Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 61 of 150
Found at i:18163805 original size:10 final size:10
Alignment explanation
Indices: 18163775--18163809 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
18163765 CATGATGAAG
18163775 TTTAATTAAT
1 TTTAATTAAT
18163785 TTTATAGTTAAT
1 TTTA-A-TTAAT
18163797 TTTAATTAAT
1 TTTAATTAAT
18163807 TTT
1 TTT
18163810 GACTATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.52
11 2 0.09
12 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTAATTAAT
Found at i:18164374 original size:16 final size:18
Alignment explanation
Indices: 18164353--18164389 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18164343 CCCTTACTGA
18164353 TCATTCA-A-CTCATCCC
1 TCATTCACATCTCATCCC
18164369 TCATTCACATCTCATCCC
1 TCATTCACATCTCATCCC
18164387 TCA
1 TCA
18164390 CACTCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.32
Consensus pattern (18 bp):
TCATTCACATCTCATCCC
Found at i:18167490 original size:25 final size:25
Alignment explanation
Indices: 18167389--18167491 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
18167379 GGCTCTTCGA
*
18167389 AGCTACCCGTTAT-TGGCTCACATG
1 AGCTTCCCGTTATATGGCTCACATG
**
18167413 AGCTTCCCG--ATGATGGCTCTTATG
1 AGCTTCCCGTTAT-ATGGCTCACATG
** * ** *
18167437 AGCTTCCCGTTATACAGCCCGGATA
1 AGCTTCCCGTTATATGGCTCACATG
18167462 AGCTTCCCGTTATATGGCTCACATG
1 AGCTTCCCGTTATATGGCTCACATG
18167487 AGCTT
1 AGCTT
18167492 TCTATTATAT
Statistics
Matches: 60, Mismatches: 15, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
22 2 0.03
24 26 0.43
25 30 0.50
26 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCACATG
Found at i:18168417 original size:15 final size:16
Alignment explanation
Indices: 18168392--18168421 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18168382 TCTCTAATTT
18168392 TTATATCTTTTTTTTG
1 TTATATCTTTTTTTTG
18168408 TTAT-TCTTTTTTTT
1 TTATATCTTTTTTTT
18168422 TTTCATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (16 bp):
TTATATCTTTTTTTTG
Found at i:18169231 original size:31 final size:31
Alignment explanation
Indices: 18169170--18169231 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
18169160 TTTAATATAT
*
18169170 ATATACATTATTTAGTTTAAATTGTCTTTTA
1 ATATACATTATTTAGTTTAAATTATCTTTTA
* *
18169201 ATATATATTATTTAGTTTAAATTATTTTTTA
1 ATATACATTATTTAGTTTAAATTATCTTTTA
18169232 TATGTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (31 bp):
ATATACATTATTTAGTTTAAATTATCTTTTA
Found at i:18169234 original size:28 final size:30
Alignment explanation
Indices: 18169169--18169241 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
18169159 TTTTAATATA
* *
18169169 TATATACATTATTTAGTTTAAATTGTCTTT
1 TATATATATTATTTAGTTTAAATTATCTTT
18169199 TAATATATATTATTTAGTTTAAATTAT-TTT
1 T-ATATATATTATTTAGTTTAAATTATCTTT
*
18169229 T-TATATGTTATTT
1 TATATATATTATTT
18169242 CAAAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 11 0.28
30 5 0.13
31 23 0.59
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (30 bp):
TATATATATTATTTAGTTTAAATTATCTTT
Found at i:18169485 original size:25 final size:25
Alignment explanation
Indices: 18169435--18169485 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
18169425 TACTTTGCAA
*
18169435 ATGATTTATTTTAAGTTATTTATAT
1 ATGATTTATTTTAAGTTACTTATAT
* *
18169460 ATGATTTTATTTTTAGTTGCTT-TAT
1 ATGA-TTTATTTTAAGTTACTTATAT
18169485 A
1 A
18169486 CATAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (25 bp):
ATGATTTATTTTAAGTTACTTATAT
Found at i:18177097 original size:16 final size:17
Alignment explanation
Indices: 18177072--18177104 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18177062 TATCTCGGGA
*
18177072 ATTAATTTA-TAAAGTT
1 ATTAAATTATTAAAGTT
18177088 ATTAAATTATTAAAGTT
1 ATTAAATTATTAAAGTT
18177105 TTTCCATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTAAATTATTAAAGTT
Found at i:18177982 original size:25 final size:23
Alignment explanation
Indices: 18177924--18177984 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 23
18177914 TTAATGGCTC
*
18177924 TCTGGAGCTTCCCGATATGACTC
1 TCTGGAGCTTCCCGATATGACTA
* * * *
18177947 GCTTGAACTTCCCGATATATGCCTA
1 TCTGGAGCTTCCCG--ATATGACTA
18177972 TCTGGAGCTTCCC
1 TCTGGAGCTTCCC
18177985 ATTAATGGCT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 11 0.39
25 17 0.61
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (23 bp):
TCTGGAGCTTCCCGATATGACTA
Found at i:18186305 original size:66 final size:66
Alignment explanation
Indices: 18186191--18186319 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
18186181 AATCTGACTG
*
18186191 AGACATGTAATAATGATGTACAAACTAAGACATAATTAATAGACTTGAAACAACTAAA-AACAAT
1 AGACATGTAATAATGATGTACAAACTAAAACATAATTAATAGACTTGAAACAACTAAAGAACAAT
18186255 C
66 C
* ** * *
18186256 AGACATGTAATAATGTTGTATGGAATTAAAACATAATTAATATGA-TTGAAATAACTAAAGAACA
1 AGACATGTAATAATGATGTA-CAAACTAAAACATAATTAATA-GACTTGAAACAACTAAAGAACA
18186320 TTTAAGTCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 19 0.35
66 30 0.55
67 6 0.11
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.26
Consensus pattern (66 bp):
AGACATGTAATAATGATGTACAAACTAAAACATAATTAATAGACTTGAAACAACTAAAGAACAAT
C
Found at i:18189005 original size:11 final size:11
Alignment explanation
Indices: 18188989--18189025 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
18188979 CAGCTAATTT
18188989 GTTAGCTGTTA
1 GTTAGCTGTTA
18189000 GTTAGCTGTTA
1 GTTAGCTGTTA
*
18189011 GTTAATCTGTTA
1 GTT-AGCTGTTA
18189023 GTT
1 GTT
18189026 TGTTCTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.19, C:0.08, G:0.24, T:0.49
Consensus pattern (11 bp):
GTTAGCTGTTA
Found at i:18211119 original size:7 final size:7
Alignment explanation
Indices: 18211109--18211163 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
18211099 AAAAAAGGAA
18211109 AAAGAAC
1 AAAGAAC
18211116 AAAGAAC
1 AAAGAAC
*
18211123 AAAGAAG
1 AAAGAAC
18211130 ATAACGGGAA-
1 A-AA---GAAC
18211140 AAAGAAC
1 AAAGAAC
18211147 AAAGAAC
1 AAAGAAC
18211154 AAAGAAC
1 AAAGAAC
18211161 AAA
1 AAA
18211164 AAAGAGGAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 3 0.07
7 31 0.74
8 2 0.05
9 2 0.05
10 1 0.02
11 3 0.07
ACGTcount: A:0.69, C:0.11, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAAC
Found at i:18212981 original size:21 final size:22
Alignment explanation
Indices: 18212955--18212997 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
18212945 TTTATAATAT
*
18212955 TTAAAATTTTATAAAAA-CATA
1 TTAAAATTCTATAAAAATCATA
18212976 TTAAAATTCTATAAAAATCATA
1 TTAAAATTCTATAAAAATCATA
18212998 AAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAATTCTATAAAAATCATA
Found at i:18213002 original size:21 final size:21
Alignment explanation
Indices: 18212957--18213004 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
18212947 TATAATATTT
* *
18212957 AAAATTTTATAAAAACATATT
1 AAAATTCTATAAAAACATATA
18212978 AAAATTCTATAAAAATCATA-A
1 AAAATTCTATAAAAA-CATATA
18212999 AAAATT
1 AAAATT
18213005 ATAAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTCTATAAAAACATATA
Found at i:18213007 original size:19 final size:19
Alignment explanation
Indices: 18212963--18213010 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
18212953 ATTTAAAATT
*
18212963 TTATAAAAACATATTAAAAT
1 TTATAAAAACATA-TAAAAA
18212983 TCTATAAAAATCATA-AAAAA
1 T-TATAAAAA-CATATAAAAA
18213003 TTATAAAA
1 TTATAAAA
18213011 TTACTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 6 0.24
21 8 0.32
22 4 0.16
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TTATAAAAACATATAAAAA
Found at i:18213412 original size:18 final size:18
Alignment explanation
Indices: 18213370--18213456 Score: 52
Period size: 18 Copynumber: 4.7 Consensus size: 18
18213360 TTCTAATACA
18213370 TTTT-TAATTTTA-ATATT
1 TTTTATAATTTTATAT-TT
**
18213387 TTAAATAATTTTATATTT
1 TTTTATAATTTTATATTT
* *
18213405 TTTTATAATTTATTAGAATT
1 TTTTATAA-TT-TTATATTT
* * * *
18213425 TATTAGATTTTTATAAGTT
1 TTTTATAATTTTAT-ATTT
18213444 TTTTATAATTTTA
1 TTTTATAATTTTA
18213457 ATAAGTTAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
17 2 0.04
18 19 0.37
19 19 0.37
20 11 0.22
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTATATTT
Found at i:18213446 original size:11 final size:10
Alignment explanation
Indices: 18213282--18213455 Score: 56
Period size: 10 Copynumber: 17.2 Consensus size: 10
18213272 TTTCTATAAA
*
18213282 TTTTATAAGT
1 TTTTATAATT
*
18213292 TTATATCAA-T
1 TTTTAT-AATT
*
18213302 TTTAAT-ATT
1 TTTTATAATT
*
18213311 TTTAAT-ATT
1 TTTTATAATT
18213320 TTTTATAATT
1 TTTTATAATT
* *
18213330 ATTTACAATT
1 TTTTATAATT
* *
18213340 TTATAATTATT
1 TT-TTATAATT
18213351 TTTTAATAA-T
1 TTTT-ATAATT
* *
18213361 TCTAATACATTT
1 TTTTATA-A-TT
* *
18213373 TTAATTTTAATA
1 TT--TTATAATT
*
18213385 TTTTA-AATAA
1 TTTTATAAT-T
*
18213395 TTTTATATTT
1 TTTTATAATT
18213405 TTTTATAATT
1 TTTTATAATT
* *
18213415 TATTAGAATT
1 TTTTATAATT
* *
18213425 TATTA-GA-T
1 TTTTATAATT
18213433 TTTTATAAGTT
1 TTTTATAA-TT
18213444 TTTTATAATT
1 TTTTATAATT
18213454 TT
1 TT
18213456 AATAAGTTAA
Statistics
Matches: 122, Mismatches: 27, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
8 6 0.05
9 23 0.19
10 61 0.50
11 23 0.19
12 5 0.04
13 1 0.01
14 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:18213463 original size:20 final size:19
Alignment explanation
Indices: 18213270--18213460 Score: 92
Period size: 19 Copynumber: 10.0 Consensus size: 19
18213260 TTTATGTTTT
18213270 TTTTTCTATAAATTTT-ATAA
1 TTTTT-TAT-AATTTTAATAA
* *
18213290 GTTTATATCAATTTTAAT-A
1 TTTTTTAT-AATTTTAATAA
* * *
18213309 TTTTTAATATTTTTTATAA
1 TTTTTTATAATTTTAATAA
* * *
18213328 TTATTTACAATTTTATAATTA
1 TTTTTTATAA-TTT-TAATAA
*
18213349 TTTTTTAATAATTCTAATACA
1 TTTTTT-ATAATTTTAATA-A
18213370 --TTTT-TAATTTTAAT-A
1 TTTTTTATAATTTTAATAA
** *
18213385 TTTTAAATAATTTT-ATAT
1 TTTTTTATAATTTTAATAA
* *
18213403 TTTTTTATAATTTATTAGAA
1 TTTTTTATAATTT-TAATAA
* * *
18213423 TTTATTA-GATTTTTATAA
1 TTTTTTATAATTTTAATAA
18213441 GTTTTTTATAATTTTAATAA
1 -TTTTTTATAATTTTAATAA
18213461 GTTAATATCA
Statistics
Matches: 125, Mismatches: 32, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
15 1 0.01
17 13 0.10
18 30 0.24
19 37 0.30
20 29 0.23
21 12 0.10
22 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTTATAATTTTAATAA
Found at i:18215644 original size:22 final size:22
Alignment explanation
Indices: 18215613--18215661 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
18215603 TCATGGACAT
*
18215613 GGAAGGTCATACTAATGAGCAA
1 GGAAGATCATACTAATGAGCAA
* *
18215635 GGAAGATCATACTAATGGGCGA
1 GGAAGATCATACTAATGAGCAA
18215657 GGAAG
1 GGAAG
18215662 TGATTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.33, T:0.16
Consensus pattern (22 bp):
GGAAGATCATACTAATGAGCAA
Found at i:18219729 original size:19 final size:19
Alignment explanation
Indices: 18219705--18219779 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
18219695 AATCTTCAAG
18219705 GATATGCAATCTTGGATAT
1 GATATGCAATCTTGGATAT
*
18219724 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
18219743 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
18219764 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
18219780 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:18226763 original size:44 final size:45
Alignment explanation
Indices: 18226710--18226992 Score: 281
Period size: 44 Copynumber: 6.4 Consensus size: 45
18226700 TTGTAGCGGT
* *
18226710 GTAGATCGAAGAAAGCAGATATTGTCTTCATTTATTGG-CGTGAA
1 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * * *
18226754 GTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAG-GAA
1 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * * *
18226798 GTGGATCGAAG-ATGCAGATCTTGTCTTCATGTATTAG-CGTGAA
1 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * * * *
18226841 GTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAA
1 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
** * ** * * *
18226886 GGGGATCGAAG-ATGCAGATCTTGTCCTTCCCATACTGGTGGCGAA
1 GTAGATCGAAGAAAGCAGATCTTGT-CTTCATATATTGGTCGTGAA
*
18226931 GTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAA
1 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* *
18226975 GTAGATCAAAGATAGCAG
1 GTAGATCGAAGAAAGCAG
18226993 GAAGTGGATC
Statistics
Matches: 191, Mismatches: 42, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.01
43 33 0.17
44 96 0.50
45 49 0.26
46 12 0.06
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (45 bp):
GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
Found at i:18226824 original size:87 final size:88
Alignment explanation
Indices: 18226713--18226968 Score: 334
Period size: 87 Copynumber: 2.9 Consensus size: 88
18226703 TAGCGGTGTA
* * * *
18226713 GATCGAAGAAAGCAGATATTGTCTTCATTTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCTTG
1 GATCGAAG-ATGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTG
*
18226778 TCTTCCTATATTGGTAG-GAAGTG
65 TCTTCCTATATTGGTAGCGAAGGG
* * *
18226801 GATCGAAGATGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGT
1 GATCGAAGATGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGT
18226866 CTTCCTATATTGGTAGCGAAGGG
66 CTTCCTATATTGGTAGCGAAGGG
** * * * *
18226889 GATCGAAGATGCAGATCTTGTCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTT
1 GATCGAAGATGCAGATCTTGT-CTTCATATATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTT
* *
18226954 GTCTTCATGTATTGG
64 GTCTTCCTATATTGG
18226969 CGTGAAGTAG
Statistics
Matches: 147, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
87 67 0.46
88 34 0.23
89 8 0.05
90 38 0.26
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (88 bp):
GATCGAAGATGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGT
CTTCCTATATTGGTAGCGAAGGG
Found at i:18227049 original size:44 final size:44
Alignment explanation
Indices: 18226993--18227181 Score: 175
Period size: 44 Copynumber: 4.3 Consensus size: 44
18226983 AAGATAGCAG
* *
18226993 GAAGTGGATCGAAGATGTAGATCTTATCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGC
* * *** * *
18227037 GAAATAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGT-GT
1 GAAGTAGATCGAAG-ATGTAGATCTTGTCTTCCCATACTGGTGGC
* * * * * * *
18227081 GAAGTAGATCGAAAATAGAAGGTCCTGTCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGAT-GTAGATCTTGTCTTCCCATACTGGTGGC
* * *
18227125 GAAGTGGATCGAAGATGCAGATCTTGTCATCCCATACTGGTGGC
1 GAAGTAGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGC
18227169 GAAGTAGATCGAA
1 GAAGTAGATCGAA
18227182 AACACCAGCC
Statistics
Matches: 114, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
43 21 0.18
44 71 0.62
45 22 0.19
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (44 bp):
GAAGTAGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGC
Found at i:18227083 original size:109 final size:110
Alignment explanation
Indices: 18226883--18227098 Score: 355
Period size: 109 Copynumber: 2.0 Consensus size: 110
18226873 TATTGGTAGC
* *
18226883 GAAGGGGATCGAAGATGCAGATCTTGTCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGGGGATCGAAGATGCAGATCTTATCCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCA
18226948 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-AAAGATAGCAG
66 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAA-ATAGCAG
* * *
18226993 GAAGTGGATCGAAGATGTAGATCTTAT-CTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGTA
1 GAAGGGGATCGAAGATGCAGATCTTATCCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCA
*
18227057 GATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAAATAG
66 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAG
18227099 AAGGTCCTGT
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
109 72 0.73
110 27 0.27
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (110 bp):
GAAGGGGATCGAAGATGCAGATCTTATCCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCA
GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAG
Found at i:18227926 original size:44 final size:44
Alignment explanation
Indices: 18227789--18228015 Score: 124
Period size: 44 Copynumber: 5.2 Consensus size: 44
18227779 AGACACTAGC
* *
18227789 CTTGCCTCCCTCGGTGGCAGTGGAACAGGTTAAAGATAACAGAT
1 CTTGCCTCCCTCGGTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
* * * * ** * * * *
18227833 ATTGCCTTCCT-GTACTGACAGTAAAGCAGATTGAAGACA-CTAG-C
1 CTTGCCTCCCTCG--GTGGCAGTGGAGCAGGTTAAAGATAGC-AGAT
*
18227877 CTTGCCTCCCTCGGTGGCAGCGGAGCAGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGGTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
* * ** * * * * * *
18227921 CTTGCCTTCCT-GTACTAACAGTGAAACAGATTGAAGACA-CTAG-C
1 CTTGCCTCCCTCG--GTGGCAGTGGAGCAGGTTAAAGATAGC-AGAT
* * *
18227965 CTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTCGGTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
18228009 CTTGCCT
1 CTTGCCT
18228016 TCCTGCACCA
Statistics
Matches: 127, Mismatches: 44, Indels: 24
0.65 0.23 0.12
Matches are distributed among these distances:
43 39 0.31
44 49 0.39
45 39 0.31
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTCGGTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
Found at i:18228057 original size:44 final size:44
Alignment explanation
Indices: 18227834--18228235 Score: 132
Period size: 44 Copynumber: 9.1 Consensus size: 44
18227824 ATAACAGATA
* * ** *
18227834 TTGCCTTCCTGTACTGACAGTAAAGCAGATTGAAGACACTAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
* *** * * * * * * *
18227878 TTGCCTCCCT-CGGTGGCAGCGGAGCAGGTTAAAGATAGCAGATC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAG-CC
* ** * * *
18227922 TTGCCTTCCTGTACTAACAGTGAAACAGATTGAAGACACTAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
* **** * * * * * * * *
18227966 TTGCCTCCCTGGGTTG-CAGTGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAG-CC
*
18228010 TTGCCTTCCTGCACCAACAGCGAAGCAGATTGAAGACACCAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
* **** * * * * * *
18228054 TTGCCTCCCTGGGTTG-CAGCGGAA-CAGGTTAAAAATAGCAGATC
1 TTGCCTTCCTGCACCGACAGC-GAAGCAGATTGAAGACACCAG-CC
* * *
18228098 TTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
* * ** * * * * * * * *
18228142 TTACCTCCCTG-AGTTG-CAACGGAGCAGGTTAAAAATAACAGATC
1 TTGCCTTCCTGCA-CCGACAGCGAAGCAGATTGAAGACACCAG-CC
* *
18228186 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACATCAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
18228230 TTGCCT
1 TTGCCT
18228236 CCTTGAGTTG
Statistics
Matches: 237, Mismatches: 109, Indels: 24
0.64 0.29 0.06
Matches are distributed among these distances:
43 70 0.30
44 100 0.42
45 67 0.28
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (44 bp):
TTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCC
Found at i:18228063 original size:351 final size:351
Alignment explanation
Indices: 18227418--18228237 Score: 1054
Period size: 351 Copynumber: 2.3 Consensus size: 351
18227408 CTGACAGTAA
* * * * * *
18227418 AGTAGATTGAAGACACTAGCCTTGCTTCCCTCTGTGGCAACGGAGCAGGTTAAGGATAGCAGATC
1 AGTAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAACGGAACAGGTTAAAGATAACAGATA
* *
18227483 TTGCCTTCTTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCG
66 TTGCCTTCCTGTACTAACAGTAAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCG
* * ** *
18227548 GAGTAGGTTAAAGATAGCAGATCTTGCCTTCTTATACTAACAACGAAGTAGGTCGAAGACACTAG
131 GAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTATACTAACAACGAAACAGATCGAAGACACTAG
* **
18227613 CCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCATGCCTTCCTGTACCGGCA
196 CCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCATGCCTTCCTGCACCAACA
* * * *
18227678 GCGAAGTAGATCAAAGACACCAGCCTTACCTCCCTGGGTTACAGCAGAGCAGGTTGAAAATTGCA
261 GCGAAGCAGATCAAAGACACCAGCCTTACCTCCCTGGGTTACAGCAGAACAGGTTAAAAATAGCA
18227743 GATCTTATCTCCCTAAGCAGTAGTGG
326 GATCTTATCTCCCTAAGCAGTAGTGG
**
18227769 AGTAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGTGGAACAGGTTAAAGATAACAGATA
1 AGTAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAACGGAACAGGTTAAAGATAACAGATA
*
18227834 TTGCCTTCCTGTACTGACAGTAAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCG
66 TTGCCTTCCTGTACTAACAGTAAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCG
* ** *
18227899 GAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAACAGATTGAAGACACTAG
131 GAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTATACTAACAACGAAACAGATCGAAGACACTAG
** *
18227964 CCTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCAACA
196 CCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCATGCCTTCCTGCACCAACA
** * * *
18228029 GCGAAGCAGATTGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTAAAAATAGCA
261 GCGAAGCAGATCAAAGACACCAGCCTTACCTCCCTGGGTTACAGCAGAACAGGTTAAAAATAGCA
** * * ** *
18228094 GATCTTGCCTTCCT--GCACCGACAACGA
326 GATCTTATCTCCCTAAGCA--G-TAGTGG
* * * * * * * *
18228121 AGCAGATCGAAGACACCAACCTTACCTCCCT-GAGTTGCAACGGAGCAGGTTAAAAATAACAGAT
1 AGTAGATTGAAGACACTAGCCTTGCCTCCCTCG-GTGGCAACGGAACAGGTTAAAGATAACAGAT
* * ** ** *
18228185 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACA-TCAGCCTTGCCTCC
65 ATTGCCTTCCTGTACTAACAGTAAAGCAGATTGAAGACACT-AGCCTTGCCTCC
18228238 TTGAGTTGCA
Statistics
Matches: 406, Mismatches: 58, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
349 3 0.01
351 304 0.75
352 99 0.24
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (351 bp):
AGTAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAACGGAACAGGTTAAAGATAACAGATA
TTGCCTTCCTGTACTAACAGTAAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCG
GAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTATACTAACAACGAAACAGATCGAAGACACTAG
CCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCATGCCTTCCTGCACCAACA
GCGAAGCAGATCAAAGACACCAGCCTTACCTCCCTGGGTTACAGCAGAACAGGTTAAAAATAGCA
GATCTTATCTCCCTAAGCAGTAGTGG
Found at i:18228249 original size:88 final size:88
Alignment explanation
Indices: 18227382--18228247 Score: 919
Period size: 88 Copynumber: 9.9 Consensus size: 88
18227372 NNNNNNNNNN
* * * * ** * *
18227382 AAAATTGCAGATCTTACCTTCCTATACTGACAGTAAAGTAGATTGAAGACACTAGCCTTGCTTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
** * *
18227447 CTCTGTGGCAACGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
** * ** *
18227470 AGGATAGCAGATCTTGCCTTCTTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
* * *
18227535 CTCGGTGGCAGCGGAGTAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * ** * * * *
18227558 AAGATAGCAGATCTTGCCTTCTTATACTAACAACGAAGTAGGTCGAAGACACTAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
*
18227623 CTGGGTTGCAGCAGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * ** * *
18227646 AAAATAGCAGATCATGCCTTCCTGTACCGGCAGCGAAGTAGATCAAAGACACCAGCCTTACCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
* * *
18227711 CTGGGTTACAGCAGAGCAGGTTG
66 CTGGGTTGCAGCGGAGCAGGTTA
* ** * * * * * * *
18227734 AAAATTGCAGATCTTATCTCCCT-AAGC-AGTAGTGGAGTAGATTGAAGACACTAGCCTTGCCTC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGA-CAGCGAAGCAGATTGAAGACACTAGCCTTGCCTC
* * * *
18227797 CCTCGGTGGCAGTGGAACAGGTTA
65 CCTGGGTTGCAGCGGAGCAGGTTA
* * * * **
18227821 AAGATAACAGATATTGCCTTCCTGTACTGACAGTAAAGCAGATTGAAGACACTAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
* *
18227886 CTCGGTGGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* ** * *
18227909 AAGATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAACAGATTGAAGACACTAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
*
18227974 CTGGGTTGCAGTGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * *
18227997 AAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATTGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
*
18228062 CTGGGTTGCAGCGGAACAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * * * *
18228085 AAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCTTACCTCC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
* *
18228150 CTGAGTTGCAACGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * *
18228173 AAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACA-TCAGCCTTGCCTC
1 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACT-AGCCTTGCCTC
* *
18228237 CTTGAGTTGCA
65 CCTGGGTTGCA
18228248 ACAGATCAAG
Statistics
Matches: 668, Mismatches: 106, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
87 62 0.09
88 605 0.91
89 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (88 bp):
AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCC
CTGGGTTGCAGCGGAGCAGGTTA
Found at i:18228633 original size:19 final size:19
Alignment explanation
Indices: 18228609--18228683 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
18228599 AATCTTCAAG
18228609 GATATGCAATCTTGGATAT
1 GATATGCAATCTTGGATAT
*
18228628 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
18228647 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
18228668 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
18228684 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:18232253 original size:18 final size:18
Alignment explanation
Indices: 18232230--18232264 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18232220 CAGTTAGGAT
18232230 CTATGTCCATTGGATGAA
1 CTATGTCCATTGGATGAA
18232248 CTATGTCCATTGGATGA
1 CTATGTCCATTGGATGA
18232265 GGTTCAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (18 bp):
CTATGTCCATTGGATGAA
Found at i:18241635 original size:6 final size:6
Alignment explanation
Indices: 18241626--18241671 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
18241616 GTAATAGGAC
* *
18241626 CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CCGAGG CCGAGG CGGA
1 CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CGGA
18241672 AACAGTCCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.61, T:0.00
Consensus pattern (6 bp):
CGGAGG
Found at i:18246590 original size:42 final size:41
Alignment explanation
Indices: 18246526--18246688 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 41
18246516 CAACTAAAAA
* * **
18246526 CGCCGTTAAAGAACATGATCTTTAGCGGCGTTTTTCCCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TATAAG
* *
18246568 CGCCGCTAAAGAAGATGTTCTTTAGCGGCGTTTTTTTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTATAAG
** *
18246609 CGCATCTAAATAACATGTTCTTTAGCGGC-TTTTTTATATGAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTATA--AG
*
18246651 CGCCGCTAAAGAACATGTTCTTTAGCGGCTCTTTTTTA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGC-GTTTTTTA
18246689 CAAAAATGCC
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
40 8 0.08
41 29 0.28
42 60 0.58
44 7 0.07
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTATAAG
Found at i:18246676 original size:83 final size:82
Alignment explanation
Indices: 18246532--18246688 Score: 224
Period size: 83 Copynumber: 1.9 Consensus size: 82
18246522 AAAACGCCGT
* * *
18246532 TAAAGAACATGATCTTTAGCGGCGTTTTTCCCTAAGCGCCGCTAAAGAAGATGTTCTTTAGCGGC
1 TAAAGAACATGATCTTTAGCGGCGTTTTTACATAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
*
18246597 GTTTTTTTTAAGCGCATC
66 -TCTTTTTTAAGCGCATC
* * * * *
18246615 TAAATAACATGTTCTTTAGCGGCTTTTTTATATGAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TAAAGAACATGATCTTTAGCGGCGTTTTTACATAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
18246680 TCTTTTTTA
66 TCTTTTTTA
18246689 CAAAAATGCC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
82 8 0.12
83 57 0.88
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (82 bp):
TAAAGAACATGATCTTTAGCGGCGTTTTTACATAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
TCTTTTTTAAGCGCATC
Found at i:18247095 original size:21 final size:21
Alignment explanation
Indices: 18247071--18247121 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
18247061 TTCTTTTGAA
*
18247071 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
18247092 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
18247113 CATCTGCTT
1 CCTCTGCTT
18247122 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.45, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:18247174 original size:87 final size:87
Alignment explanation
Indices: 18247006--18247165 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
18246996 TTCTGCTCTG
* * * *
18247006 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTTTAGCTGCAGTTCTTCATAATTCTTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATAATTCCTTTGAA
* *
18247071 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAGCTTCGCTCGCTGCAGC
* * *
18247093 CTCTGCTTCCCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATAATTCCTTTGAA
*
18247158 CTTCAGCT
66 CCTCAGCT
18247166 GTGGTCGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATAATTCCTTTGAA
CCTCAGCTTCGCTCGCTGCAGC
Found at i:18247981 original size:9 final size:9
Alignment explanation
Indices: 18247955--18248188 Score: 252
Period size: 9 Copynumber: 25.8 Consensus size: 9
18247945 ATTTGCACGG
18247955 GTAAGTTAT
1 GTAAGTTAT
* *
18247964 TTAATTTAT
1 GTAAGTTAT
18247973 GTAAGTTAT
1 GTAAGTTAT
18247982 GTAAGTTAT
1 GTAAGTTAT
18247991 GTAAGTTAT
1 GTAAGTTAT
* *
18248000 TTAATTTAT
1 GTAAGTTAT
*
18248009 GTAGGTTAT
1 GTAAGTTAT
* *
18248018 GTAAGTCCAC
1 GTAAGT-TAT
* *
18248028 GGAATTTAT
1 GTAAGTTAT
18248037 GTAAGTTAT
1 GTAAGTTAT
18248046 GTAAGTTAT
1 GTAAGTTAT
* *
18248055 TTAATTTAT
1 GTAAGTTAT
18248064 GTAAGTTAT
1 GTAAGTTAT
18248073 GTAAGTTAT
1 GTAAGTTAT
* *
18248082 TTAATTTAT
1 GTAAGTTAT
*
18248091 GTAGGTTAT
1 GTAAGTTAT
18248100 GTAAGTTAT
1 GTAAGTTAT
18248109 GTAAGTTAT
1 GTAAGTTAT
* *
18248118 TTAATTTAT
1 GTAAGTTAT
*
18248127 GCAAGTTTAT
1 GTAAG-TTAT
18248137 GTAAGTTAT
1 GTAAGTTAT
*
18248146 GTGAGTTAT
1 GTAAGTTAT
* *
18248155 TTAATTTAT
1 GTAAGTTAT
18248164 GTAAGTTAT
1 GTAAGTTAT
* *
18248173 TTAATTTAT
1 GTAAGTTAT
18248182 GTAAGTT
1 GTAAGTT
18248189 TCTATATATG
Statistics
Matches: 179, Mismatches: 44, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
9 166 0.93
10 13 0.07
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.49
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:18248230 original size:8 final size:8
Alignment explanation
Indices: 18248217--18248309 Score: 59
Period size: 8 Copynumber: 11.0 Consensus size: 8
18248207 TTGTATGTTA
18248217 GTTATTAT
1 GTTATTAT
18248225 GTTATTAT
1 GTTATTAT
18248233 GTTATTATAT
1 GTTA-T-TAT
*
18248243 AAGTTATTTAA
1 --GTTA-TTAT
18248254 GTTATTAT
1 GTTATTAT
18248262 GTTATTAT
1 GTTATTAT
*
18248270 ATAAAGTATTAT
1 GT----TATTAT
18248282 G-TA--AT
1 GTTATTAT
18248287 -TTATTAT
1 GTTATTAT
18248294 GTTATTAT
1 GTTATTAT
18248302 GTTATTAT
1 GTTATTAT
18248310 ATGTAAGTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
5 4 0.06
7 4 0.06
8 39 0.57
9 5 0.07
10 3 0.04
11 2 0.03
12 12 0.17
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (8 bp):
GTTATTAT
Found at i:18248235 original size:20 final size:20
Alignment explanation
Indices: 18248214--18248330 Score: 93
Period size: 20 Copynumber: 5.8 Consensus size: 20
18248204 ATATTGTATG
*
18248214 TTAGTTATTATGTTATTATG
1 TTAGTTATTATGTTATTATA
*
18248234 TTA-TTATATAAGTTATT-TA
1 TTAGTTAT-TATGTTATTATA
18248253 --AGTTATTATGTTATTATA
1 TTAGTTATTATGTTATTATA
* *
18248271 TAAAG-TATTATGTAATT-TA
1 T-TAGTTATTATGTTATTATA
18248290 TTATGTTATTATGTTATTATA
1 TTA-GTTATTATGTTATTATA
*
18248311 TGTAAGTTATGTAAGTTATT
1 T-T-AGTTAT-TATGTTATT
18248331 TAATTTATGT
Statistics
Matches: 78, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
17 9 0.12
18 7 0.09
19 9 0.12
20 33 0.42
21 5 0.06
22 6 0.08
23 9 0.12
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TTAGTTATTATGTTATTATA
Found at i:18248257 original size:37 final size:38
Alignment explanation
Indices: 18248210--18248330 Score: 148
Period size: 37 Copynumber: 3.3 Consensus size: 38
18248200 TTATATATTG
*
18248210 TATGTTAGTTATTATGTTATTATGTTATTATA-TAAGT
1 TATGTAAGTTATTATGTTATTATGTTATTATAGTAAGT
* *
18248247 TATTTAAGTTATTATGTTATTA---TA-TAAAGT-A-T
1 TATGTAAGTTATTATGTTATTATGTTATTATAGTAAGT
*
18248279 TATGTAATTTATTATGTTATTATGTTATTATATGTAAGT
1 TATGTAAGTTATTATGTTATTATGTTATTATA-GTAAGT
18248318 TATGTAAGTTATT
1 TATGTAAGTTATT
18248331 TAATTTATGT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
32 21 0.30
33 4 0.06
34 3 0.04
35 2 0.03
36 3 0.04
37 22 0.32
38 1 0.01
39 13 0.19
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (38 bp):
TATGTAAGTTATTATGTTATTATGTTATTATAGTAAGT
Found at i:18248296 original size:32 final size:29
Alignment explanation
Indices: 18248216--18248347 Score: 119
Period size: 32 Copynumber: 4.5 Consensus size: 29
18248206 ATTGTATGTT
*
18248216 AGTTAT-TATGTTATTATGTTATTATATA
1 AGTTATGTAAGTTATTATGTTATTATATA
*
18248244 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTATTATAT-A
* * *
18248274 AGTATTATGTAATTTATTATGTTATTATGTT
1 AG--TTATGTAAGTTATTATGTTATTATATA
* *
18248305 ATTATATGTAAGTTATGTAAGTTA-T-T-TA
1 AGT-TATGTAAGTTAT-TATGTTATTATATA
*
18248333 ATTTATGTAAGTTAT
1 AGTTATGTAAGTTAT
18248348 GCAAGCTTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
27 12 0.13
28 10 0.11
29 22 0.25
30 15 0.17
31 7 0.08
32 23 0.26
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTATTATATA
Found at i:18248306 original size:40 final size:41
Alignment explanation
Indices: 18248216--18248347 Score: 125
Period size: 40 Copynumber: 3.3 Consensus size: 41
18248206 ATTGTATGTT
*
18248216 AGTTATTATGTTATTATGT----TATTATATAAGTTATTTA
1 AGTTATTATGTTATTATATAAAGTATTATATAAGTTATTTA
* *
18248253 AGTTATTATGTTATTATATAAAGTATTATGTAATTTA-TTA
1 AGTTATTATGTTATTATATAAAGTATTATATAAGTTATTTA
* * *
18248293 TGTTATTATGTTATTATATGTAAG--TTATGTAAGTTATTTA
1 AGTTATTATGTTATTATAT-AAAGTATTATATAAGTTATTTA
* *
18248333 ATTTATGTAAGTTAT
1 AGTTAT-TATGTTAT
18248348 GCAAGCTTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
37 18 0.23
39 11 0.14
40 28 0.35
41 22 0.28
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (41 bp):
AGTTATTATGTTATTATATAAAGTATTATATAAGTTATTTA
Found at i:18248323 original size:9 final size:9
Alignment explanation
Indices: 18248309--18248371 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
18248299 TATGTTATTA
18248309 TATGTAAGT
1 TATGTAAGT
18248318 TATGTAAGT
1 TATGTAAGT
* *
18248327 TATTTAATT
1 TATGTAAGT
18248336 TATGTAAGT
1 TATGTAAGT
*
18248345 TATGCAAGCT
1 TATGTAAG-T
*
18248355 TATATACAAGT
1 TATGT--AAGT
18248366 TATGTA
1 TATGTA
18248372 TTATAACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 31 0.72
10 4 0.09
11 5 0.12
12 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:18248613 original size:16 final size:16
Alignment explanation
Indices: 18248588--18248625 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18248578 GAAAACGAAG
*
18248588 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
18248603 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
18248619 TAAATTT
1 TAAATTT
18248626 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:18248640 original size:17 final size:17
Alignment explanation
Indices: 18248618--18248654 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
18248608 TTTAATACAA
18248618 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
18248635 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
18248652 ATA
1 ATA
18248655 TAGATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:18249692 original size:27 final size:29
Alignment explanation
Indices: 18249638--18249692 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
18249628 TAATTATCAC
*
18249638 AACAATAAACTTAATAATAATTGATAAAGT
1 AACAATAAACTTAATAATAAAT-ATAAAGT
*
18249668 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATAAACTTAATAATAAATATAAA
18249693 TCAGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.22
30 14 0.61
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATAAACTTAATAATAAATATAAAGT
Found at i:18252149 original size:15 final size:15
Alignment explanation
Indices: 18252129--18252177 Score: 66
Period size: 14 Copynumber: 3.3 Consensus size: 15
18252119 ATTAACTATA
18252129 AACCCCTAAACCCAT
1 AACCCCTAAACCCAT
*
18252144 AACCCCT-AACCCCT
1 AACCCCTAAACCCAT
18252158 AA-CCCTAAACCCAT
1 AACCCCTAAACCCAT
18252172 GAACCC
1 -AACCC
18252178 TTAACCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 14 0.48
15 9 0.31
16 2 0.07
ACGTcount: A:0.37, C:0.49, G:0.02, T:0.12
Consensus pattern (15 bp):
AACCCCTAAACCCAT
Found at i:18252153 original size:7 final size:7
Alignment explanation
Indices: 18252129--18252190 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
18252119 ATTAACTATA
18252129 AACCCCT
1 AACCCCT
*
18252136 AAACCCAT
1 -AACCCCT
18252144 AACCCCT
1 AACCCCT
18252151 AACCCCT
1 AACCCCT
18252158 AA-CCCT
1 AACCCCT
*
18252164 AAACCCAT
1 -AACCCCT
*
18252172 GAACCCTT
1 -AACCCCT
18252180 AACCCC-
1 AACCCCT
18252186 AACCC
1 AACCC
18252191 TTAAACCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 9 0.20
7 22 0.48
8 15 0.33
ACGTcount: A:0.35, C:0.50, G:0.02, T:0.13
Consensus pattern (7 bp):
AACCCCT
Found at i:18252168 original size:28 final size:28
Alignment explanation
Indices: 18252132--18252219 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 28
18252122 AACTATAAAC
*
18252132 CCCTAAACCCATAACCCCTAACCCCTAA
1 CCCTAAACCCATAACCCATAACCCCTAA
*
18252160 CCCTAAACCCATGAACCCTTAACCCC-AA
1 CCCTAAACCCAT-AACCCATAACCCCTAA
* *
18252188 CCCTTAAA-CCATAATCCATAAGCCTCTAA
1 CCC-TAAACCCATAACCCATAA-CCCCTAA
18252217 CCC
1 CCC
18252220 ATATCCCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.13
28 24 0.46
29 21 0.40
ACGTcount: A:0.35, C:0.45, G:0.02, T:0.17
Consensus pattern (28 bp):
CCCTAAACCCATAACCCATAACCCCTAA
Found at i:18252178 original size:15 final size:14
Alignment explanation
Indices: 18252132--18252201 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
18252122 AACTATAAAC
18252132 CCCTAAACCCATAA
1 CCCTAAACCCATAA
*
18252146 CCCCT-AACCCCTAA
1 -CCCTAAACCCATAA
18252160 CCCTAAACCCATGAA
1 CCCTAAACCCAT-AA
* *
18252175 CCCTTAACCC-CAA
1 CCCTAAACCCATAA
18252188 CCCTTAAA-CCATAA
1 CCC-TAAACCCATAA
18252202 TCCATAAGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 11 0.24
14 19 0.42
15 15 0.33
ACGTcount: A:0.37, C:0.46, G:0.01, T:0.16
Consensus pattern (14 bp):
CCCTAAACCCATAA
Found at i:18252393 original size:20 final size:20
Alignment explanation
Indices: 18252365--18252403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18252355 AACTATAAAC
18252365 CCCTAAACCCCTAACCCCAG
1 CCCTAAACCCCTAACCCCAG
* *
18252385 CCCTTAACCCTTAACCCCA
1 CCCTAAACCCCTAACCCCA
18252404 ATCCTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.54, G:0.03, T:0.15
Consensus pattern (20 bp):
CCCTAAACCCCTAACCCCAG
Found at i:18252409 original size:20 final size:20
Alignment explanation
Indices: 18252365--18252411 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
18252355 AACTATAAAC
* *
18252365 CCCTAAACCCCTAACCCCAG
1 CCCTTAACCCCTAACCCCAA
*
18252385 CCCTTAACCCTTAACCCCAA
1 CCCTTAACCCCTAACCCCAA
*
18252405 TCCTTAA
1 CCCTTAA
18252412 ACTATATCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.49, G:0.02, T:0.19
Consensus pattern (20 bp):
CCCTTAACCCCTAACCCCAA
Found at i:18252674 original size:39 final size:39
Alignment explanation
Indices: 18252628--18252715 Score: 176
Period size: 39 Copynumber: 2.3 Consensus size: 39
18252618 CGTTTTAAAC
18252628 AAAAGCGCCAGTATTGGTTGACTATTCCGGCGTTTCTAT
1 AAAAGCGCCAGTATTGGTTGACTATTCCGGCGTTTCTAT
18252667 AAAAGCGCCAGTATTGGTTGACTATTCCGGCGTTTCTAT
1 AAAAGCGCCAGTATTGGTTGACTATTCCGGCGTTTCTAT
18252706 AAAAGCGCCA
1 AAAAGCGCCA
18252716 CCAATTTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (39 bp):
AAAAGCGCCAGTATTGGTTGACTATTCCGGCGTTTCTAT
Found at i:18253364 original size:114 final size:113
Alignment explanation
Indices: 18253131--18253450 Score: 308
Period size: 114 Copynumber: 2.8 Consensus size: 113
18253121 TTAGACAAGT
* * * *
18253131 GCCACTAAAGTCTCGAAAAGATAAATGAAAAACGACATCATTTTCTTAACAGTTTTGCGGCACTT
1 GCCACTAAAGTCTCGAAAAGATAAATGAAAAACGGCAACGTTTTCTTAACAGTTTTGCGGCGCTT
* * ** * *
18253196 CTGATAAAGCGCCACTAAAGCTTCGCTACTACGGTGTTTTCTGAAATTC
66 ATGATAAAGCGCCGCTAATTCTT-GCTACTACGGCGTTTTCTGAAATGC
* * * * *
18253245 TCCACTAACGTCTCGAAAAGATAAATGAAAAATGGCAACGTTTTCTTAACAGTCTTACGGCGCTT
1 GCCACTAAAGTCTCGAAAAGATAAATGAAAAACGGCAACGTTTTCTTAACAGTTTTGCGGCGCTT
*
18253310 ATGATAAAGCGCCGCTAATTCTTGACTA-TAGCGGCGTTTTTCAT-TAA-GC
66 ATGATAAAGCGCCGCTAATTCTTG-CTACTA-CGGCG-TTTTC-TGAAATGC
* * ** *
18253359 GCCACTAAAGTCCCCAAAACCTAAACTG-AAAACGGCAGCGTTTTTCTTAACAGTTTTTGCGGCG
1 GCCACTAAAGTCTCGAAAAGATAAA-TGAAAAACGGCAACG-TTTTCTTAACAG-TTTTGCGGCG
* * *
18253423 TTTATGACCAAA-CGCCGGTAATTCTTGC
63 CTTATGA-TAAAGCGCCGCTAATTCTTGC
18253451 ATATTGCGGT
Statistics
Matches: 169, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
113 3 0.02
114 112 0.66
115 22 0.13
116 29 0.17
117 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (113 bp):
GCCACTAAAGTCTCGAAAAGATAAATGAAAAACGGCAACGTTTTCTTAACAGTTTTGCGGCGCTT
ATGATAAAGCGCCGCTAATTCTTGCTACTACGGCGTTTTCTGAAATGC
Found at i:18254646 original size:12 final size:12
Alignment explanation
Indices: 18254629--18254657 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18254619 ATTCATGAAG
18254629 AAATTTTTTAGA
1 AAATTTTTTAGA
18254641 AAATTTTTTAGA
1 AAATTTTTTAGA
18254653 AAATT
1 AAATT
18254658 CTTCTAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
AAATTTTTTAGA
Found at i:18258366 original size:45 final size:46
Alignment explanation
Indices: 18258333--18258772 Score: 506
Period size: 46 Copynumber: 9.3 Consensus size: 46
18258323 TGTTGTCTAT
*
18258333 AGCTTTAATCTATTGCAACGCCAGGGAAA-AAGATTCGCTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
18258378 AGCTTTATTCTACTGCAATGCTAGGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
18258424 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATC---T--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
18258475 AGCTTTAATTTACTGCAACGCCAGAGAAATAAAATTCGCTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
**
18258521 AGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATC---T--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
18258572 AGCTTTAATCTACTGCAATGCTAGGGAAA-AAGATTCACTGCCTCC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* ** *
18258617 AGCTTTAATCAACTGCAACGCCAATGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
18258663 AACTTTAATCTATTCCACTACAACGCCAAGGGAAAAAAAATTCGCTGCCTTC
1 AGCTTTAATC---T--ACTGCAACGCC-AGGGAAATAAGATTCGCTGCCTTC
*
18258715 AGCTTTAATCTGCTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
18258761 AGCTTTAATCTA
1 AGCTTTAATCTA
18258773 TTCCACTGCA
Statistics
Matches: 332, Mismatches: 45, Indels: 35
0.81 0.11 0.08
Matches are distributed among these distances:
45 63 0.19
46 134 0.40
47 9 0.03
48 2 0.01
49 3 0.01
51 93 0.28
52 28 0.08
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (46 bp):
AGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:18258489 original size:97 final size:96
Alignment explanation
Indices: 18258346--18258769 Score: 510
Period size: 97 Copynumber: 4.4 Consensus size: 96
18258336 TTTAATCTAT
* *
18258346 TGCAACGCCAGGGAAA-AAGATTCGCTGCCTTCAGCTTT-ATTCTACTGCAATGCTAGGGAAATA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATT-TACTGCAACGCTAGGGAAATA
* *
18258409 AGATTCGCTACCTTCAGCTTTAATCTGTTCCAC
65 AAATTCGCTGCCTTCAGCTTTAATCTG-TCCAC
* *
18258442 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATTTACTGCAACGCCAGAGAAATAA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATTTACTGCAACGCTAGGGAAATAA
18258507 AATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
66 AATTCGCTGCCTTCAGCTTTAATCTG-TCCAC
* * *
18258539 TGCAACGCCAAAGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAATGCTAGGGAAA-AA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATTTACTGCAACGCTAGGGAAATAA
* * * *
18258603 GATTCACTGCCTCCAGCTTTAA----TCAAC
66 AATTCGCTGCCTTCAGCTTTAATCTGTCCAC
* * * * *
18258630 TGCAACGCCAATGAAATAAGATTCGCTACCTTCAACTTTAATCTATTCCACTACAACGCCAAGGG
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAA--T-TT--ACTGCAACG-CTAGGG
*
18258695 AAAAAAAATTCGCTGCCTTCAGCTTTAATCTG----C
60 AAATAAAATTCGCTGCCTTCAGCTTTAATCTGTCCAC
*
18258728 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAAT
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAAT
18258770 CTATTCCACT
Statistics
Matches: 286, Mismatches: 29, Indels: 26
0.84 0.09 0.08
Matches are distributed among these distances:
91 42 0.15
93 1 0.00
94 1 0.00
96 44 0.15
97 136 0.48
98 62 0.22
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (96 bp):
TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATTTACTGCAACGCTAGGGAAATAA
AATTCGCTGCCTTCAGCTTTAATCTGTCCAC
Found at i:18259707 original size:7 final size:7
Alignment explanation
Indices: 18259695--18259744 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
18259685 CAAGGATGAT
18259695 ATAAAAA
1 ATAAAAA
18259702 ATAAAAA
1 ATAAAAA
18259709 ATAAAAA
1 ATAAAAA
18259716 ATAAAAA
1 ATAAAAA
18259723 ATAAAAA
1 ATAAAAA
18259730 ATAAAAA
1 ATAAAAA
18259737 ATAAAAA
1 ATAAAAA
18259744 A
1 A
18259745 GGGAATTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:18262345 original size:23 final size:23
Alignment explanation
Indices: 18262319--18262369 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
18262309 CCGGACTAGG
18262319 TGTAATATCC-CGAAAATTACTAC
1 TGTAATA-CCTCGAAAATTACTAC
18262342 TGTAATACCTCGAAAATTACTAC
1 TGTAATACCTCGAAAATTACTAC
*
18262365 AGTAA
1 TGTAA
18262370 GAAAATAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCTCGAAAATTACTAC
Found at i:18272022 original size:16 final size:16
Alignment explanation
Indices: 18272001--18272034 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18271991 TTTTATGATG
* *
18272001 AAATGCTATGCAGTCA
1 AAATGCCATGCAATCA
18272017 AAATGCCATGCAATCA
1 AAATGCCATGCAATCA
18272033 AA
1 AA
18272035 GCAAAACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:18274931 original size:30 final size:30
Alignment explanation
Indices: 18274895--18274982 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 30
18274885 TAATAGGGAT
*
18274895 GACTTAATTGATCTTTAATTATTTTACAAAG
1 GACTTAATTGATTTTTAATTATTTTA-AAAG
18274926 G-CTTAATTGAATTTTTTAAAATTATTTTAAAAG
1 GACTTAATTG-A-TTTTT--AATTATTTTAAAAG
* *
18274959 GAATTACTTGATTTTTAATTATTT
1 GACTTAATTGATTTTTAATTATTT
18274983 AAGCCTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
30 16 0.33
31 2 0.04
32 9 0.18
33 6 0.12
34 16 0.33
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (30 bp):
GACTTAATTGATTTTTAATTATTTTAAAAG
Found at i:18274973 original size:33 final size:34
Alignment explanation
Indices: 18274911--18274974 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
18274901 ATTGATCTTT
*
18274911 AATTATTTTACAAAGGCTTAATTGAATTTTTTAA
1 AATTATTTTACAAAGGATTAATTGAATTTTTTAA
*
18274945 AATTATTTTA-AAAGGAATTACTTG-ATTTTT
1 AATTATTTTACAAAGG-ATTAATTGAATTTTT
18274975 AATTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (34 bp):
AATTATTTTACAAAGGATTAATTGAATTTTTTAA
Found at i:18275061 original size:19 final size:19
Alignment explanation
Indices: 18275029--18275084 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
18275019 AAATATCAAA
18275029 ATTATAGAAAATTATAAAT
1 ATTATAGAAAATTATAAAT
* *
18275048 ATTATTGAATATTATAAA-
1 ATTATAGAAAATTATAAAT
* *
18275066 AATCTAGAAAAATTATAAA
1 ATTATAG-AAAATTATAAA
18275085 ATTTTATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTATAGAAAATTATAAAT
Found at i:18275085 original size:9 final size:9
Alignment explanation
Indices: 18275026--18275172 Score: 73
Period size: 10 Copynumber: 15.3 Consensus size: 9
18275016 TGGAAATATC
18275026 AAAATTATA
1 AAAATTATA
18275035 GAAAATTATA
1 -AAAATTATA
* *
18275045 AATATTATTG
1 AAAATTA-TA
*
18275055 AATATTATA
1 AAAATTATA
*
18275064 AAAATCTAGA
1 AAAAT-TATA
18275074 AAAATTATA
1 AAAATTATA
*
18275083 AAATTTTATTA
1 AAA-ATTA-TA
**
18275094 ATATGTTATGA
1 A-AAATTAT-A
18275105 AAAA-TATGA
1 AAAATTAT-A
*
18275114 ACATATTATA
1 A-AAATTATA
* *
18275124 TAAATAATA
1 AAAATTATA
*
18275133 TAAAATTTTA
1 -AAAATTATA
18275143 AAAA-TATA
1 AAAATTATA
*
18275151 AAAACTATA
1 AAAATTATA
18275160 AAAATATATA
1 AAAAT-TATA
18275170 AAA
1 AAA
18275173 GAGATTTTAT
Statistics
Matches: 106, Mismatches: 20, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
8 7 0.07
9 41 0.39
10 46 0.43
11 11 0.10
12 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:18275154 original size:17 final size:17
Alignment explanation
Indices: 18275122--18275172 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
18275112 GAACATATTA
*
18275122 TATAAATAATAT-AAAAT
1 TATAAA-AATATAAAAAC
*
18275139 TTTAAAAATATAAAAAC
1 TATAAAAATATAAAAAC
18275156 TATAAAAATATATAAAA
1 TATAAAAATATA-AAAA
18275173 GAGATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.17
17 20 0.69
18 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAAAAATATAAAAAC
Found at i:18283176 original size:190 final size:191
Alignment explanation
Indices: 18282848--18283232 Score: 693
Period size: 190 Copynumber: 2.0 Consensus size: 191
18282838 GTGATTATGG
18282848 GTACGTTCTTTATTTTTAATGCCCCTTACTTTACATTGATAGACATAAGGTCAACACATTCCTAT
1 GTACGTTCTTTATTTTTAATGCCCCTTACTTTACATTGATAGACATAAGGTCAACACATTCCTAT
18282913 GTAGCTAGTTCTATTTTTGTAAACTTTGAGATTCCTGTTAAGAGCACTTCCGATGAGATTTCTGT
66 GTAGCTAGTTCTATTTTTGTAAACTTTGAGATTCCTGTTAAGAGCACTTCCGATGAGATTTCTGT
* * *
18282978 ACTTAGTTCGTTAGGTCAATCTGTTCGGGTGAATAGATTGTATAATAATATACCGTTGGAT
131 ACTTAGTTCGTTAAGCCAATCTGTTCGGGTGAATAGATTGTATAAGAATATACCGTTGGAT
* *
18283039 GTAC-TTCTTTATTTTTGATGCCCCTTATTTTACATTGATAGACAT-AGAGTCAACACATTCCTA
1 GTACGTTCTTTATTTTTAATGCCCCTTACTTTACATTGATAGACATAAG-GTCAACACATTCCTA
18283102 TGTAGCTAGTTCTATTTTTGTAAACTTTGAGATTCCTGTTAAGAGCACTTCCGATGAGATTTCTG
65 TGTAGCTAGTTCTATTTTTGTAAACTTTGAGATTCCTGTTAAGAGCACTTCCGATGAGATTTCTG
*
18283167 TACTTAGTTCGTTAAGCCAATTTGTTCGGGTGAATAGATTGTATAAGAATATACCGTTGGAT
130 TACTTAGTTCGTTAAGCCAATCTGTTCGGGTGAATAGATTGTATAAGAATATACCGTTGGAT
18283229 GTAC
1 GTAC
18283233 AAAGGGTTGT
Statistics
Matches: 187, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
189 2 0.01
190 181 0.97
191 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (191 bp):
GTACGTTCTTTATTTTTAATGCCCCTTACTTTACATTGATAGACATAAGGTCAACACATTCCTAT
GTAGCTAGTTCTATTTTTGTAAACTTTGAGATTCCTGTTAAGAGCACTTCCGATGAGATTTCTGT
ACTTAGTTCGTTAAGCCAATCTGTTCGGGTGAATAGATTGTATAAGAATATACCGTTGGAT
Found at i:18301761 original size:25 final size:25
Alignment explanation
Indices: 18301733--18301782 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
18301723 TAGATATACA
*
18301733 TTGCCAAATTTGAA-TGTTTTATATT
1 TTGCCAAATTCGAATTG-TTTATATT
*
18301758 TTGCCGAATTCGAATTGTTTATATT
1 TTGCCAAATTCGAATTGTTTATATT
18301783 GTCGAAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (25 bp):
TTGCCAAATTCGAATTGTTTATATT
Found at i:18301946 original size:31 final size:31
Alignment explanation
Indices: 18301818--18302056 Score: 149
Period size: 31 Copynumber: 7.7 Consensus size: 31
18301808 TATTAATTCG
* *
18301818 TATATGGTTGAACACTGCTGAAAATAAATTTT
1 TATATGGTTGAACATTGCTGAAAAT-AATTTA
*
18301850 TATATGGTT-ATACATTGCTGAAATTGAA-TTA
1 TATATGGTTGA-ACATTGCTGAAAAT-AATTTA
** * * **
18301881 TATAT-GTAT-ATTAGTTGCCG-AAATGATTCG
1 TATATGGT-TGAACA-TTGCTGAAAATAATTTA
18301911 TATATGGTTGAACATTGCTGAAAATAATTTA
1 TATATGGTTGAACATTGCTGAAAATAATTTA
* * *
18301942 TATATGGTTGTACATTGCTGAAATTGAA-TTG
1 TATATGGTTGAACATTGCTGAAAAT-AATTTA
** * *
18301973 TATAT-GTACATA-AGTTG-TCG-AAATGATTCA
1 TATATGGTTGA-ACA-TTGCT-GAAAATAATTTA
*
18302003 TATATGGTTGAACATTGCTGAAAATAATTTG
1 TATATGGTTGAACATTGCTGAAAATAATTTA
*
18302034 TATATGGTT-ATACATTGTTGAAA
1 TATATGGTTGA-ACATTGCTGAAA
18302057 TTAAATTGTT
Statistics
Matches: 157, Mismatches: 33, Indels: 35
0.70 0.15 0.16
Matches are distributed among these distances:
29 2 0.01
30 37 0.24
31 93 0.59
32 25 0.16
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.40
Consensus pattern (31 bp):
TATATGGTTGAACATTGCTGAAAATAATTTA
Found at i:18301965 original size:61 final size:62
Alignment explanation
Indices: 18301818--18302056 Score: 201
Period size: 61 Copynumber: 3.9 Consensus size: 62
18301808 TATTAATTCG
* * *
18301818 TATATGGTTGAACACTGCTGAAAATAAATTTTTATATGGTTATACATTGCTGAAATTGAA-TTA
1 TATATGGTTGAACATTGCTGAAAAT-AATTTGTATATGGTTATACATTGCTGAAAAT-AATTTA
** * * *
18301881 TATAT-GTAT-ATTAGTTGCCG-AAATGATTCGTATATGGTTGA-ACATTGCTGAAAATAATTTA
1 TATATGGT-TGAACA-TTGCTGAAAATAATTTGTATATGGTT-ATACATTGCTGAAAATAATTTA
* * * * *
18301942 TATATGGTTGTACATTGCTGAAATTGAA-TTGTATAT-GTACATA-AGTTG-TCG-AAATGATTC
1 TATATGGTTGAACATTGCTGAAAAT-AATTTGTATATGGT-TATACA-TTGCT-GAAAATAATTT
18302002 A
62 A
*
18302003 TATATGGTTGAACATTGCTGAAAATAATTTGTATATGGTTATACATTGTTGAAA
1 TATATGGTTGAACATTGCTGAAAATAATTTGTATATGGTTATACATTGCTGAAA
18302057 TTAAATTGTT
Statistics
Matches: 138, Mismatches: 21, Indels: 35
0.71 0.11 0.18
Matches are distributed among these distances:
60 4 0.03
61 90 0.65
62 33 0.24
63 11 0.08
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.40
Consensus pattern (62 bp):
TATATGGTTGAACATTGCTGAAAATAATTTGTATATGGTTATACATTGCTGAAAATAATTTA
Found at i:18302064 original size:92 final size:92
Alignment explanation
Indices: 18301813--18302070 Score: 399
Period size: 92 Copynumber: 2.8 Consensus size: 92
18301803 GGATATATTA
* *
18301813 ATTCGTATATGGTTGAACACTGCTGAAAATAAATTTTTATATGGTTATACATTGCTGAAATTGAA
1 ATTCGTATATGGTTGAACATTGCTGAAAAT-AATTTATATATGGTTATACATTGCTGAAATTGAA
* * *
18301878 TTATATATGTATATTAGTTGCCGAAATG
65 TTGTATATGTACATAAGTTGCCGAAATG
*
18301906 ATTCGTATATGGTTGAACATTGCTGAAAATAATTTATATATGGTTGTACATTGCTGAAATTGAAT
1 ATTCGTATATGGTTGAACATTGCTGAAAATAATTTATATATGGTTATACATTGCTGAAATTGAAT
*
18301971 TGTATATGTACATAAGTTGTCGAAATG
66 TGTATATGTACATAAGTTGCCGAAATG
* * * *
18301998 ATTCATATATGGTTGAACATTGCTGAAAATAATTTGTATATGGTTATACATTGTTGAAATTAAAT
1 ATTCGTATATGGTTGAACATTGCTGAAAATAATTTATATATGGTTATACATTGCTGAAATTGAAT
*
18302063 TGTTTATG
66 TGTATATG
18302071 AATATAGGAT
Statistics
Matches: 152, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
92 123 0.81
93 29 0.19
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (92 bp):
ATTCGTATATGGTTGAACATTGCTGAAAATAATTTATATATGGTTATACATTGCTGAAATTGAAT
TGTATATGTACATAAGTTGCCGAAATG
Found at i:18302120 original size:31 final size:31
Alignment explanation
Indices: 18302067--18302215 Score: 124
Period size: 31 Copynumber: 4.9 Consensus size: 31
18302057 TTAAATTGTT
* *
18302067 TATGAATATAGGA-TGCCGAATTTGATTTGTA
1 TATGAATATA-CATTGCCGAATTTGATTCGTA
* *
18302098 TATGATTATACATTGCCAAATTTGATTCGTA
1 TATGAATATACATTGCCGAATTTGATTCGTA
** * ** * *
18302129 TATGGTTATATATTATCGAA-TTGTTTGGTA
1 TATGAATATACATTGCCGAATTTGATTCGTA
* * *
18302159 TATCAATATTCATTGTCGAATTTGATTCGTA
1 TATGAATATACATTGCCGAATTTGATTCGTA
* *
18302190 TATGAATATATATTGCTGAA-TTGATT
1 TATGAATATACATTGCCGAATTTGATT
18302216 TGAGCATTAG
Statistics
Matches: 92, Mismatches: 24, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
30 29 0.32
31 63 0.68
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (31 bp):
TATGAATATACATTGCCGAATTTGATTCGTA
Found at i:18305404 original size:16 final size:16
Alignment explanation
Indices: 18305383--18305414 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18305373 ATGCTAAGCT
18305383 ACCAAACTTTAAACTA
1 ACCAAACTTTAAACTA
18305399 ACCAAACTTTAAACTA
1 ACCAAACTTTAAACTA
18305415 TCACAGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (16 bp):
ACCAAACTTTAAACTA
Found at i:18311624 original size:13 final size:13
Alignment explanation
Indices: 18311606--18311634 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18311596 TTGGGAAATA
18311606 TTTATTTTGATGT
1 TTTATTTTGATGT
18311619 TTTATTTTGATGT
1 TTTATTTTGATGT
18311632 TTT
1 TTT
18311635 TAGTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (13 bp):
TTTATTTTGATGT
Found at i:18314541 original size:282 final size:277
Alignment explanation
Indices: 18314030--18314548 Score: 580
Period size: 282 Copynumber: 1.9 Consensus size: 277
18314020 AAAAAATGGC
*
18314030 AATAGCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
1 AATACCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
* * *
18314095 TTTTTTTACTCACAATTTAAACTAATTTTCATTTTAATTTCACACATATCACGTATGTGTTATTA
66 TTTCTTTACTCACAATTTAAACTAATTTTAATTTTAATTTCACACATATCACATATGTGTTATTA
* * * * * *
18314160 TTTTTATTTTCAAATAATACATTTTTTATTTATTGTATGTTACTTTTAAAAGCATACATGTGTTC
131 TTATTAGTTTCAAATAATACATTTTTTATTTATTATATGTTACTTTTAAAAGCACACATATATTC
* * * *
18314225 TAAATATATGGTTTCTATACGCATGCGCGTGTGATAGAATTTTTAATATTGTTAATCTTGTTGGT
196 TAAATATATGGTTTCCACAAGCAT-CACGTGTGATAG-ATTTTTAATATTGTTAATCTTGTTGGT
18314290 TCAGTTGGTGTCACAAGTT
259 TCAGTTGGTGTCACAAGTT
* ** * *
18314309 AATACCATGATAAAC-ATTTAGATTGCATTTAATA-TTTTT-AATTTGATGTATTTATCTTTTTA
1 AATACCATGATAAACAATTT-GAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTT-
** * **** **
18314371 AATTTCGCTTTACTTGCAATTTAACCTAATTTTTTAATTTTAATTTTGTGCATATTGCATATGTG
64 AATTT--CTTTACTCACAATTTAAACTAA--TTTTAATTTTAATTTCACACATATCACATATGTG
* * ** *
18314436 TTGTTATTATTAGTTTCAAACT-TTACATTTTAATTATTTATTATATGTTTTTTTTAAACGCACA
125 TTATTATTATTAGTTTCAAA-TAATACATTTT--TTATTTATTATATGTTACTTTTAAAAGCACA
* * *
18314500 CCTATATTCTAAATATATTGTTTCCACAAGCAT-ATGTGTGATAGATTTT
187 CATATATTCTAAATATATGGTTTCCACAAGCATCACGTGTGATAGATTTT
18314549 CTAGTTGTAC
Statistics
Matches: 195, Mismatches: 36, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
277 18 0.09
278 14 0.07
279 27 0.14
280 18 0.09
281 5 0.03
282 60 0.31
283 1 0.01
284 52 0.27
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (277 bp):
AATACCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
TTTCTTTACTCACAATTTAAACTAATTTTAATTTTAATTTCACACATATCACATATGTGTTATTA
TTATTAGTTTCAAATAATACATTTTTTATTTATTATATGTTACTTTTAAAAGCACACATATATTC
TAAATATATGGTTTCCACAAGCATCACGTGTGATAGATTTTTAATATTGTTAATCTTGTTGGTTC
AGTTGGTGTCACAAGTT
Found at i:18316050 original size:6 final size:6
Alignment explanation
Indices: 18316030--18316073 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
18316020 ACCCTTCTTC
* **
18316030 TCCCCTT TCCTCT TCCCCT TCCCCT TCCTTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
18316074 GGGTTGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCCT
Found at i:18316057 original size:18 final size:18
Alignment explanation
Indices: 18316030--18316073 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
18316020 ACCCTTCTTC
18316030 TCCCCTTTCCTCTTCCCCT
1 TCCCC-TTCCTCTTCCCCT
*
18316049 TCCCCTTCCTTTTCCCCT
1 TCCCCTTCCTCTTCCCCT
18316067 TCCCCTT
1 TCCCCTT
18316074 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCTCTTCCCCT
Found at i:18316192 original size:25 final size:27
Alignment explanation
Indices: 18316132--18316192 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
18316122 CCAGGTAAGG
* *
18316132 CTTCTTCTCCTTCTTCTGTTCTTCATTC
1 CTTC-TCTTCTTCTTCCGTTCTTCATTC
18316160 CTT-T-TTCTTCTTCCGTTCTTCA-T-
1 CTTCTCTTCTTCTTCCGTTCTTCATTC
18316183 CTTCTCTTCT
1 CTTCTCTTCT
18316193 CAGCATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 20 0.69
26 1 0.03
28 3 0.10
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.59
Consensus pattern (27 bp):
CTTCTCTTCTTCTTCCGTTCTTCATTC
Found at i:18319610 original size:21 final size:21
Alignment explanation
Indices: 18319572--18319624 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18319562 CGTTGTTTCT
** *
18319572 AATCTCACTACTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
18319593 AATCTCACCGCTATAGTAACT
1 AATCTCACCGCTACAGTAACC
18319614 AATCTCACCGC
1 AATCTCACCGC
18319625 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:18320782 original size:17 final size:16
Alignment explanation
Indices: 18320757--18320795 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
18320747 AAACTGTTCG
*
18320757 TTTAAAATAATTTAATA
1 TTTATAATAATTTAA-A
18320774 TTTATAATAATTTAAA
1 TTTATAATAATTTAAA
18320790 TTTATA
1 TTTATA
18320796 TTTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATAATAATTTAAA
Found at i:18324066 original size:19 final size:19
Alignment explanation
Indices: 18324042--18324090 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
18324032 TTTGGTACAA
*
18324042 AGACTAAATCGTAAAAATT
1 AGACTAAATCGTAAAAACT
18324061 AGACTAAATCGTAAAAACT
1 AGACTAAATCGTAAAAACT
*
18324080 GGACTAAATCG
1 AGACTAAATCG
18324091 AATAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (19 bp):
AGACTAAATCGTAAAAACT
Found at i:18336963 original size:31 final size:31
Alignment explanation
Indices: 18336928--18336988 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
18336918 ATTATTTTGT
* *
18336928 TCACTCTTATTAGATAAGTTGTCAATTTTAA
1 TCACTCTCATTAAATAAGTTGTCAATTTTAA
* *
18336959 TCACTCTCATTAAATTAGTTGTCGATTTTA
1 TCACTCTCATTAAATAAGTTGTCAATTTTA
18336989 GTTACTCTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (31 bp):
TCACTCTCATTAAATAAGTTGTCAATTTTAA
Found at i:18336996 original size:31 final size:31
Alignment explanation
Indices: 18336921--18336996 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
18336911 AAAATTTATT
* *
18336921 ATTTT-GTTCACTCTTATTAGATAAGTTGTCA
1 ATTTTAGTT-ACTCTCATTAAATAAGTTGTCA
* * * *
18336952 ATTTTAATCACTCTCATTAAATTAGTTGTCG
1 ATTTTAGTTACTCTCATTAAATAAGTTGTCA
18336983 ATTTTAGTTACTCT
1 ATTTTAGTTACTCT
18336997 ACCGTTATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTTTAGTTACTCTCATTAAATAAGTTGTCA
Found at i:18339247 original size:14 final size:13
Alignment explanation
Indices: 18339221--18339261 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
18339211 TAATTATTGA
18339221 ATATAATTAAAAT
1 ATATAATTAAAAT
*
18339234 ATATCAATTTAAAT
1 ATAT-AATTAAAAT
18339248 ATTATAATTAAAAT
1 A-TATAATTAAAAT
18339262 TTTTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATTAAAAT
Found at i:18339266 original size:22 final size:23
Alignment explanation
Indices: 18339241--18339295 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 23
18339231 AATATATCAA
18339241 TTTAAATATTATAATTAAA-ATT
1 TTTAAATATTATAATTAAACATT
*
18339263 TTT-AA-ACTATAATTAAAGCATT
1 TTTAAATATTATAATTAAA-CATT
18339285 TTTAATATATT
1 TTTAA-ATATT
18339296 CAACATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 9 0.35
23 1 0.04
24 1 0.04
25 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAAATATTATAATTAAACATT
Found at i:18339273 original size:20 final size:21
Alignment explanation
Indices: 18339250--18339289 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
18339240 ATTTAAATAT
18339250 TATAATTAAA-ATTTTTAAAC
1 TATAATTAAACATTTTTAAAC
18339270 TATAATTAAAGCATTTTTAA
1 TATAATTAAA-CATTTTTAA
18339290 TATATTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
TATAATTAAACATTTTTAAAC
Found at i:18340209 original size:44 final size:44
Alignment explanation
Indices: 18340146--18340235 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
18340136 TATTTGTAAT
* * * * *
18340146 TTAAATTCTAATCATTTTTAAAAATATATTTATCATAGATTTTA
1 TTAAATTATAATCAATTTTAAAAATATAATTATCAAAAATTTTA
* **
18340190 TTAAATTATAATTAATTTTAAATGTATAATTATCAAAAATTTTA
1 TTAAATTATAATCAATTTTAAAAATATAATTATCAAAAATTTTA
18340234 TT
1 TT
18340236 TTGCTTTAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (44 bp):
TTAAATTATAATCAATTTTAAAAATATAATTATCAAAAATTTTA
Found at i:18340370 original size:2 final size:2
Alignment explanation
Indices: 18340363--18340429 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
18340353 AACTCATACT
18340363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18340405 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18340430 TAGAGTTGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18349559 original size:29 final size:28
Alignment explanation
Indices: 18349514--18349601 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
18349504 TTAAAATTTA
*
18349514 AAAATTCAAAATATAATTAAAACTATTTTT
1 AAAATT-AAAA-ATAATTAAAAATATTTTT
18349544 AGAAATTAAAAATAATTAAAAATA-TTTT
1 A-AAATTAAAAATAATTAAAAATATTTTT
18349572 AAAATATAAAAA-ATATTAAAAAATATTTTT
1 AAAAT-TAAAAATA-ATT-AAAAATATTTTT
18349602 GTTCAAATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
27 5 0.10
28 14 0.27
29 19 0.37
30 9 0.17
31 5 0.10
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAATTAAAAATAATTAAAAATATTTTT
Found at i:18349594 original size:10 final size:10
Alignment explanation
Indices: 18349551--18349598 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
18349541 TTTAGAAATT
18349551 AAAAATAATT-
1 AAAAAT-ATTA
*
18349561 AAAAATATTT
1 AAAAATATTA
*
18349571 TAAAATA-TA
1 AAAAATATTA
18349580 AAAAATATTA
1 AAAAATATTA
18349590 AAAAATATT
1 AAAAATATT
18349599 TTTGTTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 10 0.30
10 23 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATATTA
Found at i:18349594 original size:19 final size:19
Alignment explanation
Indices: 18349551--18349597 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18349541 TTTAGAAATT
* *
18349551 AAAAATAATTAAAAATATTT
1 AAAAAT-ATAAAAAATATTA
*
18349571 TAAAATATAAAAAATATTA
1 AAAAATATAAAAAATATTA
18349590 AAAAATAT
1 AAAAATAT
18349598 TTTTGTTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATATAAAAAATATTA
Found at i:18352306 original size:31 final size:31
Alignment explanation
Indices: 18352180--18352308 Score: 79
Period size: 31 Copynumber: 4.2 Consensus size: 31
18352170 TGGTCAAAAG
* *
18352180 AAGTTCAAGCCTCAATGTGGGAACAATTGCC
1 AAGTTCAGGCCTCAATGTGGGAAAAATTGCC
* * * * * *
18352211 TAGTCCAGGCCCCAATATGGGAACAATTGTC
1 AAGTTCAGGCCTCAATGTGGGAAAAATTGCC
* * ***
18352242 AAGTTTAGG-ATCTAACT-T-GGATAAAA--AAA
1 AAGTTCAGGCCTC-AA-TGTGGGA-AAAATTGCC
18352271 AAGTTCAGGCCTCAATGTGGGAAAAATTGCC
1 AAGTTCAGGCCTCAATGTGGGAAAAATTGCC
18352302 AAGTTCA
1 AAGTTCA
18352309 AGCTCCAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
28 1 0.01
29 15 0.21
30 9 0.13
31 44 0.63
32 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (31 bp):
AAGTTCAGGCCTCAATGTGGGAAAAATTGCC
Found at i:18359453 original size:25 final size:25
Alignment explanation
Indices: 18359366--18359467 Score: 109
Period size: 25 Copynumber: 4.1 Consensus size: 25
18359356 ATACAAGTGT
* *
18359366 GCTCATACGAG-CATATGAACGGGAA
1 GCTCATGCGAGCCATGT-AACGGGAA
*
18359391 GCTCATGCGAGCCATGTAAAGGGAA
1 GCTCATGCGAGCCATGTAACGGGAA
* *
18359416 GCTCATCCGAGCCATGTAACGGAAA
1 GCTCATGCGAGCCATGTAACGGGAA
* * *
18359441 GCTCATGCAAGCCA-ATATCGGGAA
1 GCTCATGCGAGCCATGTAACGGGAA
18359465 GCT
1 GCT
18359468 TCGGAGAGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.15
25 51 0.78
26 4 0.06
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (25 bp):
GCTCATGCGAGCCATGTAACGGGAA
Found at i:18359499 original size:25 final size:25
Alignment explanation
Indices: 18359385--18359528 Score: 102
Period size: 25 Copynumber: 5.8 Consensus size: 25
18359375 AGCATATGAA
*
18359385 CGGGAAGCTCATGCGAGCCATGTAA-
1 CGGGAAGCTCATGAGAGCCAT-TAAT
* **
18359410 AGGGAAGCTCATCCGAGCCATGTAA-
1 CGGGAAGCTCATGAGAGCCAT-TAAT
* *
18359435 CGGAAAGCTCATGCA-AGCCAAT-AT
1 CGGGAAGCTCATG-AGAGCCATTAAT
*
18359459 CGGGAAGCTTC-GGAGAGCCATTAAT
1 CGGGAAGC-TCATGAGAGCCATTAAT
* *
18359484 CGAGAAGCTCATGAGAGTCAATT-AT
1 CGGGAAGCTCATGAGAG-CCATTAAT
* *
18359509 GGGGAAGCTCGTGAGAGCCA
1 CGGGAAGCTCATGAGAGCCA
18359529 AATAACGGAA
Statistics
Matches: 95, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.02
24 19 0.20
25 70 0.74
26 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.17
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCATTAAT
Found at i:18359542 original size:50 final size:48
Alignment explanation
Indices: 18359432--18359560 Score: 120
Period size: 50 Copynumber: 2.6 Consensus size: 48
18359422 CCGAGCCATG
*
18359432 TAACGGAAAGCTCATGCAAGCCAATATCGGGAAGCTTCGGAGAGCCAT
1 TAACGGAAAGCTCATGCAAGCCAATATCGGGAAGCTTCGGAGAGCCAA
* *
18359480 TAATC-GAGAAGCTCATG-AGAGTCAATTATGGGGAAGC-TCGTGAGAGCCAAA
1 TAA-CGGA-AAGCTCATGCA-AGCCAA-TATCGGGAAGCTTCG-GAGAGCC-AA
* * *
18359531 TAACGGAAAGCTAAAGAAAGCCATATATCG
1 TAACGGAAAGCTCATGCAAGCCA-ATATCG
18359561 AGATGCTCAG
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
48 6 0.09
49 18 0.28
50 33 0.51
51 8 0.12
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (48 bp):
TAACGGAAAGCTCATGCAAGCCAATATCGGGAAGCTTCGGAGAGCCAA
Found at i:18369437 original size:25 final size:25
Alignment explanation
Indices: 18369336--18369527 Score: 149
Period size: 25 Copynumber: 7.7 Consensus size: 25
18369326 ATACAGGTAT
*
18369336 GCTCATACGAG-CATATAAACGAGAA
1 GCTCATGCGAGCCATAT-AACGAGAA
* *
18369361 GCTCTTTCGAGCCATATAAC-AGGAA
1 GCTCATGCGAGCCATATAACGA-GAA
* * * *
18369386 GCTCATGTGAGCCATGTAAAGGGAA
1 GCTCATGCGAGCCATATAACGAGAA
* *
18369411 GCTCATGCGAGCCATGTAACGAAAA
1 GCTCATGCGAGCCATATAACGAGAA
* * *
18369436 GCTCATGCGAGCTA-ATATCGTGAA
1 GCTCATGCGAGCCATATAACGAGAA
* *
18369460 GCTCATGAGAGCCA-ATTATCGAGAA
1 GCTCATGCGAGCCATA-TAACGAGAA
* * * *
18369485 GCTCGTGAGAGCCAAATAACGGGAA
1 GCTCATGCGAGCCATATAACGAGAA
* *
18369510 GCTCAAGAGAGCCATATA
1 GCTCATGCGAGCCATATA
18369528 CCGGGATGCT
Statistics
Matches: 136, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
24 20 0.15
25 110 0.81
26 6 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (25 bp):
GCTCATGCGAGCCATATAACGAGAA
Found at i:18369532 original size:25 final size:25
Alignment explanation
Indices: 18369369--18369546 Score: 153
Period size: 25 Copynumber: 7.2 Consensus size: 25
18369359 AAGCTCTTTC
* *
18369369 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* * *
18369394 GAGCCATGTAAAGGGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGA
* ** *
18369419 GAGCCATGTAACGAAAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGA
* * *
18369444 GAGCTA-ATATCGTGAAGCTCATGA
1 GAGCCATATAACGGGAAGCTCATGA
* * *
18369468 GAGCCA-ATTATCGAGAAGCTCGTGA
1 GAGCCATA-TAACGGGAAGCTCATGA
* *
18369493 GAGCCAAATAACGGGAAGCTCAAGA
1 GAGCCATATAACGGGAAGCTCATGA
* * *
18369518 GAGCCATATACCGGGATGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGA
18369543 GAGC
1 GAGC
18369547 TGTGGTAAGT
Statistics
Matches: 126, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
24 19 0.15
25 106 0.84
26 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:18371512 original size:4 final size:4
Alignment explanation
Indices: 18371503--18371527 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18371493 AGTACTCATT
18371503 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
18371528 TTGCTAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:18373736 original size:29 final size:30
Alignment explanation
Indices: 18373694--18373756 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
18373684 ATTTTTTTAG
*
18373694 AAATTATTATAAATTATA-AAAACATTATAA
1 AAATTATTAGAAATTATAGAAAAC-TTATAA
*
18373724 AAATT-TTAGAAATTATAGAAAACTTATAT
1 AAATTATTAGAAATTATAGAAAACTTATAA
18373753 AAAT
1 AAAT
18373757 CATTCAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTATTAGAAATTATAGAAAACTTATAA
Found at i:18373738 original size:18 final size:18
Alignment explanation
Indices: 18373688--18373745 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
18373678 TATTAAATTT
*
18373688 TTTTAGAAATTATTATAAA
1 TTTTAGAAATTA-TAAAAA
* *
18373707 TTATAAAAACATTATAAAAA
1 TT-TTAGAA-ATTATAAAAA
18373727 TTTTAGAAATTATAGAAAA
1 TTTTAGAAATTATA-AAAA
18373746 CTTATATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.19
19 10 0.32
20 11 0.35
21 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
TTTTAGAAATTATAAAAA
Found at i:18373867 original size:20 final size:20
Alignment explanation
Indices: 18373842--18373892 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
18373832 CATTTTAGTA
18373842 AGTTTTTAAAACATTTTT-AT
1 AGTTTTTAAAAC-TTTTTAAT
*
18373862 AGTTTTTTAATACTTTTTAAT
1 AG-TTTTTAAAACTTTTTAAT
18373883 A-TTTTTAAAA
1 AGTTTTTAAAA
18373893 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.30
20 7 0.26
21 12 0.44
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
AGTTTTTAAAACTTTTTAAT
Found at i:18376344 original size:21 final size:25
Alignment explanation
Indices: 18376320--18376406 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
18376310 TGGAATGTAT
18376320 TTATTTATTTTAAA-C-TT-TA-TA
1 TTATTTATTTTAAATCTTTCTATTA
18376341 TTATTTATTTTAAATCTTTCTATTA
1 TTATTTATTTTAAATCTTTCTATTA
* * *
18376366 TTATTTATTTTAAGTTTTTTTTATATA
1 TTATTTATTTTAA-ATCTTTCTAT-TA
*
18376393 TTATATATTTTAAA
1 TTATTTATTTTAAA
18376407 CTATGTTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
21 14 0.25
22 1 0.02
23 2 0.04
24 2 0.04
25 15 0.27
26 7 0.13
27 14 0.25
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (25 bp):
TTATTTATTTTAAATCTTTCTATTA
Found at i:18379011 original size:2 final size:2
Alignment explanation
Indices: 18379006--18379036 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18378996 ATATATATAT
18379006 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18379037 AACCCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18380032 original size:22 final size:22
Alignment explanation
Indices: 18379984--18380037 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
18379974 AGCCAAATAT
*
18379984 AAAAGTGAAAAAGCAGAAAAAA
1 AAAAGTGAAAAAGCAAAAAAAA
*
18380006 AAAAGTTAAAAAG-AAAAAAAA
1 AAAAGTGAAAAAGCAAAAAAAA
*
18380027 AGAAAGAGAAA
1 A-AAAGTGAAA
18380038 GGTAAAGTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAAGTGAAAAAGCAAAAAAAA
Found at i:18385975 original size:22 final size:21
Alignment explanation
Indices: 18385934--18385975 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
18385924 TAAATTTTTT
*
18385934 CTATATATTTATATTTATTTA
1 CTATATATTTATATTGATTTA
18385955 CTATCATATTT-TCATTGATTT
1 CTAT-ATATTTAT-ATTGATTT
18385976 TTAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.60
Consensus pattern (21 bp):
CTATATATTTATATTGATTTA
Found at i:18387457 original size:15 final size:15
Alignment explanation
Indices: 18387423--18387460 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
18387413 TATTAAAATC
*
18387423 AATTTTATTTTATTA
1 AATTTTATTTTATAA
18387438 AATTTTATTTT-TAA
1 AATTTTATTTTATAA
18387452 ATATTTTAT
1 A-ATTTTAT
18387461 ATATTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTATTTTATAA
Found at i:18388996 original size:49 final size:49
Alignment explanation
Indices: 18388943--18389040 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
18388933 TACAGTAATG
* **
18388943 AGTTGAAGTATAACTAGGGCTCCTAGCTGACAGTGGTTATGCGATCACA
1 AGTTGAAGTATAACTAGAGAGCCTAGCTGACAGTGGTTATGCGATCACA
* * * * *
18388992 AGTTGGAGTATAACTCGAGAGCCTAGTTGATAGTGGTTATGCGGTCACA
1 AGTTGAAGTATAACTAGAGAGCCTAGCTGACAGTGGTTATGCGATCACA
18389041 GGTTCATGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (49 bp):
AGTTGAAGTATAACTAGAGAGCCTAGCTGACAGTGGTTATGCGATCACA
Found at i:18392079 original size:15 final size:15
Alignment explanation
Indices: 18392056--18392085 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18392046 GACATGCACG
*
18392056 TTCTTATTACCACAC
1 TTCTCATTACCACAC
18392071 TTCTCATTACCACAC
1 TTCTCATTACCACAC
18392086 ATGTATTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
TTCTCATTACCACAC
Found at i:18393421 original size:25 final size:26
Alignment explanation
Indices: 18393388--18393446 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
18393378 TTTACCCCTA
* *
18393388 AAAATTTTTGATGATTTT-ACCCTGGT
1 AAAA-TTTTGACGATTTTGACCCTAGT
*
18393414 AAAATTTTGACGATTTTGCCCCTAGT
1 AAAATTTTGACGATTTTGACCCTAGT
18393440 AAAATTT
1 AAAATTT
18393447 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (26 bp):
AAAATTTTGACGATTTTGACCCTAGT
Found at i:18393436 original size:26 final size:25
Alignment explanation
Indices: 18393376--18393446 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
18393366 TCTCATCCCT
*
18393376 ATTTTACCCCTA--AAAATTTTTGATG
1 ATTTTA-CCCTAGTAAAA-TTTTGACG
*
18393401 ATTTTACCCTGGTAAAATTTTGACG
1 ATTTTACCCTAGTAAAATTTTGACG
*
18393426 ATTTTGCCCCTAGTAAAATTT
1 ATTTT-ACCCTAGTAAAATTT
18393447 CAAGAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 4 0.10
25 18 0.46
26 17 0.44
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGACG
Found at i:18397161 original size:15 final size:15
Alignment explanation
Indices: 18397137--18397197 Score: 104
Period size: 15 Copynumber: 4.1 Consensus size: 15
18397127 CTCTAAAGTT
18397137 AGTGGTGTTGGAAAC
1 AGTGGTGTTGGAAAC
*
18397152 AGTAGTGTTGGAAAC
1 AGTGGTGTTGGAAAC
18397167 AGTGGTGTTGGAAAC
1 AGTGGTGTTGGAAAC
*
18397182 AGTGGTGTTTGAAAC
1 AGTGGTGTTGGAAAC
18397197 A
1 A
18397198 ATTGATATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.36, T:0.28
Consensus pattern (15 bp):
AGTGGTGTTGGAAAC
Found at i:18399137 original size:22 final size:22
Alignment explanation
Indices: 18399108--18399190 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
18399098 TACACCACAC
* *
18399108 CAGAGAGCATTGTAGTGATAAG
1 CAGAGAGCACTGAAGTGATAAG
* *
18399130 TAGAGAGCACTGAAGTGCTAAG
1 CAGAGAGCACTGAAGTGATAAG
* * * *
18399152 CAGAGACCACCGAAGTGCTAAT
1 CAGAGAGCACTGAAGTGATAAG
*
18399174 CAAAGAGCA-TCGAAGTG
1 CAGAGAGCACT-GAAGTG
18399191 TTGAAAAAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (22 bp):
CAGAGAGCACTGAAGTGATAAG
Found at i:18399200 original size:22 final size:22
Alignment explanation
Indices: 18399175--18399239 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
18399165 AGTGCTAATC
18399175 AAAGAGCATCGAAGTGTTGAAA
1 AAAGAGCATCGAAGTGTTGAAA
**
18399197 AAAGAGCATCGAAGTGTTGAGT
1 AAAGAGCATCGAAGTGTTGAAA
* * *
18399219 AGAGAGCATAGAAATGTTGAA
1 AAAGAGCATCGAAGTGTTGAA
18399240 CTCGTACAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.29, T:0.20
Consensus pattern (22 bp):
AAAGAGCATCGAAGTGTTGAAA
Found at i:18416162 original size:5 final size:5
Alignment explanation
Indices: 18416152--18416182 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
18416142 TGAGCATTTG
*
18416152 ATCGA ATCGA ATTGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
18416183 AATTTTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (5 bp):
ATCGA
Found at i:18419392 original size:185 final size:186
Alignment explanation
Indices: 18419111--18419496 Score: 602
Period size: 185 Copynumber: 2.1 Consensus size: 186
18419101 AGTAAATTAA
* *
18419111 AAATTAAT-TAATA-TAATAGTACAGCAACATAAATTAAACAAAAAAAGTATGTTAAACTACATT
1 AAATTAATATAATAGTAATAGTACAACAACATAAATTAAACAAAAAAAGTATGTTAAACTACATG
* *
18419174 TTAAACTTTAAAGTTAGTTAATTGAATCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
66 TTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
* * * * *
18419239 -AGAAAAAAGTCTGTTAAGCTATCGTTTAAAATTTAAAGTTAGTTAATTGAAGCCT
131 AAAAAAAAAGTCTGTTAAACCATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
*
18419294 AAATTAATATAATAGT-ATAAGTACAACAGCATAAATTAAACCAAAAAAAGTATGTTAAACTACA
1 AAATTAATATAATAGTAAT-AGTACAACAACATAAATTAAA-CAAAAAAAGTATGTTAAACTACA
*
18419358 -GTTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTAGAATAGCATAAATTAA
64 TGTTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAA
*
18419422 ACAAAAAAAAAAGTCTGTTAAACCATAGTTTAAACTTCAAAGTTAGTTAATTGAAGCCT
129 AC-AAAAAAAAAGTCTGTTAAACCATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
18419481 AAATTAATATAATAGT
1 AAATTAATATAATAGT
18419497 GCAACAGCAT
Statistics
Matches: 185, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
183 8 0.04
184 7 0.04
185 82 0.44
186 23 0.12
187 65 0.35
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (186 bp):
AAATTAATATAATAGTAATAGTACAACAACATAAATTAAACAAAAAAAGTATGTTAAACTACATG
TTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
AAAAAAAAAGTCTGTTAAACCATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
Found at i:18419840 original size:17 final size:17
Alignment explanation
Indices: 18419818--18419869 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
18419808 TTTTCTCTAT
*
18419818 TAATATTACGTTATTAC
1 TAATATTACATTATTAC
*
18419835 TAATATTATATTATTAC
1 TAATATTACATTATTAC
**
18419852 TAATATGGCATTATTAC
1 TAATATTACATTATTAC
18419869 T
1 T
18419870 TTGGGAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:18420283 original size:19 final size:19
Alignment explanation
Indices: 18420259--18420320 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
18420249 GGAGAAGGAA
18420259 AATAGAGCGAAAATCATTC
1 AATAGAGCGAAAATCATTC
* *
18420278 AATAGAGCGAAACA-GATGC
1 AATAGAGCGAAA-ATCATTC
*
18420297 AAATAGAGCTAAAATCATTC
1 -AATAGAGCGAAAATCATTC
18420317 AATA
1 AATA
18420321 ATTCAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (19 bp):
AATAGAGCGAAAATCATTC
Found at i:18433483 original size:20 final size:19
Alignment explanation
Indices: 18433456--18433497 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
18433446 CTTTCCAAAT
18433456 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
18433475 TTTCGTTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
18433495 TTT
1 TTT
18433498 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:18435468 original size:12 final size:12
Alignment explanation
Indices: 18435451--18435481 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18435441 GAGAATCCAT
*
18435451 AAATATTTATAA
1 AAATATTCATAA
18435463 AAATATTCATAA
1 AAATATTCATAA
18435475 AAATATT
1 AAATATT
18435482 GACGGCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATTCATAA
Found at i:18440700 original size:16 final size:15
Alignment explanation
Indices: 18440675--18440709 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
18440665 AAAGTTTATA
*
18440675 ATAATTAATATATATT
1 ATAATAAATATA-ATT
18440691 ATAATAAATATAATT
1 ATAATAAATATAATT
18440706 ATAA
1 ATAA
18440710 ACTAGCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:18455974 original size:25 final size:25
Alignment explanation
Indices: 18455872--18455980 Score: 101
Period size: 25 Copynumber: 4.4 Consensus size: 25
18455862 TACACGATCA
* *
18455872 GTGAATCGGTATGCTCTTACGAGCT
1 GTGAATCAGTATGCTCTCACGAGCT
* * *
18455897 GTAAATCAGTATGCTCTCATGATCT
1 GTGAATCAGTATGCTCTCACGAGCT
* * * **
18455922 GTAAATCAATATGCTCTCGCGAATT
1 GTGAATCAGTATGCTCTCACGAGCT
* *
18455947 GTGAATCGGTATGCTCTTACGAGCT
1 GTGAATCAGTATGCTCTCACGAGCT
*
18455972 GTGAGTCAG
1 GTGAATCAG
18455981 AACTTAACTA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (25 bp):
GTGAATCAGTATGCTCTCACGAGCT
Found at i:18460295 original size:24 final size:25
Alignment explanation
Indices: 18460258--18460313 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
18460248 AAAATCTACC
*
18460258 CTAAAAAGAAAAAAGAAAACTTAAA
1 CTAAAAAGAAAAAAGAAAACCTAAA
* *
18460283 CTAAAAA-AGAAAAGAAAACCTAAC
1 CTAAAAAGAAAAAAGAAAACCTAAA
18460307 CTAAAAA
1 CTAAAAA
18460314 CTATAAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.11
Consensus pattern (25 bp):
CTAAAAAGAAAAAAGAAAACCTAAA
Done.