATG-ACAT-TTTTTTAT
* * *
17656632 TTTAAGTGACGTT-TAAATTTTGTCACAAATTTAAAATTTTATC
194 TTTAAGTGATGTTAT-AATTTTGTCACTAATTTAAAATTTTATT
* * * *
17656675 TGTGATAAA-TTTTTCTAATAGATTTTAGGTGACGTTATTAATTTTTGTCATAAA-TGTAACACT
1 TGTGATAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTG-AACACT
** * * * * * *
17656738 TTAGTTAACTATTAATGACATTACAATTTCATTACCTTTATTTTATGGTATTATATGATGATAAC
65 TTAGTTAACTATTAATGACATTACAATTTTGTCA-CATTAATGTATGGTGTTATATGACGATAAC
* * * * *
17656803 ATAAATGTCACAAAACTTTTA-CTATCAATTTTATTTGGTGAAAAAATTTTTAGTGACTTTTTTA
129 ATAAATGTCAC-AAACTTTTATC-ACCAAATTTATTTGATGAAAAATTTTTTA-TGAC-ATTTT-
*
17656867 TTTATTTTAAGTGATGTTATAA--ATGTCACTAATTTAAAATTTTATT
189 TTTATTTTAAGTGATGTTATAATTTTGTCACTAATTTAAAATTTTATT
* * * * * * *
17656913 TATGATAAATGTTTTTTGATAAATTTTAGGT--CTGTTATTAATTTTTGTCATAGATTGAATACT
1 TGTGATAAATTTTTTTTGATAGATTTTAGGTGAC-ATTATTAATTTTTGTCACAAATTGAACACT
* * ** *
17656976 TTAGTTAACTATTAATTACATTATAATTTTGTCATGTCAATGTATGGTGTTATATGACGATAACA
65 TTAGTTAACTATTAATGACATTACAATTTTGTCACATTAATGTATGGTGTTATATGACGATAACA
* **
17657041 TAAATGTCATAAACTTTTATCACCAAATTTATTTGATGGGAAATTTTTTATGACATTTTTTTATT
130 TAAATGTCACAAACTTTTATCACCAAATTTATTTGATGAAAAATTTTTTATGACATTTTTTTATT
* * * * *
17657106 TTATGTGA-GTTATAATTTTATTACCAATTTAAATTTTTATT
195 TTAAGTGATGTTATAATTTTGTCACTAATTTAAAATTTTATT
* *
17657147 TGTGACAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTTACAAATTGAACACTT
1 TGTGATAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAACACTT
* * * * * * * * *
17657212 TGGTTAACTATTAATAACATTATAATTTCGTCACATTAATATTTGATTTTATATTACGATAACAT
66 TAGTTAACTATTAATGACATTACAATTTTGTCACATTAATGTATGGTGTTATATGACGATAACAT
* * * * *
17657277 AAATGTCACAAACTTTTACCGCTAATTTTATTTGGTGAAAAATTTTTTATGACA-TTTTTTATTT
131 AAATGTCACAAACTTTTATCACCAAATTTATTTGATGAAAAATTTTTTATGACATTTTTTTATTT
*
17657341 TAGGTGATGTTATAATTTTGTCACTAA-TTAAAATTTTATT
196 TAAGTGATGTTATAATTTTGTCACTAATTTAAAATTTTATT
* *
17657381 TGTGATTAA------TTG-T---TTTT--TTG--A-TA--AATTTTTGTCACAAATTGAACACTT
1 TGTGATAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAACACTT
* ** * * * * * *
17657429 TAGTTAACTATTAATGACATCACAATTTCATCACATCAATATTTGGTGTTATATGACAACAACAA
66 TAGTTAACTATTAATGACATTACAATTTTGTCACATTAATGTATGGTGTTATATGACGATAACAT
* * * * *
17657494 AAATGTGACAAACTTTTA-CTGCCAAATTAATTTAATGGAAAATTTTT
131 AAATGTCACAAACTTTTATC-ACCAAATTTATTTGATGAAAAATTTTT
17657541 GTAACATTTT
Statistics
Matches: 731, Mismatches: 114, Indels: 60
0.81 0.13 0.07
Matches are distributed among these distances:
216 1 0.00
217 115 0.16
219 2 0.00
220 1 0.00
222 2 0.00
224 4 0.01
227 1 0.00
228 3 0.00
232 7 0.01
233 15 0.02
234 135 0.18
235 181 0.25
236 68 0.09
237 67 0.09
238 84 0.11
239 24 0.03
240 20 0.03
241 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (236 bp):
TGTGATAAATTTTTTTTGATAGATTTTAGGTGACATTATTAATTTTTGTCACAAATTGAACACTT
TAGTTAACTATTAATGACATTACAATTTTGTCACATTAATGTATGGTGTTATATGACGATAACAT
AAATGTCACAAACTTTTATCACCAAATTTATTTGATGAAAAATTTTTTATGACATTTTTTTATTT
TAAGTGATGTTATAATTTTGTCACTAATTTAAAATTTTATT
Found at i:17665483 original size:45 final size:46
Alignment explanation
Indices: 17665392--17665487 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
17665382 ATATTGCTCA
* *
17665392 TAATATCATTGAGTTTGATTTGATGGAAAAAAACAAACAAAATACT
1 TAATGTCATTGAGTCTGATTTGATGGAAAAAAACAAACAAAATACT
*
17665438 TAATGTCATTGAGTCTGATTTGATGG-AAAAAACAAACGAAATACT
1 TAATGTCATTGAGTCTGATTTGATGGAAAAAAACAAACAAAATACT
17665483 TAATG
1 TAATG
17665488 ATGTGTCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 23 0.49
46 24 0.51
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (46 bp):
TAATGTCATTGAGTCTGATTTGATGGAAAAAAACAAACAAAATACT
Found at i:17669093 original size:201 final size:198
Alignment explanation
Indices: 17668825--17669248 Score: 505
Period size: 197 Copynumber: 2.1 Consensus size: 198
17668815 TTAATAACAT
* * * *
17668825 TAATTATGTCACCAATACTGTGATGATTTATCTTTTTATCTCTAATATATCAAATTTAATCATTT
1 TAATTATGTCACCAATACTATGATGATTTATCCTTTCATCTCTAATATATCAAATTTAATAATTT
* * *
17668890 ATTTCATGATGATTATAACCTTTAATGACATT-TTTTTTATAAAAAACTAACGAAAACTAACGTC
66 ATTTCATGATGATTATAACCTTCAATGACATTCTTCTTTAT-----ACTAACGAAAACTAACATC
* * * *
17668954 ACA-AAAAAATGAAGCATAATGTGACGTTTGATTTTATTGACACGTTTGACATTATCTTATAACC
126 ACATAAAAAA-AAAACATAAGGTGACATTTGATTTTATTGACACGTTTGACATTATCTTATAACC
17669018 AATTGACGA
190 AATTGACGA
* *
17669027 TAATTATGTTACCAATACTATGATGATTTA-CCTTTCATCAT-TAATATATCAAATTTTATAATT
1 TAATTATGTCACCAATACTATGATGATTTATCCTTTCATC-TCTAATATATCAAATTTAATAATT
* ** * *
17669090 TATTTTATGATGATTATAACCTTCAATGATGTTCTTCTTTATACTAACGAAAATTAACATCATAT
65 TATTTCATGATGATTATAACCTTCAATGACATTCTTCTTTATACTAACGAAAACTAACATCACAT
* * * *
17669155 AAAAAAAAAACATAAGGTGACATTTGATTTTATTGTCATGTTTGACATTATCTTATAATCATTCA
130 AAAAAAAAAACATAAGGTGACATTTGATTTTATTGACACGTTTGACATTATCTTATAACCAAT--
*
17669220 TGACAA
193 TGACGA
* * *
17669226 TAATTGTGTCATCAATATTATGA
1 TAATTATGTCACCAATACTATGA
17669249 CAACTTACCT
Statistics
Matches: 190, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
197 68 0.36
198 6 0.03
199 24 0.13
201 56 0.29
202 36 0.19
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (198 bp):
TAATTATGTCACCAATACTATGATGATTTATCCTTTCATCTCTAATATATCAAATTTAATAATTT
ATTTCATGATGATTATAACCTTCAATGACATTCTTCTTTATACTAACGAAAACTAACATCACATA
AAAAAAAAACATAAGGTGACATTTGATTTTATTGACACGTTTGACATTATCTTATAACCAATTGA
CGA
Found at i:17669271 original size:29 final size:29
Alignment explanation
Indices: 17669239--17669301 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
17669229 TTGTGTCATC
17669239 AATATTATGACAACTTACCTTTTGTCACT
1 AATATTATGACAACTTACCTTTTGTCACT
17669268 AATATTATGACAACTTACCTTTTGTCACT
1 AATATTATGACAACTTACCTTTTGTCACT
17669297 AATAT
1 AATAT
17669302 ATCAGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (29 bp):
AATATTATGACAACTTACCTTTTGTCACT
Found at i:17669496 original size:232 final size:228
Alignment explanation
Indices: 17669054--17669504 Score: 514
Period size: 232 Copynumber: 2.0 Consensus size: 228
17669044 CTATGATGAT
* *
17669054 TTACCTTTCATCATTAATATATCAAATTTTATAATTTATTTTATGATGATTATAACCTTCAATGA
1 TTACCTTTCATCACTAATATATCAAATTTTATAATTTATTTTATGATAATTATAACCTTCAATGA
* **
17669119 TGTTCTTCTTTATACTAACGAAAATTAACATCATATAAAAAAAAAACATAAGGTGACATTTGATT
66 TGTTCTTCTTTATACTAACGAAAACTAACATCATATAAAAAAAAAACATAAAATGACATTTGATT
* * * * *
17669184 TTATTGTCATGTTTGACATTATCTTATAATCATTCATGACAATAATTGTGTCATCAATATTATGA
131 TTATTATCATGTTAGACATTATCTTACAATCATTCATGACAATAATTGTGTCATCAATACTATAA
17669249 CAACTTACCTTTTGTCACTAATATTATGACAAC
196 CAACTTACCTTTTGTCACTAATATTATGACAAC
** * * * * *
17669282 TTACCTTTTGTCACTAATATATCAGATTTTATCATTTATTTTGTGATAATTATAGCCTTTAATGA
1 TTACCTTTCATCACTAATATATCAAATTTTATAATTTATTTTATGATAATTATAACCTTCAATGA
* * * ** ** *
17669347 TGTTTTTGTTTATAAATAGCTAGCGAAAACTAACATCATA-AAAATTAATGCATAAAATGACGTT
66 TGTTCTT-CTT-T--ATA-CTAACGAAAACTAACATCATATAAAAAAAAAACATAAAATGACATT
** *
17669411 TGATTTTATTATCATAG-TAGACATTATCTTACAATCATT-AGTGATGATAATTTTGTCA-CTAA
126 TGATTTTATTATCAT-GTTAGACATTATCTTACAATCATTCA-TGACAATAATTGTGTCATC-AA
* ** *
17669473 TACTGTAATGATTTACCTTTTGTCACTAATAT
188 TACTATAACAACTTACCTTTTGTCACTAATAT
17669505 CTCATATTTT
Statistics
Matches: 183, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
228 62 0.34
229 2 0.01
230 1 0.01
231 2 0.01
232 96 0.52
233 20 0.11
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (228 bp):
TTACCTTTCATCACTAATATATCAAATTTTATAATTTATTTTATGATAATTATAACCTTCAATGA
TGTTCTTCTTTATACTAACGAAAACTAACATCATATAAAAAAAAAACATAAAATGACATTTGATT
TTATTATCATGTTAGACATTATCTTACAATCATTCATGACAATAATTGTGTCATCAATACTATAA
CAACTTACCTTTTGTCACTAATATTATGACAAC
Found at i:17670322 original size:60 final size:60
Alignment explanation
Indices: 17670253--17670417 Score: 210
Period size: 61 Copynumber: 2.7 Consensus size: 60
17670243 TGCTTTTATA
* *
17670253 CAAGGAAAATTGATACTTTCAATTTTTCCTTAAAAATATTTTTTTTT-AGAATTTTATTTT
1 CAAGAAAAATTGATA-TTTCAATTTTTCCTTAAAAATATTTTTTTTTGAAAATTTTATTTT
* *
17670313 TAAGAAAAATTGATATTTCTAACTTTTT-C-TCAAAATAATTTTTTTTTGAAAATTTTATTTT
1 CAAGAAAAATTGATATTTC-AA-TTTTTCCTTAAAAAT-ATTTTTTTTTGAAAATTTTATTTT
* *
17670374 CAAGCAAAATTGATATTTTCAACTTTTCCTTAAAAATATTTTTT
1 CAAGAAAAATTGATA-TTTCAATTTTTCCTTAAAAATATTTTTT
17670418 AGAAATTGGA
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
59 10 0.11
60 30 0.33
61 40 0.44
62 10 0.11
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.50
Consensus pattern (60 bp):
CAAGAAAAATTGATATTTCAATTTTTCCTTAAAAATATTTTTTTTTGAAAATTTTATTTT
Found at i:17670584 original size:64 final size:59
Alignment explanation
Indices: 17670438--17670625 Score: 198
Period size: 64 Copynumber: 3.1 Consensus size: 59
17670428 AATATTCTTA
* * ***
17670438 GAAATTTTATTTTCAAAAAAAATTGATACTTTCAACTTATCTGTAAAAATAATTTTTTT
1 GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTTTT
* * **
17670497 GAGAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAATGCTTTTTTTTTTTT
1 GA-AATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCCAAAA----ATAATTTTTTT
* ** *
17670561 GGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAAT-ATTTTTTA
1 -GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTTTT
17670620 GAAATT
1 GAAATT
17670626 GGAAATATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
58 6 0.06
59 8 0.07
60 41 0.38
64 50 0.47
65 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (59 bp):
GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTTTT
Found at i:17670695 original size:58 final size:57
Alignment explanation
Indices: 17670633--17670796 Score: 199
Period size: 58 Copynumber: 2.8 Consensus size: 57
17670623 ATTGGAAATA
* * *
17670633 TTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCCTCAAATTTT
1 TTTTTAGAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAATTTT
*
17670690 GTTTTTA-AAATTTTTATTTTTTAAGGAAAATT-AGTAC-TTCTAACTTTTCCCCAAATTTT
1 -TTTTTAGAAA-TTTTA-TTTTCAAGGAAAATTGA-TACTTTC-AACTTTTCCCCAAATTTT
* *
17670749 TTTTTTGAAAATTTTATTTTCAAGGAAAATTGATATTTTCAACTTTTC
1 TTTTTAG-AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
17670797 TTTAAAAATA
Statistics
Matches: 91, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
57 3 0.03
58 44 0.48
59 41 0.45
60 3 0.03
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (57 bp):
TTTTTAGAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAATTTT
Found at i:17670695 original size:77 final size:76
Alignment explanation
Indices: 17670556--17670701 Score: 222
Period size: 77 Copynumber: 1.9 Consensus size: 76
17670546 TGCTTTTTTT
* *
17670556 TTTTTGGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTAG
1 TTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTA-
17670621 AAATTGGAAATA
65 AAATTGGAAATA
* * *
17670633 TTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTCCTCAAATTTTGTTTTTA
1 TTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATAT-TTTTTA
17670697 AAATT
65 AAATT
17670702 TTTATTTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
76 17 0.27
77 46 0.73
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (76 bp):
TTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTAA
AATTGGAAATA
Done.