Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 167 of 259
Found at i:54285355 original size:24 final size:25
Alignment explanation
Indices: 54285304--54285356 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
54285294 GTCAAAATGC
* **
54285304 AATTTTTATTTTTTTAAATTTTTTA
1 AATTTTTATTTTTTGAAATTTTGAA
54285329 AATTTTT-TTTTTTGAAATTTTGAA
1 AATTTTTATTTTTTGAAATTTTGAA
54285353 AATT
1 AATT
54285357 AAACACAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
AATTTTTATTTTTTGAAATTTTGAA
Found at i:54285755 original size:53 final size:54
Alignment explanation
Indices: 54285592--54285786 Score: 319
Period size: 53 Copynumber: 3.7 Consensus size: 54
54285582 CACGTGAGCC
*
54285592 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
*
54285642 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
*
54285696 AAGGCTCAACTCACCTCTCGCAATATGA-TTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
*
54285749 AAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
54285787 TTTTTTGAAA
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
50 45 0.33
52 1 0.01
53 50 0.37
54 39 0.29
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
Found at i:54285820 original size:14 final size:14
Alignment explanation
Indices: 54285798--54285830 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54285788 TTTTTGAAAC
54285798 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
*
54285812 ACAGGAATT-AAAA
1 ACAGAAATTAAAAA
54285825 ACAGAA
1 ACAGAA
54285831 TTTGAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:54286102 original size:72 final size:72
Alignment explanation
Indices: 54285914--54287434 Score: 2524
Period size: 72 Copynumber: 21.1 Consensus size: 72
54285904 ATTAGTAAAG
* * * *
54285914 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
54285978 TTTGAAAA
65 TTTGAAAA
* *
54285986 GCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
54286051 TTTGAAAA
65 TTTGAAAA
* *
54286059 CAGAAATTGAAATTACTTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTAAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
54286124 TTGAGAAG
66 TTGA-AAA
* *
54286132 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286197 TTGAAAA
66 TTGAAAA
54286204 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286269 TTGAAAA
66 TTGAAAA
54286276 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
54286341 TTGAGAAG
66 TTGA-AAA
* * *
54286349 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTCGAGTT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286414 TTGAAAA
66 TTGAAAA
*
54286421 CAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
54286486 TTGAGAAG
66 TTGA-AAA
*
54286494 CAGAAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 CAGAAATTG-AAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
54286559 TTTGAAAA
65 TTTGAAAA
54286567 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286632 TTGAAAA
66 TTGAAAA
54286639 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286704 TTGAAAA
66 TTGAAAA
54286711 CAGAAATTGAAATTACCTCAACGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286775 TTGAAAA
66 TTGAAAA
54286782 CAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286846 TTGAAAA
66 TTGAAAA
54286853 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286918 TTGAAAA
66 TTGAAAA
54286925 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286990 TTGAAAA
66 TTGAAAA
54286997 -AGAAATTGAAATTACCTC-ACGTGTC-TGA-GCTCAACTCA-TT-TCGCAATATGAGTTGAA-T
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54287055 TTGAAAA
66 TTGAAAA
* *
54287062 TAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACACATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54287127 TTGAAAA
66 TTGAAAA
54287134 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54287199 TTGAAAA
66 TTGAAAA
* * * *
54287206 GCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
54287271 TTTGAAAA
65 TTTGAAAA
* *
54287279 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---
* *
54287344 TTTTTTAACAA
63 ATTTTGAA-AA
* ** * ** * *
54287355 CAGAAATTAAAATTACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAATTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54287419 TTGAAAAA
66 TTG-AAAA
*
54287427 CATAAATT
1 CAGAAATT
54287435 AAAAGGCTTA
Statistics
Matches: 1378, Mismatches: 50, Indels: 41
0.94 0.03 0.03
Matches are distributed among these distances:
65 8 0.01
66 35 0.03
67 9 0.01
68 13 0.01
69 12 0.01
70 23 0.02
71 147 0.11
72 716 0.52
73 292 0.21
74 60 0.04
75 6 0.00
76 57 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAA
Found at i:54286165 original size:145 final size:144
Alignment explanation
Indices: 54285914--54287434 Score: 2524
Period size: 145 Copynumber: 10.6 Consensus size: 144
54285904 ATTAGTAAAG
* * * *
54285914 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
* *
54285978 TTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
65 TTTGAAAA-CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
54286043 AGTTGAATTTTGAAAA
129 AGTTGAATTTTGAAAA
* *
54286059 CAGAAATTGAAATTACTTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTAAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
* * *
54286124 TTGAGAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGA
66 TTGA-AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
54286189 GTTGAATTTTGAAAA
130 GTTGAATTTTGAAAA
54286204 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286269 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
*
54286334 TTGAATTTTGAGAAG
131 TTGAATTTTGA-AAA
* * *
54286349 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTCGAGTT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
54286414 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
*
54286479 TTGAATTTTGAGAAG
131 TTGAATTTTGA-AAA
*
54286494 CAGAAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 CAGAAATTG-AAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
54286559 TTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
65 TTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
54286624 GTTGAATTTTGAAAA
130 GTTGAATTTTGAAAA
54286639 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286704 TTGAAAACAGAAATTGAAATTACCTCAACGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
54286768 TTGAATTTTGAAAA
131 TTGAATTTTGAAAA
54286782 CAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286846 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
54286911 TTGAATTTTGAAAA
131 TTGAATTTTGAAAA
54286925 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54286990 TTGAAAA-AGAAATTGAAATTACCTC-ACGTGTC-TGA-GCTCAACTCA-TT-TCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
54287049 TTGAA-TTTGAAAA
131 TTGAATTTTGAAAA
* *
54287062 TAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACACATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
54287127 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
54287192 TTGAATTTTGAAAA
131 TTGAATTTTGAAAA
* * * *
54287206 GCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
* *
54287271 TTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGA
65 TTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
* *
54287336 GTTGATTTTTTTTTAACAA
130 GTTGA---ATTTTGAA-AA
* ** * ** * *
54287355 CAGAAATTAAAATTACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAATTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
54287419 TTGAAAAACATAAATT
66 TTG-AAAACAGAAATT
54287435 AAAAGGCTTA
Statistics
Matches: 1313, Mismatches: 44, Indels: 35
0.94 0.03 0.03
Matches are distributed among these distances:
137 78 0.06
138 35 0.03
139 9 0.01
140 13 0.01
141 13 0.01
142 95 0.07
143 147 0.11
144 225 0.17
145 487 0.37
146 133 0.10
147 6 0.00
148 70 0.05
149 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (144 bp):
CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
TTGAATTTTGAAAA
Found at i:54286287 original size:217 final size:216
Alignment explanation
Indices: 54285910--54287424 Score: 2539
Period size: 217 Copynumber: 7.0 Consensus size: 216
54285900 TAGAATTAGT
* * *
54285910 AAAGCAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
* *
54285974 AAGTTTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAA
66 AA-TTTTGAAAA-CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
*
54286039 TATGAGTTGAATTTTGAAAACAGAAATTGAAATTACTTCAACGTGTCTTGAGGCTCAACTCATTT
129 TATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
*
54286104 CTCGCAATATGAGTTAAATTTTG
194 CTCGCAATATGAGTTGAATTTTG
*
54286127 AGAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTT
1 A-AAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
54286192 GAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
65 GAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
54286257 ATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTC
130 ATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTC
54286322 TCGCAATATGAGTTGAATTTTG
195 TCGCAATATGAGTTGAATTTTG
*
54286344 AGAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTC
1 A-AAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
* *
54286409 GAGTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAAT
65 GAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
* *
54286474 ATGAGTTGAATTTTGAGAAGCAGAAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATT
130 ATGAGTTGAATTTTGA-AAACAGAAATTG-AAATTACCTCAACGTGTCTTGAGGCTCAACTCATT
54286539 TCTCGCAATATGAGTTGAATTTTG
193 TCTCGCAATATGAGTTGAATTTTG
* *
54286563 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
54286628 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
66 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
54286693 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTC-TGAGGCTCAACTCATTTCT
131 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
54286757 CGCAATATGAGTTGAATTTTG
196 CGCAATATGAGTTGAATTTTG
*
54286778 AAAACAGAAATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
54286842 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
66 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
54286907 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
131 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
54286972 CGCAATATGAGTTGAATTTTG
196 CGCAATATGAGTTGAATTTTG
* *
54286993 AAA-AAGAAATTGAAATTACCTC-ACGTGTC-TGA-GCTCAACTCA-TT-TCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
* *
54287052 AA-TTTGAAAATAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACACATTTCTCGCAATA
66 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
54287116 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
131 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
54287181 CGCAATATGAGTTGAATTTTG
196 CGCAATATGAGTTGAATTTTG
* * *
54287202 AAAAGCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTT
1 -AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
* *
54287267 GAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAAT
65 GAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
* * * ** *
54287332 ATGAGTTGATTTTTTTTTAACAACAGAAATTAAAATTACCTCAGTGTGTCCTGAGGCTCAACTCA
130 ATGAGTTGA---ATTTTGAA-AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
** * *
54287397 CCTCTAGCAATATGAATTG-ATTTTG
191 TTTCTCGCAATATGAGTTGAATTTTG
54287422 AAA
1 AAA
54287425 AACATAAATT
Statistics
Matches: 1236, Mismatches: 44, Indels: 34
0.94 0.03 0.03
Matches are distributed among these distances:
209 146 0.12
210 20 0.02
211 19 0.02
212 16 0.01
213 6 0.00
214 185 0.15
215 106 0.09
216 33 0.03
217 356 0.29
218 218 0.18
219 64 0.05
220 12 0.01
221 55 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (216 bp):
AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
CGCAATATGAGTTGAATTTTG
Found at i:54299680 original size:15 final size:15
Alignment explanation
Indices: 54299631--54299684 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
54299621 TTTTTAGAAA
54299631 AAAAATAAAATTAACTT
1 AAAAATAAAA-T-ACTT
*
54299648 AAAAAAATAAATAC-T
1 AAAAATA-AAATACTT
*
54299663 AAAAATAAAATGCTT
1 AAAAATAAAATACTT
54299678 AAAAATA
1 AAAAATA
54299685 TATCAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.16
15 15 0.47
16 2 0.06
17 7 0.22
18 3 0.09
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAAATAAAATACTT
Found at i:54299789 original size:21 final size:21
Alignment explanation
Indices: 54299763--54299802 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54299753 AAAAAGCTCA
54299763 AAAATACGAGATTGACCGATC
1 AAAATACGAGATTGACCGATC
*
54299784 AAAATACGAGCTTGACCGA
1 AAAATACGAGATTGACCGA
54299803 GAGGGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAATACGAGATTGACCGATC
Found at i:54299849 original size:20 final size:20
Alignment explanation
Indices: 54299824--54299903 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 20
54299814 GATTCGAGCC
54299824 TTCCTTTTTTCTTTTTTCTT
1 TTCCTTTTTTCTTTTTTCTT
* *
54299844 TTCCTTTTTCCCTTTTT-TT
1 TTCCTTTTTTCTTTTTTCTT
*
54299863 TT-CTCTTTTC-TTTTTCTTT
1 TTCCTTTTTTCTTTTTTC-TT
* * *
54299882 TTTCTGTTTTCTGTTTTCTT
1 TTCCTTTTTTCTTTTTTCTT
54299902 TT
1 TT
54299904 TTCCTTCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.10
18 6 0.12
19 8 0.16
20 26 0.52
21 5 0.10
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (20 bp):
TTCCTTTTTTCTTTTTTCTT
Found at i:54299884 original size:21 final size:22
Alignment explanation
Indices: 54299858--54299914 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
54299848 TTTTTCCCTT
54299858 TTTTTTTCTCTTTTCT-TTTTC
1 TTTTTTTCTCTTTTCTGTTTTC
*
54299879 -TTTTTTCTGTTTTCTGTTTTC
1 TTTTTTTCTCTTTTCTGTTTTC
*
54299900 TTTTTTCCTTCTTTT
1 TTTTTTTC-TCTTTT
54299915 TCCTTTGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 14 0.47
21 5 0.17
22 6 0.20
23 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTTTCTCTTTTCTGTTTTC
Found at i:54299904 original size:13 final size:13
Alignment explanation
Indices: 54299830--54299920 Score: 93
Period size: 13 Copynumber: 7.2 Consensus size: 13
54299820 AGCCTTCCTT
54299830 TTTTCTTTTT-TC
1 TTTTCTTTTTCTC
*
54299842 TTTTCCTTTTTCCC
1 TTTT-CTTTTTCTC
54299856 TTTT-TTTTTCTC
1 TTTTCTTTTTCTC
*
54299868 TTTTCTTTTTCTT
1 TTTTCTTTTTCTC
*
54299881 TTTTCTGTTTTCTG
1 TTTTCT-TTTTCTC
54299895 TTTTCTTTTT-TC
1 TTTTCTTTTTCTC
*
54299907 -CTTCTTTTTC-C
1 TTTTCTTTTTCTC
54299918 TTT
1 TTT
54299921 GGCCTGCTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.14
12 17 0.26
13 23 0.35
14 17 0.26
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTTCTC
Found at i:54299920 original size:7 final size:6
Alignment explanation
Indices: 54299829--54299904 Score: 73
Period size: 7 Copynumber: 11.8 Consensus size: 6
54299819 GAGCCTTCCT
* *
54299829 TTTTTC TTTTTTC TTTTCC TTTTTCC CTTTT- TTTTTC TCTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC T-TTTTC TTTTTC
54299879 TTTTTTC TGTTTTC TGTTTTC TTTTT
1 -TTTTTC T-TTTTC T-TTTTC TTTTT
54299905 TCCTTCTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.07
6 20 0.33
7 36 0.60
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:54300210 original size:18 final size:18
Alignment explanation
Indices: 54300189--54300232 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
54300179 GTTTGGGTTG
54300189 CGGGTCGGGTCACCGGAT
1 CGGGTCGGGTCACCGGAT
* *
54300207 CGGGTCGTGTCGCCGGAT
1 CGGGTCGGGTCACCGGAT
54300225 CGGGTCGG
1 CGGGTCGG
54300233 TTTGACCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.27, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCACCGGAT
Found at i:54300285 original size:6 final size:6
Alignment explanation
Indices: 54300275--54300361 Score: 77
Period size: 6 Copynumber: 14.3 Consensus size: 6
54300265 ATTTTTTATT
* **
54300275 TTTTTCC TTTTTC -TTTTC TTTTTC TTTTTC TTTTTTC TTCTTC TCCTTC
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* * * * *
54300324 TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
54300362 CACGAGCCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.07
6 57 0.78
7 11 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:54300317 original size:3 final size:3
Alignment explanation
Indices: 54300285--54300362 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
54300275 TTTTTCCTTT
* * *
54300285 TTC TT- TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
54300330 TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54300363 ACGAGCCCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 6 0.09
3 59 0.91
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:54300419 original size:18 final size:18
Alignment explanation
Indices: 54300379--54300421 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
54300369 CCTAGCCGCC
54300379 GCGCCG-CGCCGTCGCTT
1 GCGCCGTCGCCGTCGCTT
*
54300396 GTGCCGTCGCCGTCGTCTT
1 GCGCCGTCGCCGTCG-CTT
54300415 -CGCCGTC
1 GCGCCGTC
54300422 AAGCCGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 14 0.64
19 3 0.14
ACGTcount: A:0.00, C:0.44, G:0.33, T:0.23
Consensus pattern (18 bp):
GCGCCGTCGCCGTCGCTT
Found at i:54300487 original size:20 final size:21
Alignment explanation
Indices: 54300440--54300493 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
54300430 GTCGGAGGCT
54300440 CTCTTC-TTCTTCTCCTTTCTC
1 CTCTTCTTTC-TCTCCTTTCTC
*
54300461 CTC-TCTTTCTCTCC-TTGTC
1 CTCTTCTTTCTCTCCTTTCTC
*
54300480 CTCTTCTTTTTCTC
1 CTCTTCTTTCTCTC
54300494 TTTTTTGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
20 16 0.55
21 6 0.21
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (21 bp):
CTCTTCTTTCTCTCCTTTCTC
Found at i:54300781 original size:30 final size:30
Alignment explanation
Indices: 54300741--54300835 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
54300731 ATTTAGGATT
*
54300741 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * * *
54300771 TAAGTGAAATTTAAAGAAAGTTTAAGTGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
54300801 AAAATGGAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
54300831 AAAAT
1 AAAAT
54300836 ACAATTTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 2 0.04
30 51 0.96
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54300890 original size:25 final size:25
Alignment explanation
Indices: 54300838--54300891 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
54300828 GTCAAAATAC
**
54300838 AATTTTTATTTTTTTAAATTTTTTA
1 AATTTTTATTTTTTTAAATTTTGAA
54300863 AATTTTT-TTTTTTTGAAATTTTGAA
1 AATTTTTATTTTTTT-AAATTTTGAA
54300888 AATT
1 AATT
54300892 AAACACAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
AATTTTTATTTTTTTAAATTTTGAA
Found at i:54309753 original size:119 final size:119
Alignment explanation
Indices: 54309537--54310014 Score: 753
Period size: 119 Copynumber: 4.0 Consensus size: 119
54309527 AAATAAATTG
* ** **
54309537 AAGACAGCAGATCTAGA-CTTCAGACATTTATGTTGAAGCAGATCCAAGATGATTTGGTATTCTT
1 AAGATAGCAGATCTA-ACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
* *
54309601 GTGTTTATAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
65 GTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
* *
54309656 AAGATAGCAGATCTAACCTTCAGATGATTATACTGAAGCAGATCCAGGATGATTTGGTATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
* *
54309721 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
66 TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
*
54309775 AAGATAGCAGACCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
*
54309840 TGTTTA-TAGGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
66 TGTTTACAAGG-AACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
* * *
54309894 AATATAGCAGATCTAACCTTCAGATGTTTATATTGAAGCAGATCCAAGATGATTTGGCATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
* * *
54309959 TATTTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCTCA
66 TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
54310013 AA
1 AA
54310015 CAGACTCAAG
Statistics
Matches: 331, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
118 4 0.01
119 324 0.98
120 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (119 bp):
AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
Found at i:54310042 original size:83 final size:83
Alignment explanation
Indices: 54309938--54310207 Score: 360
Period size: 83 Copynumber: 3.2 Consensus size: 83
54309928 GAAGCAGATC
* ** * * *
54309938 CAAGATGATTTGGCATTCTTGTATTTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
*
54310003 GATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* *
54310021 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATAACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
54310086 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * * * * * *
54310104 CAAGATGGTTTAAGTACCCTCGTGCTTACAAGGAACAAGTCGAGGACCTTGCAGATATGACTCTC
1 CAAGATGATTT-GGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTC
* *
54310169 AAATGTTTTCAGACAGACT
65 AAATGTTCTCAAACAGACT
*
54310188 CAAGATGATTTGACATCCTT
1 CAAGATGATTTGGCATCCTT
54310208 ACAAATCGAA
Statistics
Matches: 162, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 89 0.55
84 73 0.45
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (83 bp):
CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:54310159 original size:84 final size:83
Alignment explanation
Indices: 54309962--54310194 Score: 340
Period size: 84 Copynumber: 2.8 Consensus size: 83
54309952 ATTCTTGTAT
* * * *
54309962 TTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCTCAAACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
* * *
54310027 GGTTTGGCATCCTTGTGC
66 GGTTTAGCACCCTCGTGC
*
54310045 TTACAAGGAACAAATCGAGGACATTGCAGATATAACTCTCAAATGTTCTCAAACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
*
54310110 GGTTTAAGTACCCTCGTGC
66 GGTTT-AGCACCCTCGTGC
* * * *
54310129 TTACAAGGAACAAGTCGAGGACCTTGCAGATATGACTCTCAAATGTTTTCAGACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
54310194 G
66 G
54310195 ATTTGACATC
Statistics
Matches: 135, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 65 0.48
84 70 0.52
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (83 bp):
TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
GGTTTAGCACCCTCGTGC
Found at i:54311713 original size:17 final size:18
Alignment explanation
Indices: 54311691--54311731 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54311681 TATATTATAT
*
54311691 ATTATAA-AATTATTTTG
1 ATTATAAGAATTATTTTA
*
54311708 ATTATAAGTATTATTTTA
1 ATTATAAGAATTATTTTA
54311726 ATTATA
1 ATTATA
54311732 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTATAAGAATTATTTTA
Found at i:54311720 original size:18 final size:19
Alignment explanation
Indices: 54311699--54311741 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
54311689 ATATTATAAA
*
54311699 ATTATTTTGATTATA-AGT
1 ATTATTTTAATTATATAGT
*
54311717 ATTATTTTAATTATATATT
1 ATTATTTTAATTATATAGT
54311736 ATTATT
1 ATTATT
54311742 ACTTATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTATTTTAATTATATAGT
Found at i:54311737 original size:16 final size:16
Alignment explanation
Indices: 54311699--54311777 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
54311689 ATATTATAAA
*
54311699 ATTATTTTGATTATAAGT
1 ATTATTTTAATTAT-A-T
54311717 ATTATTTTAATTATAT
1 ATTATTTTAATTATAT
*
54311733 ATTATTATTACTTATTATGT
1 ATTATT-TTA---ATTATAT
** *
54311753 ATTATTTTTCTTAAAT
1 ATTATTTTAATTATAT
54311769 ATTATTTTA
1 ATTATTTTA
54311778 CATCTCTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
16 19 0.38
17 4 0.08
18 13 0.26
19 2 0.04
20 12 0.24
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (16 bp):
ATTATTTTAATTATAT
Found at i:54311852 original size:12 final size:12
Alignment explanation
Indices: 54311808--54311859 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
54311798 ATATTTTCAC
54311808 ATATATTATATTT
1 ATATATTAT-TTT
*
54311821 AT-TAATTA-TAT
1 ATAT-ATTATTTT
54311832 ATATATTATTTT
1 ATATATTATTTT
*
54311844 ATATGTTATTTT
1 ATATATTATTTT
54311856 ATAT
1 ATAT
54311860 TATATCTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 8 0.24
12 19 0.58
13 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
ATATATTATTTT
Found at i:54311872 original size:12 final size:12
Alignment explanation
Indices: 54311811--54311872 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
54311801 TTTTCACATA
54311811 TATTATATTTAT
1 TATTATATTTAT
*
54311823 TAATTATATATA-
1 T-ATTATATTTAT
54311835 TATTAT-TTTAT
1 TATTATATTTAT
*
54311846 ATGTTAT-TTTA-
1 -TATTATATTTAT
*
54311857 TATTATATCTAT
1 TATTATATTTAT
54311869 TATT
1 TATT
54311873 TTTCTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.20
11 8 0.20
12 15 0.38
13 9 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:54311935 original size:18 final size:19
Alignment explanation
Indices: 54311912--54311959 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
54311902 ATATAATCTT
54311912 TATTATGTT-TTATTTTTA
1 TATTATGTTATTATTTTTA
* *
54311930 TATTAT-TTATTGTTTTTT
1 TATTATGTTATTATTTTTA
54311948 TATATATGTTAT
1 TAT-TATGTTAT
54311960 ATATATCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (19 bp):
TATTATGTTATTATTTTTA
Found at i:54314898 original size:22 final size:22
Alignment explanation
Indices: 54314871--54314914 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54314861 ATTATTATTG
*
54314871 ATTAATTAGTTTAATTAGATAA
1 ATTAATTAGTTTAATTAAATAA
**
54314893 ATTAATTTTTTTAATTAAATAA
1 ATTAATTAGTTTAATTAAATAA
54314915 TTTTCTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTAATTAGTTTAATTAAATAA
Found at i:54314917 original size:17 final size:18
Alignment explanation
Indices: 54314890--54314923 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54314880 TTTAATTAGA
*
54314890 TAAATTAATTTTTTTAAT
1 TAAATTAATTTTCTTAAT
54314908 TAAA-TAATTTTCTTAA
1 TAAATTAATTTTCTTAA
54314924 CCCAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTAATTTTCTTAAT
Found at i:54317693 original size:18 final size:18
Alignment explanation
Indices: 54317670--54317706 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54317660 TATCATGCCA
*
54317670 TTTATATCTTTTAATAAT
1 TTTATATCTTTTAAAAAT
*
54317688 TTTATATTTTTTAAAAAT
1 TTTATATCTTTTAAAAAT
54317706 T
1 T
54317707 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATCTTTTAAAAAT
Found at i:54322686 original size:21 final size:21
Alignment explanation
Indices: 54322662--54322714 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
54322652 CACTGTTTCT
*
54322662 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
54322683 AATCTCACCGCTTCAGTAACT
1 AATCTCACCGCTACAGTAACC
54322704 AATCTCACCGC
1 AATCTCACCGC
54322715 CACCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:54331679 original size:46 final size:46
Alignment explanation
Indices: 54331626--54331844 Score: 209
Period size: 46 Copynumber: 4.7 Consensus size: 46
54331616 GTTATTGTTG
* *
54331626 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCATTGAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGAGA
*
54331672 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATG-AGA
* * * * *
54331718 GCCAGTGTAAGACATATTTGGGATATGCATCGGC-TACGAGATGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGATGAGA
*
54331764 G-TCAGTGTAAGACCATGT-TAGGGACATGGCATC-G-ATTTGAGAT-ATGA
1 GCT-AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCA-TCGAGATGA-GA
*
54331811 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
54331845 TCACCTTACC
Statistics
Matches: 147, Mismatches: 13, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
45 2 0.01
46 91 0.62
47 47 0.32
48 7 0.05
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGAGA
Found at i:54336014 original size:21 final size:21
Alignment explanation
Indices: 54335990--54336051 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
54335980 AGTTTATTTA
*
54335990 ATATTT-AATATTTTATCTTTT
1 ATATTTAAATATTAT-TCTTTT
54336011 ATATTTAAATATTATTCTTTT
1 ATATTTAAATATTATTCTTTT
**
54336032 GATA-GAAAATATTATTCTTT
1 -ATATTTAAATATTATTCTTT
54336052 AATAGTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (21 bp):
ATATTTAAATATTATTCTTTT
Found at i:54336015 original size:28 final size:29
Alignment explanation
Indices: 54335967--54336023 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
54335957 AATATTTTAA
54335967 TAATATTTTATATAGTTTATTT-AATATT
1 TAATATTTTATATAGTTTATTTAAATATT
* *
54335995 TAATATTTTATCT-TTTATATTTAAATATT
1 TAATATTTTATATAGTT-TATTTAAATATT
54336024 ATTCTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TAATATTTTATATAGTTTATTTAAATATT
Found at i:54336061 original size:20 final size:21
Alignment explanation
Indices: 54336016--54336061 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
54336006 CTTTTATATT
*
54336016 TAAATATTATTCTTTTGATAG
1 TAAATATTATTCTTTTAATAG
*
54336037 AAAATATTATTC-TTTAATAG
1 TAAATATTATTCTTTTAATAG
54336057 TAAAT
1 TAAAT
54336062 TGATGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAATATTATTCTTTTAATAG
Found at i:54338879 original size:29 final size:30
Alignment explanation
Indices: 54338812--54338880 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
54338802 TATCAAAGTT
*
54338812 ATACATGAACTATGATTTAATATTCAATTTG
1 ATACATGAACTATGATTT-ATATGCAATTTG
* *
54338843 ATATATGAACTTTGATTT-TATGCAATTTG
1 ATACATGAACTATGATTTATATGCAATTTG
54338872 ATACATGAA
1 ATACATGAA
54338881 TATTAAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (30 bp):
ATACATGAACTATGATTTATATGCAATTTG
Found at i:54346910 original size:20 final size:20
Alignment explanation
Indices: 54346887--54346924 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54346877 ACTAAAAAAA
*
54346887 TTTAAACTAATTTTTAAATT
1 TTTAAAATAATTTTTAAATT
54346907 TTTAAAATAATTTTTAAA
1 TTTAAAATAATTTTTAAA
54346925 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAAATAATTTTTAAATT
Found at i:54346933 original size:20 final size:20
Alignment explanation
Indices: 54346894--54346933 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54346884 AAATTTAAAC
* **
54346894 TAATTTTTAAATTTTTAAAA
1 TAATTTTTAAAATTAAAAAA
54346914 TAATTTTTAAAATTAAAAAA
1 TAATTTTTAAAATTAAAAAA
54346934 ATAAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTTTAAAATTAAAAAA
Found at i:54348520 original size:17 final size:17
Alignment explanation
Indices: 54348498--54348540 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
54348488 TATATCGAAC
54348498 TATTCAAACTCAATGAG
1 TATTCAAACTCAATGAG
54348515 TATTCAAACTCAATGAG
1 TATTCAAACTCAATGAG
54348532 TATTCAAAC
1 TATTCAAAC
54348541 ATTCACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (17 bp):
TATTCAAACTCAATGAG
Found at i:54348755 original size:18 final size:18
Alignment explanation
Indices: 54348734--54348918 Score: 162
Period size: 18 Copynumber: 10.3 Consensus size: 18
54348724 TCGGTTATCT
54348734 AGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
* **
54348752 AGTAA-AATCAGGTATTC
1 AGTAACAGTCAATTATTC
* *
54348769 AGTAACAATTAAGTTATTC
1 AGTAACAGTCAA-TTATTC
54348788 AGTAACAGTC-ATTCATTC
1 AGTAACAGTCAATT-ATTC
* * * *
54348806 TGTGACAATCAGTTATTC
1 AGTAACAGTCAATTATTC
*
54348824 AGTAA-TGATCAATTATTC
1 AGTAACAG-TCAATTATTC
* * *
54348842 AGTAATATTCAGTTATTC
1 AGTAACAGTCAATTATTC
*
54348860 AGTAACAGTCTAA-TATCC
1 AGTAACAGTC-AATTATTC
*
54348878 AGTAACAGTCAATTATCC
1 AGTAACAGTCAATTATTC
*
54348896 GGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
54348914 AGTAA
1 AGTAA
54348919 TAATCAGTTA
Statistics
Matches: 132, Mismatches: 27, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
17 18 0.14
18 98 0.74
19 16 0.12
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (18 bp):
AGTAACAGTCAATTATTC
Found at i:54348863 original size:72 final size:71
Alignment explanation
Indices: 54348729--54348930 Score: 208
Period size: 72 Copynumber: 2.8 Consensus size: 71
54348719 ATTGATCGGT
* * ** * *
54348729 TATCTAGTAACAGTCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCAGTAAC
1 TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAA-TATTCAGTTATTCAGTAAC
*
54348794 AGTC-AT
65 AGTCTAA
* * * * *
54348800 TCATTCTGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
54348865 CAGTCTAA
64 CAGTCTAA
* * * * *
54348873 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
54348931 TTATACCTTT
Statistics
Matches: 105, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
71 1 0.01
72 88 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:54348929 original size:18 final size:18
Alignment explanation
Indices: 54348635--54348930 Score: 161
Period size: 18 Copynumber: 16.1 Consensus size: 18
54348625 TCATTAACAA
* *
54348635 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAGTTAT
* *
54348652 TCAATAACAGTCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
54348670 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAGTTAT
* * *
54348688 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAGTTAT
*
54348706 TCAGTATCGATCAATTGATCGGTTA-
1 TCAGTA---A-C-A---ATCAGTTAT
* *
54348731 TCTAGTAACAGTCAATTAT
1 TC-AGTAACAATCAGTTAT
*
54348750 TCAGTAA-AATCAGGTAT
1 TCAGTAACAATCAGTTAT
*
54348767 TCAGTAACAATTAAGTTAT
1 TCAGTAACAA-TCAGTTAT
*
54348786 TCAGTAACAGTCA-TTCAT
1 TCAGTAACAATCAGTT-AT
* *
54348804 TCTGTGACAATCAGTTAT
1 TCAGTAACAATCAGTTAT
** *
54348822 TCAGTAATGATCAATTAT
1 TCAGTAACAATCAGTTAT
* *
54348840 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
54348858 TCAGTAACAGTCTA-ATAT
1 TCAGTAACAATC-AGTTAT
* * *
54348876 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
* * * *
54348894 CCGGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
*
54348912 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAGTTAT
54348930 T
1 T
54348931 TTATACCTTT
Statistics
Matches: 213, Mismatches: 49, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.09
18 156 0.73
19 20 0.09
21 2 0.01
22 1 0.00
23 2 0.01
25 2 0.01
26 10 0.05
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TCAGTAACAATCAGTTAT
Found at i:54350950 original size:31 final size:32
Alignment explanation
Indices: 54350894--54350956 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
54350884 CACACTTGTC
*
54350894 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
54350926 ATAATATAAT-TATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
54350957 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:54360490 original size:40 final size:40
Alignment explanation
Indices: 54360407--54360498 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 40
54360397 GTACCTTTTG
* * *
54360407 GTGTGTAGGGTTGGATGGGTTGATTATATCCCTAAACTTT
1 GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
* * *
54360447 GTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCACA-TG-
1 GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
*
54360485 GTGTGTTGGGTTGG
1 GTGTGTAGGGTTGG
54360499 TTGGAGATGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 13 0.29
39 1 0.02
40 31 0.69
ACGTcount: A:0.14, C:0.12, G:0.37, T:0.37
Consensus pattern (40 bp):
GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
Found at i:54363471 original size:46 final size:45
Alignment explanation
Indices: 54363418--54363623 Score: 168
Period size: 46 Copynumber: 4.4 Consensus size: 45
54363408 TTGTGGGCTT
* * *
54363418 GTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCTT
1 GTGTAAGACATGTCTGGGACATGCATCGGCCACA-GACGAGAGCTA
* * * *
54363464 GTATAAGACCATGTCTGGGATATGGAATCGG-CATCGAGACGAGTGCTA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-C-AGACGAGAGCTA
* * *
54363512 CTGTAAGACATGTTTGGGACATGCATCGGCCTCAAGACGTA-AG-TCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGACG-AGAGCT-A
* * *
54363558 GTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAG-TCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGACGAGAGCT-A
54363604 GTGTAAGACCATGTCTGGGA
1 GTGTAAGA-CATGTCTGGGA
54363624 TATGGCATTG
Statistics
Matches: 130, Mismatches: 21, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
45 2 0.02
46 67 0.52
47 40 0.31
48 20 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (45 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCCACAGACGAGAGCTA
Found at i:54367811 original size:46 final size:46
Alignment explanation
Indices: 54367678--54367813 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
54367668 TTATCTTCGA
* * * * * *
54367678 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
*
54367724 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAAACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54367770 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
54367814 TTCAGAAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.05
46 76 0.95
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:54374136 original size:46 final size:46
Alignment explanation
Indices: 54374082--54374300 Score: 232
Period size: 46 Copynumber: 4.7 Consensus size: 46
54374072 ATTGTGGGCT
* *
54374082 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGAGAGTC
* *
54374128 TGTGTAAGACCATGTCTAGGG-CATGGCATCGG-CACCGAGATGAGTG-C
1 AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCCA-CGAGATGAGAGTC
* * *
54374175 TAATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATG-AGAGTC
* *
54374222 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
*
54374268 AGTGTAAGACAATGTCTGGGATATGGCATCGGC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
54374301 ACTCTACCCC
Statistics
Matches: 147, Mismatches: 13, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
45 1 0.01
46 75 0.51
47 38 0.26
48 32 0.22
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
Found at i:54380524 original size:3 final size:3
Alignment explanation
Indices: 54380516--54380548 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
54380506 AAACCGACCT
54380516 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54380549 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54380769 original size:26 final size:25
Alignment explanation
Indices: 54380726--54380774 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
54380716 ATGAAATAAG
*
54380726 AATTATATATGCTGTTTAATAAATTA
1 AATTATATATACTGTTT-ATAAATTA
* *
54380752 AATTATATATATTTTTTATAAAT
1 AATTATATATACTGTTTATAAAT
54380775 ATTAAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
AATTATATATACTGTTTATAAATTA
Found at i:54386795 original size:25 final size:25
Alignment explanation
Indices: 54386757--54386823 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
54386747 TCTCGAGCCA
* *
54386757 TATAACAGGAAGCTCATGTGAGTTG
1 TATAACAAGAAGCTCATCTGAGTTG
* * * *
54386782 TATGACGAGAAGCTTATCTGGGTTG
1 TATAACAAGAAGCTCATCTGAGTTG
*
54386807 TATAACAAGAGGCTCAT
1 TATAACAAGAAGCTCAT
54386824 AAGAGCCATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (25 bp):
TATAACAAGAAGCTCATCTGAGTTG
Found at i:54386845 original size:24 final size:24
Alignment explanation
Indices: 54386818--54386894 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
54386808 ATAACAAGAG
54386818 GCTCATAAGAGCCATAATCGGGAA
1 GCTCATAAGAGCCATAATCGGGAA
* *
54386842 GCTCATATGAGCCAATAAT-GGGTA
1 GCTCATAAGAGCC-ATAATCGGGAA
* * *
54386866 GTTC-TGAAGAGCCATTAAACAGGAA
1 GCTCAT-AAGAGCCA-TAATCGGGAA
54386891 GCTC
1 GCTC
54386895 CGGATCGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
23 2 0.05
24 28 0.68
25 11 0.27
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (24 bp):
GCTCATAAGAGCCATAATCGGGAA
Found at i:54386957 original size:25 final size:26
Alignment explanation
Indices: 54386926--54386994 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
54386916 GCCATATCGG
*
54386926 GAAGCTC-CGGAGAGCCATTAATCAA
1 GAAGCTCACGAAGAGCCATTAATCAA
* * *
54386951 GAAGCTCACAAAGAGCC-TTTATCGA
1 GAAGCTCACGAAGAGCCATTAATCAA
54386976 GAAGCTCACGAAGAGCCAT
1 GAAGCTCACGAAGAGCCAT
54386995 ATATCAGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 29 0.78
26 8 0.22
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (26 bp):
GAAGCTCACGAAGAGCCATTAATCAA
Found at i:54390456 original size:122 final size:122
Alignment explanation
Indices: 54390239--54390482 Score: 461
Period size: 122 Copynumber: 2.0 Consensus size: 122
54390229 AGCCAACTAG
54390239 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
1 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
*
54390304 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGTTATTTGGGATGTCTTAA
66 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
54390361 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
1 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
* *
54390426 CCATATACTTATATATGTGTAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
66 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
54390483 AGTGAGTCTC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (122 bp):
TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
Found at i:54391309 original size:57 final size:57
Alignment explanation
Indices: 54391191--54391386 Score: 234
Period size: 56 Copynumber: 3.5 Consensus size: 57
54391181 ATTATTTTGG
* * * * * ** **
54391191 TAATAAACAATAATGGACAACAACAATTAAATA-TCAGTTTGACAGTTTAATTACAA
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
* * * *
54391247 TAATAAATAACAATGAAGAACAATAATTAAACACCCTTTTTGACAACTTAATTTCAG
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
* *
54391304 TAATAAATAACAATGAACAACAACAATTGAACACCCTTTTT-ACAACTTAATTGCAA
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
*
54391360 TAATAAATAACAATAAACAACAACAAT
1 TAATAAATAACAATGAACAACAACAAT
54391387 ATGAACAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
56 66 0.55
57 54 0.45
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (57 bp):
TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
Found at i:54391393 original size:57 final size:57
Alignment explanation
Indices: 54391228--54391393 Score: 235
Period size: 57 Copynumber: 2.9 Consensus size: 57
54391218 TAAATATCAG
** * * *
54391228 TTTGACAGTTTAATTACAATAATAAATAACAATGAAGAACAATAATTAAACACCCTT
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
* *
54391285 TTTGACAACTTAATTTCAGTAATAAATAACAATGAACAACAACAATTGAACACCCTT
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
* *
54391342 TTT-ACAACTTAATTGCAATAATAAATAACAATAAACAACAACAATATGAACA
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAAT-TGAACA
54391394 AAAATACACC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 39 0.40
57 59 0.60
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (57 bp):
TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
Found at i:54393785 original size:63 final size:63
Alignment explanation
Indices: 54393699--54393898 Score: 192
Period size: 63 Copynumber: 3.2 Consensus size: 63
54393689 TGACCAAACT
* * ** * * *
54393699 GTGTAACTCGCTGTTTTGAGTGTAAAAACCACATGGCCAGGAACACG-GACGTGTGCCTAGGTC
1 GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAG-CGTATGCCCAGGCC
* *
54393762 GTGTAACTCACTATTTTGGGTGTAAAAACCACACAGCCAGGGACACGAGCGTATGCCCAGGCC
1 GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAGCGTATGCCCAGGCC
* * * * * * *
54393825 CTGTAACTCACTGTTTAT-AATAT-AAAACCACACAGCCAGGGACA-TAGGCGTGTGCCCAGGCC
1 GTGTAACTCACTATTT-TGAGTGTAAAAACCACACAGCCAGGAACACGA-GCGTATGCCCAGGCC
*
54393887 ATGTAACTCACT
1 GTGTAACTCACT
54393899 GTTTGTGCTT
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
61 1 0.01
62 46 0.39
63 68 0.58
64 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (63 bp):
GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAGCGTATGCCCAGGCC
Found at i:54393918 original size:62 final size:62
Alignment explanation
Indices: 54393786--54393902 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
54393776 TTTGGGTGTA
* *
54393786 AAAACCACACAGCCAGGGACACGAGCGTATGCCCAGGCCCTGTAACTCACTGTTTATAATAT
1 AAAACCACACAGCCAGGGACAAGAGCGTATGCCCAGGCCATGTAACTCACTGTTTATAATAT
*
54393848 AAAACCACACAGCCAGGGACATAG-GCGTGTGCCCAGGCCATGTAACTCACTGTTT
1 AAAACCACACAGCCAGGGACA-AGAGCGTATGCCCAGGCCATGTAACTCACTGTTT
54393903 GTGCTTGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 50 0.98
63 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (62 bp):
AAAACCACACAGCCAGGGACAAGAGCGTATGCCCAGGCCATGTAACTCACTGTTTATAATAT
Found at i:54397983 original size:21 final size:21
Alignment explanation
Indices: 54397959--54398002 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54397949 GAAAAAGGCA
*
54397959 AGAAAAAAAGAAAAGATAAAT
1 AGAAAAAAAGAAAAGAGAAAT
*
54397980 AGAAAAAAGGAAAAGAGAAAT
1 AGAAAAAAAGAAAAGAGAAAT
54398001 AG
1 AG
54398003 TTGAAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
AGAAAAAAAGAAAAGAGAAAT
Found at i:54411144 original size:14 final size:14
Alignment explanation
Indices: 54411117--54411152 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
54411107 TTGTTTGACT
*
54411117 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
*
54411131 GAATATGATTTCTG
1 GAAAATGATTTCTG
54411145 GAAAATGA
1 GAAAATGA
54411153 CTTGTTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:54412349 original size:17 final size:17
Alignment explanation
Indices: 54412327--54412361 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54412317 TATCATTAAT
*
54412327 ATTAATTGTATAACACA
1 ATTAATTATATAACACA
*
54412344 ATTAATTATATAATACA
1 ATTAATTATATAACACA
54412361 A
1 A
54412362 AATTGTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (17 bp):
ATTAATTATATAACACA
Found at i:54414698 original size:16 final size:16
Alignment explanation
Indices: 54414674--54414712 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54414664 AAATTTAGAA
54414674 TATAATTAAAA-ATAAT
1 TATAATTAAAATA-AAT
*
54414690 TATATTTAAAATAAAT
1 TATAATTAAAATAAAT
54414706 TATAATT
1 TATAATT
54414713 GAATAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATTAAAATAAAT
Found at i:54415216 original size:37 final size:37
Alignment explanation
Indices: 54415166--54415236 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
54415156 CTTGCTTTCG
*
54415166 ATTGAGGTGGAAACTTGAGAAGAGAAACAATCGGTCA
1 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGGTCA
54415203 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGG
1 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGG
54415237 ATAGTGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.18
Consensus pattern (37 bp):
ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGGTCA
Found at i:54425692 original size:43 final size:44
Alignment explanation
Indices: 54425591--54425704 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 44
54425581 GGTTACCGAG
* * *
54425591 ATGTGATTACATGTAAGACCATGTCTGGGAAATTGTCATCGTTA
1 ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
* * * *
54425635 AT-TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT-
1 ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
* * *
54425677 ATGTGATAACATGTAAGGCCATATCTGG
1 ATGTGATTACATGTAAGACCATGTCTGG
54425705 ATATGGCATT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.04
43 52 0.93
44 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
Found at i:54432081 original size:11 final size:10
Alignment explanation
Indices: 54432067--54432114 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
54432057 AATAAAAGAC
*
54432067 AAAATAAAGT
1 AAAATAAAAT
54432077 GAAAATGAAAAT
1 -AAAAT-AAAAT
54432089 AAAATAAAAT
1 AAAATAAAAT
54432099 AAAAATAAAAAT
1 -AAAAT-AAAAT
54432111 AAAA
1 AAAA
54432115 ATGATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.15
11 19 0.58
12 9 0.27
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:54432087 original size:6 final size:5
Alignment explanation
Indices: 54432067--54432114 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 5
54432057 AATAAAAGAC
*
54432067 AAAAT AAAGT GAAAAT GAAAAT AAAAT AAAAT AAAAAT AAAAAT AAAA
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAA
54432115 ATGATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:54432115 original size:6 final size:6
Alignment explanation
Indices: 54432078--54432116 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
54432068 AAATAAAGTG
*
54432078 AAAATG AAAAT- AAAAT- AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
54432117 GATAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:54432123 original size:12 final size:12
Alignment explanation
Indices: 54432078--54432125 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
54432068 AAATAAAGTG
54432078 AAAATGAAAAT-
1 AAAATGAAAATA
54432089 AAAAT-AAAATA
1 AAAATGAAAATA
*
54432100 AAAATAAAAATA
1 AAAATGAAAATA
*
54432112 AAAATGATAATA
1 AAAATGAAAATA
54432124 AA
1 AA
54432126 TAAATAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 5 0.15
11 10 0.30
12 18 0.55
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:54432129 original size:22 final size:22
Alignment explanation
Indices: 54432056--54432114 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
54432046 CTTCAAAAGT
* * *
54432056 AAATAAAAGACAAAATAAAGTGA
1 AAATAAAA-ATAAAATAAAATAA
*
54432079 AAATGAAAATAAAATAAAATAA
1 AAATAAAAATAAAATAAAATAA
54432101 AAATAAAAATAAAA
1 AAATAAAAATAAAA
54432115 ATGATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATAAAAATAAAATAAAATAA
Found at i:54433445 original size:17 final size:20
Alignment explanation
Indices: 54433411--54433449 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
54433401 ATCAAAGTAG
54433411 TAAAAATAATAGTAATATCC
1 TAAAAATAATAGTAATATCC
54433431 TAAAAAT-ATA-T-ATATCC
1 TAAAAATAATAGTAATATCC
54433448 TA
1 TA
54433450 TCATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 3 0.16
20 7 0.37
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAAATAATAGTAATATCC
Found at i:54439532 original size:28 final size:28
Alignment explanation
Indices: 54439480--54439534 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
54439470 GTTTCATTCA
54439480 AAACTATTTTAATCTTTTAATATATTTTT
1 AAACTATTTTAA-CTTTTAATATATTTTT
*
54439509 AAACTATTTTTAA-TTTTGATATATTT
1 AAACTA-TTTTAACTTTTAATATATTT
54439535 AATTTATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 6 0.25
30 6 0.25
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (28 bp):
AAACTATTTTAACTTTTAATATATTTTT
Found at i:54439549 original size:16 final size:15
Alignment explanation
Indices: 54439517--54439557 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
54439507 TTAAACTATT
54439517 TTTAATTTTGATATA
1 TTTAATTTTGATATA
*
54439532 TTTAATTTATGTTATA
1 TTTAATTT-TGATATA
54439548 TTTAATTTTG
1 TTTAATTTTG
54439558 TCTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTAATTTTGATATA
Found at i:54450770 original size:86 final size:86
Alignment explanation
Indices: 54450663--54450827 Score: 269
Period size: 86 Copynumber: 1.9 Consensus size: 86
54450653 GCGCCTATCT
*
54450663 GGCCCACACGACCAAAATTGGCCTTGGCTATGTGGATCACACGGCCTGGCCCAGAATT-TCACAC
1 GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCT-ACAC
54450727 GCCCATGTGGTTCACTCGTGTG
65 GCCCATGTGGTTCACTCGTGTG
* * *
54450749 GGCCCACACGACCCAAATTGGCCTTGGCCGTGTGGATCACACGGGCTGGCCCAGAATTCTACACG
1 GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCTACACG
*
54450814 CCCGTGTGGTTCAC
66 CCCATGTGGTTCAC
54450828 CCATACGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 72 0.99
87 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.21
Consensus pattern (86 bp):
GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCTACACG
CCCATGTGGTTCACTCGTGTG
Found at i:54453291 original size:60 final size:57
Alignment explanation
Indices: 54453159--54453293 Score: 153
Period size: 60 Copynumber: 2.3 Consensus size: 57
54453149 TTCATATAAT
* ** * *
54453159 AATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATGAAATTATATTTAAT
1 AATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATGAAAATATATTTAAC
* * *
54453217 AATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATAATAAAATATATTTAAC
1 AATAATTATATTAAAATATGGTTAAATTATATATTA-TTTTAT--GAAAATATATTTAAC
*
54453277 AATAATTTTATTAAAAT
1 AATAATTATATTAAAAT
54453294 TTAATAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 18 0.28
58 19 0.30
60 27 0.42
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
AATAATTATATTAAAATATGGTTAAATTATATATTATTTTATGAAAATATATTTAAC
Found at i:54453485 original size:16 final size:16
Alignment explanation
Indices: 54453464--54453518 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
54453454 TGAATTATTG
54453464 ATTACAGCTTTATTCC
1 ATTACAGCTTTATTCC
*
54453480 ATTACAG-TTCTATTCA
1 ATTACAGCTT-TATTCC
* *
54453496 ATGACAGCCTTATTCC
1 ATTACAGCTTTATTCC
54453512 ATTACAG
1 ATTACAG
54453519 TGAACCAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (16 bp):
ATTACAGCTTTATTCC
Found at i:54453869 original size:13 final size:13
Alignment explanation
Indices: 54453851--54453876 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54453841 CTCAAAAATT
54453851 AAGTATTGAAAAA
1 AAGTATTGAAAAA
54453864 AAGTATTGAAAAA
1 AAGTATTGAAAAA
54453877 TTAAATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AAGTATTGAAAAA
Found at i:54453887 original size:15 final size:15
Alignment explanation
Indices: 54453844--54453888 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
54453834 TGATAAACTC
54453844 AAAAATTAAGTATTG
1 AAAAATTAAGTATTG
54453859 AAAAA--AAGTATTG
1 AAAAATTAAGTATTG
*
54453872 AAAAATTAAATATTG
1 AAAAATTAAGTATTG
54453887 AA
1 AA
54453889 TTTAAGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 13 0.48
15 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:54459262 original size:256 final size:256
Alignment explanation
Indices: 54458805--54459317 Score: 884
Period size: 256 Copynumber: 2.0 Consensus size: 256
54458795 TTTTGGTGTA
* * *
54458805 AAACGACCAAGGCGTTAGGCCTCAGGGAGTCTGCGCTGCAGAGGCACAAGGAGGGGGTGTGGTGC
1 AAACGACCAAGGCGTTAGGCCTCAGGGAGGCTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTGC
54458870 ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
66 ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
* * *
54458935 TTTGGGTTATATTGGGCCGTTGTAATTTCGACTGATAACTATTGTAAATGGACTTTGATACTTGG
131 TTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTGA
*
54459000 ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTGGGCTATT
196 ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
*
54459061 AAACGACCAAGGCGTTAGGCCTTAGGG-GGCGTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTG
1 AAACGACCAAGGCGTTAGGCCTCAGGGAGGC-TGCGCTACAGAGGCACAAGGAGGGGGTGCGGTG
*
54459125 CATTACGGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGA
65 CATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGA
* *
54459190 ATTTGGGTTATATTGGGCCATTGTAATTTGGGCTAATAACTATTGTAAATGGACTTTGATACTTG
130 ATTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTG
* * *
54459255 AACTTATTTGTTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGGGCAAATTAGGCTATT
195 AACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
54459317 A
1 A
54459318 CAGCTACCCA
Statistics
Matches: 242, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
255 2 0.01
256 240 0.99
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.37
Consensus pattern (256 bp):
AAACGACCAAGGCGTTAGGCCTCAGGGAGGCTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTGC
ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
TTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTGA
ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
Found at i:54459650 original size:89 final size:88
Alignment explanation
Indices: 54459534--54459836 Score: 247
Period size: 89 Copynumber: 3.4 Consensus size: 88
54459524 TATAGCTTTG
* *
54459534 ATCTGTTCCACTGCTACTTCAAGGAGATAATG-TTTATAGCTTTAATATGCTCTACTACAACTTC
1 ATCTGCTCCACTGCTACTTCAAGGAGATAA-GATTTATAGCTTCAATATGCTC-ACTACAACTTC
54459598 AGAGAGATAAGATTTGCTATCTTCA
64 AGAGAGATAAGATTTGCTATCTTCA
* * * *
54459623 ATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGTGGCTTCAATATGCTCACTGCAACTTCAG
1 ATCTGCTCCACTGCTACTTCAAGGAGATAAGATTTATAGCTTCAATATGCTCACTACAACTTCAG
* * *
54459688 GGAGATAAGATTCGCCATGGTAACTTCA
66 AGAGATAAGATT-----TGCTATCTTCA
* ** * * * * * * *
54459716 ATCCG-TCTTGCTGCAACTTC-AGGAGAATGAGATTTACTATCTTCGATTTATTC-CACTCCAAA
1 ATCTGCTC-CACTGCTACTTCAAGGAG-ATAAGATTTA-TAGCTTC-A-ATATGCTCACTACAAC
* * *
54459778 TTCAGGGAGATAAGATCTG-TAACTTCA
61 TTCAGAGAGATAAGATTTGCTATCTTCA
* *
54459805 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 ATCTGCTCCACTGCTACTTCAAGGAGATAAGA
54459837 CTTGTGGCTT
Statistics
Matches: 173, Mismatches: 28, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
88 24 0.14
89 72 0.42
90 8 0.05
92 6 0.03
93 30 0.17
94 5 0.03
95 24 0.14
96 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (88 bp):
ATCTGCTCCACTGCTACTTCAAGGAGATAAGATTTATAGCTTCAATATGCTCACTACAACTTCAG
AGAGATAAGATTTGCTATCTTCA
Found at i:54459987 original size:95 final size:95
Alignment explanation
Indices: 54459767--54460021 Score: 235
Period size: 95 Copynumber: 2.8 Consensus size: 95
54459757 TTCGATTTAT
* * * * * * * *
54459767 TCCACTCCAAATTCAGGGAGATAAGA-TCTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACT-TGTAGCTTTAATATGCTCTACTACAACTTTAGGGAG
*
54459831 AT-A-A---G-A-CTTGTGGCTTTAGTCTGC
65 ATAAGATTTGTAGCTTGTGGCTTTAGTCTAC
* * * * *
54459855 TCCACTGCAACTTCAGGGAGATTAGGCTTTTAGCTTTAATATGCT-TCATTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAATATGCTCT-ACTACAACTTTAGGGAG
*
54459919 ATAAGATTTGTAGCTTGTAGG-TTTAGTCTAT
65 ATAAGATTTGTAGCTTGT-GGCTTTAGTCTAC
* *
54459950 TCCACTGTAACTTCAGGGAGATAAGACTTGT-GTCTTTAATCTGCTCTACTACAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAG-CTTTAATATGCTCTACTACAACTTTAGGGAG
*
54460014 TTAAGATT
65 ATAAGATT
54460022 CGTCATGATG
Statistics
Matches: 134, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
88 52 0.39
89 2 0.01
90 1 0.01
93 1 0.01
94 2 0.01
95 73 0.54
96 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (95 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAATATGCTCTACTACAACTTTAGGGAGA
TAAGATTTGTAGCTTGTGGCTTTAGTCTAC
Found at i:54460012 original size:44 final size:43
Alignment explanation
Indices: 54459528--54460019 Score: 188
Period size: 44 Copynumber: 10.9 Consensus size: 43
54459518 GTAACTTATA
* * * * * * *
54459528 GCTTTGATCTGTTCCACTGCTACTTCAAGGAGATAATG-TTTAT
1 GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAA-GACTTGT
* * * *
54459571 AGCTTTAATATGCTCTACTACAACTTCAGAGAGATAAGATTTGCT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTG-T
* * * * *
54459616 ATCTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* *
54459660 GGCTTCAATATGCTC-ACTGCAACTTCAGGGAGATAAGA-TTCGCCAT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTT-G---T
* * * * * *
54459706 GGTAACTTCAATCCG-TCTTGCTGCAACTTCA-GGAGAATGAGATTTACT
1 -G---CTTTAATCTGCTC-TACTGCAACTTCAGGGAG-ATAAGACTT-GT
* ** * ** * * *
54459754 ATCTTCGATTTATTCCACTCCAAATTCAGGGAGATAAGA-TCTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACT-TGT
* * *
54459798 AACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * * * *
54459842 GGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATTAGGCTTTT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * * *
54459886 AGCTTTAATATGCT-TCATTGCAACTTTAGGGAGATAAGATTTGT
1 -GCTTTAATCTGCTCT-ACTGCAACTTCAGGGAGATAAGACTTGT
** * *
54459930 AGCTTGTAGGTTTAGTCTATTCCACTGTAACTTCAGGGAGATAAGACTTGT
1 -GCTT-TA-----A-TCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * *
54459981 GTCTTTAATCTGCTCTACTACAACTTTAGGGAGTTAAGA
1 G-CTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGA
54460020 TTCGTCATGA
Statistics
Matches: 344, Mismatches: 77, Indels: 54
0.72 0.16 0.11
Matches are distributed among these distances:
42 2 0.01
43 24 0.07
44 180 0.52
45 62 0.18
46 9 0.03
48 3 0.01
49 12 0.03
50 20 0.06
51 32 0.09
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (43 bp):
GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
Found at i:54466204 original size:15 final size:16
Alignment explanation
Indices: 54466184--54466215 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54466174 GCGATCCTCT
54466184 CTTGAA-AAATTAAAA
1 CTTGAATAAATTAAAA
54466199 CTTGAATAAATTAAAA
1 CTTGAATAAATTAAAA
54466215 C
1 C
54466216 AAGTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (16 bp):
CTTGAATAAATTAAAA
Found at i:54466911 original size:26 final size:25
Alignment explanation
Indices: 54466882--54466937 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
54466872 TATATAAGAA
54466882 ATAAGTGGAAAATAAAATAAATATAT
1 ATAAGTGGAAAAT-AAATAAATATAT
** **
54466908 ATAAAGTTTAAGGTAAATAAATATAT
1 AT-AAGTGGAAAATAAATAAATATAT
54466934 ATAA
1 ATAA
54466938 AAAACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
27 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (25 bp):
ATAAGTGGAAAATAAATAAATATAT
Found at i:54466991 original size:3 final size:3
Alignment explanation
Indices: 54466977--54467055 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
54466967 AGAAATAGAG
* * *
54466977 AAT AAT AA- AAT AAT AA- AAT AAT AA- AAT AAAG AAT GAAC AAG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT
*
54467021 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54467056 GGAATAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.09
3 54 0.84
4 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:54472515 original size:23 final size:23
Alignment explanation
Indices: 54472485--54472531 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
54472475 GCAAAGTTGT
54472485 ATACTCCTCCACAGTAGGTACTA
1 ATACTCCTCCACAGTAGGTACTA
54472508 ATACTCCTCCACAGTAGGTACTA
1 ATACTCCTCCACAGTAGGTACTA
54472531 A
1 A
54472532 ATCTACCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (23 bp):
ATACTCCTCCACAGTAGGTACTA
Found at i:54474400 original size:3 final size:3
Alignment explanation
Indices: 54474392--54474435 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
54474382 AGGAAGGGTA
* * *
54474392 AAT AAT AAT AAT GAT AAT AAT AAT ACT AAT AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54474436 AAACAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:54480807 original size:10 final size:10
Alignment explanation
Indices: 54480788--54480831 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
54480778 AATTTTAGCT
54480788 TTTATCTTTA
1 TTTATCTTTA
*
54480798 TTTATATTTA
1 TTTATCTTTA
*
54480808 TTTACCTTTA
1 TTTATCTTTA
*
54480818 ATTATCTTTA
1 TTTATCTTTA
54480828 TTTA
1 TTTA
54480832 ATTGTATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:54480842 original size:20 final size:20
Alignment explanation
Indices: 54480794--54480842 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
54480784 AGCTTTTATC
*
54480794 TTTATTTATATTTATTTACC
1 TTTATTTATATTTATTTACA
* *
54480814 TTTAATTATCTTTATTTA-A
1 TTTATTTATATTTATTTACA
54480833 TTGTATTTAT
1 TT-TATTTAT
54480843 TTTTTAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTATTTATATTTATTTACA
Found at i:54481985 original size:23 final size:25
Alignment explanation
Indices: 54481940--54481990 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
54481930 GGGAAAAAGG
*
54481940 TATGACCGTTTTTTTGAAGAGAGGT
1 TATGACCGTTTTGTTGAAGAGAGGT
54481965 TATGACCGTTTTGTTGAAGAGAGGT
1 TATGACCGTTTTGTTGAAGAGAGGT
54481990 T
1 T
54481991 CTCTTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (25 bp):
TATGACCGTTTTGTTGAAGAGAGGT
Found at i:54482324 original size:24 final size:24
Alignment explanation
Indices: 54482296--54482348 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54482286 GTTCTAGAAA
* * *
54482296 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATAAGCATAATAT
*
54482320 ATTTAGCATTTATAAGCATAATTT
1 ATTTAGCATTTATAAGCATAATAT
54482344 ATTTA
1 ATTTA
54482349 TGGTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTAGCATTTATAAGCATAATAT
Found at i:54484595 original size:42 final size:42
Alignment explanation
Indices: 54484545--54484656 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
54484535 TACAGCCTAC
54484545 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
1 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
* * * *
54484587 GCACACGCCAATGTCCTTACCTGTGTGGCTCAGACGGCCTGG
1 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
54484629 GCACACGCTC-ATGTCCTTGGCC-GTGTGG
1 GCACACGC-CAATGTCCTT-GCCTGTGTGG
54484657 TTCTAAAGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (42 bp):
GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
Found at i:54491969 original size:25 final size:25
Alignment explanation
Indices: 54491938--54492050 Score: 111
Period size: 25 Copynumber: 4.6 Consensus size: 25
54491928 TTTCGATACT
*
54491938 CAACTCGTATGAGCTTCCCGTTATA
1 CAACTCGCATGAGCTTCCCGTTATA
* *
54491963 CAGCTCGCATGAGCTTCCCGTTATT
1 CAACTCGCATGAGCTTCCCGTTATA
* * * *
54491988 TAGCTCGCATGAGCTTCCCATTATT
1 CAACTCGCATGAGCTTCCCGTTATA
** * *
54492013 CAACTCAAACGAGCTTACCGTT-TA
1 CAACTCGCATGAGCTTCCCGTTATA
*
54492037 CAACTCGTATGAGC
1 CAACTCGCATGAGC
54492051 ATACATGAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 12 0.17
25 60 0.83
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (25 bp):
CAACTCGCATGAGCTTCCCGTTATA
Found at i:54495492 original size:36 final size:36
Alignment explanation
Indices: 54495452--54495521 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
54495442 ATTTATTAGC
54495452 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
1 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
54495488 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGG
1 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGG
54495522 AGTTTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (36 bp):
ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
Found at i:54498433 original size:23 final size:22
Alignment explanation
Indices: 54498407--54498507 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
54498397 CTCATATGAA
* *
54498407 CTTACCGTTTTAGCTCATTCGAG
1 CTTACCGTTTCAGCTC-TACGAG
*
54498430 CTTACCGATTT-AGCTCGTAAGAG
1 CTTACCG-TTTCAGCTC-TACGAG
54498453 CTTACCGTTTCAGCTCTACGAAG
1 CTTACCGTTTCAGCTCTACG-AG
*
54498476 CTTA-C-TATTCAGCTCTTCGGAG
1 CTTACCGT-TTCAGCTCTAC-GAG
54498498 CTTACCGTTT
1 CTTACCGTTT
54498508 ATCAACTCAG
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.02
22 23 0.35
23 38 0.58
24 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (22 bp):
CTTACCGTTTCAGCTCTACGAG
Found at i:54498459 original size:46 final size:45
Alignment explanation
Indices: 54498407--54498507 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
54498397 CTCATATGAA
* * *
54498407 CTTACCGTTTTAGCTCATTCG-AGCTTACCGATTTAGCTCGTAAGAG
1 CTTACCGTTTCAGCTC-TACGAAGCTTA-CGATTCAGCTCGTAAGAG
* * **
54498453 CTTACCGTTTCAGCTCTACGAAGCTTACTATTCAGCTCTTCGGAG
1 CTTACCGTTTCAGCTCTACGAAGCTTACGATTCAGCTCGTAAGAG
54498498 CTTACCGTTT
1 CTTACCGTTT
54498508 ATCAACTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
45 26 0.55
46 21 0.45
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (45 bp):
CTTACCGTTTCAGCTCTACGAAGCTTACGATTCAGCTCGTAAGAG
Found at i:54498489 original size:22 final size:22
Alignment explanation
Indices: 54498461--54498502 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54498451 AGCTTACCGT
54498461 TTCAGCTCTACGAAGCTTACTA
1 TTCAGCTCTACGAAGCTTACTA
* *
54498483 TTCAGCTCTTCGGAGCTTAC
1 TTCAGCTCTACGAAGCTTAC
54498503 CGTTTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (22 bp):
TTCAGCTCTACGAAGCTTACTA
Found at i:54498719 original size:9 final size:9
Alignment explanation
Indices: 54498684--54498729 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
54498674 TAAGAGCTAT
*
54498684 ATGATTTAC
1 ATGAATTAC
54498693 ATGAATT--
1 ATGAATTAC
54498700 AT-AAGTTAC
1 ATGAA-TTAC
54498709 ATGAATTAC
1 ATGAATTAC
54498718 ATGAATTAC
1 ATGAATTAC
54498727 ATG
1 ATG
54498730 GATTTTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
9 24 0.75
10 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (9 bp):
ATGAATTAC
Found at i:54503151 original size:40 final size:39
Alignment explanation
Indices: 54503086--54503171 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
54503076 TTTGTATATA
**
54503086 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCA-TTT
* * *
54503126 TAGCCGAAGCTATTTCGAACCGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
54503165 TAGCCGA
1 TAGCCGA
54503172 TAAGTCGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
Found at i:54509372 original size:23 final size:24
Alignment explanation
Indices: 54509346--54509412 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 24
54509336 TTACTCATAT
*
54509346 GAGCTTACTGTTTCAGCTCATT-G
1 GAGCTTACCGTTTCAGCTCATTCG
*
54509369 GAGCTTACCATTT-AGCTC-TTCG
1 GAGCTTACCGTTTCAGCTCATTCG
54509391 GAGCTTACCGTTTATCAGCTCA
1 GAGCTTACCG-TT-TCAGCTCA
54509413 GGAGGAGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 15 0.42
23 13 0.36
24 1 0.03
25 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (24 bp):
GAGCTTACCGTTTCAGCTCATTCG
Found at i:54513754 original size:16 final size:16
Alignment explanation
Indices: 54513735--54513766 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54513725 TATTTAAGAG
54513735 TTTTTTTCTTATTATA
1 TTTTTTTCTTATTATA
54513751 TTTTTTTCTTATTATA
1 TTTTTTTCTTATTATA
54513767 AATACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTCTTATTATA
Found at i:54516616 original size:17 final size:17
Alignment explanation
Indices: 54516569--54516616 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
54516559 ATAAACATTA
54516569 AAATATTTAA-ATTTATT
1 AAATATTTAATA-TTATT
*
54516586 ATATATTT-ATATTATT
1 AAATATTTAATATTATT
54516602 AAATATTTAATATTA
1 AAATATTTAATATTA
54516617 CAAGTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATTTAATATTATT
Found at i:54516907 original size:11 final size:11
Alignment explanation
Indices: 54516888--54516918 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54516878 ATAGTTTTTA
*
54516888 AATTATTTAAT
1 AATTTTTTAAT
54516899 AATTTTTTAAT
1 AATTTTTTAAT
54516910 AATTTTTTA
1 AATTTTTTA
54516919 TGTCATTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
AATTTTTTAAT
Found at i:54518043 original size:3 final size:3
Alignment explanation
Indices: 54518035--54518069 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54518025 ATTTTTAAGT
54518035 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54518070 GTAGTGTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54519497 original size:9 final size:8
Alignment explanation
Indices: 54519481--54519587 Score: 58
Period size: 8 Copynumber: 12.8 Consensus size: 8
54519471 GACTTTTTAC
54519481 ATTATTAT
1 ATTATTAT
54519489 ATATATTAT
1 AT-TATTAT
54519498 -TTATTAT
1 ATTATTAT
* *
54519505 ACTTTTTAG
1 A-TTATTAT
54519514 ATTATTAT
1 ATTATTAT
54519522 ATATATTAT
1 AT-TATTAT
54519531 -TTATTAT
1 ATTATTAT
*
54519538 ACTTTATTTT
1 A--TTATTAT
54519548 ACTTATT-T
1 A-TTATTAT
54519556 ATTTATTTAT
1 A-TTA-TTAT
* *
54519566 TTTATTGT
1 ATTATTAT
* *
54519574 ATTTTTTT
1 ATTATTAT
54519582 ATTATT
1 ATTATT
54519588 GGTTTGTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
7 12 0.16
8 29 0.38
9 28 0.36
10 8 0.10
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (8 bp):
ATTATTAT
Found at i:54519509 original size:33 final size:33
Alignment explanation
Indices: 54519472--54519542 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
54519462 TTTAGTTTGG
54519472 ACTTTTTACATTATTATATATATTATTTATTAT
1 ACTTTTTACATTATTATATATATTATTTATTAT
*
54519505 ACTTTTTAGATTATTATATATATTATTTATTAT
1 ACTTTTTACATTATTATATATATTATTTATTAT
54519538 ACTTT
1 ACTTT
54519543 ATTTTACTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (33 bp):
ACTTTTTACATTATTATATATATTATTTATTAT
Found at i:54519538 original size:12 final size:12
Alignment explanation
Indices: 54519481--54519566 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
54519471 GACTTTTTAC
54519481 ATTA-TTATATAT
1 ATTATTTAT-TAT
54519493 ATTATTTATTAT
1 ATTATTTATTAT
* *
54519505 A--CTTT-TTAG
1 ATTATTTATTAT
54519514 ATTA-TTATATAT
1 ATTATTTAT-TAT
54519526 ATTATTTATTAT
1 ATTATTTATTAT
54519538 ACTTTATTTTACTTAT
1 A--TTA-TTTA-TTAT
54519554 -TTATTTATT-T
1 ATTATTTATTAT
54519564 ATT
1 ATT
54519567 TTATTGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 23
0.69 0.05 0.27
Matches are distributed among these distances:
9 4 0.07
10 6 0.10
11 5 0.08
12 22 0.37
13 11 0.19
14 3 0.05
15 4 0.07
16 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (12 bp):
ATTATTTATTAT
Found at i:54519544 original size:26 final size:25
Alignment explanation
Indices: 54519515--54519586 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
54519505 ACTTTTTAGA
54519515 TTATTATATATATTATTTATTATACT
1 TTATTATAT-TATTATTTATTATACT
* *
54519541 TTATTTTACTTATTTATTTATT-TATT
1 TTATTATA-TTA-TTATTTATTATACT
*
54519567 TTATTGTATT-TT-TTTATTAT
1 TTATTATATTATTATTTATTAT
54519587 TGGTTTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
25 2 0.05
26 19 0.47
27 10 0.25
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (25 bp):
TTATTATATTATTATTTATTATACT
Found at i:54519569 original size:13 final size:13
Alignment explanation
Indices: 54519527--54519584 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
54519517 ATTATATATA
*
54519527 TTATTTATTATACT
1 TTATTTATT-TATT
*
54519541 TTATTTTACTTA-T
1 TTA-TTTATTTATT
54519554 TTATTTATTTATT
1 TTATTTATTTATT
54519567 TTATTGTATTT-TT
1 TTATT-TATTTATT
54519580 TTATT
1 TTATT
54519585 ATTGGTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 7 0.18
13 17 0.44
14 10 0.26
15 5 0.13
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:54519578 original size:31 final size:32
Alignment explanation
Indices: 54519485--54519566 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
54519475 TTTTACATTA
54519485 TTATATATATTATTTATTATACTTT-TTAGATTA-
1 TTATATATATTATTTATTATACTTTATT---TTAC
54519518 TTATATATATTATTTATTATACTTTATTTTAC
1 TTATATATATTATTTATTATACTTTATTTTAC
*
54519550 TTATTTAT-TTATTTATT
1 TTATATATATTATTTATT
54519567 TTATTGTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 12 0.26
32 7 0.15
33 25 0.54
34 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (32 bp):
TTATATATATTATTTATTATACTTTATTTTAC
Found at i:54519604 original size:4 final size:4
Alignment explanation
Indices: 54519527--54519584 Score: 53
Period size: 4 Copynumber: 13.2 Consensus size: 4
54519517 ATTATATATA
*
54519527 TTAT TTAT TATACT TTATT TTAC TTAT TTAT TTAT TTATT TTAT TGTAT
1 TTAT TTAT T-TA-T TTA-T TTAT TTAT TTAT TTAT TTA-T TTAT T-TAT
*
54519576 TTTT TTAT T
1 TTAT TTAT T
54519585 ATTGGTTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 27 0.60
5 16 0.36
6 2 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:54521948 original size:35 final size:34
Alignment explanation
Indices: 54521909--54522020 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 34
54521899 TGTTTTCGAG
54521909 GGACTAGCACTTTTGAGCATTGATGTGTTTTGGTT
1 GGACTAGC-CTTTTGAGCATTGATGTGTTTTGGTT
* * * **
54521944 GGACTAGCTCTTATGAGAAAT-AGTGTGTTTTGGAA
1 GGACTAGC-CTTTTGAGCATTGA-TGTGTTTTGGTT
* * *
54521979 GGATTAG-CTTGTGTAAGCATCTGGTGTGTTTTGGTT
1 GGACTAGCCTT-T-TGAGCAT-TGATGTGTTTTGGTT
54522015 GGACTA
1 GGACTA
54522021 ACGATGTACT
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
33 3 0.05
34 1 0.02
35 37 0.65
36 16 0.28
ACGTcount: A:0.21, C:0.10, G:0.30, T:0.39
Consensus pattern (34 bp):
GGACTAGCCTTTTGAGCATTGATGTGTTTTGGTT
Found at i:54523541 original size:23 final size:23
Alignment explanation
Indices: 54523510--54523563 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
54523500 GTAGTTCCTG
*
54523510 ACTCATTTAAATGGTGTGGGATT
1 ACTCATTTAAACGGTGTGGGATT
*
54523533 ACTCGTTTAAACGGTGTGGGATT
1 ACTCATTTAAACGGTGTGGGATT
54523556 ACTCATTT
1 ACTCATTT
54523564 TTGAAACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (23 bp):
ACTCATTTAAACGGTGTGGGATT
Found at i:54525009 original size:23 final size:22
Alignment explanation
Indices: 54524983--54525051 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
54524973 TATATAATGC
54524983 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
54525006 AATAAGGATGAAACAATAAT--
1 AATAACAATGAAACAAAAATAA
* *
54525026 AATAA-AATAAAATAAAAATAA
1 AATAACAATGAAACAAAAATAA
54525047 CAATA
1 -AATA
54525052 CATTAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
22 11 0.31
23 10 0.28
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:54525028 original size:3 final size:3
Alignment explanation
Indices: 54525020--54525098 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
54525010 AGGATGAAAC
* *
54525020 AAT AAT AAT AA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
*
54525065 AAT AAT AAT AAT GAT AAT ACA- AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT
54525099 GATGATGTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 5 0.08
3 51 0.81
4 5 0.08
5 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54525116 original size:28 final size:28
Alignment explanation
Indices: 54525061--54525116 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
54525051 ACATTAATAA
*
54525061 TAATAATAATAATAATGATAATACAAAT
1 TAATAATAATAATAATGATAATAAAAAT
* *
54525089 TAATAATAATGATGATG-TAAGTAAAAAT
1 TAATAATAATAATAATGATAA-TAAAAAT
54525117 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (28 bp):
TAATAATAATAATAATGATAATAAAAAT
Found at i:54525237 original size:3 final size:3
Alignment explanation
Indices: 54525229--54525367 Score: 58
Period size: 3 Copynumber: 45.7 Consensus size: 3
54525219 GATAGAAAAG
* * *
54525229 ATA ATA ATA ACGTA TTA ATA AGA ATA ATA ATA AT- ATA ATA ATT ATGGA
1 ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A
* * * *
54525277 A-A A-A ATA ATA TTA AT- ATT TTAA ATA A-G ATA ATA ATA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA
* * *
54525320 GA-A AGTA GTA GTA ATA ATA ATA ATA ATA A-A GATA ATA ATA AAA ATA
1 -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
54525366 AT
1 AT
54525368 TAATTTGAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
2 11 0.10
3 83 0.79
4 8 0.08
5 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54525270 original size:23 final size:22
Alignment explanation
Indices: 54525173--54525270 Score: 65
Period size: 23 Copynumber: 4.3 Consensus size: 22
54525163 TTAATTAGCC
* *
54525173 TAATAATATGATAATAATATTA
1 TAATAATAAGATAATAATAATA
* *
54525195 GTAACAATACAG-TAATAGTAATA
1 -TAATAATA-AGATAATAATAATA
* **
54525218 -AGATAGAAAAGATAATAATAACG
1 TA-ATA-ATAAGATAATAATAATA
*
54525241 TATTAATAAGAATAATAATAATA
1 TAATAATAAG-ATAATAATAATA
54525264 TAATAAT
1 TAATAAT
54525271 TATGGAAAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
21 1 0.02
22 8 0.15
23 44 0.80
24 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (22 bp):
TAATAATAAGATAATAATAATA
Found at i:54526318 original size:23 final size:24
Alignment explanation
Indices: 54526266--54526325 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
54526256 TTTAAACCTT
*
54526266 GCAGGTGGCAGAGCAAGCGGAGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
* * *
54526290 GTAGGTGGCTGA-CAAACGGTGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
54526313 GCAGGTGGTCAGA
1 GCAGGTGG-CAGA
54526326 AGATTAGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.27, C:0.15, G:0.47, T:0.12
Consensus pattern (24 bp):
GCAGGTGGCAGAGCAAACGGAGGA
Found at i:54526934 original size:44 final size:43
Alignment explanation
Indices: 54526751--54527406 Score: 193
Period size: 44 Copynumber: 14.7 Consensus size: 43
54526741 TGCTCCATTG
**
54526751 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAATCTA
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATCTA
** * *
54526795 CTCCACTTTATCTTCAGGGAGATAAGATTTGTGG--T-AAT-TCG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCT-A
* * * * * *
54526836 CTCCTCTACAACTTCA-GAGGTATGAGATTTGCTGTCTTCAGTCTG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTG-TGGCTTCAATCTA
* * *
54526881 CTCCGCTGCAACTTCAGGAAGATAGGACTTGTGGCTTCAATCTA
1 CTCCACTGCAACTTCAGG-AGATAAGATTTGTGGCTTCAATCTA
* * * ** *
54526925 CTCCACTGCAACTTCAAGTAGATAAGATTTTCCATGGTAGATTTGATCCGA
1 CTCCACTGCAACTTC-AGGAGATAAGA--TT---T-GTGGCTTCAAT-CTA
* * * * * * **
54526976 C-CTACTGCAACTTCA-GAGGTATAAGACTCGTCGTTTAAATCCG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTGTGGCTTCAATCTA
* * * * *
54527019 CTCCACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* * * *** * * *
54527064 CCCCGCTGCAACTTCAGGGAGATAAGACTTGTAATTTTAACCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
* * * *
54527108 CTCCACTGCAATTTCAAGGAGATAAG-GTT-T-GCTAT-GATCTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCT-TCAATCTA
* * * * * *
54527149 CTCTATTGCAACTTCAGCGAGATAAGATCTATAATTTATAGCTTCAATTTG
1 CTCCACTGCAACTTCAG-GAGATAAG-------ATTTGTGGCTTCAATCTA
* * * ** * *
54527200 TTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGG-AGATAAGATTTG-TGGCTTCAATCTA
* * *** * * *
54527245 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* ** *
54527290 CTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAA-CTTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATC-TA
* * ** *
54527334 CTCCACTGTAATTTCAGGGAGATAAGATTAATGGCTTCGATCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
54527378 CTCCACTGCAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCA-GGAGATAAGATT
54527407 CACCATCTTC
Statistics
Matches: 457, Mismatches: 109, Indels: 92
0.69 0.17 0.14
Matches are distributed among these distances:
39 2 0.00
40 4 0.01
41 49 0.11
42 5 0.01
43 7 0.02
44 180 0.39
45 135 0.30
46 9 0.02
47 1 0.00
48 2 0.00
49 5 0.01
50 28 0.06
51 30 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGAGATAAGATTTGTGGCTTCAATCTA
Found at i:54527254 original size:45 final size:45
Alignment explanation
Indices: 54527018--54527416 Score: 237
Period size: 45 Copynumber: 8.9 Consensus size: 45
54527008 GTTTAAATCC
* * * * *
54527018 GCTCCACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * * * **
54527063 ACCCCGCTGCAACTTCAGGGAGATAAGACTT-G-TAAT-TTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCT-ATCTTCAGTCT
* * * * *
54527107 GCTCCACTGCAATTTCAAGGAGATAAGGTTTGCTA---TGA-TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * * *** * *
54527148 GCTCTATTGCAACTTCAGCGAGATAAGATCTATAATTTATAGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-CGCTAT--CTTCAGTCT
* * *
54527199 GTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * *
54527244 GCTCCACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * *
54527289 GCTCCACTGCAACTTCAAGGAGATAAGACTT-G-TAACTTCA-ACTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTCAGTC-T
* * ** **
54527333 GCTCCACTGTAATTTCAGGGAGATAAGATT-AATGGCTTC-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAG-TCT
* * *
54527377 ACTCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
54527417 GATCTATTCC
Statistics
Matches: 269, Mismatches: 65, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
41 24 0.09
42 2 0.01
43 6 0.02
44 95 0.35
45 108 0.40
46 3 0.01
47 3 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 24 0.09
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
Done.