Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 19 of 213
Found at i:5230725 original size:40 final size:40
Alignment explanation
Indices: 5230671--5231127 Score: 465
Period size: 40 Copynumber: 11.0 Consensus size: 40
5230661 GAGTACAAAG
* *
5230671 AAATC-AGATCTTATCTCTCTAAGCAGTAGTAGAGCAGATC-
1 AAATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CA
*
5230711 ACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAA
1 AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--A
* *
5230753 AGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-
1 A-AATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CA
*
5230795 ACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAA
1 AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--A
* *
5230837 AGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-
1 A-AATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CA
*
5230878 ACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAA
1 AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--A
* *
5230920 AGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA
1 A-AATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC---A
* *
5230964 GAAACCAAGTCTTATCTCTCTAAGCAGTAGTGGAGCAGATC-
1 -AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CA
*
5231005 ACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAA
1 AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--A
* * ** **
5231047 AGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGTGGATT
1 A-AATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACA
** *
5231089 GCATCAAGTCTTATCTCTCTAAGCAGTAGTGGAGCAGAC
1 AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC
5231128 GAAAGAAACC
Statistics
Matches: 353, Mismatches: 40, Indels: 48
0.80 0.09 0.11
Matches are distributed among these distances:
39 4 0.01
40 158 0.45
41 11 0.03
42 5 0.01
43 77 0.22
44 95 0.27
45 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (40 bp):
AAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACA
Found at i:5230763 original size:84 final size:83
Alignment explanation
Indices: 5230667--5231126 Score: 569
Period size: 84 Copynumber: 5.5 Consensus size: 83
5230657 AGTAGAGTAC
* * *
5230667 AAAGAAATCAGATCTTATCTCTCTAAGCAGTAGTAGAGCAGATCACATCAAGTCTTATCTCCCTA
1 AAAGAAACCAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTA
5230732 AGCAGTAGTGGAGCAGACG
65 AGCAGTAGTGGAGCAGACG
5230751 AAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTA
1 AAAGAAACCAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTA
5230816 AGCAGTAGTGGAGCAGACG
65 AGCAGTAGTGGAGCAGACG
5230835 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
1 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
5230900 GCAGTAGTGGAGCAGACG
66 GCAGTAGTGGAGCAGACG
* *
5230918 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAAGTCTTATCTC
1 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCAAGTCTTATCTC
*
5230982 TCTAAGCAGTAGTGGAGCAGATC-
61 CCTAAGCAGTAGTGGAGCAGA-CG
* * * * * *
5231005 --A-CATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTC
1 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTC
*
5231066 CCTAAGCAGTAGTGGAG-TG--G
61 CCTAAGCAGTAGTGGAGCAGACG
** * * * *
5231086 ATTGCATCAAGTCTTATCTCTCTAAGCAGTAGTGGAGCAGA
1 AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
5231127 CGAAAGAAAC
Statistics
Matches: 347, Mismatches: 17, Indels: 24
0.89 0.04 0.06
Matches are distributed among these distances:
82 3 0.01
83 119 0.34
84 188 0.54
85 1 0.00
87 35 0.10
88 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (83 bp):
AAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
GCAGTAGTGGAGCAGACG
Found at i:5230871 original size:127 final size:124
Alignment explanation
Indices: 5230717--5231126 Score: 526
Period size: 127 Copynumber: 3.3 Consensus size: 124
5230707 GATCACATCA
*
5230717 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCAG
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-AAACAAG-TCTTATCTCCCTAAGCAG
* * *
5230781 TAGTGGAGCAGATC-A-CATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
61 TAGTGGAGCAGA-CAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* *
5230844 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAAGTCTTATCTCCCTAAGCAGTAGTG
5230909 GAGCAGACGAAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
66 GAGCAGAC--AAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * *
5230970 AAGTCTTATCTCTCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 -AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAAGTCTTATCTCCCTAAGCAGTAGT
* ** * * *
5231035 GGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAG-TG--GATTGCATCA
65 GGAGCAGAC--AAGAAACCAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
*
5231095 AGTCTTATCTCTCTAAGCAGTAGTGGAGCAGA
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
5231127 CGAAAGAAAC
Statistics
Matches: 263, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
122 1 0.00
123 30 0.11
124 36 0.14
125 7 0.03
126 45 0.17
127 117 0.44
128 27 0.10
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (124 bp):
AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAAGTCTTATCTCCCTAAGCAGTAGTG
GAGCAGACAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
Found at i:5231442 original size:10 final size:11
Alignment explanation
Indices: 5231423--5231459 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5231413 AACAAAACAA
5231423 AAAATAAA-CC
1 AAAATAAACCC
*
5231433 AAAATTAACCC
1 AAAATAAACCC
5231444 AAAATAAACCC
1 AAAATAAACCC
5231455 AAAAT
1 AAAAT
5231460 GCCAGCCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.65, C:0.22, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAATAAACCC
Found at i:5237158 original size:41 final size:42
Alignment explanation
Indices: 5237136--5237215 Score: 137
Period size: 41 Copynumber: 1.9 Consensus size: 42
5237126 AAAGTCTAAA
5237136 TGTTTAAAAATATATATATGAAA-TTTAAAAAAATCCTAATAG
1 TGTTTAAAAA-ATATATATGAAATTTTAAAAAAATCCTAATAG
5237178 TGTTTAAAAAATATATATGAAA-TTTAAAAAAATCCTAA
1 TGTTTAAAAAATATATATGAAATTTTAAAAAAATCCTAA
5237216 CATTATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
41 28 0.74
42 10 0.26
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (42 bp):
TGTTTAAAAAATATATATGAAATTTTAAAAAAATCCTAATAG
Found at i:5238271 original size:17 final size:16
Alignment explanation
Indices: 5238232--5238276 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
5238222 ACTTTTTAAA
*
5238232 AAATTTTATAATAATT
1 AAATTTTATAAAAATT
*
5238248 AATATTTTTTAAAAATAT
1 AA-ATTTTATAAAAAT-T
5238266 AAATTTTATAA
1 AAATTTTATAA
5238277 GGTTGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 19 0.79
18 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTTTATAAAAATT
Found at i:5240456 original size:3 final size:3
Alignment explanation
Indices: 5240444--5240485 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5240434 CATGAATGTT
5240444 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5240486 ACAGTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5242601 original size:12 final size:14
Alignment explanation
Indices: 5242571--5242603 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5242561 CATGAATACA
5242571 CAATTCATATGTCT
1 CAATTCATATGTCT
5242585 CAATTCATAT-T-T
1 CAATTCATATGTCT
5242597 CAATTCA
1 CAATTCA
5242604 CTGCCCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.42
Consensus pattern (14 bp):
CAATTCATATGTCT
Found at i:5243068 original size:24 final size:24
Alignment explanation
Indices: 5243023--5243069 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5243013 TATATACACC
5243023 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
5243047 AATTC-ATCACATAGTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
5243070 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:5243820 original size:13 final size:13
Alignment explanation
Indices: 5243783--5243821 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5243773 GACTACTGTT
*
5243783 TTTTAATTTTAATA
1 TTTT-ATTTTATTA
*
5243797 TGTTATTTTATTA
1 TTTTATTTTATTA
5243810 TTTTATTTTATT
1 TTTTATTTTATT
5243822 TTATTTCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:5244649 original size:13 final size:13
Alignment explanation
Indices: 5244601--5244652 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 13
5244591 TTATTATTAT
5244601 TATTATTATTCTTTG
1 TATTA-TATT-TTTG
5244616 TATATATATTTTTG
1 TAT-TATATTTTTG
*
5244630 T-TT-TATTTTTT
1 TATTATATTTTTG
5244641 TATTATATTTTT
1 TATTATATTTTT
5244653 ACTCTTCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 8 0.24
12 3 0.09
13 8 0.24
14 5 0.15
15 7 0.21
16 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTATATTTTTG
Found at i:5244739 original size:16 final size:16
Alignment explanation
Indices: 5244720--5244768 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
5244710 TTTTATCGTA
5244720 TTTCTTATTTATTTAT
1 TTTCTTATTTATTTAT
5244736 TTTCTT-TATTA-TTAT
1 TTTCTTAT-TTATTTAT
*
5244751 TTTACTTA-ATATTTAT
1 TTT-CTTATTTATTTAT
5244767 TT
1 TT
5244769 ATTTATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTATTTATTTAT
Found at i:5245212 original size:72 final size:72
Alignment explanation
Indices: 5245095--5245238 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
5245085 TCTTTTCAAA
* * *
5245095 CTCAAGTTTTAAACAATCTCGGGAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCGTGATCCC
1 CTCAAGTTTTAAACAATCTCGGAAATTAAAAAGAGATCGAGTCCTAACTTACTGGGCATGATCCC
5245160 TTTTTTT
66 TTTTTTT
**
5245167 CTCAAGTTTTAAATGATCTCGGAAATTAAGAAA-AGATCGAGTCCTAACTTACTGGGCATGATCC
1 CTCAAGTTTTAAACAATCTCGGAAATTAA-AAAGAGATCGAGTCCTAACTTACTGGGCATGATCC
*
5245231 TTTTTTTT
65 CTTTTTTT
5245239 TAATCCGAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 62 0.95
73 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (72 bp):
CTCAAGTTTTAAACAATCTCGGAAATTAAAAAGAGATCGAGTCCTAACTTACTGGGCATGATCCC
TTTTTTT
Found at i:5246269 original size:5 final size:5
Alignment explanation
Indices: 5246259--5246307 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
5246249 ATTTTTTTAT
5246259 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
5246308 CTTAATTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:5255562 original size:13 final size:13
Alignment explanation
Indices: 5255544--5255568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5255534 AATAAACTTC
5255544 TGAAAAATACAAT
1 TGAAAAATACAAT
5255557 TGAAAAATACAA
1 TGAAAAATACAA
5255569 ACCTTCTCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (13 bp):
TGAAAAATACAAT
Found at i:5263449 original size:10 final size:9
Alignment explanation
Indices: 5263436--5263602 Score: 54
Period size: 9 Copynumber: 17.6 Consensus size: 9
5263426 AATTATAAAA
5263436 AAAAACTTAT
1 AAAAA-TTAT
5263446 AAAAATTTAT
1 AAAAA-TTAT
5263456 AATAAA-TAT
1 AA-AAATTAT
5263465 AATAAATTAT
1 AA-AAATTAT
**
5263475 AAAAATCCT
1 AAAAATTAT
5263484 -AAAATTAAT
1 AAAAATT-AT
*
5263493 AAAATTTATT
1 AAAAATTA-T
* *
5263503 TAAAATGTTT
1 AAAAAT-TAT
*
5263513 AAAATTATTAA
1 AAAA--ATTAT
*
5263524 AAAAAGTAT
1 AAAAATTAT
* * *
5263533 CAGAATTCT
1 AAAAATTAT
*
5263542 TAAAA--AT
1 AAAAATTAT
*
5263549 AAAAATTGT
1 AAAAATTAT
5263558 CAATAAATTAT
1 -AA-AAATTAT
*
5263569 AAAAAATAT
1 AAAAATTAT
*
5263578 TAAAATTGAT
1 AAAAATT-AT
*
5263588 ATAAACTTAT
1 A-AAAATTAT
5263598 AAAAA
1 AAAAA
5263603 AATCATAAAA
Statistics
Matches: 113, Mismatches: 30, Indels: 29
0.66 0.17 0.17
Matches are distributed among these distances:
7 5 0.04
8 5 0.04
9 42 0.37
10 39 0.35
11 20 0.18
12 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5263474 original size:19 final size:18
Alignment explanation
Indices: 5263443--5263480 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5263433 AAAAAAAACT
5263443 TATAAAAATTTATAATAAA
1 TATAAAAATTTATAA-AAA
5263462 TATAATAAA-TTATAAAAA
1 TATAA-AAATTTATAAAAA
5263480 T
1 T
5263481 CCTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 11 0.61
20 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAAATTTATAAAAA
Found at i:5264095 original size:9 final size:9
Alignment explanation
Indices: 5264083--5264304 Score: 89
Period size: 10 Copynumber: 23.8 Consensus size: 9
5264073 CTTTTAACAT
5264083 TTTTTATAA
1 TTTTTATAA
5264092 TTTTTATTAA
1 TTTTTA-TAA
*
5264102 TTTTATAGAA
1 TTTT-TATAA
* *
5264112 TTTTAATACG
1 TTTTTATA-A
**
5264122 TACTTATAAA
1 TTTTTAT-AA
*
5264132 ATTTTA-AA
1 TTTTTATAA
*
5264140 TATTTTAAATA
1 T-TTTTATA-A
*
5264151 TGTTTTTTTAA
1 T-T-TTTATAA
*
5264162 T-TTTATAT
1 TTTTTATAA
5264170 TTTTTTATAA
1 T-TTTTATAA
*
5264180 TTTATTAGAA
1 TTT-TTATAA
5264190 TTTTTAT-A
1 TTTTTATAA
5264198 TTTTTATAA
1 TTTTTATAA
* *
5264207 TATTTATAG
1 TTTTTATAA
*
5264216 TAGTTTATAA
1 T-TTTTATAA
*
5264226 TATTTATAA
1 TTTTTATAA
*
5264235 GTTTATATCAA
1 -TTTTTAT-AA
*
5264246 TTTTCAT-A
1 TTTTTATAA
5264254 -TTTT-TAA
1 TTTTTATAA
* *
5264261 TATATAATAA
1 T-TTTTATAA
5264271 TTTTTATAA
1 TTTTTATAA
5264280 -TTTTATAA
1 TTTTTATAA
*
5264288 TTTTTAATCA
1 TTTTT-ATAA
5264298 TTTTTAT
1 TTTTTAT
5264305 GGGAAAAATA
Statistics
Matches: 157, Mismatches: 35, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 25 0.16
9 48 0.31
10 65 0.41
11 10 0.06
12 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5264105 original size:19 final size:18
Alignment explanation
Indices: 5264083--5264304 Score: 89
Period size: 19 Copynumber: 11.9 Consensus size: 18
5264073 CTTTTAACAT
5264083 TTTTTATAATTTTTATTAA
1 TTTTTATAATTTTTA-TAA
* * *
5264102 TTTTATAGAATTTTAATACG
1 TTTT-TATAATTTTTATA-A
** *
5264122 TACTTATAAAATTTTA-AA
1 TTTTTAT-AATTTTTATAA
* *
5264140 TATTTTAAATATGTTTTTTTAA
1 T-TTTTATA-AT-T-TTTATAA
*
5264162 T-TTTATATTTTTTTATAA
1 TTTTTATAAT-TTTTATAA
*
5264180 TTTATTAGAATTTTTAT-A
1 TTT-TTATAATTTTTATAA
* *
5264198 TTTTTATAATATTTATAG
1 TTTTTATAATTTTTATAA
* *
5264216 TAGTTTATAATATTTATAA
1 T-TTTTATAATTTTTATAA
* *
5264235 GTTTATATCAATTTTCAT-A
1 -TTTTTAT-AATTTTTATAA
* *
5264254 -TTTT-TAATATATAATAA
1 TTTTTATAAT-TTTTATAA
5264271 TTTTTATAA-TTTTATAA
1 TTTTTATAATTTTTATAA
*
5264288 TTTTTAATCATTTTTAT
1 TTTTT-ATAATTTTTAT
5264305 GGGAAAAATA
Statistics
Matches: 148, Mismatches: 35, Indels: 40
0.66 0.16 0.18
Matches are distributed among these distances:
15 3 0.02
16 5 0.03
17 26 0.18
18 21 0.14
19 51 0.34
20 36 0.24
21 3 0.02
22 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:5264184 original size:17 final size:18
Alignment explanation
Indices: 5264148--5264182 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5264138 AATATTTTAA
5264148 ATATGTTTTTTTAATTTT
1 ATATGTTTTTTTAATTTT
5264166 ATAT-TTTTTTATAATTT
1 ATATGTTTTTT-TAATTT
5264183 ATTAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
ATATGTTTTTTTAATTTT
Found at i:5264214 original size:17 final size:18
Alignment explanation
Indices: 5264173--5264293 Score: 92
Period size: 19 Copynumber: 6.7 Consensus size: 18
5264163 TTTATATTTT
* *
5264173 TTTATAATTTATTAGAATT
1 TTTATAATTT-TTATAATA
5264192 TTTAT-ATTTTTATAATA
1 TTTATAATTTTTATAATA
* *
5264209 TTTATAGTAGTTTATAATA
1 TTTATAAT-TTTTATAATA
*
5264228 TTTATAAGTTTATATCAAT-
1 TTTATAA-TTTTTAT-AATA
5264247 TTTCAT-A-TTTT-TAATA
1 TTT-ATAATTTTTATAATA
*
5264263 TATAATAATTTTTATAAT-
1 T-TTATAATTTTTATAATA
5264281 TTTATAATTTTTA
1 TTTATAATTTTTA
5264294 ATCATTTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.04
16 4 0.05
17 27 0.33
18 10 0.12
19 32 0.39
20 6 0.07
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTATAATTTTTATAATA
Found at i:5274216 original size:27 final size:27
Alignment explanation
Indices: 5274186--5274252 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
5274176 CCTATCAGGT
5274186 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
5274213 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
5274240 AGGCGCCAATGAA
1 AGGCGCCAATGAA
5274253 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:5274275 original size:19 final size:19
Alignment explanation
Indices: 5274251--5274381 Score: 72
Period size: 19 Copynumber: 6.6 Consensus size: 19
5274241 GGCGCCAATG
5274251 AATATTGTAATTTTGTATT
1 AATATTGTAATTTTGTATT
*
5274270 AATATTGTAATTAT-T-TT
1 AATATTGTAATTTTGTATT
* *
5274287 -ATAAT-TAAATTTGTATTT
1 AATATTGTAATTTTGTA-TT
* *
5274305 ATAGTTTTGGATTAGTATTTTGTATG
1 A-A-TATT-G--TA--ATTTTGTATT
*
5274331 AATATTGTAATTTTTTATAT
1 AATATTGTAATTTTGTAT-T
* *
5274351 GAATATTATAATTTTGTATG
1 -AATATTGTAATTTTGTATT
5274371 AATATTGTAAT
1 AATATTGTAAT
5274382 ATTATAATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
15 5 0.06
16 5 0.06
17 2 0.02
18 3 0.04
19 31 0.37
20 1 0.01
21 20 0.24
23 1 0.01
24 3 0.04
25 3 0.04
26 2 0.02
27 7 0.08
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
AATATTGTAATTTTGTATT
Found at i:5274383 original size:27 final size:27
Alignment explanation
Indices: 5274352--5274435 Score: 150
Period size: 27 Copynumber: 3.1 Consensus size: 27
5274342 TTTTTATATG
5274352 AATATTATAATTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTGT
5274379 AATATTATAATTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTGT
* *
5274406 AATTTTGTAATTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTGT
5274433 AAT
1 AAT
5274436 GTCGGGATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (27 bp):
AATATTATAATTTTGTATGAATATTGT
Found at i:5274403 original size:19 final size:19
Alignment explanation
Indices: 5274321--5274435 Score: 89
Period size: 19 Copynumber: 6.1 Consensus size: 19
5274311 TTGGATTAGT
5274321 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
* *
5274340 ATTTTTTATATGAATATTATA
1 A--TTTTGTATGAATATTGTA
5274361 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
* *
5274380 A-TAT-TAT-AATTTTGTATGA
1 ATTTTGTATGAATATTG--T-A
* *
5274399 ATATTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
5274415 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
5274434 AT
1 AT
5274436 GTCGGGATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.16
17 4 0.05
18 4 0.05
19 38 0.50
20 1 0.01
21 17 0.22
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:5274558 original size:60 final size:60
Alignment explanation
Indices: 5274476--5274597 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
5274466 TGTATGAATG
* * * *
5274476 TTGTAATTATTTTATAAATAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTATAAATAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
5274536 TTGTAATTA-TTTA-AAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTATAAA--TAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
5274596 TT
1 TT
5274598 AGTTTAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 3 0.05
59 4 0.07
60 48 0.87
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTATAAATAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:5274675 original size:38 final size:38
Alignment explanation
Indices: 5274630--5274711 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
5274620 CATATAAAGT
5274630 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
*
5274668 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
5274706 TTATAA
1 TTATAA
5274712 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
Found at i:5274788 original size:15 final size:15
Alignment explanation
Indices: 5274744--5274788 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
5274734 TGTTGTTAAC
*
5274744 TAATTTAATTTTATA
1 TAATTAAATTTTATA
*
5274759 TAATGTAACTTTTATA
1 TAAT-TAAATTTTATA
5274775 TAATTAAATTTTAT
1 TAATTAAATTTTAT
5274789 TTGATTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATTAAATTTTATA
Found at i:5274900 original size:21 final size:21
Alignment explanation
Indices: 5274857--5274919 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
5274847 CATTTTTTTT
* * *
5274857 ATTACAAAATTACAAACACAAA
1 ATTACAATATT-CATACAAAAA
* *
5274879 ATTATAATATTCATATAAAAA
1 ATTACAATATTCATACAAAAA
5274900 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
5274920 TACTAATCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 25 0.74
22 9 0.26
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTACAATATTCATACAAAAA
Found at i:5275069 original size:27 final size:27
Alignment explanation
Indices: 5274989--5275055 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5274979 AATTACAATA
* *
5274989 TTCATTAGCGTCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
5275016 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
5275043 TTCATTGGCGCCT
1 TTCATTGGCGCCT
5275056 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.31, G:0.21, T:0.33
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:5275114 original size:11 final size:11
Alignment explanation
Indices: 5275098--5275141 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
5275088 ACCGTATTTT
5275098 TTAAAAAAATA
1 TTAAAAAAATA
5275109 TT-AAAAAATA
1 TTAAAAAAATA
5275119 -TAAAAAAA-A
1 TTAAAAAAATA
*
5275128 TTAAAAAATTA
1 TTAAAAAAATA
5275139 TTA
1 TTA
5275142 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 2 0.07
10 21 0.72
11 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:5279227 original size:31 final size:29
Alignment explanation
Indices: 5279162--5279236 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
5279152 ATAACGTTTC
* *
5279162 AAATAAATAGAATATATATAAAAATTAGA
1 AAATAAATAGAATATATAGAAAAATTAAA
*
5279191 CAATAAATA-AATAATAATAGAAACAATTAAA
1 AAATAAATAGAAT-AT-ATAGAAA-AATTAAA
*
5279222 AAATAAATAGTATAT
1 AAATAAATAGAATAT
5279237 TTAAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 6 0.16
31 16 0.43
32 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAAATAGAATATATAGAAAAATTAAA
Found at i:5281126 original size:97 final size:95
Alignment explanation
Indices: 5280940--5281236 Score: 522
Period size: 95 Copynumber: 3.1 Consensus size: 95
5280930 ACTACTACTT
* * *
5280940 AGGGAGATAAAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCCTCTT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
5281005 CGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
*
5281035 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATC
5281100 TTCGATCTTCAATCTATTCCACTGCCAAATAC
64 TTCGATCTTCAATCTATTCCACTGCCAAATAC
*
5281132 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATATT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
*
5281197 TGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
5281227 AGGGAGATAG
1 AGGGAGATAG
5281237 GATCTGTTTT
Statistics
Matches: 193, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
95 101 0.52
97 92 0.48
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (95 bp):
AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
CGATCTTCAATCTATTCCACTGCCAAATAC
Found at i:5281312 original size:44 final size:43
Alignment explanation
Indices: 5281255--5282093 Score: 769
Period size: 44 Copynumber: 19.1 Consensus size: 43
5281245 TTTCAATCCG
* *
5281255 CTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5281299 CTTCACACCAATATATGAATACAAGATCTGCTTTTTTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTT-CGATCTA
* * * * *
5281344 CTTCACCACCAGTATGGGAAGACAAAATCTGC-ATCTTAGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5281388 CTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5281432 CTTCACACCAATACATGAAGACAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5281476 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
** *
5281520 CTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
5281564 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5281608 CTTTGCCACCAA-ATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 C-TT-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5281651 CTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * * * *
5281695 CTTCACGCCAATACATGAAGATAAGATCTGATTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5281739 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5281783 CTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
5281827 CTTCACGCCAATA-CGTGAAGATAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAG-GAAGACAAGATCTGCTATCTTCGATCTA
*
5281871 CTTCGCCACCAATAT-GGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5281914 TTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5281958 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5282002 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5282046 TTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
5282090 CTTC
1 CTTC
5282094 TTGCCCCGGG
Statistics
Matches: 637, Mismatches: 123, Indels: 70
0.77 0.15 0.08
Matches are distributed among these distances:
41 4 0.01
42 23 0.04
43 133 0.21
44 351 0.55
45 99 0.16
46 26 0.04
47 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
CTTCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
Found at i:5281534 original size:132 final size:132
Alignment explanation
Indices: 5281250--5282093 Score: 1395
Period size: 132 Copynumber: 6.4 Consensus size: 132
5281240 CTGTTTTTCA
* ** * *
5281250 ATCCGCTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * *
5281315 GAATACAAGATCTGCTTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCT
66 GAAGACAAGATCTGC-TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
*
5281380 TAG
130 TCG
* * *
5281383 ATCCACTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281448 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5281513 CG
131 CG
** *
5281515 ATCCACTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281580 GAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCAA-ATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5281644 CG
131 CG
*
5281646 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
5281711 GAAGATAAGATCTGATTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5281776 CG
131 CG
* *
5281778 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACGT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281843 GAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5281907 CG
131 CG
* *
5281909 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281974 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5282039 CG
131 CG
* *
5282041 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTC
5282094 TTGCCCCGGG
Statistics
Matches: 673, Mismatches: 36, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
131 248 0.37
132 352 0.52
133 73 0.11
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CG
Found at i:5281724 original size:263 final size:263
Alignment explanation
Indices: 5281250--5282093 Score: 1384
Period size: 263 Copynumber: 3.2 Consensus size: 263
5281240 CTGTTTTTCA
* * * *
5281250 ATCCGCTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * *
5281315 GAATACAAGATCTGCTTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCT
66 GAAGACAAGATCTGC-TTTCTGCGATCTACTTCGCCACCA-AATGGGAAGACAAGATCTGCATCT
* * * *
5281380 TAGATCCACTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATA
129 TCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATA
5281445 CATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCAT
194 CATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCAT
*
5281510 CGTCG
259 CTTCG
* *
5281515 ATCCACTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281580 GAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCAAATGGGAAGACAAGATCTGCATCTTC
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAAATGGGAAGACAAGATCTGCATCTTC
*
5281645 GATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACA
131 GATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACA
* *
5281710 TGAAGATAAGATCTGATTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
196 TGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
5281775 TCG
261 TCG
* * *
5281778 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACGT
1 ATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5281843 GAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAA-ATGGGAAGACAAGATCTGCATCTT
* *
5281907 CGATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATAC
130 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATAC
*
5281972 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
195 ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
5282037 TTCG
260 TTCG
* * *
5282041 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
1 ATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC
5282094 TTGCCCCGGG
Statistics
Matches: 542, Mismatches: 36, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
263 446 0.82
264 23 0.04
265 73 0.13
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (263 bp):
ATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAAATGGGAAGACAAGATCTGCATCTTC
GATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACA
TGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
TCG
Found at i:5282321 original size:136 final size:136
Alignment explanation
Indices: 5282101--5282755 Score: 1068
Period size: 136 Copynumber: 4.8 Consensus size: 136
5282091 TTCTTGCCCC
** * * * *
5282101 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAAT--CAGGGAGGTAAAATCCGCCGTCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
** * * * *
5282164 TCAACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAGTCTATTCTACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
5282229 AATACA
131 AATACA
5282235 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
*
5282300 TTGATCTGCTTCGCTGCCAAATACATGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
*
5282365 AATATA
131 AATACA
*
5282371 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGT--CAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
* *
5282434 TTGATCTGCTTCTCTGCCAAATACACGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
5282499 AATACA
131 AATACA
*
5282505 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
5282570 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
*
5282635 GATACA
131 AATACA
*
5282641 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
* *
5282706 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTG-ATATCTTCAA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
5282756 CCAGATCTGC
Statistics
Matches: 489, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
134 165 0.34
135 1 0.00
136 323 0.66
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (136 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
AATACA
Found at i:5282582 original size:270 final size:270
Alignment explanation
Indices: 5282101--5282755 Score: 1098
Period size: 270 Copynumber: 2.4 Consensus size: 270
5282091 TTCTTGCCCC
** * * * *
5282101 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* * * *
5282166 AACCTGCTT-TGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAGTCTATTCTACTGCCAA
66 GATCTGCTTCT-CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
*
5282230 ATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGC
130 ATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGC
*
5282295 CATCTTTGATCTGCTTCGCTGCCAAATACATGAAGGCAAGATCTGCAATCTTCAATCTATTCCAC
195 CATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCAC
*
5282360 TGCCAAATATA
260 TGCCAAATACA
* *
5282371 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
*
5282436 GATCTGCTTCTCTGCCAAATACACGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
5282501 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
131 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
5282566 ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
196 ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
*
5282631 GCCAGATACA
261 GCCAAATACA
*
5282641 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
5282706 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTG-ATATCTTCAA
64 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
5282756 CCAGATCTGC
Statistics
Matches: 360, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
270 289 0.80
271 2 0.01
272 69 0.19
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (270 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
GCCAAATACA
Found at i:5282826 original size:42 final size:41
Alignment explanation
Indices: 5282778--5282912 Score: 96
Period size: 42 Copynumber: 3.2 Consensus size: 41
5282768 CAAACGAGAG
5282778 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATG-AGGA
* * * * * * * *
5282820 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAAACGA-GA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTC-AATGAGGA
*
5282863 GTGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATG-AGGA
5282906 AGGCAAG
1 AGGCAAG
5282913 ATCTGATAAC
Statistics
Matches: 65, Mismatches: 18, Indels: 20
0.63 0.17 0.19
Matches are distributed among these distances:
41 15 0.23
42 18 0.28
43 6 0.09
44 11 0.17
45 15 0.23
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (41 bp):
AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGAGGA
Found at i:5282830 original size:86 final size:86
Alignment explanation
Indices: 5282703--5282965 Score: 409
Period size: 86 Copynumber: 3.0 Consensus size: 86
5282693 AAATCTGCCA
* * * *
5282703 TCTTCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGATATCTTCAACCAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTA
5282768 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* * *
5282790 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
*
5282855 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
*
5282876 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
* * *
5282941 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
5282962 TCTT
1 TCTT
5282966 TAATTTTCAC
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 141 0.88
87 19 0.12
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:5287116 original size:19 final size:20
Alignment explanation
Indices: 5287092--5287135 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5287082 CGTGAAAGTC
* *
5287092 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
5287111 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
5287131 -AATGC
1 TAATGC
5287136 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:5291210 original size:97 final size:95
Alignment explanation
Indices: 5291024--5291320 Score: 522
Period size: 95 Copynumber: 3.1 Consensus size: 95
5291014 ACTACTACTT
* * *
5291024 AGGGAGATAAAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCCTCTT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
5291089 CGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
*
5291119 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATC
5291184 TTCGATCTTCAATCTATTCCACTGCCAAATAC
64 TTCGATCTTCAATCTATTCCACTGCCAAATAC
*
5291216 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATATT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
*
5291281 TGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
5291311 AGGGAGATAG
1 AGGGAGATAG
5291321 GATCTGTTTT
Statistics
Matches: 193, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
95 101 0.52
97 92 0.48
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (95 bp):
AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
CGATCTTCAATCTATTCCACTGCCAAATAC
Found at i:5291396 original size:44 final size:43
Alignment explanation
Indices: 5291339--5292177 Score: 769
Period size: 44 Copynumber: 19.1 Consensus size: 43
5291329 TTTCAATCCG
* *
5291339 CTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5291383 CTTCACACCAATATATGAATACAAGATCTGCT-TTTTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTT-CGATCTA
* * * * *
5291427 CTTCACCACCAGTATGGGAAGACAAAATCTGC-ATCTTAGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5291471 CTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5291515 CTTCACACCAATACATGAAGACAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5291559 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
** *
5291603 CTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
5291647 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5291691 CTTTGCCACCAA-ATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 C-TT-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5291734 CTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * * * *
5291778 CTTCACGCCAATACATGAAGATAAGATCTGATTTCTGCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5291822 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
5291866 CTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
5291910 CTTCACGCCAATA-CGTGAAGATAAGATCTGCTTTCTGCGATCTA
1 CTTC-CACCAATATAG-GAAGACAAGATCTGCTATCTTCGATCTA
* *
5291954 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5291998 TTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5292042 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 CTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* *
5292086 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 CTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
5292130 TTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTA
1 CTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
5292174 CTTC
1 CTTC
5292178 TTGCCCCGGG
Statistics
Matches: 637, Mismatches: 123, Indels: 70
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.00
42 17 0.03
43 133 0.21
44 355 0.56
45 123 0.19
46 7 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
CTTCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
Found at i:5291527 original size:132 final size:132
Alignment explanation
Indices: 5291334--5292177 Score: 1411
Period size: 132 Copynumber: 6.4 Consensus size: 132
5291324 CTGTTTTTCA
* ** * *
5291334 ATCCGCTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * *
5291399 GAATACAAGATCTGCTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5291464 AG
131 CG
* * *
5291466 ATCCACTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5291531 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5291596 CG
131 CG
** *
5291598 ATCCACTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5291663 GAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCAA-ATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5291727 CG
131 CG
*
5291729 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
5291794 GAAGATAAGATCTGATTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5291859 CG
131 CG
* *
5291861 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACGT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5291926 GAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5291991 CG
131 CG
* *
5291993 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
5292058 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5292123 CG
131 CG
* *
5292125 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTC
5292178 TTGCCCCGGG
Statistics
Matches: 675, Mismatches: 36, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
131 123 0.18
132 552 0.82
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CG
Found at i:5292069 original size:395 final size:396
Alignment explanation
Indices: 5291334--5292177 Score: 1411
Period size: 395 Copynumber: 2.1 Consensus size: 396
5291324 CTGTTTTTCA
* ** *
5291334 ATCCGCTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATACAT
* * * *
5291399 GAATACAAGATCTGCTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCTT
66 GAAGACAAGATCTGATTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAAATCTGCATCTT
* *
5291464 AGATCCACTTCCTATCAATATAAGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATAC
131 AGATCCACTTCCTACCAATATAAGAAGATAGGATCTGCTACCTTCGATCTACTTCACACCAATAC
5291529 ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
196 ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
* *
5291594 GTCGATCCACTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCACGCCAAT
261 GTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCTATCTTCGATCTACTTCACGCCAAT
*
5291659 ACATGAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCAA-ATGGGAAGACAAGATCTGCA
326 ACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
5291723 TCTTCG
391 TCTTCG
* *
5291729 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATACAT
* * *
5291794 GAAGATAAGATCTGATTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGATTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAAATCTGCATCTT
* * *
5291859 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATAC
131 AGATCCACTTCCTACCAATATAAGAAGATAGGATCTGCTACCTTCGATCTACTTCACACCAATAC
* *
5291924 GTGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
196 ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
* * * *
5291989 TTCGATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAAT
261 GTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCTATCTTCGATCTACTTCACGCCAAT
*
5292054 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
326 ACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
5292119 TCTTCG
391 TCTTCG
* *
5292125 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTC
5292178 TTGCCCCGGG
Statistics
Matches: 417, Mismatches: 31, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
395 341 0.82
396 76 0.18
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (396 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACACCAATACAT
GAAGACAAGATCTGATTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAAATCTGCATCTT
AGATCCACTTCCTACCAATATAAGAAGATAGGATCTGCTACCTTCGATCTACTTCACACCAATAC
ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
GTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCTATCTTCGATCTACTTCACGCCAAT
ACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
TCTTCG
Found at i:5292405 original size:136 final size:136
Alignment explanation
Indices: 5292185--5292839 Score: 1068
Period size: 136 Copynumber: 4.8 Consensus size: 136
5292175 TTCTTGCCCC
** * * * *
5292185 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAAT--CAGGGAGGTAAAATCCGCCGTCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
** * * * *
5292248 TCAACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAGTCTATTCTACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
5292313 AATACA
131 AATACA
5292319 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
*
5292384 TTGATCTGCTTCGCTGCCAAATACATGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
*
5292449 AATATA
131 AATACA
*
5292455 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGT--CAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
* *
5292518 TTGATCTGCTTCTCTGCCAAATACACGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
5292583 AATACA
131 AATACA
*
5292589 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
5292654 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
*
5292719 GATACA
131 AATACA
*
5292725 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
* *
5292790 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTG-ATATCTTCAA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
5292840 CCAGATCTGC
Statistics
Matches: 489, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
134 165 0.34
135 1 0.00
136 323 0.66
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (136 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
AATACA
Found at i:5292666 original size:270 final size:270
Alignment explanation
Indices: 5292185--5292839 Score: 1098
Period size: 270 Copynumber: 2.4 Consensus size: 270
5292175 TTCTTGCCCC
** * * * *
5292185 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* * * *
5292250 AACCTGCTT-TGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAGTCTATTCTACTGCCAA
66 GATCTGCTTCT-CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
*
5292314 ATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGC
130 ATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGC
*
5292379 CATCTTTGATCTGCTTCGCTGCCAAATACATGAAGGCAAGATCTGCAATCTTCAATCTATTCCAC
195 CATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCAC
*
5292444 TGCCAAATATA
260 TGCCAAATACA
* *
5292455 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
*
5292520 GATCTGCTTCTCTGCCAAATACACGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
5292585 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
131 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
5292650 ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
196 ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
*
5292715 GCCAGATACA
261 GCCAAATACA
*
5292725 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
5292790 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTG-ATATCTTCAA
64 TCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
5292840 CCAGATCTGC
Statistics
Matches: 360, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
270 289 0.80
271 2 0.01
272 69 0.19
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (270 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC
ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
GCCAAATACA
Found at i:5292910 original size:42 final size:41
Alignment explanation
Indices: 5292862--5292996 Score: 96
Period size: 42 Copynumber: 3.2 Consensus size: 41
5292852 CAAACGAGAG
5292862 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATG-AGGA
* * * * * * * *
5292904 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAAACGA-GA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTC-AATGAGGA
*
5292947 GTGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATG-AGGA
5292990 AGGCAAG
1 AGGCAAG
5292997 ATCTGATAAC
Statistics
Matches: 65, Mismatches: 18, Indels: 20
0.63 0.17 0.19
Matches are distributed among these distances:
41 15 0.23
42 18 0.28
43 6 0.09
44 11 0.17
45 15 0.23
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (41 bp):
AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGAGGA
Found at i:5292914 original size:86 final size:86
Alignment explanation
Indices: 5292787--5293049 Score: 409
Period size: 86 Copynumber: 3.0 Consensus size: 86
5292777 AAATCTGCCA
* * * *
5292787 TCTTCGATCTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGATATCTTCAACCAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTA
5292852 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* * *
5292874 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
*
5292939 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
*
5292960 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
* * *
5293025 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
5293046 TCTT
1 TCTT
5293050 TAATTTTCAC
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 141 0.88
87 19 0.12
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:5297200 original size:19 final size:20
Alignment explanation
Indices: 5297176--5297219 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5297166 CGTGAAAGTC
* *
5297176 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
5297195 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
5297215 -AATGC
1 TAATGC
5297220 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:5299417 original size:31 final size:29
Alignment explanation
Indices: 5299352--5299426 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
5299342 ATAACGTTTC
* *
5299352 AAATAAATAGAATATATATAAAAATTAGA
1 AAATAAATAGAATATATAGAAAAATTAAA
*
5299381 CAATAAATA-AATAATAATAGAAACAATTAAA
1 AAATAAATAGAAT-AT-ATAGAAA-AATTAAA
*
5299412 AAATAAATAGTATAT
1 AAATAAATAGAATAT
5299427 TTAAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 6 0.16
31 16 0.43
32 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAAATAGAATATATAGAAAAATTAAA
Found at i:5301491 original size:30 final size:30
Alignment explanation
Indices: 5301455--5301514 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5301445 AAGTTTACAA
5301455 GTCCAAAATCAAACTCATACCACATTTTAT
1 GTCCAAAATCAAACTCATACCACATTTTAT
* *
5301485 GTCCAAAATCGAACTCATGCCACATTTTAT
1 GTCCAAAATCAAACTCATACCACATTTTAT
5301515 ATAATCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (30 bp):
GTCCAAAATCAAACTCATACCACATTTTAT
Found at i:5302529 original size:21 final size:21
Alignment explanation
Indices: 5302505--5302557 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5302495 GGTTTAGACT
5302505 GTGTGACAG-GGGTACATGGCC
1 GTGTGACAGAGGG-ACATGGCC
* * *
5302526 GTGTGGCTGAGGGACATGTCC
1 GTGTGACAGAGGGACATGGCC
5302547 GTGTGAGCAGA
1 GTGTGA-CAGA
5302558 CTATATAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (21 bp):
GTGTGACAGAGGGACATGGCC
Found at i:5311791 original size:63 final size:63
Alignment explanation
Indices: 5311714--5311847 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 63
5311704 TGCAAGGGTG
* * *
5311714 ACACGAGTGAGACACACAGGCGTATGTCCAGGAC-GTGTAACTAACTAAGTTCATATTAGAGTC
1 ACACGGGTAAGACACACAGGCGTATGTCCAGG-CTGTGTAACTAACTAAGTTCATATTAGAGAC
* * * * * *
5311777 ACACGGGTAAGACACACGGGCGTGTGTCCAGGCTGTGTAACTCACTGAGTTTATATTTGAGAC
1 ACACGGGTAAGACACACAGGCGTATGTCCAGGCTGTGTAACTAACTAAGTTCATATTAGAGAC
*
5311840 ACATGGGT
1 ACACGGGT
5311848 GTGCACCAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 1 0.02
63 59 0.98
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (63 bp):
ACACGGGTAAGACACACAGGCGTATGTCCAGGCTGTGTAACTAACTAAGTTCATATTAGAGAC
Found at i:5314848 original size:17 final size:17
Alignment explanation
Indices: 5314823--5314873 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
5314813 ATTTATATTA
* *
5314823 ATATTTTAATGATAAAT
1 ATATATTAATAATAAAT
*
5314840 ATATATTAAAAATATAA-
1 ATATATTAATAATA-AAT
5314857 ATATATTAATAATAAAT
1 ATATATTAATAATAAAT
5314874 TTTTTAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATATATTAATAATAAAT
Found at i:5315018 original size:21 final size:21
Alignment explanation
Indices: 5314994--5315033 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5314984 TTAGGTCCAA
*
5314994 TTGTTAATATTGTTAATTTTC
1 TTGTCAATATTGTTAATTTTC
* *
5315015 TTGTCAATTTTGTTTATTT
1 TTGTCAATATTGTTAATTT
5315034 GACATTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.65
Consensus pattern (21 bp):
TTGTCAATATTGTTAATTTTC
Found at i:5316071 original size:5 final size:5
Alignment explanation
Indices: 5316061--5316090 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5316051 ACTATTTAAA
5316061 GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT
5316091 AGTAGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GATAT
Found at i:5317468 original size:19 final size:19
Alignment explanation
Indices: 5317444--5317506 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
5317434 AAAAATTTAC
5317444 AAATATAATTCTATTTATT
1 AAATATAATTCTATTTATT
* *
5317463 AAATATTATT-AATATTATT
1 AAATATAATTCTAT-TTATT
*
5317482 AAAAATAATTCTATTTATT
1 AAATATAATTCTATTTATT
5317501 AAATAT
1 AAATAT
5317507 TATTTTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 2 0.06
19 32 0.89
20 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATAATTCTATTTATT
Found at i:5317525 original size:38 final size:38
Alignment explanation
Indices: 5317448--5317524 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
5317438 ATTTACAAAT
*
5317448 ATAATTCTATTTATTAAATATTATTAATATTATTAAAA
1 ATAATTCTATTTATTAAATATTATTAATATTAATAAAA
**
5317486 ATAATTCTATTTATTAAATATTATTTTTATTTAATAAAA
1 ATAATTCTATTTATTAAATATTATTAATA-TTAATAAAA
5317525 TGTTGTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (38 bp):
ATAATTCTATTTATTAAATATTATTAATATTAATAAAA
Found at i:5318706 original size:14 final size:13
Alignment explanation
Indices: 5318685--5318715 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5318675 TTTTTTGTTC
5318685 TTTCTCTTTTCTT
1 TTTCTCTTTTCTT
5318698 TTTCTTCTTTTCTT
1 TTTC-TCTTTTCTT
5318712 TTTC
1 TTTC
5318716 GCCATATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTCTTTTCTT
Found at i:5318715 original size:20 final size:20
Alignment explanation
Indices: 5318676--5318713 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5318666 TTGTTCCCTT
*
5318676 TTTTTGTTCTTTCTCTTTTC
1 TTTTTCTTCTTTCTCTTTTC
5318696 TTTTTCTTCTTT-TCTTTT
1 TTTTTCTTCTTTCTCTTTT
5318714 TCGCCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTCTTCTTTCTCTTTTC
Found at i:5331467 original size:9 final size:9
Alignment explanation
Indices: 5331455--5331526 Score: 63
Period size: 9 Copynumber: 7.6 Consensus size: 9
5331445 AATAAATCAG
5331455 AAAAATATA
1 AAAAATATA
* *
5331464 AAAATTATT
1 AAAAATATA
5331473 AAAAATATCA
1 AAAAATAT-A
*
5331483 AAAAATTATT
1 AAAAA-TATA
*
5331493 AAAATTAATA
1 AAAAAT-ATA
*
5331503 AAAACTTATA
1 AAAA-ATATA
5331513 AAAAATATA
1 AAAAATATA
5331522 AAAAA
1 AAAAA
5331527 ATATTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
9 24 0.47
10 22 0.43
11 5 0.10
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATATA
Found at i:5331477 original size:10 final size:10
Alignment explanation
Indices: 5331462--5331570 Score: 80
Period size: 10 Copynumber: 10.8 Consensus size: 10
5331452 CAGAAAAATA
5331462 TAAAAATTAT
1 TAAAAATTAT
5331472 TAAAAA-TAT
1 TAAAAATTAT
*
5331481 CAAAAAATTAT
1 -TAAAAATTAT
*
5331492 T-AAAATTAA
1 TAAAAATTAT
5331501 TAAAAACTTA-
1 TAAAAA-TTAT
*
5331511 TAAAAAATAT
1 TAAAAATTAT
* *
5331521 AAAAAAATAT
1 TAAAAATTAT
* *
5331531 TTAAAATTTT
1 TAAAAATTAT
*
5331541 ATAAAAATTCT
1 -TAAAAATTAT
5331552 TAAAAACTTAT
1 TAAAAA-TTAT
*
5331563 TTAAAATT
1 TAAAAATT
5331571 TAATTTAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
9 13 0.16
10 44 0.56
11 22 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:5331482 original size:29 final size:29
Alignment explanation
Indices: 5331450--5331525 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
5331440 ATGAAAATAA
*
5331450 ATCAGAAAAATATAAAAATTATTAAAAA-T
1 ATCA-AAAAATATAAAAATTAATAAAAACT
*
5331479 ATCAAAAAATTATTAAAATTAATAAAAACTT
1 ATCAAAAAA-TATAAAAATTAATAAAAAC-T
5331510 AT-AAAAAATATAAAAA
1 ATCAAAAAATATAAAAA
5331526 AATATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 27 0.66
30 6 0.15
31 3 0.07
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (29 bp):
ATCAAAAAATATAAAAATTAATAAAAACT
Found at i:5331488 original size:20 final size:19
Alignment explanation
Indices: 5331455--5331557 Score: 100
Period size: 20 Copynumber: 5.3 Consensus size: 19
5331445 AATAAATCAG
5331455 AAAAATAT-AAAAATTATT
1 AAAAATATAAAAAATTATT
5331473 AAAAATATCAAAAAATTATT
1 AAAAATAT-AAAAAATTATT
* * *
5331493 AAAATTAATAAAAACTTATA
1 AAAAAT-ATAAAAAATTATT
*
5331513 AAAAATATAAAAAAATATTT
1 AAAAATATAAAAAATTA-TT
* * *
5331533 AAAATTTTATAAAAATTCTT
1 AAAAATATA-AAAAATTATT
5331553 AAAAA
1 AAAAA
5331558 CTTATTTAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.12
19 9 0.13
20 43 0.63
21 8 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATATAAAAAATTATT
Found at i:5333360 original size:14 final size:14
Alignment explanation
Indices: 5333330--5333375 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
5333320 AAATATTAAA
5333330 ATTTTT-TATTT-T
1 ATTTTTATATTTAT
5333342 ATTTTTATATTTAT
1 ATTTTTATATTTAT
*
5333356 ATTTTTA-AATTAT
1 ATTTTTATATTTAT
*
5333369 AATTTTA
1 ATTTTTA
5333376 AGAAGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 6 0.20
13 16 0.53
14 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTTATATTTAT
Found at i:5334947 original size:6 final size:6
Alignment explanation
Indices: 5334936--5334962 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5334926 CATAAATAGC
5334936 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
5334963 GACAGGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:5337253 original size:51 final size:51
Alignment explanation
Indices: 5337148--5337255 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
5337138 CTGTGTAAGT
* * * * * *
5337148 ATTGACAGAATGTATAAATGTTATGTGCTAAATTTGTTGAACCATGACTAA
1 ATTGACAAAATGTATAAATGTTAAGAGCTAAATTTGTTAAACCAAGACCAA
* * ** *
5337199 ATTGACAAAATGTGTAAATTTTAAGAGCTAAATTTGTTAAATTAAGACCGA
1 ATTGACAAAATGTATAAATGTTAAGAGCTAAATTTGTTAAACCAAGACCAA
5337250 ATTGAC
1 ATTGAC
5337256 TAGAAAATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (51 bp):
ATTGACAAAATGTATAAATGTTAAGAGCTAAATTTGTTAAACCAAGACCAA
Found at i:5339000 original size:114 final size:113
Alignment explanation
Indices: 5338719--5339396 Score: 873
Period size: 114 Copynumber: 6.0 Consensus size: 113
5338709 AAAATAAGCA
* * *
5338719 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAGACTTCAGCCCAACAACGCTGTTTTCTGAGCTGA
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGA
** *
5338784 GAAGGATTTAGTGGCAATTTTACGAAAGCGCCGCTAATGCTCA-GTCT
66 GAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGGTCT
* * * *
5338831 TTAGCGGCATTTTTCGGAAAGCGCCGCAAAAACACTTCAGTCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGC-AAAATACTTCAGCCCAACGACGCCGTTTTCTGAGC-T
** * * *
5338896 TCG-GGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTTAGGTCC
64 GAGAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGGTCT
* *
5338945 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAGTTCTTCAGCCCAACGACGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA-TACTTCAGCCCAACGACGCCGTTTTCTGAGC-T
** * * *
5339010 TCG-GGGATTTAGTGGCGTTTTTATTAAAGCGCCGCTAATACTCAGAG-CT
64 GAGAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAG-GTCT
* * *
5339059 TTAGTGGCGTTTGTGGGAAAGCGCCACAACAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAA-AATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
* * * *
5339124 AGAATGATTTAGTGGCGTTTTTATGTAGGCGCCGCTAAAGCTCAGGTCT
65 AGAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGGTCT
*
5339173 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAGAATACTTCAGCCCAACGACGCCGTTTTTTGAGCTG
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAA-AATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
* * *
5339238 AGAAGGATTTAGTGGCGTTTTTATGTAAGCGCTGCTAATGCTCAAGTCT
65 AGAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGGTCT
*
5339287 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACTTCAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGC-AAAATACTTCAGCCCAACGACGCCGTTTTCTGAGC-T
** * * * *
5339352 TCG-GGGATTTAGTGGCATTTTTATG-AAGCGCCACTAATACTCAGG
64 GAGAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGG
5339397 GATGTAAAAT
Statistics
Matches: 498, Mismatches: 58, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
112 25 0.05
113 90 0.18
114 376 0.76
115 7 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGA
GAAGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATGCTCAGGTCT
Found at i:5339250 original size:342 final size:339
Alignment explanation
Indices: 5338719--5339395 Score: 1005
Period size: 342 Copynumber: 2.0 Consensus size: 339
5338709 AAAATAAGCA
* * *
5338719 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAGACTTCAGCCCAACAACGCTGTTTTCTGAGCTGA
1 TTAGCGGCGTTTGTGGGAAAGCGCCACAAAAGACTTCAGCCCAACAACGCCGTTTTCTGAGCTGA
*
5338784 GAAGGATTTAGTGGCAATTTTACGAAAGCGCCGCTAATGCTCAGTCTTTAGCGGCATTTTTCGGA
66 GAAGGATTTAGTGGCAATTTTACGAAAGCGCCGCTAAAGCTCAGTCTTTAGCGGCATTTTTCGGA
* ** *
5338849 AAGCGCCGCAAAAACACTTCAGTCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGT
131 AAGCGCCGCAAAAACACTTCAGCCCAACGACGCCGTTTTCTGAGCTTGAGAGGATTTAGTGGCGT
* * * *
5338914 TTTTATGAAAGCGCCGCTAATGCTTAGGTCCTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAGTT
196 TTTTATGAAAGCGCCGCTAATGCTCAAGTCCTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATA
* * *
5338979 CTTCAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCG
261 CTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCATTTTTA-TAAAGCGCCA
5339044 CTAATACTCAGAGCT
325 CTAATACTCAGAGCT
* * *
5339059 TTAGTGGCGTTTGTGGGAAAGCGCCACAACAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
1 TTAGCGGCGTTTGTGGGAAAGCGCCACAA-AAGACTTCAGCCCAACAACGCCGTTTTCTGAGCTG
* ** * * * * *
5339124 AGAATGATTTAGTGGCGTTTTTATGTAGGCGCCGCTAAAGCTCAGGTCTTTAGCGGCGTTTTTGG
65 AGAAGGATTTAGTGGCAATTTTACGAAAGCGCCGCTAAAGCTCA-GTCTTTAGCGGCATTTTTCG
* * *
5339189 GAAAGCGCCGCAAGAATACTTCAGCCCAACGACGCCGTTTTTTGAGC-TGAGAAGGATTTAGTGG
129 GAAAGCGCCGCAAAAACACTTCAGCCCAACGACGCCGTTTTCTGAGCTTGAG-AGGATTTAGTGG
* * *
5339253 CGTTTTTATGTAAGCGCTGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
193 CGTTTTTATGAAAGCGCCGCTAATGCTCAAGTCCTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
* *
5339318 ATACTTCAGCCCAACGATGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCATTTTTATGAAGCGC
258 ATACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCATTTTTATAAAGCGC
5339383 CACTAATACTCAG
323 CACTAATACTCAG
5339396 GGATGTAAAA
Statistics
Matches: 300, Mismatches: 34, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
340 26 0.09
341 90 0.30
342 184 0.61
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (339 bp):
TTAGCGGCGTTTGTGGGAAAGCGCCACAAAAGACTTCAGCCCAACAACGCCGTTTTCTGAGCTGA
GAAGGATTTAGTGGCAATTTTACGAAAGCGCCGCTAAAGCTCAGTCTTTAGCGGCATTTTTCGGA
AAGCGCCGCAAAAACACTTCAGCCCAACGACGCCGTTTTCTGAGCTTGAGAGGATTTAGTGGCGT
TTTTATGAAAGCGCCGCTAATGCTCAAGTCCTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATA
CTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCATTTTTATAAAGCGCCAC
TAATACTCAGAGCT
Found at i:5339663 original size:14 final size:15
Alignment explanation
Indices: 5339630--5339663 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5339620 TAAGTTTTAT
5339630 AGATTATGGAATTAG
1 AGATTATGGAATTAG
5339645 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
5339659 GGATT
1 AGATT
5339664 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:5339703 original size:7 final size:7
Alignment explanation
Indices: 5339703--5339753 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
5339693 TTATGGGTTA
5339703 TTAGGGG
1 TTAGGGG
*
5339710 TTAGGGA
1 TTAGGGG
5339717 TTAGGGG
1 TTAGGGG
*
5339724 TTAAGGG
1 TTAGGGG
5339731 TTAGGGG
1 TTAGGGG
5339738 TTA--GG
1 TTAGGGG
5339743 TTAGGGG
1 TTAGGGG
5339750 TTAG
1 TTAG
5339754 ATGTTAAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 5 0.13
7 33 0.87
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:5339759 original size:19 final size:20
Alignment explanation
Indices: 5339703--5339769 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
5339693 TTATGGGTTA
*
5339703 TTAGGGGTTAG-GGATTAGGGG
1 TTAGGGGTTAGAGG-TTA-AGG
* *
5339724 TTAAGGGTTAGGGGTT-AGG
1 TTAGGGGTTAGAGGTTAAGG
*
5339743 TTAGGGGTTAGATGTTAAGAG
1 TTAGGGGTTAGAGGTTAAG-G
5339764 TTAGGG
1 TTAGGG
5339770 ATTTAGGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 15 0.39
20 2 0.05
21 19 0.50
22 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.31
Consensus pattern (20 bp):
TTAGGGGTTAGAGGTTAAGG
Found at i:5339865 original size:7 final size:7
Alignment explanation
Indices: 5339853--5339975 Score: 183
Period size: 7 Copynumber: 17.6 Consensus size: 7
5339843 TAAATAAGGT
5339853 TTAGGGG
1 TTAGGGG
5339860 TTAGGGG
1 TTAGGGG
5339867 TTAGGGG
1 TTAGGGG
* *
5339874 TTAGAGA
1 TTAGGGG
*
5339881 TCAGGGG
1 TTAGGGG
*
5339888 TTAAGGG
1 TTAGGGG
*
5339895 TTAAGGG
1 TTAGGGG
*
5339902 TTAAGGG
1 TTAGGGG
5339909 TTAGGGG
1 TTAGGGG
5339916 TTAGGGG
1 TTAGGGG
5339923 TTAGGGG
1 TTAGGGG
5339930 TTAGGGG
1 TTAGGGG
5339937 TTAGGGG
1 TTAGGGG
5339944 TTAGGGG
1 TTAGGGG
5339951 TTAGGGG
1 TTAGGGG
5339958 TTAGGGG
1 TTAGGGG
*
5339965 TTAGGGT
1 TTAGGGG
5339972 TTAG
1 TTAG
5339976 ATTAATTAGT
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 107 1.00
ACGTcount: A:0.19, C:0.01, G:0.51, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:5340095 original size:103 final size:105
Alignment explanation
Indices: 5339909--5340113 Score: 270
Period size: 103 Copynumber: 2.0 Consensus size: 105
5339899 GGGTTAAGGG
* * * * * * *
5339909 TTAGGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGTTT
1 TTAGGGGTTAGGGGTTAGGGGTTAAGGATTAGGGATTAGGAGTTACGGGTTAGGGGTTAAGATTT
** *
5339974 AGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGT
66 AGATTAATTAGTACTTTTTAATTTACATATTAAATAAAGT
* * *
5340014 TTAGGGGTTAGGGGTTAGGGGTTAAGGATTATGGATTTGGAG-T-CGGGTTAGGGTTTAAGATTT
1 TTAGGGGTTAGGGGTTAGGGGTTAAGGATTAGGGATTAGGAGTTACGGGTTAGGGGTTAAGATTT
*
5340077 GGATTAATTAGTACTTTTTAATTTACATATTAAATAA
66 AGATTAATTAGTACTTTTTAATTTACATATTAAATAA
5340114 GTTCTTTATA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
103 49 0.57
104 1 0.01
105 36 0.42
ACGTcount: A:0.26, C:0.01, G:0.33, T:0.40
Consensus pattern (105 bp):
TTAGGGGTTAGGGGTTAGGGGTTAAGGATTAGGGATTAGGAGTTACGGGTTAGGGGTTAAGATTT
AGATTAATTAGTACTTTTTAATTTACATATTAAATAAAGT
Found at i:5340215 original size:21 final size:21
Alignment explanation
Indices: 5340162--5340215 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
5340152 TAAAGATTAT
5340162 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
5340183 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
5340204 TAATTTAAAATT
1 TAATTTAAAATT
5340216 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:5340230 original size:8 final size:8
Alignment explanation
Indices: 5340205--5340238 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5340195 TGAATATAAT
5340205 AATT-TAA
1 AATTGTAA
5340212 AATTGTAAA
1 AATTGT-AA
5340221 AATTGTAA
1 AATTGTAA
5340229 AATTGTAA
1 AATTGTAA
5340237 AA
1 AA
5340239 AAATTGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.16
8 13 0.52
9 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (8 bp):
AATTGTAA
Found at i:5340252 original size:9 final size:9
Alignment explanation
Indices: 5340210--5340239 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5340200 ATAATAATTT
5340210 AAAATTGTA
1 AAAATTGTA
5340219 AAAATTGT-
1 AAAATTGTA
5340227 AAAATTGTA
1 AAAATTGTA
5340236 AAAA
1 AAAA
5340240 AATTGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (9 bp):
AAAATTGTA
Found at i:5340258 original size:20 final size:19
Alignment explanation
Indices: 5340218--5340260 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5340208 TTAAAATTGT
**
5340218 AAAAATTGTAAAATTGTAA
1 AAAAATTGTAAAATTACAA
5340237 AAAAATTGTCAAAATTACAA
1 AAAAATTGT-AAAATTACAA
5340257 AAAA
1 AAAA
5340261 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAATTGTAAAATTACAA
Found at i:5340261 original size:19 final size:19
Alignment explanation
Indices: 5340205--5340252 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 19
5340195 TGAATATAAT
5340205 AATT-TAAAATTGT--AAA
1 AATTGTAAAATTGTAAAAA
5340221 AATTGTAAAATTGTAAAAA
1 AATTGTAAAATTGTAAAAA
5340240 AATTGTCAAAATT
1 AATTGT-AAAATT
5340253 ACAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
19 9 0.32
20 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (19 bp):
AATTGTAAAATTGTAAAAA
Found at i:5340276 original size:18 final size:18
Alignment explanation
Indices: 5340255--5340296 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5340245 TCAAAATTAC
*
5340255 AAAAAATAAAATTA-AAAT
1 AAAAAATAAAA-AAGAAAT
5340273 AAAAAATAAAAAAGAAAT
1 AAAAAATAAAAAAGAAAT
5340291 AAAAAA
1 AAAAAA
5340297 AACTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAAAAGAAAT
Found at i:5340353 original size:47 final size:47
Alignment explanation
Indices: 5340293--5340389 Score: 131
Period size: 47 Copynumber: 2.1 Consensus size: 47
5340283 AAAGAAATAA
** * *
5340293 AAAAAACTAAAATTTTTATTTTTACCTAATTTTTATAAATATTACTT
1 AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACCT
* * *
5340340 AAAAAACTGAAATTGATAATTTTATCTAATTTTTTTAAATATTACCT
1 AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACCT
5340387 AAA
1 AAA
5340390 TTAACAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (47 bp):
AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACCT
Found at i:5342322 original size:7 final size:7
Alignment explanation
Indices: 5342310--5342361 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
5342300 TATTTCTTTA
5342310 TTTTCTG
1 TTTTCTG
5342317 TTTTCTG
1 TTTTCTG
*
5342324 TTTTCTA
1 TTTTCTG
*
5342331 TTTTTTG
1 TTTTCTG
5342338 TTTTCTG
1 TTTTCTG
*
5342345 TTTTGCTA
1 TTTT-CTG
5342353 TTTTCTG
1 TTTTCTG
5342360 TT
1 TT
5342362 GAATGAAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.73
Consensus pattern (7 bp):
TTTTCTG
Found at i:5342334 original size:21 final size:22
Alignment explanation
Indices: 5342308--5342361 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
5342298 TATATTTCTT
5342308 TATTTTCTGTTTTCTGTTTT-C
1 TATTTTCTGTTTTCTGTTTTGC
*
5342329 TATTTTTTGTTTTCTGTTTTGC
1 TATTTTCTGTTTTCTGTTTTGC
5342351 TATTTTCTGTT
1 TATTTTCTGTT
5342362 GAATGAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (22 bp):
TATTTTCTGTTTTCTGTTTTGC
Found at i:5343006 original size:53 final size:53
Alignment explanation
Indices: 5342949--5343098 Score: 237
Period size: 53 Copynumber: 2.8 Consensus size: 53
5342939 GACTTGAATA
**
5342949 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATT
* * * *
5343002 TATTACTTAAATATGTTACTCAGATGCATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATT
*
5343055 TTTTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
5343099 AAGTATATAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 87 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATT
Found at i:5343020 original size:13 final size:13
Alignment explanation
Indices: 5342932--5343089 Score: 88
Period size: 13 Copynumber: 12.0 Consensus size: 13
5342922 ATTTACTCTT
* *
5342932 AATATATGACTTG
1 AATATATTACTTA
5342945 AATATATTACTTA
1 AATATATTACTTA
*
5342958 AATAAATTACTTA
1 AATATATTACTTA
*
5342971 AATACATTACTTA
1 AATATATTACTTA
*
5342984 CTAA-A-ATTTCGTTA
1 --AATATATTAC-TTA
*
5342998 AATTTATTACTTA
1 AATATATTACTTA
* *
5343011 AATATGTTACTCA
1 AATATATTACTTA
* **
5343024 GATGCATTACTTA
1 AATATATTACTTA
* **
5343037 CTAAAAT-TTGGTTA
1 --AATATATTACTTA
* *
5343051 AATTTTTTACTTA
1 AATATATTACTTA
*
5343064 AATATGTTACTTA
1 AATATATTACTTA
*
5343077 AATACATTACTTA
1 AATATATTACTTA
5343090 CTAAAATTTA
Statistics
Matches: 108, Mismatches: 29, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
12 5 0.05
13 87 0.81
14 13 0.12
15 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.44
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:5343273 original size:9 final size:9
Alignment explanation
Indices: 5343230--5343333 Score: 106
Period size: 9 Copynumber: 11.8 Consensus size: 9
5343220 TATGTACAAG
5343230 AACTTACAT
1 AACTTACAT
* *
5343239 AATTTACAC
1 AACTTACAT
*
5343248 AACTTATAT
1 AACTTACAT
*
5343257 AACCTACAT
1 AACTTACAT
5343266 AACTTACAT
1 AACTTACAT
5343275 AA--TACA-
1 AACTTACAT
5343281 AAGCTTACAT
1 AA-CTTACAT
* *
5343291 AACTGAAAT
1 AACTTACAT
* *
5343300 AGCTTACAC
1 AACTTACAT
5343309 AACTTACAT
1 AACTTACAT
5343318 AACTTACAT
1 AACTTACAT
5343327 AACTTAC
1 AACTTAC
5343334 TGTAAGCACT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
6 2 0.03
7 4 0.05
9 67 0.89
10 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:5343474 original size:30 final size:29
Alignment explanation
Indices: 5343411--5343527 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 29
5343401 AAAAAAATAA
* *
5343411 AAATTGCATTTTGACACCTAAACTTT-TCCT
1 AAATTTCATTTTGAC-CCTAAACTTTCT-TT
5343441 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCTTT
* * *
5343471 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCTTT
* * *
5343501 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTGACCCTAAACTTTCT
5343528 AAAAATTACA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 57 0.78
31 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCTTT
Found at i:5343793 original size:10 final size:10
Alignment explanation
Indices: 5343774--5343823 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
5343764 TTTTTCGAAG
*
5343774 GAAAAAAGAA
1 GAAAAGAGAA
5343784 GAAAAGAGAA
1 GAAAAGAGAA
5343794 GAAAAGAGAA
1 GAAAAGAGAA
* *
5343804 -AGAGGAGAA
1 GAAAAGAGAA
5343813 GAAAAGA-AA
1 GAAAAGAGAA
5343822 GA
1 GA
5343824 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:5343824 original size:17 final size:19
Alignment explanation
Indices: 5343777--5343819 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5343767 TTCGAAGGAA
5343777 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
5343795 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
5343814 AAAAGA
1 AAAAGA
5343820 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:5343885 original size:3 final size:3
Alignment explanation
Indices: 5343879--5343924 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
5343869 GCTAGACTTT
*
5343879 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
5343925 AGAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5343897 original size:10 final size:10
Alignment explanation
Indices: 5343882--5343910 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5343872 AGACTTTGAA
5343882 GAAGAAGAAG
1 GAAGAAGAAG
5343892 GAAGAAGAAG
1 GAAGAAGAAG
5343902 GAAGAAGAA
1 GAAGAAGAA
5343911 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:5343897 original size:13 final size:13
Alignment explanation
Indices: 5343879--5343924 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
5343869 GCTAGACTTT
5343879 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
5343892 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
5343905 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
5343916 GAAGAAGAA
1 GAAGAAGAA
5343925 AGAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:5344224 original size:22 final size:22
Alignment explanation
Indices: 5344199--5344274 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 22
5344189 GCAGCCCAGC
*
5344199 AGAAAAAAAAGGAAGAAAAAGA
1 AGAAAAAAAAAGAAGAAAAAGA
*
5344221 AGAAAAAAGAAAAAAAGAAAAAGGA
1 AG-AAAAA-AAAAGAAGAAAAA-GA
*
5344246 AAAAAGAAAAAAGAA-AAAAAGA
1 AGAAA-AAAAAAGAAGAAAAAGA
5344268 AGAAAAA
1 AGAAAAA
5344275 GGGAGTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
21 2 0.04
22 8 0.18
23 10 0.22
24 20 0.44
25 5 0.11
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAGAAGAAAAAGA
Found at i:5344232 original size:7 final size:7
Alignment explanation
Indices: 5344215--5344264 Score: 73
Period size: 7 Copynumber: 6.9 Consensus size: 7
5344205 AAAAGGAAGA
5344215 AAAAGAAG
1 AAAA-AAG
5344223 AAAAAAG
1 AAAAAAG
5344230 AAAAAAAG
1 -AAAAAAG
*
5344238 AAAAAGG
1 AAAAAAG
5344245 AAAAAAG
1 AAAAAAG
5344252 AAAAAAG
1 AAAAAAG
5344259 AAAAAA
1 AAAAAA
5344265 AGAAGAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
7 28 0.72
8 11 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5344234 original size:8 final size:8
Alignment explanation
Indices: 5344211--5344275 Score: 75
Period size: 8 Copynumber: 8.4 Consensus size: 8
5344201 AAAAAAAAGG
5344211 AAGAAAAA
1 AAGAAAAA
5344219 GAAG-AAAA
1 -AAGAAAAA
5344227 AAGAAAAA
1 AAGAAAAA
5344235 AAG--AAA
1 AAGAAAAA
*
5344241 AAGGAAAA
1 AAGAAAAA
5344249 AAG-AAAA
1 AAGAAAAA
5344256 AAGAAAAA
1 AAGAAAAA
5344264 AAGAAGAAA
1 AAGAA-AAA
5344273 AAG
1 AAG
5344276 GGAGTTCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.12
7 10 0.20
8 26 0.51
9 9 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:5344238 original size:15 final size:15
Alignment explanation
Indices: 5344211--5344273 Score: 92
Period size: 15 Copynumber: 4.1 Consensus size: 15
5344201 AAAAAAAAGG
5344211 AAGAAAAAGAAGAAAA
1 AAGAAAAA-AAGAAAA
5344227 AAGAAAAAAAG-AAA
1 AAGAAAAAAAGAAAA
*
5344241 AAGGAAAAAAGAAAA
1 AAGAAAAAAAGAAAA
5344256 AAGAAAAAAAGAAGAA
1 AAGAAAAAAAGAA-AA
5344272 AA
1 AA
5344274 AGGGAGTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.30
15 18 0.42
16 12 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:5344271 original size:32 final size:35
Alignment explanation
Indices: 5344199--5344276 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 35
5344189 GCAGCCCAGC
*
5344199 AGAAAAAAAAGGAAGAAAAAGAAGAAAAAAGAAAA
1 AGAAGAAAAAGGAAGAAAAAGAAGAAAAAAGAAAA
5344234 A-AAGAAAAAGG-A-AAAAAGAA-AAAAGAA-AAAA
1 AGAAGAAAAAGGAAGAAAAAGAAGAAAA-AAGAAAA
5344265 AGAAGAAAAAGG
1 AGAAGAAAAAGG
5344277 GAGTTCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 9 0.22
32 20 0.50
33 1 0.03
34 9 0.22
35 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (35 bp):
AGAAGAAAAAGGAAGAAAAAGAAGAAAAAAGAAAA
Found at i:5344837 original size:18 final size:19
Alignment explanation
Indices: 5344812--5344867 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
5344802 GAAATTTTCG
**
5344812 AATTTTCGCGTTT-TCAAA
1 AATTTTCGCGTTTGAAAAA
* *
5344830 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTGAAAAA
5344849 AATTTTCGCGTTT-AAAAA
1 AATTTTCGCGTTTGAAAAA
5344867 A
1 A
5344868 TTTCTCGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTTCGCGTTTGAAAAA
Found at i:5344885 original size:37 final size:37
Alignment explanation
Indices: 5344812--5344885 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
5344802 GAAATTTTCG
* * * *
5344812 AATTTTCGCGTTTTCAAAAGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
5344849 AATTTTCGCG-TTTAAAAAATTTCTCGTATTTCAAAAA
1 AATTTTCGCGTTTTAAAAAATTT-TCGTATTTCAAAAA
5344886 TTGTCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
Found at i:5344952 original size:16 final size:16
Alignment explanation
Indices: 5344931--5344991 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
5344921 TCCTCGTGCT
5344931 TTTAAAAATTCTCATG
1 TTTAAAAATTCTCATG
* *
5344947 TTTAAAAAATCTTCGTG
1 TTTAAAAATTC-TCATG
*
5344964 TTTTCAAAATTCT-AGTG
1 -TTTAAAAATTCTCA-TG
5344981 TTTCAAAAATT
1 TTT-AAAAATT
5344992 TTCTTGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 13 0.37
17 13 0.37
18 9 0.26
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (16 bp):
TTTAAAAATTCTCATG
Found at i:5344972 original size:18 final size:18
Alignment explanation
Indices: 5344812--5345248 Score: 139
Period size: 17 Copynumber: 24.5 Consensus size: 18
5344802 GAAATTTTCG
*
5344812 AATTTTCGCGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
* **
5344830 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGTGTTT-TCAAA
* *
5344849 AATTTTCGCG-TTTAAAA
1 AATTTTCGTGTTTTCAAA
*
5344866 AATTTCTCGT-ATTTCAAA
1 AATTT-TCGTGTTTTCAAA
* * *
5344884 AATTGTCGT-TTTTTACA
1 AATTTTCGTGTTTTCAAA
* *
5344901 AATTTTCGTGCTTTCAAT
1 AATTTTCGTGTTTTCAAA
**
5344919 AATCCTCGTGCTTTT-AAA
1 AATTTTCGTG-TTTTCAAA
* * *
5344937 AATTCTCATG-TTTAAAA
1 AATTTTCGTGTTTTCAAA
*
5344954 AATCTTCGTGTTTTC-AA
1 AATTTTCGTGTTTTCAAA
* *
5344971 AATTCTAGTG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
*
5344988 AATTTTCTTGTTTTCAAAAAA
1 AATTTTCGTGTTTTC---AAA
** *
5345009 AAAATTCGTGTTTTAAAAAAAA
1 AATTTTCGTGTTTT----CAAA
5345031 AATATTTCCGTGTTTT-AAA
1 AAT-TTT-CGTGTTTTCAAA
5345050 AATTTTCGTGTTTT-AAA
1 AATTTTCGTGTTTTCAAA
* *
5345067 AATTCTCGT-ATTT-AAA
1 AATTTTCGTGTTTTCAAA
***
5345083 ATATTTT--T-TTAAGAAA
1 A-ATTTTCGTGTTTTCAAA
*
5345099 AAATTT--TG-TTTCAAAA
1 AATTTTCGTGTTTTC-AAA
* * *
5345115 AAATGTCTTGTTTT-AAA
1 AATTTTCGTGTTTTCAAA
*
5345132 AA-TTCCG-GTGTTTCAAAAA
1 AATTTTCGTGT-TTTC--AAA
* *
5345151 AAATGTCGTGTTTT-AAGA
1 AATTTTCGTGTTTTCAA-A
* *
5345169 AAATTTCGTTTTTTTTCAAA
1 AATTTTCG--TGTTTTCAAA
*
5345189 AATTTTCGTG-TTTCTAA
1 AATTTTCGTGTTTTCAAA
* *
5345206 AATATTCGTG-TTT-ACA
1 AATTTTCGTGTTTTCAAA
*
5345222 AATTCTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
*
5345240 AATTCTCGT
1 AATTTTCGT
5345249 ATTTAAAAAA
Statistics
Matches: 315, Mismatches: 67, Indels: 74
0.69 0.15 0.16
Matches are distributed among these distances:
15 10 0.03
16 40 0.13
17 105 0.33
18 80 0.25
19 28 0.09
20 19 0.06
21 18 0.06
22 5 0.02
23 2 0.01
24 8 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (18 bp):
AATTTTCGTGTTTTCAAA
Found at i:5345030 original size:24 final size:24
Alignment explanation
Indices: 5345003--5345051 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5344993 TCTTGTTTTC
5345003 AAAAAAAAAATT-CGTGTTTTAAA
1 AAAAAAAAAATTCCGTGTTTTAAA
* *
5345026 AAAAAAATATTTCCGTGTTTTAAA
1 AAAAAAAAAATTCCGTGTTTTAAA
5345050 AA
1 AA
5345052 TTTTCGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (24 bp):
AAAAAAAAAATTCCGTGTTTTAAA
Found at i:5345115 original size:16 final size:18
Alignment explanation
Indices: 5345096--5345133 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5345086 TTTTTTTAAG
5345096 AAAAAAT-T-TTGTTTCA
1 AAAAAATGTCTTGTTTCA
*
5345112 AAAAAATGTCTTGTTTTA
1 AAAAAATGTCTTGTTTCA
5345130 AAAA
1 AAAA
5345134 TTCCGGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (18 bp):
AAAAAATGTCTTGTTTCA
Found at i:5345230 original size:16 final size:16
Alignment explanation
Indices: 5345186--5345257 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
5345176 GTTTTTTTTC
*
5345186 AAAAATTTTCGTGTTT
1 AAAAATTCTCGTGTTT
*
5345202 CTAAAATAT-TCGTGTTT
1 -AAAAAT-TCTCGTGTTT
*
5345219 ACAAATTCTCGTGTTTT
1 AAAAATTCTCGTG-TTT
*
5345236 CAAAAATTCTCGTATTT
1 -AAAAATTCTCGTGTTT
5345253 AAAAA
1 AAAAA
5345258 AAAACTTTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 14 0.30
17 19 0.41
18 12 0.26
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (16 bp):
AAAAATTCTCGTGTTT
Found at i:5345258 original size:18 final size:18
Alignment explanation
Indices: 5345221--5345259 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5345211 TCGTGTTTAC
* **
5345221 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTATTTAAAA
5345239 AAATTCTCGTATTTAAAA
1 AAATTCTCGTATTTAAAA
5345257 AAA
1 AAA
5345260 AACTTTCGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (18 bp):
AAATTCTCGTATTTAAAA
Found at i:5356514 original size:21 final size:22
Alignment explanation
Indices: 5356466--5356508 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5356456 TGGTGGTTGT
*
5356466 TGTTTGTGGTTTACGGGTTTAA
1 TGTTTATGGTTTACGGGTTTAA
5356488 TGTTTATGGTTTA-GGGTTTAA
1 TGTTTATGGTTTACGGGTTTAA
5356509 GATTTACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.51
Consensus pattern (22 bp):
TGTTTATGGTTTACGGGTTTAA
Found at i:5356519 original size:21 final size:22
Alignment explanation
Indices: 5356473--5356519 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5356463 TGTTGTTTGT
*
5356473 GGTTTACGGGTTTAATGTTTAT
1 GGTTTACGGGTTTAATGTTTAC
5356495 GGTTTA-GGGTTTAA-GATTTAC
1 GGTTTACGGGTTTAATG-TTTAC
5356516 GGTT
1 GGTT
5356520 AATTTGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.47
Consensus pattern (22 bp):
GGTTTACGGGTTTAATGTTTAC
Found at i:5356633 original size:21 final size:21
Alignment explanation
Indices: 5356603--5356661 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5356593 CAGGGTTTAA
* *
5356603 GTTTACGATTTAGGGTTTGGG
1 GTTTAAGATTTACGGTTTGGG
* **
5356624 GTTTAGGATTTATAGTTTGGG
1 GTTTAAGATTTACGGTTTGGG
5356645 GTTTAAGATTTACGGTT
1 GTTTAAGATTTACGGTT
5356662 AGGCTTACAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (21 bp):
GTTTAAGATTTACGGTTTGGG
Found at i:5357032 original size:21 final size:22
Alignment explanation
Indices: 5357008--5357050 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5356998 AATATATTGA
*
5357008 TGTATTTA-TTTTTTAAAAATG
1 TGTAATTATTTTTTTAAAAATG
5357029 TGTAATTATTTTTTTAAAAATG
1 TGTAATTATTTTTTTAAAAATG
5357051 CATTACTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (22 bp):
TGTAATTATTTTTTTAAAAATG
Found at i:5358683 original size:18 final size:18
Alignment explanation
Indices: 5358643--5358686 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5358633 GTATTTTATG
**
5358643 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
5358661 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
5358679 CTTGGGTT
1 ATTGGGTT
5358687 TAGATTGGGT
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:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:5358997 original size:25 final size:25
Alignment explanation
Indices: 5358966--5359016 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5358956 TTGCATAATA
*
5358966 ATTCTTACTCTATAGCTTATCAAAT
1 ATTCTTACTCTATAGCTTATAAAAT
5358991 ATTCTTACTCTATAGCTTATAAAAT
1 ATTCTTACTCTATAGCTTATAAAAT
5359016 A
1 A
5359017 ATTAAATTGT
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:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (25 bp):
ATTCTTACTCTATAGCTTATAAAAT
Found at i:5359784 original size:43 final size:44
Alignment explanation
Indices: 5359710--5359803 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
5359700 GTCATGTCTA
* *
5359710 TAGCGGCGTTGGTGGAAAAGAACGCCGCTAAAGAACATTACTTT
1 TAGCGGCGTTGGTGGAAAAGAACGCCACTAAAGAACATTACCTT
* *
5359754 TAGCGGCGTTTGT-GAAGAA-AACGCTACTAAAGAACATTACCTT
1 TAGCGGCGTTGGTGGAA-AAGAACGCCACTAAAGAACATTACCTT
5359797 TAGCGGC
1 TAGCGGC
5359804 ATTTTCGAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 31 0.69
44 14 0.31
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (44 bp):
TAGCGGCGTTGGTGGAAAAGAACGCCACTAAAGAACATTACCTT
Found at i:5360819 original size:1 final size:1
Alignment explanation
Indices: 5360813--5360860 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
5360803 TGATAAGCAG
* * * *
5360813 TTTTTTTTTTTTATTATTTTTTTTTTTTTTTATTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5360861 ATTTCTATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.06, C:0.00, G:0.02, T:0.92
Consensus pattern (1 bp):
T
Found at i:5360835 original size:17 final size:16
Alignment explanation
Indices: 5360813--5360864 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
5360803 TGATAAGCAG
*
5360813 TTTTTTTTTTTTATTA
1 TTTTTTTTTTTTTTTA
5360829 TTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTA
5360845 TTTTTTTTTGTTTTTTA
1 TTTTTTTTT-TTTTTTA
5360862 TTT
1 TTT
5360865 CTATATTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 24 0.71
17 10 0.29
ACGTcount: A:0.08, C:0.00, G:0.02, T:0.90
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTA
Found at i:5360837 original size:19 final size:18
Alignment explanation
Indices: 5360813--5360864 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 18
5360803 TGATAAGCAG
5360813 TTTTTTTTTTTTATTATTT
1 TTTTTTTTTTTTATT-TTT
5360832 TTTTTTTTTTTTA-TTTT
1 TTTTTTTTTTTTATTTTT
*
5360849 TTTTTGTTTTTTATTT
1 TTTTTTTTTTTTATTT
5360865 CTATATTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 15 0.48
18 3 0.10
19 13 0.42
ACGTcount: A:0.08, C:0.00, G:0.02, T:0.90
Consensus pattern (18 bp):
TTTTTTTTTTTTATTTTT
Found at i:5361282 original size:21 final size:21
Alignment explanation
Indices: 5361253--5361299 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5361243 GAAGCGCAGT
*
5361253 ATTTCTTTTTTAAA-ACGA-A
1 ATTTTTTTTTTAAATACGAGA
5361272 AGTTTTTTTTTTAAATACGAGA
1 A-TTTTTTTTTTAAATACGAGA
5361294 ATTTTT
1 ATTTTT
5361300 GAAAACACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 9 0.38
22 2 0.08
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (21 bp):
ATTTTTTTTTTAAATACGAGA
Found at i:5361298 original size:16 final size:16
Alignment explanation
Indices: 5361279--5361350 Score: 65
Period size: 16 Copynumber: 4.3 Consensus size: 16
5361269 GAAAGTTTTT
*
5361279 TTTTTAAATACGAGAA
1 TTTTTAAACACGAGAA
5361295 TTTTTGAAAACACGAGAA
1 TTTTT--AAACACGAGAA
*
5361313 TTTGTAAACACGA-ATA
1 TTTTTAAACACGAGA-A
* *
5361329 TTTTAGAAACACGAAAA
1 TTTT-TAAACACGAGAA
5361346 TTTTT
1 TTTTT
5361351 GGAAAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
15 1 0.02
16 17 0.37
17 13 0.28
18 15 0.33
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (16 bp):
TTTTTAAACACGAGAA
Found at i:5361427 original size:18 final size:16
Alignment explanation
Indices: 5361406--5361457 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
5361396 AACACGGGAA
5361406 TTTTTAAAACAAGACATT
1 TTTTTAAAACAA-A-ATT
*
5361424 TTTTTGAAACAAAATTT
1 TTTTTAAAACAAAA-TT
5361441 TTTCTTAAAA-AAAATT
1 TTT-TTAAAACAAAATT
5361457 T
1 T
5361458 AAATACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
18 16 0.53
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (16 bp):
TTTTTAAAACAAAATT
Found at i:5361502 original size:18 final size:17
Alignment explanation
Indices: 5361462--5361720 Score: 121
Period size: 17 Copynumber: 14.5 Consensus size: 17
5361452 AAATTTAAAT
*
5361462 ACGAGAATTTTTAAAAC
1 ACGAAAATTTTTAAAAC
5361479 ACGAAAATTTTTAAAAC
1 ACGAAAATTTTTAAAAC
5361496 ACGGAAATATTTTTTTTTAAAAC
1 AC-GAAA-A----TTTTTAAAAC
*
5361519 ACGAAATTTTTTTTTGAAAAC
1 ACGAAA---ATTTTT-AAAAC
* *
5361540 AAGAAAATTTTTGAAAC
1 ACGAAAATTTTTAAAAC
* * *
5361557 ACTAGAATTTTGAAAAC
1 ACGAAAATTTTTAAAAC
* *
5361574 ACGAAGATTTTTGAAAC
1 ACGAAAATTTTTAAAAC
* *
5361591 ATGAGAA-TTTTAAAAGC
1 ACGAAAATTTTTAAAA-C
** * *
5361608 ACGAGGATTATTGAAAGC
1 ACGAAAATT-TTTAAAAC
* * *
5361626 ACGAAGATTTATAAAAA
1 ACGAAAATTTTTAAAAC
* * *
5361643 ACGACAA-TTTTGAAAT
1 ACGAAAATTTTTAAAAC
5361659 ACGAGAAA-TTTT-AAAC
1 ACGA-AAATTTTTAAAAC
* *
5361675 GCGAAAATTTTTTTCAAAC
1 ACGAAAA--TTTTTAAAAC
*
5361694 ACGAAAACTTTTGAAAAC
1 ACGAAAA-TTTTTAAAAC
*
5361712 GCGAAAATT
1 ACGAAAATT
5361721 CGAAAATTTC
Statistics
Matches: 184, Mismatches: 41, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
15 3 0.02
16 23 0.12
17 73 0.40
18 37 0.20
19 16 0.09
20 5 0.03
21 10 0.05
22 4 0.02
23 12 0.07
24 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
ACGAAAATTTTTAAAAC
Done.