Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 121 of 295
Found at i:41565892 original size:24 final size:23
Alignment explanation
Indices: 41565821--41565903 Score: 85
Period size: 25 Copynumber: 3.4 Consensus size: 23
41565811 AGAAAGTGCT
* * *
41565821 AAAAGGGCTATGCCCCAATTTACC
1 AAAAGGGCTTTGCCCC-AGTTATC
41565845 AAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
41565870 AAAATGGGCTTTGCCCCAGTTATT
1 AAAA-GGGCTTTGCCCCAGTTATC
41565894 AAAAGAGGCT
1 AAAAG-GGCT
41565904 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
23 1 0.02
24 17 0.33
25 33 0.65
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:41566165 original size:31 final size:30
Alignment explanation
Indices: 41566110--41566192 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 30
41566100 CGCTTACAGT
*
41566110 AAAGGCTTCGG-CCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATGATTTATGA
41566140 AAAGGCTTCGGCCCAGTAATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATGATTTATGA
41566171 AAAGGCTTCGGCCCAGTATATG
1 AAAGGCTTCGGCCCAGTATATG
41566193 TCGAGACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 16 0.32
31 34 0.68
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATGATTTATGA
Found at i:41566264 original size:34 final size:33
Alignment explanation
Indices: 41566220--41566291 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
41566210 CTTAGGCCCA
** *
41566220 TACTGCTACTGTTTAAGGGCTAAGGCCCAGATTG
1 TACTGCTACTGAAT-AGGGCTAAGGCCAAGATTG
* **
41566254 TACTGTTACTGAATAGGGCTTTGGCCAAGATTG
1 TACTGCTACTGAATAGGGCTAAGGCCAAGATTG
41566287 TACTG
1 TACTG
41566292 ACACTGTGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (33 bp):
TACTGCTACTGAATAGGGCTAAGGCCAAGATTG
Found at i:41569268 original size:27 final size:27
Alignment explanation
Indices: 41569229--41569344 Score: 137
Period size: 27 Copynumber: 4.3 Consensus size: 27
41569219 CGTACCTGAA
41569229 CCCTTATGAGATAAAATGACTGTTTTG
1 CCCTTATGAGATAAAATGACTGTTTTG
* *
41569256 CCCTTATGTGATAAAAT-AATGATTTTG
1 CCCTTATGAGATAAAATGACTG-TTTTG
* * * *
41569283 CCCTTCTAAGGTAAAATGA-TGGTTTTA
1 CCCTTATGAGATAAAATGACT-GTTTTG
*
41569310 CCCTTATGAGGTAAAATGACTGTTTTG
1 CCCTTATGAGATAAAATGACTGTTTTG
41569337 CCCTTATG
1 CCCTTATG
41569345 TGATGTATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
26 3 0.04
27 69 0.92
28 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (27 bp):
CCCTTATGAGATAAAATGACTGTTTTG
Found at i:41569710 original size:18 final size:18
Alignment explanation
Indices: 41569670--41569723 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
41569660 AGGATTTGCA
* *
41569670 TACTGTTTACTGTTATTC
1 TACTGTTTACTGTTACTG
* *
41569688 CACTGATTACTGTTACTG
1 TACTGTTTACTGTTACTG
41569706 TACTGTTTACTGTTACTG
1 TACTGTTTACTGTTACTG
41569724 CAATGGGCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (18 bp):
TACTGTTTACTGTTACTG
Found at i:41570179 original size:17 final size:17
Alignment explanation
Indices: 41570159--41570197 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41570149 ATAAACGAGA
41570159 TTTTGAAA-TAAATAACT
1 TTTTGAAAGTAAAT-ACT
41570176 TTTT-AAAGTAAATACT
1 TTTTGAAAGTAAATACT
41570192 TTTTGA
1 TTTTGA
41570198 TAGTGACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (17 bp):
TTTTGAAAGTAAATACT
Found at i:41572366 original size:85 final size:85
Alignment explanation
Indices: 41572216--41572378 Score: 195
Period size: 85 Copynumber: 1.9 Consensus size: 85
41572206 GTCTGAGACA
* * * * * **
41572216 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTTTGGGA
1 TCGTGTAAGACCCTATCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGGGA
41572281 CATTGGCATTGTATCTAATT
66 CATTGGCATTGTATCTAATT
* * *
41572301 TCGTGTAAGACCCTATCTGGGATAGAGGCATCGATATTGA-A-TTACATGTAAGACCACGTCCGG
1 TCGTGTAAGACCCTATCTGGGACACAGGCATCG--ATTGAGATTTACATATAAGACCACGTCCGG
*
41572364 GACGTTGGCATTGTA
64 GACATTGGCATTGTA
41572379 CTTGGTTATG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 59 0.91
86 1 0.02
87 5 0.08
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (85 bp):
TCGTGTAAGACCCTATCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGGGA
CATTGGCATTGTATCTAATT
Found at i:41573825 original size:47 final size:47
Alignment explanation
Indices: 41573744--41574035 Score: 494
Period size: 47 Copynumber: 6.2 Consensus size: 47
41573734 ATCTACTTGT
* * * *
41573744 ATATATACACTTTCACATTCATCATATCGTCCATTCGGCCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* *
41573791 ATATACACACTTTCACATTAATCACATTGGCCATTAGGCCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* *
41573838 ATATATACACTTTCACATGCATCACATTGGCCATTCGGCCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
41573885 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
41573932 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
*
41573979 ATATACACACTTTCACATTCATCACATTGGCCATTCGACCTTATCAC
1 ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
*
41574026 ATATATACAC
1 ATATACACAC
41574036 CTTGTACATC
Statistics
Matches: 231, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 231 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
ATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
Found at i:41573886 original size:22 final size:22
Alignment explanation
Indices: 41573858--41573980 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 22
41573848 TTTCACATGC
41573858 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
41573880 ATCACATAT-ACACACTTTC-ACATT
1 ATCACAT-TGGC-CA--TTCGGCCTT
41573904 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
41573927 ATCACATAT-ACACACTTTC-ACATT
1 ATCACAT-TGGC-CA--TTCGGCCTT
41573951 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41573974 ATCACAT
1 ATCACAT
41573981 ATACACACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
22 29 0.39
23 12 0.16
24 12 0.16
25 22 0.29
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41577635 original size:40 final size:40
Alignment explanation
Indices: 41577579--41577980 Score: 579
Period size: 40 Copynumber: 10.1 Consensus size: 40
41577569 GAATACACAT
* * *
41577579 CACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
41577619 CACCAGCACGAATGCTCTTCGGGACTTAACCCTGATATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
41577659 CTCTAGCACAAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * *
41577699 CACCAGCACGAATTCTCTTCGGGACTTAGCCCGGATACAT
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
41577739 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
41577779 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATACAT
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
41577819 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAAATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * * *
41577859 CACCAGTATGAATGCTCTTCGGGACTTAGCCCGGATACAT
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
41577899 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACAT
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
41577939 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
41577979 CA
1 CA
41577981 TACTGAACTT
Statistics
Matches: 319, Mismatches: 43, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 319 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:41577691 original size:80 final size:80
Alignment explanation
Indices: 41577575--41577975 Score: 640
Period size: 80 Copynumber: 5.0 Consensus size: 80
41577565 GCCCGAATAC
* * *
41577575 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
* *
41577640 GGACTTAACCCTGAT
66 GGACTTAGCCCGGAT
* * * * * *
41577655 ATAACTCTAGCACAAATGCTCTTCGAGACTTAGCCCGGATATAACACCAGCACGAATTCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
41577720 GGACTTAGCCCGGAT
66 GGACTTAGCCCGGAT
*
41577735 ACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
41577800 GGACTTAGCCCGGAT
66 GGACTTAGCCCGGAT
* * *
41577815 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAAATAACACCAGTATGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
41577880 GGACTTAGCCCGGAT
66 GGACTTAGCCCGGAT
* * *
41577895 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
41577960 GGACTTAGCCCGGAT
66 GGACTTAGCCCGGAT
41577975 A
1 A
41577976 TAACATACTG
Statistics
Matches: 295, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 295 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (80 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
GGACTTAGCCCGGAT
Found at i:41579625 original size:47 final size:47
Alignment explanation
Indices: 41579562--41580096 Score: 872
Period size: 47 Copynumber: 11.4 Consensus size: 47
41579552 CCCTTCGGGA
* * * *
41579562 CTTATCACATTTATACACTTTCATATCCATCACATTGGCCATTCGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
41579609 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41579656 CTTATCTCATATATACACTTTCACATTCATCACGTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41579703 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41579750 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41579797 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
41579844 CTTATCACATATACACACTTTCACATTAATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41579891 CTTATCACATATATACACTTTCACATGCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41579938 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41579985 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41580032 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41580079 CTTATCACATATATACAC
1 CTTATCACATATATACAC
41580097 CTTGTACATC
Statistics
Matches: 458, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 458 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:41584786 original size:21 final size:21
Alignment explanation
Indices: 41584760--41584802 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41584750 AACACGGATC
41584760 TTGTTATTATTTTTTGAATTA
1 TTGTTATTATTTTTTGAATTA
41584781 TTGTTATTATTTTTTGAATTA
1 TTGTTATTATTTTTTGAATTA
41584802 T
1 T
41584803 ATCATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (21 bp):
TTGTTATTATTTTTTGAATTA
Found at i:41589214 original size:40 final size:40
Alignment explanation
Indices: 41589014--41589248 Score: 221
Period size: 39 Copynumber: 6.0 Consensus size: 40
41589004 ACTTGAAACC
* *
41589014 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * *
41589053 AATACCAGCTCGA-AGCCTGCGGGACTTT-TGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * * *
41589092 ATTTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * *
41589131 AATTTCAGCACATAGCCTGC-GGACCTTAAGTCCGGGTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * *
41589170 AATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGATAA
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * *
41589210 AATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCAGATA
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATA
41589249 CACATCAAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
38 17 0.10
39 95 0.58
40 52 0.32
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
Found at i:41592014 original size:29 final size:29
Alignment explanation
Indices: 41591969--41592026 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41591959 CCCACGATCG
41591969 TGTGCCCCAATACCTATATAAACCCCTCA
1 TGTGCCCCAATACCTATATAAACCCCTCA
*
41591998 TGTGCCCCAATATCTATATAAACCCCTCA
1 TGTGCCCCAATACCTATATAAACCCCTCA
41592027 CTATTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.26
Consensus pattern (29 bp):
TGTGCCCCAATACCTATATAAACCCCTCA
Found at i:41593530 original size:8 final size:8
Alignment explanation
Indices: 41593517--41593541 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41593507 AGGAGGACCC
41593517 AGCCTCTT
1 AGCCTCTT
41593525 AGCCTCTT
1 AGCCTCTT
41593533 AGCCTCTT
1 AGCCTCTT
41593541 A
1 A
41593542 CTAATGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.36, G:0.12, T:0.36
Consensus pattern (8 bp):
AGCCTCTT
Found at i:41597474 original size:46 final size:46
Alignment explanation
Indices: 41597416--41597636 Score: 198
Period size: 46 Copynumber: 4.7 Consensus size: 46
41597406 ATTCGTGTTT
* *
41597416 GAGCAAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
* * ** *
41597462 GAGATAGTGTAAGACCATGTCTGGGACATGACATCGG-TATTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCA-CAATATGA
* * *
41597510 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACAT-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATGA
* * *
41597557 -AGCCAGTGTAAGACATGTTTGGGACATGCATCGGCTACAATATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
* * *
41597602 TAG-TCAGTGTAAGACCATGTTTGGTACATGGCATC
1 GAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATC
41597637 AACTTGAGAT
Statistics
Matches: 142, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
44 3 0.02
45 2 0.01
46 62 0.44
47 45 0.32
48 30 0.21
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
Found at i:41597518 original size:48 final size:44
Alignment explanation
Indices: 41597421--41597546 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 44
41597411 TGTTTGAGCA
41597421 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGAT
1 AGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTATGAGAGAT
* * *
41597467 AGTGTAAGACCATGTCTGGGACATGACATCGG-TATTGAGATGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCCATT---ATGAGAGAT
41597515 AGTGTAAGACATGTCTGGGACATGCATCGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC
41597547 TCGAGACATA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
45 3 0.04
46 15 0.21
47 30 0.43
48 22 0.31
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATTATGAGAGAT
Found at i:41597651 original size:93 final size:94
Alignment explanation
Indices: 41597469--41597686 Score: 230
Period size: 93 Copynumber: 2.3 Consensus size: 94
41597459 TGAGAGATAG
* ** * * *
41597469 TGTAAGACCATGTCTGGGACATGACATCGG-TATTGAGATGA-GGGCTAGTGTAAGACATGTCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTA-CAATATGATAGTC-AGTGTAAGACATGTCTG
** *
41597532 GGACATGCATCGGCCTCGAGACATAAGCCAG
64 GGACATGCATCGAACTCGAGACATAAGCCAA
* *
41597563 TGTAAGA-CATGTTTGGGACAT-GCATCGGCTACAATATGATAGTCAGTGTAAGACCATGTTTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTACAATATGATAGTCAGTGTAAGA-CATGTCTGG
* * *
41597626 TACATGGCATC-AACTTGAGATATAAGCCAA
65 GACAT-GCATCGAACTCGAGACATAAGCCAA
*
41597656 TGTAAGACCGTGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTCTGGGACATGGCATCGGC
41597687 ACCTTACCCT
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
92 20 0.20
93 50 0.49
94 24 0.24
95 8 0.08
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (94 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCTACAATATGATAGTCAGTGTAAGACATGTCTGGG
ACATGCATCGAACTCGAGACATAAGCCAA
Found at i:41597660 original size:47 final size:47
Alignment explanation
Indices: 41597515--41597683 Score: 150
Period size: 47 Copynumber: 3.6 Consensus size: 47
41597505 GATGAGGGCT
* ** * *
41597515 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACATAAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-AACTAGAGATATAAGCC
** * *
41597561 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCTACA-ATATGATAGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCAACTAGAGATAT-A-AGCC
* *
41597607 AGTGTAAGACCATGTTTGGTACATGGCATCAACTTGAGATATAAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCAACTAGAGATATAAGCC
* * *
41597654 AATGTAAGACCGTGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTTTGGGACATGGCATC
41597684 GGCACCTTAC
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
44 3 0.03
45 5 0.05
46 39 0.38
47 42 0.41
48 9 0.09
49 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCAACTAGAGATATAAGCC
Found at i:41597670 original size:140 final size:140
Alignment explanation
Indices: 41597421--41597686 Score: 342
Period size: 140 Copynumber: 1.9 Consensus size: 140
41597411 TGTTTGAGCA
*
41597421 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGATAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGATAGTGTAAGACCATGTCTGG
* ** * *
41597486 GACATGACATCGGTATTGAGATGAGGGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCG
66 GACATGACATC-GAATTGAGATGAAAGCCAATGTAAGACATGTCTGGGACATGGCATCGGCCTCG
41597550 AGACATAAGCC
130 AGACATAAGCC
* * * *
41597561 AGTGTAAGACATGTTTGGGACATGCATCGGCTACAATATGATAG-TCAGTGTAAGACCATGTTTG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGAT-AGTGTAAGACCATGTCTG
* * *
41597625 GTACATGGCATC-AACTTGAGAT-ATAAGCCAATGTAAGACCGTGTCTGGGACATGGCATCGGC
65 GGACATGACATCGAA-TTGAGATGA-AAGCCAATGTAAGA-CATGTCTGGGACATGGCATCGGC
41597687 ACCTTACCCT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 2 0.02
139 18 0.17
140 80 0.74
141 8 0.07
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGATAGTGTAAGACCATGTCTGG
GACATGACATCGAATTGAGATGAAAGCCAATGTAAGACATGTCTGGGACATGGCATCGGCCTCGA
GACATAAGCC
Found at i:41600869 original size:40 final size:40
Alignment explanation
Indices: 41600807--41601022 Score: 314
Period size: 40 Copynumber: 5.4 Consensus size: 40
41600797 AAACCAAGTA
* * *
41600807 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
41600846 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41600886 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41600926 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
41600966 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41601006 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
41601023 CGTTATCATC
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.08
40 151 0.92
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41608902 original size:40 final size:40
Alignment explanation
Indices: 41608840--41609055 Score: 314
Period size: 40 Copynumber: 5.4 Consensus size: 40
41608830 AAACCAAGTA
* * *
41608840 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
41608879 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41608919 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41608959 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
41608999 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41609039 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
41609056 CGTTATCATC
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.08
40 151 0.92
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41611663 original size:44 final size:45
Alignment explanation
Indices: 41611598--41611690 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 45
41611588 AAAATGGAAT
41611598 AGGGAGAGAAAAAAGTAAGAATCGAAGGCAAGTAGTGCCCCATAG
1 AGGGAGAGAAAAAAGTAAGAATCGAAGGCAAGTAGTGCCCCATAG
*
41611643 AGGGAGAG-AAAAAGTAAGAATCGAAGGCAAGTAGTGCCCTATAG
1 AGGGAGAGAAAAAAGTAAGAATCGAAGGCAAGTAGTGCCCCATAG
41611687 AGGG
1 AGGG
41611691 GTAGACCACA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 39 0.83
45 8 0.17
ACGTcount: A:0.43, C:0.12, G:0.33, T:0.12
Consensus pattern (45 bp):
AGGGAGAGAAAAAAGTAAGAATCGAAGGCAAGTAGTGCCCCATAG
Found at i:41615990 original size:46 final size:45
Alignment explanation
Indices: 41615905--41616027 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 45
41615895 TGTGTGAGCT
* * *
41615905 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-TAAGCC
1 AGTGTAAAACATGTATGGGACATGCATC-GACTCAAGATGAT-AGCC
*
41615951 AGTGTAAAACATGTATGGGACATGCATCGACT-ATGAGATGATAGTC
1 AGTGTAAAACATGTATGGGACATGCATCGACTCA--AGATGATAGCC
* *
41615997 AGTGTAAGACCATGTTTGGGACATGGCATCG
1 AGTGTAA-AACATGTATGGGACAT-GCATCG
41616028 GCACCTTACC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
44 1 0.02
45 3 0.05
46 41 0.62
47 15 0.23
48 6 0.09
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAAACATGTATGGGACATGCATCGACTCAAGATGATAGCC
Found at i:41618597 original size:27 final size:26
Alignment explanation
Indices: 41618566--41618679 Score: 129
Period size: 27 Copynumber: 4.3 Consensus size: 26
41618556 TGGAGGAAGC
*
41618566 GTTCTTGTGGCTATGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* *
41618592 ATTTCTGGTGGCTACGCCACAAATATCT
1 -GTTCTGGTGGCTATGCCAC-AATATCT
*
41618620 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
41618646 GTATCTGGTGACTCTGTCACAATATTT
1 GT-TCTGGTGGCTATGCCACAATATCT
41618673 GTTCTGG
1 GTTCTGG
41618680 CAACCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.18
27 55 0.72
28 7 0.09
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:41625667 original size:19 final size:20
Alignment explanation
Indices: 41625643--41625689 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
41625633 ACGTTAATGG
* *
41625643 TTGTTTTTAGTATG-TTTAA
1 TTGTTTTTAATACGCTTTAA
41625662 TTGTTTTTAATACGCTTTAA
1 TTGTTTTTAATACGCTTTAA
41625682 TTAGTTTT
1 TT-GTTTT
41625690 AATTGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 7 0.29
21 5 0.21
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (20 bp):
TTGTTTTTAATACGCTTTAA
Found at i:41626738 original size:28 final size:28
Alignment explanation
Indices: 41626698--41626766 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
41626688 CACGGGCTAA
* *
41626698 GACACGGGTGTGTCATGATCGTGTGAAG
1 GACACGGGCGTGTCATGATCGTATGAAG
* *
41626726 GACACAGGCGTGTCATGGTCGTATGAAG
1 GACACGGGCGTGTCATGATCGTATGAAG
41626754 GACACGGGCGTGT
1 GACACGGGCGTGT
41626767 GTCAGGCCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (28 bp):
GACACGGGCGTGTCATGATCGTATGAAG
Found at i:41636808 original size:23 final size:23
Alignment explanation
Indices: 41636782--41636828 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
41636772 GATCGTCACC
41636782 ACACCATCGAACCTCATTTTGGT
1 ACACCATCGAACCTCATTTTGGT
*
41636805 ACACTATCGAACCTCATTTTGGT
1 ACACCATCGAACCTCATTTTGGT
41636828 A
1 A
41636829 TTTTGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (23 bp):
ACACCATCGAACCTCATTTTGGT
Found at i:41643610 original size:66 final size:64
Alignment explanation
Indices: 41643489--41643745 Score: 218
Period size: 66 Copynumber: 3.9 Consensus size: 64
41643479 TGGATGATAC
* ** * * *
41643489 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGT-GTACAAGAGAGCTA
1 AGATA-TATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTA
*
41643552 CA
63 CG
*
41643554 AGATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC
1 AGA-TAT-ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC
41643619 G
64 G
* * * * * * *
41643620 GGATATATGTAGCTAGGCCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTA
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
41643685 CG
63 CG
* * * *
41643687 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
41643746 CGAACTATAT
Statistics
Matches: 156, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 24 0.15
65 8 0.05
66 70 0.45
67 34 0.22
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:41647353 original size:43 final size:43
Alignment explanation
Indices: 41647290--41647383 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
41647280 ATTGTGATTA
* * * ** *
41647290 CATGTCTAGGACATTGGCATCGTTATATGATTTCGTGTAAGAC
1 CATGTCTGGGACATTAGCATCGATATATGATAACATGTAAGAC
*
41647333 CATGTCTGGGACATTAGCATCGATATGTGATAACATGTAAGAC
1 CATGTCTGGGACATTAGCATCGATATATGATAACATGTAAGAC
*
41647376 CATATCTG
1 CATGTCTG
41647384 AGATATGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
CATGTCTGGGACATTAGCATCGATATATGATAACATGTAAGAC
Found at i:41653007 original size:16 final size:15
Alignment explanation
Indices: 41652982--41653036 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 15
41652972 TGAATCCTCC
41652982 TATT-TTTTTATTCAT
1 TATTATTTTTATTC-T
*
41652997 TCTTATTTTTATT-T
1 TATTATTTTTATTCT
41653011 TATT-TTTTT-TTCT
1 TATTATTTTTATTCT
*
41653024 TTTTATTTTTATT
1 TATTATTTTTATT
41653037 TTGATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
12 2 0.06
13 9 0.27
14 9 0.27
15 5 0.15
16 8 0.24
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TATTATTTTTATTCT
Found at i:41653010 original size:6 final size:6
Alignment explanation
Indices: 41652999--41653077 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
41652989 TTATTCATTC
* *
41652999 TTATTT TTA-TT TTA-TT TT-TTT TTCTTT TTATTT TTATTT TGATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
* * *
41653044 TTATTT TCA-TT TCAATT TTATTATT TTATTT TTA
1 TTATTT TTATTT TTATTT TTA-T-TT TTATTT TTA
41653078 AAGACATATC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 18 0.29
6 38 0.61
7 1 0.02
8 5 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:41653013 original size:5 final size:5
Alignment explanation
Indices: 41653003--41653075 Score: 51
Period size: 5 Copynumber: 13.8 Consensus size: 5
41652993 TCATTCTTAT
* *
41653003 TTTTA TTTTA TTTTT TTTTCT TTTTA TTTTTA TTTTGA TTTTTA TTTTCA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA -TTTTA TTTT-A -TTTTA TTTT-A
*
41653053 TTTCAA TTTTA --TTA TTTTA TTTT
1 TTT-TA TTTTA TTTTA TTTTA TTTT
41653076 TAAAGACATA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 3 0.05
5 29 0.52
6 20 0.36
7 4 0.07
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:41653013 original size:21 final size:21
Alignment explanation
Indices: 41652987--41653032 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
41652977 CCTCCTATTT
41652987 TTTTATTCATTCTTATTTTTA
1 TTTTATTCATTCTTATTTTTA
** * *
41653008 TTTTATTTTTTTTTCTTTTTA
1 TTTTATTCATTCTTATTTTTA
41653029 TTTT
1 TTTT
41653033 TATTTTGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTATTCATTCTTATTTTTA
Found at i:41655963 original size:13 final size:13
Alignment explanation
Indices: 41655947--41655979 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41655937 TTTAATTAAA
*
41655947 TTAGTTAATTAGT
1 TTAGATAATTAGT
41655960 TTAGATAATTAGT
1 TTAGATAATTAGT
41655973 TTA-ATAA
1 TTAGATAA
41655980 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:41657767 original size:14 final size:13
Alignment explanation
Indices: 41657739--41657775 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
41657729 ATCCTGGAAT
41657739 ATTAA-AACAATA
1 ATTAAGAACAATA
41657751 ATTAAGAACACATA
1 ATTAAGAACA-ATA
41657765 ATTAAGAACAA
1 ATTAAGAACAA
41657776 GTCAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 13 0.57
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (13 bp):
ATTAAGAACAATA
Found at i:41659428 original size:40 final size:40
Alignment explanation
Indices: 41659384--41659651 Score: 423
Period size: 40 Copynumber: 6.7 Consensus size: 40
41659374 GCTACTTGCT
41659384 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
41659424 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
41659464 CAAATGCCTTCGGGACTCAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
41659504 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
41659544 CAAATGCCTTCGGGACTCAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
41659584 CAAATGCCTTAGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
41659623 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
41659652 CATCCGAATA
Statistics
Matches: 208, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
38 1 0.00
39 32 0.15
40 174 0.84
41 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41661667 original size:20 final size:21
Alignment explanation
Indices: 41661644--41661686 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
41661634 CACGCCCGTG
*
41661644 TGAAATGTGTA-TAAATGGCA
1 TGAAATGTGTATTAAATAGCA
41661664 TGAAATGTGTATTAAATAGCA
1 TGAAATGTGTATTAAATAGCA
41661685 TG
1 TG
41661687 TTTTGGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
TGAAATGTGTATTAAATAGCA
Found at i:41674404 original size:22 final size:22
Alignment explanation
Indices: 41674379--41674421 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41674369 ATACATAACA
41674379 TATTTAACTATTATA-TATGTAT
1 TATTT-ACTATTATATTATGTAT
*
41674401 TATTTATTATTATATTATGTA
1 TATTTACTATTATATTATGTA
41674422 ATGTTCTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TATTTACTATTATATTATGTAT
Found at i:41674608 original size:20 final size:20
Alignment explanation
Indices: 41674567--41674608 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41674557 TTTAGTAATA
*
41674567 ATTATATAATATGTTATTAT
1 ATTATATAATATGTTATCAT
41674587 ATTATATAATA-GTATATCAT
1 ATTATATAATATGT-TATCAT
41674607 AT
1 AT
41674609 GTTACAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTATATAATATGTTATCAT
Found at i:41678799 original size:18 final size:18
Alignment explanation
Indices: 41678776--41678813 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41678766 GGGAGATACG
41678776 AACAAAAGGAAGAAAAAA
1 AACAAAAGGAAGAAAAAA
41678794 AACAAAAGGAAGAAAAAA
1 AACAAAAGGAAGAAAAAA
41678812 AA
1 AA
41678814 TAGAACAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
AACAAAAGGAAGAAAAAA
Found at i:41681740 original size:14 final size:14
Alignment explanation
Indices: 41681704--41681747 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
41681694 CATGGTTAGT
41681704 ATTTTGAT-AG-AA
1 ATTTTGATAAGAAA
*
41681716 A-TTTCATAAGAAA
1 ATTTTGATAAGAAA
41681729 ATTTTGATAAGAAA
1 ATTTTGATAAGAAA
41681743 ATTTT
1 ATTTT
41681748 ATTGATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 3 0.11
13 3 0.11
14 16 0.59
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (14 bp):
ATTTTGATAAGAAA
Found at i:41684446 original size:79 final size:82
Alignment explanation
Indices: 41684335--41684519 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
41684325 GCTACTCGTT
* *
41684335 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* *
41684398 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
41684415 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
* *
41684478 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
41684495 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41684520 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:41684519 original size:40 final size:41
Alignment explanation
Indices: 41684335--41684519 Score: 204
Period size: 40 Copynumber: 4.6 Consensus size: 41
41684325 GCTACTCGTT
* * *
41684335 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* * *
41684375 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* *
41684415 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTAGCA
* * *
41684454 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTAGCA
41684495 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41684520 CATCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 77 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
Found at i:41689921 original size:27 final size:27
Alignment explanation
Indices: 41689880--41689933 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41689870 TGTCATGTGA
* *
41689880 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
41689907 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
41689934 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:41690708 original size:16 final size:16
Alignment explanation
Indices: 41690687--41690728 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41690677 TGCATGTGAT
41690687 AGGGAATTATCCTAAC
1 AGGGAATTATCCTAAC
*
41690703 AGGGAATTATCTTAAC
1 AGGGAATTATCCTAAC
**
41690719 TTGGAATTAT
1 AGGGAATTAT
41690729 GACTAAGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (16 bp):
AGGGAATTATCCTAAC
Found at i:41702969 original size:20 final size:22
Alignment explanation
Indices: 41702930--41702969 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41702920 GATTAATTTG
41702930 TGAAATATGCAAATTAAATGGT
1 TGAAATATGCAAATTAAATGGT
*
41702952 TGAAATGTG-AAA-TAAATG
1 TGAAATATGCAAATTAAATG
41702970 AAAGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (22 bp):
TGAAATATGCAAATTAAATGGT
Found at i:41708445 original size:29 final size:27
Alignment explanation
Indices: 41708386--41708446 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
41708376 AATGATGACC
41708386 GTGTGTGACACACGGCCTGGTATATGG
1 GTGTGTGACACACGGCCTGGTATATGG
41708413 GTGTGTGACACACGGCCTGGTATATGG
1 GTGTGTGACACACGGCCTGGTATATGG
*
41708440 GAGTGTG
1 GTGTGTG
41708447 GTTAGGCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.26
Consensus pattern (27 bp):
GTGTGTGACACACGGCCTGGTATATGG
Found at i:41712398 original size:40 final size:39
Alignment explanation
Indices: 41712345--41712432 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
41712335 GGGCTAAGCC
* * *
41712345 CCGACGGCTTTTATGCTAGTGACTATATCCGGACTAAGA
1 CCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGA
*
41712384 TCCGAAGGCATTTATGCTAGTGACCATATCCGGGCTAAGA
1 -CCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGA
41712424 CTCGAAGGC
1 C-CGAAGGC
41712433 CTTGTGCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGA
Found at i:41720624 original size:40 final size:38
Alignment explanation
Indices: 41720564--41720707 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 38
41720554 TATTCGAATG
*
41720564 ATATCCGGGCTAAGCCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAG-ACCGAAGGCTTTTAT-CTAGTGACT
* * *
41720604 ATATCCAGACTAAGATCCGAAGGCATTTGTA-CGAGTTG-CT
1 ATATCCGGGCTAAGA-CCGAAGGC-TTT-TATCTAG-TGACT
* *
41720644 ATATCCGGGCTAAGACCGGAAGGCATTTAATCTAGTGACC
1 ATATCCGGGCTAAGACC-GAAGGC-TTTTATCTAGTGACT
41720684 ATATCCGGGCTAAGACTCGAAGGC
1 ATATCCGGGCTAAGAC-CGAAGGC
41720708 CTTGTGCGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
39 5 0.06
40 74 0.85
41 6 0.07
42 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (38 bp):
ATATCCGGGCTAAGACCGAAGGCTTTTATCTAGTGACT
Found at i:41720697 original size:80 final size:79
Alignment explanation
Indices: 41720564--41720743 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 79
41720554 TATTCGAATG
* * *
41720564 ATATCCGGGCTAAGCCCCGAAGGCTTTTATGCTAGTGACTATATCCAGACTAAGA-TCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCTTTAATGCTAGTGACCATATCCAGACTAAGACT-CGAAGGC
* *
41720628 ATTTGTACGAGTTGCT
65 -CTTGTACGAGTGGCT
* * *
41720644 ATATCCGGGCTAAGACCGGAAGGCATTTAAT-CTAGTGACCATATCCGGGCTAAGACTCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTAATGCTAGTGACCATATCCAGACTAAGACTCGAAGGC
* *
41720708 CTTGTGCGAGTGGTT
65 CTTGTACGAGTGGCT
41720723 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
41720744 ATACTTGGGT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 12 0.14
79 17 0.20
80 50 0.58
81 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTAATGCTAGTGACCATATCCAGACTAAGACTCGAAGGCC
TTGTACGAGTGGCT
Found at i:41723685 original size:59 final size:57
Alignment explanation
Indices: 41723540--41723717 Score: 227
Period size: 59 Copynumber: 3.1 Consensus size: 57
41723530 CATATCTACA
* * *
41723540 TCAAAATAACTCCTAATTTATTAAATGAAACAATATAAAATAATTTGTACAAATATAT
1 TCAAAACAACT-CTATTTTATTAAATGAAACAATATAAAATAATTTGTACAAAAATAT
*
41723598 TCAAAACAA--CTATTTTATTGAATGAAACAATATAAATATAATTTGTACAAAAATAT
1 TCAAAACAACTCTATTTTATTAAATGAAACAATATAAA-ATAATTTGTACAAAAATAT
* * **
41723654 TTAAAAGAACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTAAACAAAAAT-T
1 TCAAAACAAC-TCTATTTTATTAAATGAAACAATAT-AAAATAATTTGTACAAAAATAT
41723712 TCAAAA
1 TCAAAA
41723718 ATAAATCAAT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
55 25 0.24
56 25 0.24
58 14 0.13
59 38 0.36
60 3 0.03
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (57 bp):
TCAAAACAACTCTATTTTATTAAATGAAACAATATAAAATAATTTGTACAAAAATAT
Found at i:41737282 original size:26 final size:25
Alignment explanation
Indices: 41737228--41737276 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41737218 GAAAATATAA
*
41737228 AAATAAAATATTATTCTTTTGATAG
1 AAATAAAATATTATTCTTTTAATAG
41737253 AAATAGAAATATTATT-TTTTAATA
1 AAATA-AAATATTATTCTTTTAATA
41737277 TTAAATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
AAATAAAATATTATTCTTTTAATAG
Found at i:41737380 original size:26 final size:25
Alignment explanation
Indices: 41737316--41737388 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
41737306 AATTGTTTTG
*
41737316 TTAATTATGTATTTA-AAATATTATTT
1 TTAATTA--TATTTATAGATATTATTT
*
41737342 TT-ATTATAATTATAGATATTATTT
1 TTAATTATATTTATAGATATTATTT
41737366 CTTAATTATATTTATAGATATTA
1 -TTAATTATATTTATAGATATTA
41737389 AAATTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.12
24 10 0.24
25 6 0.15
26 20 0.49
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (25 bp):
TTAATTATATTTATAGATATTATTT
Found at i:41737399 original size:26 final size:24
Alignment explanation
Indices: 41737325--41737405 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 24
41737315 GTTAATTATG
* *
41737325 TATTTA-AAATATTATTTTTATTA
1 TATTTATAGATATTAATTTTATTA
* *
41737348 TAATTATAGATATTATTTCTTAATTA
1 TATTTATAGATATTAATT-TT-ATTA
41737374 TATTTATAGATATTAAAATTTTATTA
1 TATTTATAGATATT--AATTTTATTA
41737400 T-TTTAT
1 TATTTAT
41737406 TTTGAATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 5 0.10
24 10 0.20
25 7 0.14
26 22 0.45
27 2 0.04
28 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTATAGATATTAATTTTATTA
Found at i:41742477 original size:28 final size:28
Alignment explanation
Indices: 41742432--41742503 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
41742422 AGGTGCCTAT
*
41742432 ATATAAAATTTTAATAAAAAT-ATAT-A
1 ATATAAAATTTAAATAAAAATAATATAA
41742458 ATATAAAATATTAAATTAAAAATAATATAA
1 ATATAAAAT-TTAAA-TAAAAATAATATAA
* *
41742488 ATATATATTTTAAATA
1 ATATAAAATTTAAATA
41742504 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 9 0.23
27 4 0.10
28 9 0.23
29 9 0.23
30 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATAAAATTTAAATAAAAATAATATAA
Found at i:41742500 original size:29 final size:28
Alignment explanation
Indices: 41742432--41742502 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
41742422 AGGTGCCTAT
41742432 ATATAAAATTTT-AA-TAAAAATATATA
1 ATATAAAATTTTAAATTAAAAATATATA
*
41742458 ATATAAAATATTAAATTAAAAATAATATA
1 ATATAAAATTTTAAATTAAAAAT-ATATA
*
41742487 A-ATATATATTTTAAAT
1 ATATA-AAATTTTAAAT
41742503 ATTTCAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 11 0.29
27 2 0.05
28 10 0.26
29 15 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATAAAATTTTAAATTAAAAATATATA
Found at i:41743316 original size:31 final size:32
Alignment explanation
Indices: 41743254--41743319 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
41743244 GTAAGGGTTA
*
41743254 ATTTCATTTTTTAAAATATTATTTAATATTTTT
1 ATTTCATTTTTT-AAATATTATTAAATATTTTT
41743287 ATTTCATTTTTT-AAT-TTAATTAAATATTTTT
1 ATTTCATTTTTTAAATATT-ATTAAATATTTTT
41743318 AT
1 AT
41743320 AATTTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.06
31 17 0.55
33 12 0.39
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTCATTTTTTAAATATTATTAAATATTTTT
Found at i:41745099 original size:23 final size:24
Alignment explanation
Indices: 41745053--41745104 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
41745043 ATTATGAGTG
**
41745053 AATAAGAAACATAAATAACTAAGT
1 AATAAGAAACATAAATAAAAAAGT
*
41745077 AATAAGAAA-ATAAGTAAAAAAGT
1 AATAAGAAACATAAATAAAAAAGT
41745100 AATAA
1 AATAA
41745105 TAATGCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.19
Consensus pattern (24 bp):
AATAAGAAACATAAATAAAAAAGT
Found at i:41745161 original size:3 final size:3
Alignment explanation
Indices: 41745155--41745211 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
41745145 TAATACGTCA
* * *
41745155 AAT AAT AAA AATT AAT AAT AAT AAT AA- AAGT AAT AAT AAT AAT GAG
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
41745201 AAT ATAT AAT A
1 AAT A-AT AAT A
41745212 TATAGTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.05
3 35 0.80
4 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41745188 original size:18 final size:19
Alignment explanation
Indices: 41745155--41745197 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
41745145 TAATACGTCA
*
41745155 AATAATAAAAATTAATAAT
1 AATAATAAAAAGTAATAAT
41745174 AATAAT-AAAAGTAATAAT
1 AATAATAAAAAGTAATAAT
41745192 AATAAT
1 AATAAT
41745198 GAGAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAATAAAAAGTAATAAT
Found at i:41746818 original size:10 final size:10
Alignment explanation
Indices: 41746805--41746837 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
41746795 TTTTCTCCTC
41746805 TTTTTTTTAT
1 TTTTTTTTAT
41746815 TTTTTTTTAT
1 TTTTTTTTAT
41746825 GTTTTTTTTAT
1 -TTTTTTTTAT
41746836 TT
1 TT
41746838 ATATGTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:41746818 original size:21 final size:21
Alignment explanation
Indices: 41746794--41746837 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41746784 TTTGGGGTAA
*
41746794 TTTTTCTCCTCTTTTTTTTAT
1 TTTTTCTCATCTTTTTTTTAT
* * *
41746815 TTTTTTTTATGTTTTTTTTAT
1 TTTTTCTCATCTTTTTTTTAT
41746836 TT
1 TT
41746838 ATATGTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTTCTCATCTTTTTTTTAT
Found at i:41746819 original size:11 final size:11
Alignment explanation
Indices: 41746805--41746837 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41746795 TTTTCTCCTC
41746805 TTTTTTTTA-T
1 TTTTTTTTATT
*
41746815 TTTTTTTTATG
1 TTTTTTTTATT
41746826 TTTTTTTTATT
1 TTTTTTTTATT
41746837 T
1 T
41746838 ATATGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:41747967 original size:87 final size:87
Alignment explanation
Indices: 41747821--41748261 Score: 675
Period size: 87 Copynumber: 5.1 Consensus size: 87
41747811 TTTGATTTTC
*
41747821 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
1 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
41747886 GGGGGTTAAGATCTGTAAATTT
66 GGGGGTTAAGATCTGTAAATTT
* *
41747908 AACCTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
1 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
*
41747973 GGGGGTTAAGATTTGTAAATTT
66 GGGGGTTAAGATCTGTAAATTT
* * *
41747995 AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCATCTTCAATCTGTTTCCCTACTGCTTA
1 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
* **
41748060 GAGGGTTAAGATCTGTAAATCC
66 GGGGGTTAAGATCTGTAAATTT
* * ** *
41748082 AACCTGTTATCCTACTGCTTAGGGGTTTGAGGTTCATCGCCTTCGATCTGTTTCCCTACTGCTTA
1 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
* *
41748147 AGGGGTTGAGATCTGTAAATTT
66 GGGGGTTAAGATCTGTAAATTT
* * * * *
41748169 AGCCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCTACTGCTTA
1 AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
41748234 GGGGGTTAAGATCTGTAAATTT
66 GGGGGTTAAGATCTGTAAATTT
*
41748256 AGCCTG
1 AACCTG
41748262 CTCCATTGCG
Statistics
Matches: 320, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 320 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (87 bp):
AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTA
GGGGGTTAAGATCTGTAAATTT
Found at i:41748343 original size:43 final size:44
Alignment explanation
Indices: 41748259--41748350 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 44
41748249 TAAATTTAGC
* * * *
41748259 CTGCTCCATTGCGACTTCAAGGAGATGAGACTTGTAGCTTCAGT
1 CTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAGCTTCAAT
* *
41748303 CTGCTCCACTGC-ACTTCAGGGAGATAAGGCTAGT-GACTTCAAT
1 CTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAG-CTTCAAT
41748346 CTGCT
1 CTGCT
41748351 TTGCTGAGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 29 0.71
44 11 0.27
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAGCTTCAAT
Found at i:41758278 original size:19 final size:20
Alignment explanation
Indices: 41758254--41758291 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41758244 GGTACCACCA
41758254 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41758273 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41758292 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41758582 original size:46 final size:46
Alignment explanation
Indices: 41758515--41758686 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
41758505 AACCCGCCCC
* * *
41758515 TAAGTGAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
41758561 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
41758609 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
* *
41758654 TAGGGGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
41758687 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 58 0.55
47 28 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:41758629 original size:93 final size:93
Alignment explanation
Indices: 41758520--41758690 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
41758510 GCCCCTAAGT
* * * *
41758520 GAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCAA
41758585 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
41758613 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGGGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCAA
41758678 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41758691 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41762640 original size:3 final size:3
Alignment explanation
Indices: 41762634--41762676 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
41762624 TAATACGTCA
*
41762634 AAT AAT AAA AATT AAT AAT AAT AAT AA- AAGT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
41762677 GAGAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.83
4 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41762667 original size:18 final size:19
Alignment explanation
Indices: 41762634--41762676 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
41762624 TAATACGTCA
*
41762634 AATAATAAAAATTAATAAT
1 AATAATAAAAAGTAATAAT
41762653 AATAAT-AAAAGTAATAAT
1 AATAATAAAAAGTAATAAT
41762671 AATAAT
1 AATAAT
41762677 GAGAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAATAAAAAGTAATAAT
Found at i:41764901 original size:7 final size:7
Alignment explanation
Indices: 41764889--41764913 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41764879 TAACATAGTC
41764889 TATTTAG
1 TATTTAG
41764896 TATTTAG
1 TATTTAG
41764903 TATTTAG
1 TATTTAG
41764910 TATT
1 TATT
41764914 ATGTATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41765303 original size:31 final size:31
Alignment explanation
Indices: 41765268--41765333 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
41765258 CATTCCAGAG
*
41765268 TTAGTGTGAGATACAGATTACATGTCATGGT
1 TTAGTGTGAGATACAGATTACATGACATGGT
* *
41765299 TTAGTGTGTGATACGGATTACATGACATGGT
1 TTAGTGTGAGATACAGATTACATGACATGGT
41765330 TTAG
1 TTAG
41765334 GATCCATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (31 bp):
TTAGTGTGAGATACAGATTACATGACATGGT
Found at i:41765964 original size:59 final size:59
Alignment explanation
Indices: 41765895--41766071 Score: 248
Period size: 60 Copynumber: 3.0 Consensus size: 59
41765885 CATTGATTTA
41765895 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTT
1 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTT
* * **
41765954 TTTTTAAATATTTTTGTAAAAATTATTTTTTATATTGTTTCATTTAACGAAATAGAAGTT
1 TTTTTGAATATTTTTGTACAAATTA-TTTTTATATTGTTTCATTTAATAAAATAGAAGTT
* * * * * *
41766014 CTTTTGAATATGTTTGTACAAATTA-TTTTCTATTATTTCATTTAATAAATTAGGAGTT
1 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTT
41766072 ATTTCGATGT
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
58 27 0.26
59 23 0.22
60 53 0.51
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (59 bp):
TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTT
Found at i:41770799 original size:21 final size:20
Alignment explanation
Indices: 41770771--41770813 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41770761 GATTCCAAAA
41770771 TTATTATT-TTATTAAATTTT
1 TTATTATTCTT-TTAAATTTT
*
41770791 TTATATATTCTTTTAGATTTT
1 TTAT-TATTCTTTTAAATTTT
41770812 TT
1 TT
41770814 TAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTATTATTCTTTTAAATTTT
Found at i:41770846 original size:18 final size:19
Alignment explanation
Indices: 41770807--41770848 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
41770797 ATTCTTTTAG
*
41770807 ATTTTTTTAAAAATTTATA
1 ATTTTTTTAAAAATATATA
*
41770826 ATTTTTTTTAAAATATA-A
1 ATTTTTTTAAAAATATATA
41770844 ATTTT
1 ATTTT
41770849 AGAATTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTTTAAAAATATATA
Found at i:41771773 original size:21 final size:20
Alignment explanation
Indices: 41771747--41771816 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
41771737 TCCACACGGG
41771747 TGTGCCTCAGACACACGGCCA
1 TGTGCCTCAGACACACGG-CA
***
41771768 TGTGCCTCTCTTCACACGAGCA
1 TGTGCCTC-AGACACACG-GCA
* *
41771790 TGTGCCTCAGCCACACAGTCA
1 TGTGCCTCAGACACAC-GGCA
41771811 TGTGCC
1 TGTGCC
41771817 CCTCTTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 21 0.54
22 17 0.44
23 1 0.03
ACGTcount: A:0.20, C:0.37, G:0.21, T:0.21
Consensus pattern (20 bp):
TGTGCCTCAGACACACGGCA
Found at i:41771791 original size:22 final size:23
Alignment explanation
Indices: 41771758--41771828 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 23
41771748 GTGCCTCAGA
41771758 CACACG-GCCATGTGCCTCTCTT
1 CACACGAGCCATGTGCCTCTCTT
*
41771780 CACACGAG-CATGTGCCTCAGC--
1 CACACGAGCCATGTGCCTC-TCTT
* *
41771801 CACAC-AGTCATGTGCCCCTCTT
1 CACACGAGCCATGTGCCTCTCTT
41771823 CACACG
1 CACACG
41771829 GGCTTTAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
20 3 0.08
21 14 0.35
22 21 0.52
23 2 0.05
ACGTcount: A:0.20, C:0.41, G:0.18, T:0.21
Consensus pattern (23 bp):
CACACGAGCCATGTGCCTCTCTT
Found at i:41771799 original size:43 final size:43
Alignment explanation
Indices: 41771747--41771828 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
41771737 TCCACACGGG
* *
41771747 TGTGCCTCAGACACACGGCCATGTGCCTCTCTTCACACGAGCA
1 TGTGCCTCAGACACACAGCCATGTGCCCCTCTTCACACGAGCA
* *
41771790 TGTGCCTCAGCCACACAGTCATGTGCCCCTCTTCACACG
1 TGTGCCTCAGACACACAGCCATGTGCCCCTCTTCACACG
41771829 GGCTTTAGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (43 bp):
TGTGCCTCAGACACACAGCCATGTGCCCCTCTTCACACGAGCA
Found at i:41774246 original size:14 final size:15
Alignment explanation
Indices: 41774227--41774255 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41774217 AAAAAAATTC
41774227 AATATTAA-TATTTA
1 AATATTAACTATTTA
41774241 AATATTAACTATTTA
1 AATATTAACTATTTA
41774256 TTAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTAACTATTTA
Found at i:41776950 original size:3 final size:3
Alignment explanation
Indices: 41776942--41776978 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41776932 CTAATATGGT
41776942 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 A
41776979 GCTTAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41779225 original size:10 final size:9
Alignment explanation
Indices: 41779204--41779248 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
41779194 TATTTTAGGT
*
41779204 ATTTTTAAA
1 ATTTTTATA
41779213 ATTTTTATGA
1 ATTTTTAT-A
41779223 ATTTTTTATA
1 A-TTTTTATA
*
41779233 ACTTTTATA
1 ATTTTTATA
41779242 ATTTTTA
1 ATTTTTA
41779249 CTGTGAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 20 0.65
10 4 0.13
11 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:41779230 original size:20 final size:19
Alignment explanation
Indices: 41779205--41779247 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
41779195 ATTTTAGGTA
*
41779205 TTTTTAAAATTTTTATGAAT
1 TTTTTAAAACTTTTAT-AAT
*
41779225 TTTTTATAACTTTTATAAT
1 TTTTTAAAACTTTTATAAT
41779244 TTTT
1 TTTT
41779248 ACTGTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTAAAACTTTTATAAT
Found at i:41783986 original size:34 final size:34
Alignment explanation
Indices: 41783941--41784008 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
41783931 CAGTATCAAA
*
41783941 TATGCAGTAGGGCCTTAGCCCATCACACTATTAG
1 TATGCAGTAGGGCCTTAACCCATCACACTATTAG
* *
41783975 TATGCATTAGGGCCTTAACCCATCACAGTATTAG
1 TATGCAGTAGGGCCTTAACCCATCACACTATTAG
41784009 CATCAGTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (34 bp):
TATGCAGTAGGGCCTTAACCCATCACACTATTAG
Found at i:41785054 original size:17 final size:18
Alignment explanation
Indices: 41785029--41785064 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41785019 TAGAGAATAG
41785029 AGAAAAAGAGA-AAAAAA
1 AGAAAAAGAGAGAAAAAA
*
41785046 AGAAGAAGAGAGAAAAAA
1 AGAAAAAGAGAGAAAAAA
41785064 A
1 A
41785065 CTTAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAGAGAAAAAA
Found at i:41787554 original size:22 final size:22
Alignment explanation
Indices: 41787529--41787575 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
41787519 TAATTTAGTC
41787529 ATTCTACATTTCATACTTCAAA
1 ATTCTACATTTCATACTTCAAA
*
41787551 ATTCTACATTTCATATTTCAAA
1 ATTCTACATTTCATACTTCAAA
41787573 ATT
1 ATT
41787576 TAAGTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTCTACATTTCATACTTCAAA
Found at i:41790842 original size:46 final size:48
Alignment explanation
Indices: 41790737--41790961 Score: 205
Period size: 46 Copynumber: 4.8 Consensus size: 48
41790727 ACATTGTGAG
* * *
41790737 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGACGTA
* *
41790784 ATGCTAGTGTAAGA-CGTGTCTGGGACAT-GCATCAGCCTCGAGACGTA
1 A-GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGACGTA
* * *
41790831 AGCCAGCGTAAGA-CATGTCTGGGACAT-GCATC-GGCTACGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-CGAGACGTA
* * * * * *
41790876 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCAACATAGATATGCTA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGACG-TA
* **
41790924 GAACTTGTGTAAGACCATGTCTGGGACATGGCATCAGC
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC
41790962 ACCTGACCCC
Statistics
Matches: 146, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
44 10 0.07
45 17 0.12
46 59 0.40
47 18 0.12
48 11 0.08
50 31 0.21
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGACGTA
Found at i:41798680 original size:18 final size:19
Alignment explanation
Indices: 41798657--41798707 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
41798647 ATTTATGTGT
41798657 ATTTTATAGTTTTTT-TAA
1 ATTTTATAGTTTTTTATAA
* *
41798675 ATTTTATGAATTTTTTATAT
1 ATTTTAT-AGTTTTTTATAA
*
41798695 CTTTTATAGTTTT
1 ATTTTATAGTTTT
41798708 GACGAATCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
ATTTTATAGTTTTTTATAA
Found at i:41811410 original size:21 final size:21
Alignment explanation
Indices: 41811383--41811433 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
41811373 TTGCCCAGTT
* *
41811383 CTAAAGGAGACTTAGGTTAAT
1 CTAAAGGAGACTCAGGTTAAG
* *
41811404 TTAAAGGATACTCAGGTTAAG
1 CTAAAGGAGACTCAGGTTAAG
41811425 CTAAAGGAG
1 CTAAAGGAG
41811434 GGTTGTCTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (21 bp):
CTAAAGGAGACTCAGGTTAAG
Found at i:41816229 original size:29 final size:29
Alignment explanation
Indices: 41816194--41816255 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
41816184 TATTCGACAC
41816194 CTTTAATTAATAGAATTTAACTTTTGCAT
1 CTTTAATTAATAGAATTTAACTTTTGCAT
41816223 CTTTAATTAATAGAATTTAACTTTTGCAT
1 CTTTAATTAATAGAATTTAACTTTTGCAT
41816252 CTTT
1 CTTT
41816256 TATAATTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.50
Consensus pattern (29 bp):
CTTTAATTAATAGAATTTAACTTTTGCAT
Found at i:41820767 original size:32 final size:30
Alignment explanation
Indices: 41820721--41820790 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 30
41820711 ATTCCAAAAA
*
41820721 TAATATTATTTTAATAGT-TTTATATTAAATT
1 TAATATTATCTTAATAGTATTT-TATT-AATT
41820752 TAATACTTATCTTAATAGTATTTTATTAATT
1 TAATA-TTATCTTAATAGTATTTTATTAATT
*
41820783 TAACATTA
1 TAATATTA
41820791 AAGTAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 13 0.37
32 16 0.46
33 3 0.09
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATATTATCTTAATAGTATTTTATTAATT
Found at i:41826622 original size:51 final size:51
Alignment explanation
Indices: 41826546--41826662 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 51
41826536 CAGATCACAT
* *
41826546 TTATCACTTGTCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
* *
41826597 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
41826648 TTATCACTTGTCACT
1 TTATCACTTGTCACT
41826663 AATCAGAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
Found at i:41834019 original size:33 final size:33
Alignment explanation
Indices: 41833982--41834045 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
41833972 TTACACAAAA
41833982 ACCGTGCCGTAAAATTTCAACCAATTTAAAACT
1 ACCGTGCCGTAAAATTTCAACCAATTTAAAACT
41834015 ACCGTGCCGTAAAATTTCAACCAATTTAAAA
1 ACCGTGCCGTAAAATTTCAACCAATTTAAAA
41834046 TTTTTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (33 bp):
ACCGTGCCGTAAAATTTCAACCAATTTAAAACT
Found at i:41836151 original size:43 final size:43
Alignment explanation
Indices: 41836052--41836215 Score: 181
Period size: 43 Copynumber: 3.9 Consensus size: 43
41836042 AAGTCTAAAT
** ** *
41836052 TCAT-TCACCGGCATT-TCTCCTGCTAGGCTTGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATA
* * *
41836093 TCATTTCACCAGCATTATAGACTGCTAGGCCC-AAGGCCCAATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAA-GCCCAATA
* * **
41836136 TTATCTCACTGGCATTATAGCCTGCTAGGCCCGAAGCCTGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATA
*
41836179 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGC
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGC
41836216 TCGTATATCA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
41 4 0.04
42 12 0.12
43 84 0.82
44 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (43 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATA
Found at i:41837115 original size:70 final size:70
Alignment explanation
Indices: 41836998--41837132 Score: 234
Period size: 70 Copynumber: 1.9 Consensus size: 70
41836988 TAGCACATAA
* * * *
41836998 CACCATGATTTTGTCCTAATTTGGACAGCCAATAATTTACAGTATTACAGCAGCATATTAATTAG
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAGCATTACAGCAGCAAATTAATTAG
41837063 CTAAG
66 CTAAG
41837068 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAGCATTACAGCAGCAAATTAATTAG
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAGCATTACAGCAGCAAATTAATTAG
41837133 TAATAAACTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (70 bp):
CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAGCATTACAGCAGCAAATTAATTAG
CTAAG
Found at i:41838696 original size:51 final size:51
Alignment explanation
Indices: 41838620--41838736 Score: 216
Period size: 51 Copynumber: 2.3 Consensus size: 51
41838610 CAGATCACAT
41838620 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
41838671 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
41838722 TTATCACTTGTCACT
1 TTATCACTTGTCACT
41838737 GATCAGAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:41842354 original size:23 final size:23
Alignment explanation
Indices: 41842324--41842374 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
41842314 GCTATAATAT
41842324 GGAAATGGCCATAACATGACAAA
1 GGAAATGGCCATAACATGACAAA
41842347 GGAAATGGCCATAACATGACAAA
1 GGAAATGGCCATAACATGACAAA
41842370 GGAAA
1 GGAAA
41842375 ATTGAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.49, C:0.16, G:0.24, T:0.12
Consensus pattern (23 bp):
GGAAATGGCCATAACATGACAAA
Found at i:41842879 original size:23 final size:22
Alignment explanation
Indices: 41842814--41842879 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
41842804 TCAATAGATG
*
41842814 ACTTCTGTTACTAGTACTTCGTT
1 ACTTCTGTTACTAGTACTT-TTT
*
41842837 ACTTCTGTTATTAGTACTTTTAT
1 ACTTCTGTTACTAGTACTTTT-T
* *
41842860 ACTTTTGTTACTAGCACTTT
1 ACTTCTGTTACTAGTACTTT
41842880 GGTGCTTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.52
Consensus pattern (22 bp):
ACTTCTGTTACTAGTACTTTTT
Found at i:41854407 original size:8 final size:8
Alignment explanation
Indices: 41854365--41854389 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41854355 ATATAGACTA
41854365 AATAAAAT
1 AATAAAAT
41854373 AATAAAAT
1 AATAAAAT
41854381 AATAAAAT
1 AATAAAAT
41854389 A
1 A
41854390 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:41854413 original size:29 final size:31
Alignment explanation
Indices: 41854362--41854430 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
41854352 TATATATAGA
*
41854362 CTAAATAAAATAATAAAATAATAA-AA-TAT
1 CTAATTAAAATAATAAAATAATAACAATTAT
* *
41854391 CTTATTAAAAT-ATTAAATAAATAACAATTAT
1 CTAATTAAAATAATAAAAT-AATAACAATTAT
41854422 CTAATTAAA
1 CTAATTAAA
41854431 TAACTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 14 0.42
30 2 0.06
31 11 0.33
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAACAATTAT
Found at i:41860660 original size:18 final size:19
Alignment explanation
Indices: 41860622--41860662 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
41860612 TTTCTATTAA
41860622 TAAAAATATATTTAATTAAT
1 TAAAAATATATTTAA-TAAT
41860642 TAAAAATATATTTAA-AAT
1 TAAAAATATATTTAATAAT
41860660 TAA
1 TAA
41860663 TTTATTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAATATATTTAATAAT
Found at i:41860664 original size:22 final size:20
Alignment explanation
Indices: 41860617--41860656 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41860607 GTTGGTTTCT
41860617 ATTAA-TAAAAATATATTTA
1 ATTAATTAAAAATATATTTA
41860636 ATTAATTAAAAATATATTTA
1 ATTAATTAAAAATATATTTA
41860656 A
1 A
41860657 AATTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAATTAAAAATATATTTA
Found at i:41861494 original size:2 final size:2
Alignment explanation
Indices: 41861487--41861519 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41861477 GTTTAATGTT
41861487 TA TA TA TA 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 TA TA TA TA T
41861520 TATTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41863630 original size:27 final size:27
Alignment explanation
Indices: 41863600--41863777 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
41863590 ATATTGAGCC
* * *
41863600 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
41863627 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
41863654 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
41863682 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
41863709 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
41863736 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
41863763 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41863778 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:41863693 original size:55 final size:55
Alignment explanation
Indices: 41863600--41863777 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
41863590 ATATTGAGCC
* * *
41863600 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
41863654 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
41863709 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
41863763 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41863778 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:41863739 original size:82 final size:81
Alignment explanation
Indices: 41863621--41863776 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
41863611 TGCTATACAA
* * *
41863621 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
41863686 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
41863703 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
41863767 CACTTAGTGC
65 CACTTAGTGC
41863777 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41871735 original size:27 final size:27
Alignment explanation
Indices: 41871705--41871882 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
41871695 ATATTGAGCC
* * *
41871705 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
41871732 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
41871759 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
41871787 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
41871814 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
41871841 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
41871868 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41871883 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:41871798 original size:55 final size:55
Alignment explanation
Indices: 41871705--41871882 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
41871695 ATATTGAGCC
* * *
41871705 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
41871759 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
41871814 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
41871868 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41871883 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:41871844 original size:82 final size:81
Alignment explanation
Indices: 41871726--41871881 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
41871716 TGCTATACAA
* * *
41871726 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
41871791 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
41871808 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
41871872 CACTTAGTGC
65 CACTTAGTGC
41871882 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41875975 original size:21 final size:20
Alignment explanation
Indices: 41875911--41875987 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
41875901 AAGCTCATTG
41875911 AACAGAAACCCATAAGGGTTA
1 AACAGAAACCCATAA-GGTTA
* * * *
41875932 AACTGGAACTCGA-AAGAGCTA
1 AACAGAAAC-CCATAAG-GTTA
41875953 AACAGAAACCCAATAAGGTTA
1 AACAGAAACCC-ATAAGGTTA
* *
41875974 AACTGAAACTCATA
1 AACAGAAACCCATA
41875988 CGAGTTAACT
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
20 5 0.12
21 32 0.76
22 5 0.12
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (20 bp):
AACAGAAACCCATAAGGTTA
Found at i:41882658 original size:12 final size:12
Alignment explanation
Indices: 41882641--41882673 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
41882631 AGCCACACAC
41882641 CCGTGTGCTAGG
1 CCGTGTGCTAGG
41882653 CCGTGTGCTAGG
1 CCGTGTGCTAGG
41882665 CCGTGTGCT
1 CCGTGTGCT
41882674 TCACACGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.27, G:0.39, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:41883641 original size:21 final size:21
Alignment explanation
Indices: 41883574--41883641 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41883564 AAGCTGAACG
41883574 GAAACCC-ATAAGGGTTAAACT
1 GAAACCCAAT-AGGGTTAAACT
* * *
41883595 GAAACTCGAA-AGAGCTAAA-T
1 GAAAC-CCAATAGGGTTAAACT
41883615 GAAAACCCAATAGGGTTAAACT
1 G-AAACCCAATAGGGTTAAACT
41883637 GAAAC
1 GAAAC
41883642 TCATACGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
20 5 0.14
21 27 0.75
22 3 0.08
23 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (21 bp):
GAAACCCAATAGGGTTAAACT
Found at i:41883653 original size:21 final size:21
Alignment explanation
Indices: 41883587--41883654 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41883577 ACCCATAAGG
41883587 GTTAAACTGAAACTCGAA-AGA
1 GTTAAACTGAAACTC-AATAGA
* * *
41883608 GCTAAA-TGAAAACCCAATAGG
1 GTTAAACTG-AAACTCAATAGA
41883629 GTTAAACTGAAACTC-ATACGA
1 GTTAAACTGAAACTCAATA-GA
41883650 GTTAA
1 GTTAA
41883655 CTAAAGCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 7 0.19
21 28 0.76
22 2 0.05
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (21 bp):
GTTAAACTGAAACTCAATAGA
Found at i:41891281 original size:18 final size:18
Alignment explanation
Indices: 41891258--41891295 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41891248 TTTTTCATTT
41891258 TTGTTTACTACTGTTTTG
1 TTGTTTACTACTGTTTTG
* *
41891276 TTGTTTGCTATTGTTTTG
1 TTGTTTACTACTGTTTTG
41891294 TT
1 TT
41891296 ATTGTTTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (18 bp):
TTGTTTACTACTGTTTTG
Found at i:41891298 original size:11 final size:11
Alignment explanation
Indices: 41891279--41891336 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
41891269 TGTTTTGTTG
41891279 TTTGCTATTGT
1 TTTGCTATTGT
*
41891290 TTTGTTATTGT
1 TTTGCTATTGT
***
41891301 TTTGCTACCAT
1 TTTGCTATTGT
*
41891312 TTTGCTATTAT
1 TTTGCTATTGT
* *
41891323 ATTGCTATTAT
1 TTTGCTATTGT
41891334 TTT
1 TTT
41891337 ATTGTTATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.16, C:0.10, G:0.12, T:0.62
Consensus pattern (11 bp):
TTTGCTATTGT
Found at i:41891335 original size:22 final size:22
Alignment explanation
Indices: 41891280--41891336 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
41891270 GTTTTGTTGT
* * * *
41891280 TTGCTATTGTTTTGTTATTGTT
1 TTGCTATTATTTTGCTATTATA
**
41891302 TTGCTACCATTTTGCTATTATA
1 TTGCTATTATTTTGCTATTATA
41891324 TTGCTATTATTTT
1 TTGCTATTATTTT
41891337 ATTGTTATTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.61
Consensus pattern (22 bp):
TTGCTATTATTTTGCTATTATA
Found at i:41892222 original size:20 final size:19
Alignment explanation
Indices: 41892182--41892310 Score: 67
Period size: 20 Copynumber: 6.7 Consensus size: 19
41892172 TTTTCCCATA
41892182 AAAAATAATTAAAA--ATCAT
1 AAAAAT-ATTAAAATTAT-AT
41892201 AAAAATATTAAAATTGATAT
1 AAAAATATTAAAATT-ATAT
**
41892221 AAACTTATTAAAATTATA-
1 AAAAATATTAAAATTATAT
*
41892239 AAAAAAACTTATAAA-TAT-T
1 AAAAATA-TTA-AAATTATAT
* * *
41892258 ATAAATTATAATAAATTATAA
1 A-AAAATATTA-AAATTATAT
41892279 AAAAATA-T-AAATTA-AT
1 AAAAATATTAAAATTATAT
41892295 AAAAATTATTTAAAAT
1 AAAAA-TA-TTAAAAT
41892311 CTTTAAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
16 6 0.07
17 8 0.09
18 11 0.13
19 23 0.27
20 34 0.40
21 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATATTAAAATTATAT
Found at i:41892249 original size:22 final size:22
Alignment explanation
Indices: 41892221--41892262 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
41892211 AAATTGATAT
41892221 AAACTTATTAAA-ATTATAAAAA
1 AAACTTA-TAAATATTATAAAAA
41892243 AAACTTATAAATATTATAAA
1 AAACTTATAAATATTATAAA
41892263 TTATAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACTTATAAATATTATAAAAA
Found at i:41892399 original size:11 final size:10
Alignment explanation
Indices: 41892351--41892417 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 10
41892341 ATCTTGAAAT
*
41892351 ATTATAAAAA
1 ATTATATAAA
*
41892361 ATTATAAAAA
1 ATTATATAAA
**
41892371 AGAAT-TAAA
1 ATTATATAAA
*
41892380 AATAT-TAAA
1 ATTATATAAA
41892389 ATTGATATAAA
1 ATT-ATATAAA
*
41892400 CTTATA-AAA
1 ATTATATAAA
41892409 ATTATATAA
1 ATTATATAA
41892418 GAAATCATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 20 0.43
10 20 0.43
11 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
ATTATATAAA
Done.