Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 55 of 240
Found at i:18449033 original size:21 final size:20
Alignment explanation
Indices: 18449009--18449047 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18448999 TAAAAAAAAT
18449009 TATAATATTTTTATGAATAAG
1 TATAATATTTTTAT-AATAAG
*
18449030 TATATTATTTTTATAATA
1 TATAATATTTTTATAATA
18449048 TATAACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATAATATTTTTATAATAAG
Found at i:18449666 original size:17 final size:17
Alignment explanation
Indices: 18449636--18449673 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
18449626 TCAAATATTA
18449636 AAAATTGAAATAAAAT-
1 AAAATTGAAATAAAATC
*
18449652 AAAATTTAAAGTAAAATC
1 AAAATTGAAA-TAAAATC
18449670 AAAA
1 AAAA
18449674 GAAATGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAATTGAAATAAAATC
Found at i:18451217 original size:17 final size:17
Alignment explanation
Indices: 18451187--18451232 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
18451177 CAATTAAGTT
* *
18451187 ATTTTTGAAGTTTTAAA
1 ATTTTTAAAATTTTAAA
* *
18451204 GTTTTTTAAATTTTAAA
1 ATTTTTAAAATTTTAAA
18451221 ATTTTTAAAATT
1 ATTTTTAAAATT
18451233 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
ATTTTTAAAATTTTAAA
Found at i:18456519 original size:24 final size:24
Alignment explanation
Indices: 18456490--18456541 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
18456480 TTTCTAGAAG
*
18456490 ATTTAGTATTTATTAGTATAGTAT
1 ATTTAGCATTTATTAGTATAGTAT
*
18456514 ATTTAGCATTTATTAGTATAGTTT
1 ATTTAGCATTTATTAGTATAGTAT
18456538 ATTT
1 ATTT
18456542 GACTTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAGTAT
Found at i:18460132 original size:27 final size:28
Alignment explanation
Indices: 18460073--18460143 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
18460063 ATAAAATTTG
*
18460073 TTATAATTA-TA-A-ATTTAACAAATAT
1 TTATAATTATTACATATTTAACAAATAC
18460098 TGTGATAATTATTACATATTTAA-AAATAC
1 T-T-ATAATTATTACATATTTAACAAATAC
18460127 TTATAATTTAATTACAT
1 TTATAA-TT-ATTACAT
18460144 TTATTATTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 11 0.29
28 5 0.13
29 14 0.37
30 6 0.16
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (28 bp):
TTATAATTATTACATATTTAACAAATAC
Found at i:18462315 original size:49 final size:49
Alignment explanation
Indices: 18462258--18462362 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
18462248 TCATGTGTTA
* * *
18462258 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
18462307 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
18462356 TAATTTT
1 TAATTTT
18462363 TTTTCTTAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:18463783 original size:21 final size:20
Alignment explanation
Indices: 18463738--18463784 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18463728 AAATAATAAA
*
18463738 TTAG-ATTATACATTATTTT
1 TTAGTATTATACATTATATT
*
18463757 TATAGTATTATATATTATGATT
1 T-TAGTATTATACATTAT-ATT
18463779 TTAGTA
1 TTAGTA
18463785 AATTCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 16 0.70
22 3 0.13
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (20 bp):
TTAGTATTATACATTATATT
Found at i:18463818 original size:10 final size:10
Alignment explanation
Indices: 18463800--18463874 Score: 68
Period size: 10 Copynumber: 7.9 Consensus size: 10
18463790 ATATAAGAAT
*
18463800 AATTATATTG
1 AATTATATTA
*
18463810 AATTTTATTA
1 AATTATATTA
*
18463820 AATTATATTG
1 AATTATATTA
*
18463830 AATTTTATTA
1 AATTATATTA
*
18463840 AATTATATTT
1 AATTATATTA
18463850 AA-TA-A-T-
1 AATTATATTA
*
18463856 AATTATTTTA
1 AATTATATTA
18463866 AATTATATT
1 AATTATATT
18463875 TTATAATATT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 1 0.02
9 3 0.06
10 42 0.82
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
AATTATATTA
Found at i:18463825 original size:20 final size:20
Alignment explanation
Indices: 18463800--18463848 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
18463790 ATATAAGAAT
18463800 AATTATATTGAATTTTATTA
1 AATTATATTGAATTTTATTA
18463820 AATTATATTGAATTTTATTA
1 AATTATATTGAATTTTATTA
18463840 AATTATATT
1 AATTATATT
18463849 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AATTATATTGAATTTTATTA
Found at i:18463859 original size:26 final size:26
Alignment explanation
Indices: 18463837--18463886 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
18463827 TTGAATTTTA
18463837 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTTAATAATAATTATT
*
18463863 TTAAATTATATTTTATAAT-ATTAT
1 TTAAATTATATTTAATAATAATTAT
18463887 ATATTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAAATTATATTTAATAATAATTATT
Found at i:18463859 original size:56 final size:54
Alignment explanation
Indices: 18463767--18463981 Score: 157
Period size: 56 Copynumber: 3.7 Consensus size: 54
18463757 TATAGTATTA
18463767 TATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATTTTATTAAAT
1 TATATTA--ATTTTAGTAAATTCATATAAGAATAATTATATTGAATTTTATTAAAT
* * * * *
18463823 TATATTGAATTTTATTAAATT-ATATTTAATAATAATTATTTTAAATTATATTTTATAATATT
1 TATATT-AATTTTAGTAAATTCATA--TAAGAATAATTATATTGAA-T-T-TTAT-TAA-A-T
*
18463885 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 -TATATTA--ATTTTAGTAAATTCATATAAGAATAATT-ATATT--GAATTTTATTAAAT
* * *
18463945 TATA-TATTTTTATTAAATT-ATATTTAATAATAATTAT
1 TATATTAATTTTAGTAAATTCATA--TAAGAATAATTAT
18463982 GTTAAAATAT
Statistics
Matches: 126, Mismatches: 15, Indels: 36
0.71 0.08 0.20
Matches are distributed among these distances:
54 3 0.02
55 15 0.12
56 35 0.28
57 11 0.09
58 3 0.02
59 7 0.06
60 4 0.03
61 2 0.02
62 5 0.04
63 18 0.14
64 17 0.13
65 4 0.03
66 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (54 bp):
TATATTAATTTTAGTAAATTCATATAAGAATAATTATATTGAATTTTATTAAAT
Found at i:18463891 original size:119 final size:118
Alignment explanation
Indices: 18463749--18463987 Score: 392
Period size: 119 Copynumber: 2.0 Consensus size: 118
18463739 TAGATTATAC
*
18463749 ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATT-GAA
1 ATTATTTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATTAGAA
*
18463812 TTTTATTAAATTATATTGAATTTTATTAAATTATATTTAATAATAATTATTTTAA
66 TTTTATTAAATTATA-T-AATTTTATTAAATTATATTTAATAATAATTATGTTAA
*
18463867 ATTATATTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTAT-TTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATT-AG
*
18463932 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
64 AATTTTATTAAATTATATAATTTTATTAAATTATATTTAATAATAATTATGTTAA
18463987 A
1 A
18463988 ATATGATTAA
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
118 5 0.04
119 48 0.42
120 41 0.36
121 1 0.01
122 18 0.16
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (118 bp):
ATTATTTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTAATATTAGAA
TTTTATTAAATTATATAATTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:18463892 original size:22 final size:24
Alignment explanation
Indices: 18463867--18463913 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
18463857 ATTATTTTAA
18463867 ATTAT-ATTTTA-TAATATT-ATAT
1 ATTATGATTTTAGTAA-ATTCATAT
18463889 ATTATGATTTTAGTAAATTCATAT
1 ATTATGATTTTAGTAAATTCATAT
18463913 A
1 A
18463914 AGAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTATGATTTTAGTAAATTCATAT
Found at i:18463928 original size:37 final size:37
Alignment explanation
Indices: 18463879--18463950 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
18463869 TATATTTTAT
*
18463879 AATATTATATATTATG-ATTTTAGTAAATTCATATAAG
1 AATATTATATATTAAGAATTTTAGTAAATT-ATATAAG
*
18463916 AATATT-TAATATTAAGAATTTTATTAAATTATATA
1 AATATTAT-ATATTAAGAATTTTAGTAAATTATATA
18463951 TTTTTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 18 0.58
38 12 0.39
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (37 bp):
AATATTATATATTAAGAATTTTAGTAAATTATATAAG
Found at i:18464215 original size:45 final size:44
Alignment explanation
Indices: 18464126--18464232 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 44
18464116 ATTACAACAT
* *
18464126 CATTCTATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
18464170 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
* * *
18464215 CATTACAGTGAACCAAAC
1 CATTCCATTCAACCAAAC
18464233 GTGCCCTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.41
45 31 0.57
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:18466132 original size:22 final size:21
Alignment explanation
Indices: 18466099--18466139 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18466089 CTTACGAATT
*
18466099 TTCACTTGTAATATGATTAAA
1 TTCACTTGTAATATCATTAAA
*
18466120 TTCATTTGATAATATCATTA
1 TTCACTTG-TAATATCATTA
18466140 TCATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (21 bp):
TTCACTTGTAATATCATTAAA
Found at i:18467033 original size:63 final size:63
Alignment explanation
Indices: 18466952--18467108 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 63
18466942 ACATAATAAG
* * * * * * *
18466952 ACACACAATAATTCCCTGCATCAACACCTTCAGCTCTAGTTTATTTTACATAAGCATC-ACAAC
1 ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGC-TCTACAAC
* *
18467015 ACACACAATCATTTCCTGCATCAGCACATTTAACACCAGTTTATTTTACACAAGCTCTACAAC
1 ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGCTCTACAAC
* *
18467078 ACGCACAATCA-TTCTTTGCATCAACACATTC
1 ACACACAATCATTTC-CTGCATCAACACATTC
18467109 TCCAGGGGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 5 0.06
63 74 0.94
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (63 bp):
ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGCTCTACAAC
Found at i:18469641 original size:29 final size:28
Alignment explanation
Indices: 18469587--18469641 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
18469577 CCTTTTTACT
*
18469587 TTTCCCTCAAACTTTTACTCCTTCCCAC
1 TTTCCCTCAAACTTTTACTCCCTCCCAC
18469615 TTTCCC-CAAAACTTTTACTCCCCTCCC
1 TTTCCCTC-AAACTTTTACT-CCCTCCC
18469642 CTCCTAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 17 0.71
29 6 0.25
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTCCCTCAAACTTTTACTCCCTCCCAC
Found at i:18485753 original size:98 final size:98
Alignment explanation
Indices: 18485630--18485822 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 98
18485620 TAAAATTATG
* *
18485630 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGGTTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
18485695 AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
* * *
18485728 AAGGAAATATTCTGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
18485793 AAATCTTGGATGAGTGGATGTTCTTTTAAA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAA
18485823 GTTTTATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
Found at i:18490626 original size:25 final size:25
Alignment explanation
Indices: 18490595--18490644 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
18490585 AGAAGGAGAT
*
18490595 AGAAAAAAGGTAGGAAAGAAGAAGG
1 AGAAAAAAGGCAGGAAAGAAGAAGG
18490620 AGAAAAAAGGCAGGAAAGAAGAAGG
1 AGAAAAAAGGCAGGAAAGAAGAAGG
18490645 GCGCGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.02
Consensus pattern (25 bp):
AGAAAAAAGGCAGGAAAGAAGAAGG
Found at i:18496108 original size:44 final size:45
Alignment explanation
Indices: 18496049--18496170 Score: 153
Period size: 45 Copynumber: 2.7 Consensus size: 45
18496039 GATCGCATCT
18496049 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCA
* *
18496093 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATAGCA
* *
18496138 AATCTTCTCTCCCTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
18496171 TTAAAGCCGG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
43 3 0.04
44 29 0.43
45 31 0.46
46 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Found at i:18496162 original size:45 final size:44
Alignment explanation
Indices: 18495888--18496170 Score: 162
Period size: 44 Copynumber: 6.5 Consensus size: 44
18495878 TCTTATTCTT
* *
18495888 CTGAAGTTGTAGTGGGGCAGACTGAAG-ATAG-AAAGTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCAAA-TCTTATCTCC
* * *
18495933 CTGAAGTTGCAGTGGAGCAG-TTCAA--AACCAATAATCCTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACT-AAGTAAGC-A-AATCTTATCTCC
* * * * * **
18495977 CTGAAGTTGCGGTGGAGCAGATTAA--AATCTCAGATCTTGTCTTT
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAA--GCAAATCTTATCTCC
* * * * * *
18496021 CTGAAGTTGCAGAGGA-CAGA-T-CG-CATCTAGTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCTCC
*
18496061 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTC
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCTC-C
* * *
18496105 CTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCAAATCTTCTCTCC
1 CTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAATCTTATCTCC
18496150 CTGAAGTTGCAGTGGAGCAGA
1 CTGAAGTTGCAGTGGAGCAGA
18496171 TTAAAGCCGG
Statistics
Matches: 188, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
40 24 0.13
41 4 0.02
42 4 0.02
43 9 0.05
44 89 0.47
45 54 0.29
46 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCTCC
Found at i:18496231 original size:217 final size:212
Alignment explanation
Indices: 18495874--18496404 Score: 608
Period size: 217 Copynumber: 2.5 Consensus size: 212
18495864 TCGAAAATTA
* *
18495874 CAAGTCTTATTCTTCTGAAGTTGTAGTGGGGCAGACTGAAGATAG-AAAGTCTTATCTCCCTGAA
1 CAAGTCTTA-TCTCCTGAAGTTGCAGT-GGGCAGACTGAAGAT-GCAAA-TCTTATCTCCCTGAA
* * * * *
18495938 GTTGCAGTGGAGCAG-TTCAAAACCAATAATCCTATCTCCCTGAAGTTGCGGTGGAGCAGATTAA
62 GTTGCAGTGGAGCAGATT-AAAGCCGATAATCCTATCTCACTGAAGTGGCAGTGGAGCAGATTAA
* * * * * *
18496002 AATCTCAGATCTTGTCTTTCTGAAGTTGCAGAGGACAGATCGCATCTAGTCTTATCTCCCTGAAG
126 AATCTCAGATCTTATCTCTCTGAAGTGGCAGAGGACAGATCGCATCCAATCCTATCTCCCTGAAG
18496067 TTGCAGTGGAGCAGACTAAGTAAG
191 TTGCAGTGGAGCAGACTAA--AAG
* *
18496091 CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTCTCTCCCTGAAG
1 CAAGTCTTAT-CTCCTGAAGTTGCAGTG-GGCAGACTGAAGAT-GCAAATCTTATCTCCCTGAAG
* * * *
18496156 TTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCACTGAAGTGGTAGTGG-GCGGTTTAAAA
63 TTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCACTGAAGTGGCAGTGGAGCAGATTAAAA
* *
18496220 TCTCAAGATCTTATCTCTCTGAAGTGGCAGAGGGCAGATTGCATCCAATCCTATCTCCCTGAAGT
128 TCTC-AGATCTTATCTCTCTGAAGTGGCAGAGGACAGATCGCATCCAATCCTATCTCCCTGAAGT
* * *
18496285 TGCAGTGGAGCGGATTAAAAT
192 TGCAGTGGAGCAGACTAAAAG
* * * * *
18496306 CTCAGATCTTATCTCTCTGAAGTTGCAGAGGGCAGA-TCG--CAT-CTAATCCTATCTCCCTGAA
1 C-AAG-TCTTATCTC-CTGAAGTTGCAGTGGGCAGACT-GAAGATGCAAATCTTATCTCCCTGAA
*
18496367 GTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTC
62 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
18496405 CCTAAGCAGT
Statistics
Matches: 271, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
212 52 0.19
214 2 0.01
215 4 0.01
216 26 0.10
217 182 0.67
218 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (212 bp):
CAAGTCTTATCTCCTGAAGTTGCAGTGGGCAGACTGAAGATGCAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGCCGATAATCCTATCTCACTGAAGTGGCAGTGGAGCAGATTAAAATCT
CAGATCTTATCTCTCTGAAGTGGCAGAGGACAGATCGCATCCAATCCTATCTCCCTGAAGTTGCA
GTGGAGCAGACTAAAAG
Found at i:18496282 original size:40 final size:41
Alignment explanation
Indices: 18496231--18496384 Score: 168
Period size: 40 Copynumber: 3.7 Consensus size: 41
18496221 CTCAAGATCT
* *
18496231 TATCTCTCTGAAGTGGCAGAGG-GCAGATTGCATCCAATCC
1 TATCTCCCTGAAGTTGCAGAGGAGCAGATTGCATCCAATCC
* * ** *
18496271 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCT
1 TATCTCCCTGAAGTTGCAGAGGAGCAGATT-GCATC-CA-ATCC
* * *
18496315 TATCTCTCTGAAGTTGCAGAGG-GCAGATCGCATCTAATCC
1 TATCTCCCTGAAGTTGCAGAGGAGCAGATTGCATCCAATCC
*
18496355 TATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 TATCTCCCTGAAGTTGCAGAGGAGCAGATT
18496385 AAAGCCGACA
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
40 42 0.46
41 13 0.14
42 6 0.07
43 7 0.08
44 23 0.25
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (41 bp):
TATCTCCCTGAAGTTGCAGAGGAGCAGATTGCATCCAATCC
Found at i:18496282 original size:84 final size:84
Alignment explanation
Indices: 18496182--18496387 Score: 315
Period size: 84 Copynumber: 2.5 Consensus size: 84
18496172 TAAAGCCGGT
* * *
18496182 AATCCTATCTCACTGAAGTGGTAGTGG-GCGGTTTAAAATCTCAAGATCTTATCTCTCTGAAGTG
1 AATCCTATCTCCCTGAAGTGGCAGTGGAGCGGATTAAAATCTC-AGATCTTATCTCTCTGAAGTG
*
18496246 GCAGAGGGCAGATTGCATCC
65 GCAGAGGGCAGATCGCATCC
* *
18496266 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTGGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTGG
*
18496331 CAGAGGGCAGATCGCATCT
66 CAGAGGGCAGATCGCATCC
* *
18496350 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AATCCTATCTCCCTGAAGTGGCAGTGGAGCGGATTAAA
18496388 GCCGACAATC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 99 0.88
85 14 0.12
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (84 bp):
AATCCTATCTCCCTGAAGTGGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTGG
CAGAGGGCAGATCGCATCC
Found at i:18496405 original size:44 final size:43
Alignment explanation
Indices: 18495926--18496407 Score: 230
Period size: 44 Copynumber: 11.2 Consensus size: 43
18495916 TAGAAAGTCT
* *
18495926 TATCTCCCTGAAGTTGCAGTGGAGCAG-TTCAAAACCAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCC-ACAATCC
* ** * *
18495970 TATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAATCTCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-ATCC
* ** * * * *
18496014 TGTCTTTCTGAAGTTGCAGAGGA-CAGA-T--CG-CATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-C-AATCC
* ** *
18496054 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAA-TCC
* * * *
18496098 TATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-AATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCACAATCC
* **
18496143 TCTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAATCC
* * * * * * *
18496187 TATCTCACTGAAGTGGTAGTGG-GCGGTTTAAAATCTCA-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CACA-ATCC
* * * ** *
18496231 TATCTCTCTGAAGTGGCAGAGG-GCAGATTGCA-TC-CAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAATCC
* ** * *
18496271 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-ATCC
* * *
18496315 TATCTCTCTGAAGTTGCAGAGG-GCAGA-T--CG-CATCTAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-C-AATCC
18496355 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAATCC
18496399 TATCTCCCT
1 TATCTCCCT
18496408 AAGCAGTAGC
Statistics
Matches: 335, Mismatches: 68, Indels: 70
0.71 0.14 0.15
Matches are distributed among these distances:
39 2 0.01
40 69 0.21
41 20 0.06
42 8 0.02
43 24 0.07
44 173 0.52
45 29 0.09
46 7 0.02
47 1 0.00
48 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAATCC
Found at i:18496426 original size:84 final size:84
Alignment explanation
Indices: 18496182--18496413 Score: 238
Period size: 84 Copynumber: 2.8 Consensus size: 84
18496172 TAAAGCCGGT
* * * * * * * *
18496182 AATCCTATCTCACTGAAGTGGTAGTGG-GCGGTTTAAAATCTCA-AGATCTTATCTCTCTGAAGT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-C-CACAGATCCTATCTCCCTGAAGC
* *
18496245 GGCAGAGGGCAGATTGCATCC
64 AGCAGAGGGCAGATCGCATCC
* * * * * **
18496266 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCCTATCTCCCTGAAGCAG
*
18496331 CAGAGGGCAGATCGCATCT
66 CAGAGGGCAGATCGCATCC
*
18496350 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-ATCCTATCTCCCT-AAGCA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ACAGATCCTATCTCCCTGAAGCA
18496413 G
65 G
18496414 TAGCGGAGCA
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
83 5 0.04
84 111 0.87
85 12 0.09
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (84 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCCTATCTCCCTGAAGCAG
CAGAGGGCAGATCGCATCC
Found at i:18498621 original size:98 final size:98
Alignment explanation
Indices: 18498498--18498690 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 98
18498488 TAAAATCATG
* * *
18498498 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGGTTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTACCCTAACGTATTGGGTGTGATTTCTT
18498563 AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
* *
18498596 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTACCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTACCCTAACGTATTGGGTGTGATTTCTT
*
18498661 AAATCTTGGATGAGTGGATGTTCTTTTAAA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAA
18498691 GTTTTATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTACCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAATA
Found at i:18508603 original size:46 final size:46
Alignment explanation
Indices: 18508525--18508710 Score: 266
Period size: 46 Copynumber: 4.0 Consensus size: 46
18508515 ACAATTCTAT
* * * *
18508525 AACTTAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAG
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
18508571 AACTAAGTATGGTTTTCTTCACTGCAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
18508617 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTAT-AC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTT-TCAC
* * * *
18508663 AACTCAGTATGGCTTTCTTCAGTGAAACACCATAGCTACATTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
18508709 AA
1 AA
18508711 TTTTCCATGG
Statistics
Matches: 127, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 125 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:18509947 original size:17 final size:17
Alignment explanation
Indices: 18509925--18509961 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18509915 AAATTCTTTT
18509925 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
* *
18509942 TAAATCATAGAATTCAC
1 TAAATCACAAAATTCAC
18509959 TAA
1 TAA
18509962 TTCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:18514967 original size:46 final size:46
Alignment explanation
Indices: 18514900--18515085 Score: 291
Period size: 46 Copynumber: 4.0 Consensus size: 46
18514890 ATAATGCTAT
* * *
18514900 AACTCAGTATGGTTTCCTTCACTAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
18514946 AACTCAGTATGGTTTTTTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
** *
18514992 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTAAATTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
18515038 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTTAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
18515084 AA
1 AA
18515086 TTTTCCATGG
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:18516264 original size:17 final size:17
Alignment explanation
Indices: 18516239--18516275 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18516229 AAATTCTTTT
*
18516239 TAAATCACAAAATTCAC
1 TAAACCACAAAATTCAC
*
18516256 TAAACCACAGAATTCAC
1 TAAACCACAAAATTCAC
18516273 TAA
1 TAA
18516276 TTCAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22
Consensus pattern (17 bp):
TAAACCACAAAATTCAC
Found at i:18520915 original size:45 final size:45
Alignment explanation
Indices: 18520851--18520944 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
18520841 AACAGATACT
* *
18520851 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
18520896 CGGTGGAATCAGCACATAGCAACCATCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
18520941 CGGT
1 CGGT
18520945 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:18521127 original size:101 final size:101
Alignment explanation
Indices: 18520948--18521132 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
18520938 GTTCGGTTCA
* * *
18520948 CATAGTAGCCTGCACATAGTACTACATATGTGACCATTACCATCCAATACATGTAGTATCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCAATACACGTAGTAGCCTGCA
18521013 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
18521050 CATAGTAGCCTGCACATAGTACTACACATGCT-ACC-TATCATTCCAGTATACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATG-TGACCATACCA-TCCAATACACGTAGTAGCCTGC
18521113 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
18521133 CCATCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 32 0.43
103 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCAATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:18525552 original size:34 final size:33
Alignment explanation
Indices: 18525464--18525553 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
18525454 GAATATAATA
18525464 AAAAT-ATATTTTT-ATTTTTA-TTTTTTATTTT
1 AAAATAAT-TTTTTAATTTTTATTTTTTTATTTT
* **
18525495 AAAATACTTTTAAAATATTTTTATTTTTTTATTTTT
1 AAAATAATTTT-TTA-ATTTTTATTTTTTTA-TTTT
*
18525531 AAAATAATTTTTTAATGTTTATT
1 AAAATAATTTTTTAATTTTTATT
18525554 AAAAAATGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
31 8 0.17
32 1 0.02
34 15 0.33
35 8 0.17
36 14 0.30
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (33 bp):
AAAATAATTTTTTAATTTTTATTTTTTTATTTT
Found at i:18530692 original size:21 final size:22
Alignment explanation
Indices: 18530668--18530722 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
18530658 GTCTTAAATT
18530668 TAAATATAATATAATA-TAAAA
1 TAAATATAATATAATATTAAAA
*** *
18530689 TAAATATTCGACAATATTAAAA
1 TAAATATAATATAATATTAAAA
18530711 -AAATATAATATA
1 TAAATATAATATA
18530723 TGCATTGGAA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATAATATAATATTAAAA
Found at i:18532286 original size:16 final size:17
Alignment explanation
Indices: 18532257--18532290 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18532247 AGGTAAAAAG
18532257 ACTAAAAATATATTTAT
1 ACTAAAAATATATTTAT
*
18532274 ACTAAAAA-CTATTTAT
1 ACTAAAAATATATTTAT
18532290 A
1 A
18532291 ATACAGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
ACTAAAAATATATTTAT
Found at i:18535690 original size:18 final size:17
Alignment explanation
Indices: 18535669--18535716 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
18535659 CTATTTTAAA
18535669 CTTTAATTAATTTTATTT
1 CTTTAATTAA-TTTATTT
*
18535687 CTTTAATT-ATTTCTTT
1 CTTTAATTAATTTATTT
*
18535703 -TTTAATTAAATTAT
1 CTTTAATTAATTTAT
18535717 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.27
16 10 0.38
17 1 0.04
18 8 0.31
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTAATTAATTTATTT
Found at i:18535723 original size:17 final size:18
Alignment explanation
Indices: 18535700--18535740 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
18535690 TAATTATTTC
*
18535700 TTTTTTAATTAAATTATA
1 TTTTTAAATTAAATTATA
*
18535718 TTTTTAAAATTATATTATA
1 TTTTT-AAATTAAATTATA
18535737 TTTT
1 TTTT
18535741 AAACTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTAAATTATA
Found at i:18544134 original size:66 final size:65
Alignment explanation
Indices: 18544021--18544153 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 65
18544011 CAAATTGCTT
* * *
18544021 AACTTAAAGCGGAGACAGCATCGAGGGAAGCAGAGGCTCAAAGAAAATATGAAGAACTCCAGCTA
1 AACTTAAAGCGGAGACAGCAGCGAGGGAAGCAGAGGC-CAAAAAAAATATGAAGAACTCCAACTA
18544086 C
65 C
* * *
18544087 AACTTAAAGTGGAGGCAGCAGCGAGGGAAGCAGAGG-CAAGCAAAAAATATGACGAACTCCAACT
1 AACTTAAAGCGGAGACAGCAGCGAGGGAAGCAGAGGCCAA--AAAAAATATGAAGAACTCCAACT
18544151 AC
64 AC
18544153 A
1 A
18544154 GCTTCAGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
64 3 0.05
66 56 0.95
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (65 bp):
AACTTAAAGCGGAGACAGCAGCGAGGGAAGCAGAGGCCAAAAAAAATATGAAGAACTCCAACTAC
Found at i:18545427 original size:23 final size:24
Alignment explanation
Indices: 18545392--18545437 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
18545382 TAATAAAAAT
18545392 ATATTTAAAATATTTTT-TAATTG
1 ATATTTAAAATATTTTTATAATTG
* *
18545415 ATATTTTATATATTTTTATAATT
1 ATATTTAAAATATTTTTATAATT
18545438 AAATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTTAAAATATTTTTATAATTG
Found at i:18555955 original size:48 final size:52
Alignment explanation
Indices: 18555885--18555983 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
18555875 AATAATTATT
18555885 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
18555933 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
18555984 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:18555965 original size:17 final size:17
Alignment explanation
Indices: 18555940--18555973 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18555930 ATAATTTTAA
*
18555940 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
18555957 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
18555974 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:18555990 original size:17 final size:16
Alignment explanation
Indices: 18555945--18555992 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
18555935 TTTAAATTTT
18555945 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
18555962 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
18555976 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
18555993 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:18556047 original size:54 final size:54
Alignment explanation
Indices: 18555989--18556167 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
18555979 ATAATCATAT
18555989 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
18556043 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
18556106 TA
54 -A
*
18556108 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
18556163 ATTAT
1 ATTAT
18556168 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:18556050 original size:61 final size:61
Alignment explanation
Indices: 18555985--18556172 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
18555975 AGTTATAATC
18555985 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
18556046 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
18556105 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
18556166 ATATATT
1 ATATATT
18556173 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:18556064 original size:18 final size:17
Alignment explanation
Indices: 18556033--18556067 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18556023 ATTATTAAGA
18556033 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
18556050 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
18556068 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:18556106 original size:120 final size:120
Alignment explanation
Indices: 18555982--18556204 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
18555972 ATTAGTTATA
18555982 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
18556047 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
18556102 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
18556167 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
18556205 TAAATATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:18556181 original size:18 final size:17
Alignment explanation
Indices: 18556153--18556187 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18556143 ATTATTAAGA
*
18556153 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18556170 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18556188 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18556199 original size:54 final size:54
Alignment explanation
Indices: 18556016--18556201 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
18556006 TTCATATAAG
* *
18556016 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
18556070 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
18556133 AAG
53 -TT
* *
18556136 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
18556190 AATAATAATTAT
1 AATAATAATTAT
18556202 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:18556308 original size:144 final size:147
Alignment explanation
Indices: 18556141--18556412 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
18556131 ATAAGAATAT
*
18556141 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
18556206 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
18556268 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
18556285 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
18556350 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
18556413 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:18556325 original size:18 final size:17
Alignment explanation
Indices: 18556297--18556331 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18556287 ATTATTAAGA
*
18556297 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18556314 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18556332 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18556542 original size:44 final size:45
Alignment explanation
Indices: 18556493--18556587 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
18556483 TTACACCTCT
* *
18556493 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
18556537 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
18556582 ATTACA
1 ATTACA
18556588 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:18556587 original size:16 final size:16
Alignment explanation
Indices: 18556566--18556598 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18556556 TTGATTTGCT
*
18556566 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
18556582 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
18556598 A
1 A
18556599 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:18556608 original size:21 final size:21
Alignment explanation
Indices: 18556579--18556621 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18556569 ACACCTCTAT
*
18556579 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18556600 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18556621 T
1 T
18556622 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:18556913 original size:31 final size:30
Alignment explanation
Indices: 18556876--18556953 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
18556866 CCCTTTGACC
*
18556876 AAAAATACAAAGATTAAAATTAA-CAAATTT
1 AAAAATACAAAGAATAAAATTAATCAAA-TT
*
18556906 AAAAAATATAAA-AACTAAAATTAATCAAATT
1 -AAAAATACAAAGAA-TAAAATTAATCAAATT
18556937 -AAAATACAAAGAATAAA
1 AAAAATACAAAGAATAAA
18556954 TCTGCAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 13 0.32
30 3 0.07
31 21 0.51
32 4 0.10
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (30 bp):
AAAAATACAAAGAATAAAATTAATCAAATT
Found at i:18563223 original size:31 final size:31
Alignment explanation
Indices: 18563188--18563247 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
18563178 AAGTTTGGGT
*
18563188 AGTGGTGTCCATGGGAAAGGCGGCACCAAGG
1 AGTGGTGCCCATGGGAAAGGCGGCACCAAGG
*
18563219 AGTGGTGCCCATGGGAAAGGTGGCACCAA
1 AGTGGTGCCCATGGGAAAGGCGGCACCAA
18563248 AGTACTGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.40, T:0.13
Consensus pattern (31 bp):
AGTGGTGCCCATGGGAAAGGCGGCACCAAGG
Found at i:18566594 original size:22 final size:22
Alignment explanation
Indices: 18566567--18566668 Score: 84
Period size: 25 Copynumber: 4.4 Consensus size: 22
18566557 CACTAATGAA
18566567 CAGAGAGCACTAAAGTGCTATA-
1 CAGAGAGCAC-AAAGTGCTATAT
*
18566589 CAGAGAGCACATATGTGCTA-AT
1 CAGAGAGCACA-AAGTGCTATAT
*
18566611 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCA-CAAAGTGCT-AT-AT
18566636 CAGAGAGCACCAACA-TGCTAATAAT
1 CAGAGAGCA-CAA-AGTGCT-AT-AT
18566661 CAGAGAGC
1 CAGAGAGC
18566669 GCGCTAAAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.03
22 32 0.46
23 3 0.04
25 33 0.47
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (22 bp):
CAGAGAGCACAAAGTGCTATAT
Found at i:18566641 original size:25 final size:25
Alignment explanation
Indices: 18566607--18566668 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
18566597 ACATATGTGC
*
18566607 TAATCAGAGAGCACCAACGTGCTAA
1 TAATCAGAGAGCACCAACATGCTAA
18566632 TAATCAGAGAGCACCAACATGCTAA
1 TAATCAGAGAGCACCAACATGCTAA
18566657 TAATCAGAGAGC
1 TAATCAGAGAGC
18566669 GCGCTAAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (25 bp):
TAATCAGAGAGCACCAACATGCTAA
Found at i:18566655 original size:47 final size:44
Alignment explanation
Indices: 18566567--18566657 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 44
18566557 CACTAATGAA
* **
18566567 CAGAGAGCACTAAAGTGCTATACAGAGAGCACATATGTGCTAAT
1 CAGAGAGCACCAAAGTGCTATACAGAGAGCACATACATGCTAAT
*
18566611 CAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCA-ACATGCTAAT
1 CAGAGAGCACCAAAGTGCT-AT-A-CAGAGAGCA-CATACATGCTAAT
18566658 AATCAGAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
44 17 0.44
45 2 0.05
46 1 0.03
47 17 0.44
48 2 0.05
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (44 bp):
CAGAGAGCACCAAAGTGCTATACAGAGAGCACATACATGCTAAT
Found at i:18567642 original size:8 final size:8
Alignment explanation
Indices: 18567622--18567675 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
18567612 TTTCTATTTG
18567622 TTAT-ATA
1 TTATAATA
18567629 TATATAATA
1 T-TATAATA
18567638 TTATAATA
1 TTATAATA
18567646 TTATAATA
1 TTATAATA
*
18567654 ATATAATTA
1 TTATAA-TA
*
18567663 ATATAATA
1 TTATAATA
18567671 CTTAT
1 -TTAT
18567676 TTATTAAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 1 0.02
8 25 0.61
9 15 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
TTATAATA
Found at i:18569650 original size:7 final size:7
Alignment explanation
Indices: 18569611--18569636 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18569601 CGAAACAGAG
18569611 AAGGAGA
1 AAGGAGA
18569618 AAGGAGA
1 AAGGAGA
18569625 AAGGAGA
1 AAGGAGA
18569632 AAGGA
1 AAGGA
18569637 AAAAAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AAGGAGA
Found at i:18570531 original size:25 final size:25
Alignment explanation
Indices: 18570503--18570583 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
18570493 ACTTTAGCGC
*
18570503 GCTCTCTGATTTTTAGCAC-TTCAGT
1 GCTCTCTGATTATTAGCACGTT-AGT
*
18570528 GCTCTTTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * *
18570553 GCTCCCTGATTACTAGCATGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
18570578 GCTCTC
1 GCTCTC
18570584 CGTTTAGCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 46 0.96
26 2 0.04
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:18571537 original size:16 final size:16
Alignment explanation
Indices: 18571516--18571546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18571506 AAAATAAAAA
*
18571516 AAATTAATCAGAAACT
1 AAATTAATCAAAAACT
18571532 AAATTAATCAAAAAC
1 AAATTAATCAAAAAC
18571547 ATTTATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATTAATCAAAAACT
Found at i:18571874 original size:32 final size:32
Alignment explanation
Indices: 18571811--18571893 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
18571801 CCCTTTCTTC
* *
18571811 TTTCCTTCTCTTCTCTTCT-CTTTTTTTCCCT
1 TTTCCTTCTCTTCTATTCTCCTCTTTTTCCCT
*
18571842 TTTCCTTCTATTCTATTCTCCTCTTTTTCCCT
1 TTTCCTTCTCTTCTATTCTCCTCTTTTTCCCT
* *
18571874 TCTCCTTCTCTTCTTTTCTC
1 TTTCCTTCTCTTCTATTCTC
18571894 TATTCTGCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 17 0.38
32 28 0.62
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTCCTTCTCTTCTATTCTCCTCTTTTTCCCT
Found at i:18576571 original size:14 final size:13
Alignment explanation
Indices: 18576551--18576585 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
18576541 CATAAAAGAG
18576551 ATAAATAATTAAA
1 ATAAATAATTAAA
18576564 ATTAAATAATTAAA
1 A-TAAATAATTAAA
18576578 ATAAATAA
1 ATAAATAA
18576586 GCAAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATAATTAAA
Found at i:18578012 original size:30 final size:31
Alignment explanation
Indices: 18577978--18578035 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
18577968 CATTATTATC
*
18577978 CAAAA-AAATGAAAAGCAAAGTTGGAGCTCT
1 CAAAATAAATGAAAAGCAAAGTTAGAGCTCT
*
18578008 CAAAATAAATGAAAAGCAACGTTAGAGC
1 CAAAATAAATGAAAAGCAAAGTTAGAGC
18578036 GATGATTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.16
Consensus pattern (31 bp):
CAAAATAAATGAAAAGCAAAGTTAGAGCTCT
Found at i:18579299 original size:21 final size:21
Alignment explanation
Indices: 18579275--18579315 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18579265 GTGGCGACCA
*
18579275 GGGAAAAAGAAAACGAAAAAT
1 GGGAAAAAGAAAAAGAAAAAT
18579296 GGGAAAAAGAAAAAGAAAAA
1 GGGAAAAAGAAAAAGAAAAA
18579316 AAGGTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (21 bp):
GGGAAAAAGAAAAAGAAAAAT
Found at i:18595098 original size:16 final size:17
Alignment explanation
Indices: 18595065--18595100 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18595055 TAATCTAATT
18595065 TATTTGATATATTTAAA
1 TATTTGATATATTTAAA
18595082 TATTTGATATA-TTAAA
1 TATTTGATATATTTAAA
18595098 TAT
1 TAT
18595101 ATTTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTGATATATTTAAA
Found at i:18595521 original size:17 final size:19
Alignment explanation
Indices: 18595490--18595529 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
18595480 CGTAGCTTTT
18595490 AAAATAAAATAAAAACT-A
1 AAAATAAAATAAAAACTGA
*
18595508 AAAATAAAGT-AAAACTGA
1 AAAATAAAATAAAAACTGA
18595526 AAAA
1 AAAA
18595530 AGTGAGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAATAAAATAAAAACTGA
Found at i:18598629 original size:37 final size:36
Alignment explanation
Indices: 18598578--18598647 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
18598568 ATTCCAAAAA
*
18598578 TAATATTATTTTAATAGT-TTATTATTAAATTAAATT
1 TAATATTATCTTAATAGTATT-TTATTAAATTAAATT
*
18598614 TAATAATTATCTTAATAGTATTTTATTAATTTAA
1 TAAT-ATTATCTTAATAGTATTTTATTAAATTAA
18598648 TATTAAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 4 0.13
37 24 0.80
38 2 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTTTATTAAATTAAATT
Found at i:18599754 original size:21 final size:21
Alignment explanation
Indices: 18599697--18599765 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
18599687 AAGTTCATGA
*
18599697 ATAAACCACCAATCTTTACAG
1 ATAAACCACCAATGTTTACAG
* *
18599718 ATAAACCACTAATGTTTGCAG
1 ATAAACCACCAATGTTTACAG
* * *
18599739 ATAAACCACCAGTGTTCATAG
1 ATAAACCACCAATGTTTACAG
18599760 ATAAAC
1 ATAAAC
18599766 TGCCAGTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (21 bp):
ATAAACCACCAATGTTTACAG
Found at i:18601697 original size:36 final size:37
Alignment explanation
Indices: 18601645--18601717 Score: 139
Period size: 36 Copynumber: 2.0 Consensus size: 37
18601635 CGGGATACAT
18601645 GGCATAAGGGCTAGCTTACGCTTTTCGAAGTATAGTC
1 GGCATAAGGGCTAGCTTACGCTTTTCGAAGTATAGTC
18601682 GGCATAA-GGCTAGCTTACGCTTTTCGAAGTATAGTC
1 GGCATAAGGGCTAGCTTACGCTTTTCGAAGTATAGTC
18601718 TGTTTAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.81
37 7 0.19
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (37 bp):
GGCATAAGGGCTAGCTTACGCTTTTCGAAGTATAGTC
Found at i:18605845 original size:20 final size:20
Alignment explanation
Indices: 18605820--18605863 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
18605810 CACAAAATAC
18605820 ACAAAATTTGTCCACACTAT
1 ACAAAATTTGTCCACACTAT
18605840 ACAAAATTTGTCCACACTAT
1 ACAAAATTTGTCCACACTAT
18605860 ACAA
1 ACAA
18605864 GGGCTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (20 bp):
ACAAAATTTGTCCACACTAT
Found at i:18605936 original size:27 final size:27
Alignment explanation
Indices: 18605905--18605956 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
18605895 CACACATTTC
*
18605905 ATTT-ATTTCACATTTTAGTCCCTAAAA
1 ATTTAATTTCACAATTTAG-CCCTAAAA
18605932 ATTTAATTTCACAATTTAGCCCTAA
1 ATTTAATTTCACAATTTAGCCCTAA
18605957 TTACTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (27 bp):
ATTTAATTTCACAATTTAGCCCTAAAA
Found at i:18605966 original size:27 final size:28
Alignment explanation
Indices: 18605909--18605970 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
18605899 CATTTCATTT
* * *
18605909 ATTTCACATTTTAGTCCCTAAAAATTTA
1 ATTTCACAATTTAGTCCCTAAAAACTCA
**
18605937 ATTTCACAATTTAG-CCCTAATTACTCA
1 ATTTCACAATTTAGTCCCTAAAAACTCA
18605964 ATTTCAC
1 ATTTCAC
18605971 CAATAATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (28 bp):
ATTTCACAATTTAGTCCCTAAAAACTCA
Found at i:18607197 original size:30 final size:29
Alignment explanation
Indices: 18607162--18607282 Score: 165
Period size: 29 Copynumber: 4.0 Consensus size: 29
18607152 AATAAACACA
*
18607162 AAAAAATTTAGAAAATTAAAAAAAGTATTTT
1 AAAATATTTA-AAAA-TAAAAAAAGTATTTT
18607193 AAAAATATTTTAAAAAT-AAAAAAGTATTTT
1 -AAAATA-TTTAAAAATAAAAAAAGTATTTT
18607223 AAAATATTTTAAAAATAAAAAAAGTATTTT
1 AAAATA-TTTAAAAATAAAAAAAGTATTTT
18607253 AAAATATTTAAAAATAAAAAAA-TATATTT
1 AAAATATTTAAAAATAAAAAAAGTAT-TTT
18607282 A
1 A
18607283 TTATATTCGA
Statistics
Matches: 85, Mismatches: 1, Indels: 9
0.89 0.01 0.09
Matches are distributed among these distances:
28 3 0.04
29 36 0.42
30 32 0.38
31 1 0.01
32 9 0.11
33 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATATTTAAAAATAAAAAAAGTATTTT
Found at i:18607214 original size:29 final size:29
Alignment explanation
Indices: 18607180--18607282 Score: 163
Period size: 30 Copynumber: 3.5 Consensus size: 29
18607170 TAGAAAATTA
18607180 AAAAAAGTATTTTAAAAATATTTTAAAAAT
1 AAAAAAGTATTTT-AAAATATTTTAAAAAT
18607210 AAAAAAGTATTTTAAAATATTTTAAAAAT
1 AAAAAAGTATTTTAAAATATTTTAAAAAT
18607239 AAAAAAAGTATTTTAAAATA-TTTAAAAAT
1 -AAAAAAGTATTTTAAAATATTTTAAAAAT
*
18607268 AAAAAAATATATTTA
1 AAAAAAGTAT-TTTA
18607283 TTATATTCGA
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
28 9 0.13
29 29 0.41
30 32 0.46
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAAAGTATTTTAAAATATTTTAAAAAT
Found at i:18607931 original size:23 final size:23
Alignment explanation
Indices: 18607905--18607950 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18607895 TACTTGCACA
18607905 CTTAGTGCATAATTGCCAAACTT
1 CTTAGTGCATAATTGCCAAACTT
18607928 CTTAGTGCATAATTGCCAAACTT
1 CTTAGTGCATAATTGCCAAACTT
18607951 TCTTGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (23 bp):
CTTAGTGCATAATTGCCAAACTT
Found at i:18610284 original size:20 final size:20
Alignment explanation
Indices: 18610242--18610296 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
18610232 TAGCGATAAC
*
18610242 AAAATTGAAACCAAAAGACA
1 AAAATTGAAAACAAAAGACA
* *
18610262 AAAATTGAAGAACAAAGGAAA
1 AAAATTGAA-AACAAAAGACA
18610283 AATAACTTGAAAAC
1 AA-AA-TTGAAAAC
18610297 GTTGAACAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 10 0.34
22 5 0.17
23 5 0.17
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAATTGAAAACAAAAGACA
Found at i:18615580 original size:28 final size:29
Alignment explanation
Indices: 18615517--18615585 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
18615507 AGGAAAAGGA
*
18615517 AAGGAAAAAGAATAGAAAGAAAAAAAAAG
1 AAGGAAAAGGAATAGAAAGAAAAAAAAAG
* * *
18615546 AATGAAAAGGAAT-GAAAGAAAAGAAAAT
1 AAGGAAAAGGAATAGAAAGAAAAAAAAAG
*
18615574 AAGGAAAGGGAA
1 AAGGAAAAGGAA
18615586 AAAAAATAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.06
Consensus pattern (29 bp):
AAGGAAAAGGAATAGAAAGAAAAAAAAAG
Found at i:18622928 original size:20 final size:20
Alignment explanation
Indices: 18622891--18622933 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
18622881 TAAAATACCA
** * *
18622891 AAAAACCCAACGATCAAAGC
1 AAAAACCCAAAAAACAAACC
18622911 AAAAACCCAAAAAACAAACC
1 AAAAACCCAAAAAACAAACC
18622931 AAA
1 AAA
18622934 TCCGAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.28, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAACCCAAAAAACAAACC
Found at i:18623200 original size:24 final size:23
Alignment explanation
Indices: 18623152--18623205 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
18623142 ACAAATACGT
* *
18623152 TTTCAGATACAGATTCAAATATA
1 TTTCATATACAGAATCAAATATA
* *
18623175 TTCTCATATACAGAATCAACTGTA
1 TT-TCATATACAGAATCAAATATA
18623199 TTTCATA
1 TTTCATA
18623206 ATCGGATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (23 bp):
TTTCATATACAGAATCAAATATA
Found at i:18630135 original size:17 final size:17
Alignment explanation
Indices: 18630113--18630146 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18630103 GACCATATAT
18630113 GGGATATTACGTGTAAG
1 GGGATATTACGTGTAAG
18630130 GGGATATTACGTGTAAG
1 GGGATATTACGTGTAAG
18630147 ACCATATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (17 bp):
GGGATATTACGTGTAAG
Found at i:18630230 original size:43 final size:43
Alignment explanation
Indices: 18630139--18630295 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
18630129 GGGGATATTA
* *
18630139 CGTGTAAGACCATATCTGGGATA-TGGCATTGATATGAGACTT
1 CGTGTAAGACCATGTCTGGGATATTGGCATCGATATGAGACTT
* * *
18630181 CGTGTAAGTCCATGTCTGGGATATTGACATCGATATGTGA-TT
1 CGTGTAAGACCATGTCTGGGATATTGGCATCGATATGAGACTT
** * *
18630223 CCGTGTAAGACCATGGATGGGCTATTGGCATCGATACGAGA-TT
1 -CGTGTAAGACCATGTCTGGGATATTGGCATCGATATGAGACTT
* * * *
18630266 ACATGTAAGACTATATATGGGATA-TGGCAT
1 -CGTGTAAGACCATGTCTGGGATATTGGCAT
18630296 TGTTACAGTA
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
42 29 0.31
43 66 0.69
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGATATTGGCATCGATATGAGACTT
Found at i:18635329 original size:8 final size:8
Alignment explanation
Indices: 18635316--18635343 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
18635306 GTAAAAATAT
18635316 TTATTTTA
1 TTATTTTA
18635324 TTATTTTA
1 TTATTTTA
18635332 TTATTTTA
1 TTATTTTA
18635340 TTAT
1 TTAT
18635344 GGTTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:18636691 original size:43 final size:42
Alignment explanation
Indices: 18636536--18636700 Score: 152
Period size: 43 Copynumber: 3.9 Consensus size: 42
18636526 TTAGGGTTAC
*
18636536 CGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
1 CGAGATTACGTGTAAGACCATATATGGGATATGGCATCGATA
* * * * ** * *
18636578 TGAGACTT-TGTGTAAGTCCATGTCCGTGACATTGGCATCGATA
1 CGAGA-TTACGTGTAAGACCATATATGGGATA-TGGCATCGATA
* * * ** *
18636621 TGTGATTCCGTGTAAGACCATGGATGGGCTATTGGCATCGATA
1 CGAGATTACGTGTAAGACCATATATGGGATA-TGGCATCGATA
*
18636664 CGAGATTACATGTAAGACCATATATGGGATATGGCAT
1 CGAGATTACGTGTAAGACCATATATGGGATATGGCAT
18636701 TGTTACAGTA
Statistics
Matches: 97, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
42 29 0.30
43 68 0.70
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (42 bp):
CGAGATTACGTGTAAGACCATATATGGGATATGGCATCGATA
Found at i:18642112 original size:37 final size:36
Alignment explanation
Indices: 18642071--18642143 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
18642061 CTTGAAATAA
*
18642071 AATATAATT-TAATAAGAATTTAATTTTATATTATTTT
1 AATATAATTCTAA-AAGAATTAAATTTT-TATTATTTT
*
18642108 AATATAATTCTAAATGAATTAAATTTTTATTATTTT
1 AATATAATTCTAAAAGAATTAAATTTTTATTATTTT
18642144 GTAATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 9 0.27
37 21 0.64
38 3 0.09
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (36 bp):
AATATAATTCTAAAAGAATTAAATTTTTATTATTTT
Found at i:18642710 original size:45 final size:47
Alignment explanation
Indices: 18642660--18642753 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 47
18642650 ATTGGCCACT
* *
18642660 TATAAATAATTAATAATAAATAATATGTAATTTATTTAAA-A-TTAG
1 TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTTAG
* *
18642705 TATAAATAATTCATAATAAATATTATATAATTTAATTAAATATTTAG
1 TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTTAG
18642752 TA
1 TA
18642754 AGCCAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 36 0.84
46 1 0.02
47 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (47 bp):
TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTTAG
Found at i:18645187 original size:38 final size:38
Alignment explanation
Indices: 18645079--18645190 Score: 109
Period size: 38 Copynumber: 2.9 Consensus size: 38
18645069 ACCTAGTGAG
* * *
18645079 TACATGTTAAGCGTGTCAACTGCTAGTGTTAAATTGAA
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
* * * * * *
18645117 TGCATGATAAGCATGTTGATTGGC-AATTTTGAATTGAA
1 TACATGTTAAGCATGTTAACT-GCTAGTGTTGAATTGAA
* *
18645155 TACATGTTAAGCATGTTTACTACTAGTGTTGAATTG
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTG
18645191 TTCATAGCTT
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
37 1 0.02
38 53 0.95
39 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (38 bp):
TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
Found at i:18649939 original size:85 final size:86
Alignment explanation
Indices: 18649795--18649956 Score: 238
Period size: 85 Copynumber: 1.9 Consensus size: 86
18649785 CAAATAAGTA
* * * *
18649795 GTGGCTCGTCCACAAAACCCAGTGGCAGTTTGTTTAATCTGCAAATAAGTTGTACACTCACAACA
1 GTGGCTCGTCCACAAAACCCAATGGCAGTTTGTTTAACCTGCAAACAAGTCGTACACTCACAACA
18649860 AGTGGCAGTAACTGTAAATAT
66 AGTGGCAGTAACTGTAAATAT
* *
18649881 GTGGCTCGTCCAC-AAACCCAATGGCAGTTTGTTTAACCTG-AAACCATGTCGTGCACTCACAAC
1 GTGGCTCGTCCACAAAACCCAATGGCAGTTTGTTTAACCTGCAAA-CAAGTCGTACACTCACAAC
*
18649944 AAGTGGTAGTAAC
65 AAGTGGCAGTAAC
18649957 CGAAAATGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 3 0.04
85 52 0.76
86 13 0.19
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (86 bp):
GTGGCTCGTCCACAAAACCCAATGGCAGTTTGTTTAACCTGCAAACAAGTCGTACACTCACAACA
AGTGGCAGTAACTGTAAATAT
Found at i:18650178 original size:165 final size:165
Alignment explanation
Indices: 18649906--18650231 Score: 526
Period size: 165 Copynumber: 2.0 Consensus size: 165
18649896 ACCCAATGGC
* *
18649906 AGTTTGTTTAACCTGAAACCATGTCGTGCACTCACAACAAGTGGTAGTAACCGAAAATGATTTTA
1 AGTTTGTTTAACCTGAAACCATGTCGTGCACTCACAACAAGTGGCAGCAACCGAAAATGATTTTA
* *
18649971 TCTAATATACTAGTGGTTTACCTACGTTTTTCTTTACAAAGTGGCAGTTTATCTACAAACTAGTG
66 TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTACAAACCAGTG
* * *
18650036 GTGGCTCGTCTACAATCCAGATTGATATGTTAGAT
131 GTGGCTCGTCCACAATCAAGAGTGATATGTTAGAT
* * * *
18650071 AGTTTGTTTAACCTGAAACCATGTTGTGCACTCACAATAAGTGGCAGCAACTGCAAATGATTTTA
1 AGTTTGTTTAACCTGAAACCATGTCGTGCACTCACAACAAGTGGCAGCAACCGAAAATGATTTTA
* *
18650136 TCTAATATGCTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTGCAAACCAGTG
66 TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTACAAACCAGTG
*
18650201 GTGGCTCGTCCACAATCAAGAGTGATGTGTT
131 GTGGCTCGTCCACAATCAAGAGTGATATGTT
18650232 GCAGAGTTGG
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
165 147 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (165 bp):
AGTTTGTTTAACCTGAAACCATGTCGTGCACTCACAACAAGTGGCAGCAACCGAAAATGATTTTA
TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTACAAACCAGTG
GTGGCTCGTCCACAATCAAGAGTGATATGTTAGAT
Found at i:18651710 original size:22 final size:22
Alignment explanation
Indices: 18651685--18651727 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18651675 TCTTTAAATC
*
18651685 TCAAA-GAGTAAGTGGATATTTT
1 TCAAATGAGAAAGT-GATATTTT
18651707 TCAAATGAGAAAGTGATATTT
1 TCAAATGAGAAAGTGATATTT
18651728 CCCTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (22 bp):
TCAAATGAGAAAGTGATATTTT
Found at i:18671264 original size:86 final size:84
Alignment explanation
Indices: 18671121--18671285 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 84
18671111 CACATGCATA
* * * *
18671121 AGGTTGAGTTCTTACTCTTAATGAATTCATAGCCAGGGTTTGGATGGTCCTATTGAGACAGACTT
1 AGGTTGAGTTATTACTCTTAATGAATTCATAACCAGGGTTTGGATGATCCTACTGAGACAGACTT
18671186 GATGAATTCACTGACATGT
66 GATGAATTCACTGACATGT
* * *
18671205 AGGTTGAGTTTATTACTCTTAATGAGTTCATATATCAGGGTTTGGGTGATCCTACTGAGACAGAC
1 AGGTTGAG-TTATTACTCTTAATGAATTCATA-ACCAGGGTTTGGATGATCCTACTGAGACAGAC
18671270 TTGATGAATTCACTGA
64 TTGATGAATTCACTGA
18671286 ATTTAAATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 8 0.11
85 21 0.29
86 43 0.60
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (84 bp):
AGGTTGAGTTATTACTCTTAATGAATTCATAACCAGGGTTTGGATGATCCTACTGAGACAGACTT
GATGAATTCACTGACATGT
Found at i:18671783 original size:23 final size:23
Alignment explanation
Indices: 18671738--18671783 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18671728 TATTTTTAGC
*
18671738 AGTTACAAACCATTATTTCCAAT
1 AGTTACAAACCATTATTTACAAT
*
18671761 AGTTACAAACTATT-TCTTACAAT
1 AGTTACAAACCATTAT-TTACAAT
18671784 TACAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (23 bp):
AGTTACAAACCATTATTTACAAT
Found at i:18673028 original size:28 final size:28
Alignment explanation
Indices: 18672988--18673044 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
18672978 CTTTGTATAG
*
18672988 ATGTCCTCATTGGTTTTGCTTGGCAAAC
1 ATGTCCTCATTGGTTTTGCTTGACAAAC
18673016 ATGTCCTCATTGGTTTTGCTTGACAAAC
1 ATGTCCTCATTGGTTTTGCTTGACAAAC
18673044 A
1 A
18673045 AATGACTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (28 bp):
ATGTCCTCATTGGTTTTGCTTGACAAAC
Found at i:18694968 original size:17 final size:17
Alignment explanation
Indices: 18694946--18694985 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
18694936 TCGGTAATAT
18694946 TATTATTAATCTATTAG
1 TATTATTAATCTATTAG
* *
18694963 TATTATTAATTTATTAT
1 TATTATTAATCTATTAG
18694980 TATTAT
1 TATTAT
18694986 CACCGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
TATTATTAATCTATTAG
Found at i:18694980 original size:14 final size:16
Alignment explanation
Indices: 18694943--18694984 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
18694933 TATTCGGTAA
18694943 TATTATTATTAATCTAT
1 TATTATTATTAA-CTAT
*
18694960 TAGTATTATTAA-T-T
1 TATTATTATTAACTAT
18694974 TATTATTATTA
1 TATTATTATTA
18694985 TCACCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 1 0.04
17 11 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTATTATTAACTAT
Found at i:18697105 original size:54 final size:54
Alignment explanation
Indices: 18697021--18697129 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
18697011 TAGATTGATG
* * *
18697021 TCAACTAACTTGTGACACCAAACCCTTAAAATATTTAATATTTGTACAGATACA
1 TCAACTAACTTGTGACACCAAACCCGTAAAAGACTTAATATTTGTACAGATACA
*
18697075 TCAACTAACTTGTGACACCAAACCCGTAAAAGACTTGATATTTGTACAGATACA
1 TCAACTAACTTGTGACACCAAACCCGTAAAAGACTTAATATTTGTACAGATACA
18697129 T
1 T
18697130 AGACCTTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (54 bp):
TCAACTAACTTGTGACACCAAACCCGTAAAAGACTTAATATTTGTACAGATACA
Found at i:18699669 original size:237 final size:237
Alignment explanation
Indices: 18699254--18699728 Score: 941
Period size: 237 Copynumber: 2.0 Consensus size: 237
18699244 ACCAAATCAT
18699254 AAGACATCTTGAAAATCCAAAGCTTGAAAACATGCACCAAGGAAAACTATCCTCTTGACAAATCA
1 AAGACATCTTGAAAATCCAAAGCTTGAAAACATGCACCAAGGAAAACTATCCTCTTGACAAATCA
*
18699319 ACATTCTCAACAAAGTACTAAAAAATAGGAAATAATGTCTTTCATCAGATTTTAAATTTTTAAAT
66 ACATTCTCAACAAAGTACTAAAAAACAGGAAATAATGTCTTTCATCAGATTTTAAATTTTTAAAT
18699384 AAATAAGAATCTGACCTGTAATAGTTATTAGATGTAGAACTCAATGGAAGGCCCAACCCCAAGAA
131 AAATAAGAATCTGACCTGTAATAGTTATTAGATGTAGAACTCAATGGAAGGCCCAACCCCAAGAA
18699449 AGATTAGAAATCATCAATTAAATGTATCAAACTAAACTATAA
196 AGATTAGAAATCATCAATTAAATGTATCAAACTAAACTATAA
18699491 AAGACATCTTGAAAATCCAAAGCTTGAAAACATGCACCAAGGAAAACTATCCTCTTGACAAATCA
1 AAGACATCTTGAAAATCCAAAGCTTGAAAACATGCACCAAGGAAAACTATCCTCTTGACAAATCA
18699556 ACATTCTCAACAAAGTACTAAAAAACAGGAAATAATGTCTTTCATCAGATTTTAAATTTTTAAAT
66 ACATTCTCAACAAAGTACTAAAAAACAGGAAATAATGTCTTTCATCAGATTTTAAATTTTTAAAT
18699621 AAATAAGAATCTGACCTGTAATAGTTATTAGATGTAGAACTCAATGGAAGGCCCAACCCCAAGAA
131 AAATAAGAATCTGACCTGTAATAGTTATTAGATGTAGAACTCAATGGAAGGCCCAACCCCAAGAA
18699686 AGATTAGAAATCATCAATTAAATGTATCAAACTAAACTATAA
196 AGATTAGAAATCATCAATTAAATGTATCAAACTAAACTATAA
18699728 A
1 A
18699729 CCCCATGAAA
Statistics
Matches: 237, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 237 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (237 bp):
AAGACATCTTGAAAATCCAAAGCTTGAAAACATGCACCAAGGAAAACTATCCTCTTGACAAATCA
ACATTCTCAACAAAGTACTAAAAAACAGGAAATAATGTCTTTCATCAGATTTTAAATTTTTAAAT
AAATAAGAATCTGACCTGTAATAGTTATTAGATGTAGAACTCAATGGAAGGCCCAACCCCAAGAA
AGATTAGAAATCATCAATTAAATGTATCAAACTAAACTATAA
Found at i:18700304 original size:21 final size:20
Alignment explanation
Indices: 18700280--18700320 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
18700270 TTAAAATCAG
*
18700280 GTTTGGTTTGAAAAGCTGCTT
1 GTTTGGGTTGAAAAG-TGCTT
18700301 GTTTGGGTTGAAAAGTGCTT
1 GTTTGGGTTGAAAAGTGCTT
18700321 TTGAATCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (20 bp):
GTTTGGGTTGAAAAGTGCTT
Found at i:18700864 original size:19 final size:19
Alignment explanation
Indices: 18700833--18700886 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
18700823 GAAATTTTTT
18700833 ATTTTTTATATATTCTTTAG
1 ATTTTTTATATATT-TTTAG
*
18700853 ATTTTTTA-ATATTTTTAA
1 ATTTTTTATATATTTTTAG
*
18700871 AATTTTTATA-ATTTTT
1 ATTTTTTATATATTTTT
18700887 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 17 0.55
19 6 0.19
20 8 0.26
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTTATATATTTTTAG
Found at i:18700882 original size:20 final size:20
Alignment explanation
Indices: 18700835--18700892 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
18700825 AATTTTTTAT
*
18700835 TTTTTAT-ATATTCTTT-AGA
1 TTTTTATAATATT-TTTAAAA
18700854 TTTTT-TAATATTTTTAAAA
1 TTTTTATAATATTTTTAAAA
*
18700873 TTTTTATAATTTTTTTAAAA
1 TTTTTATAATATTTTTAAAA
18700893 ATATAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.12
19 17 0.50
20 13 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTATAATATTTTTAAAA
Found at i:18700916 original size:18 final size:17
Alignment explanation
Indices: 18700894--18700949 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
18700884 TTTTTAAAAA
18700894 TATAAATTTTGGAATTT
1 TATAAATTTTGGAATTT
18700911 TCATAAATACTTT-GAATTT
1 T-ATAAAT--TTTGGAATTT
*
18700930 TAAAAATTATTGTGAATTT
1 TATAAATT-TTG-GAATTT
18700949 T
1 T
18700950 TTTTTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 11 0.34
19 14 0.44
20 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:18705702 original size:3 final size:3
Alignment explanation
Indices: 18705694--18705737 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
18705684 TTTAGTTTCC
* *
18705694 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
18705738 ACCCCTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:18706810 original size:61 final size:62
Alignment explanation
Indices: 18706669--18706810 Score: 155
Period size: 61 Copynumber: 2.3 Consensus size: 62
18706659 TGATCCTAAA
* ** ** *
18706669 TATAAAACATTCAACAAATTTAGTTCTCAATGTTTACAAAATTTTTCATTTTAATTTGAATT
1 TATAAAAAATTCAACAAATTTAGCCCTCAAAATTTACAAAATTTTTCATCTTAATTTGAATT
* * * * *
18706731 TAAAAAAAATT-AATAAATTTAGCCCTCAAAATTTATAAAATTTTTCGA-CTTAGTTTTAATT
1 TATAAAAAATTCAACAAATTTAGCCCTCAAAATTTACAAAATTTTTC-ATCTTAATTTGAATT
18706792 T-TAAAAAATTCAACAAATT
1 TATAAAAAATTCAACAAATT
18706811 AATTTTCGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
60 8 0.12
61 47 0.72
62 10 0.15
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (62 bp):
TATAAAAAATTCAACAAATTTAGCCCTCAAAATTTACAAAATTTTTCATCTTAATTTGAATT
Found at i:18711669 original size:65 final size:65
Alignment explanation
Indices: 18711565--18711695 Score: 208
Period size: 65 Copynumber: 2.0 Consensus size: 65
18711555 CAATTAATTG
* * *
18711565 AAGGTATTAACTATTCGTGTTAATTTTGATATCTCAAGCTTTTGATATAACAACATTTAAGATAA
1 AAGGTATCAACTATACGAGTTAATTTTGATATCTCAAGCTTTTGATATAACAACATTTAAGATAA
* * *
18711630 AAGGTATCAATTATACGAGTTAATTTTGATGTCTCAAGCTTTTGATATAACAATATTTAAGATAA
1 AAGGTATCAACTATACGAGTTAATTTTGATATCTCAAGCTTTTGATATAACAACATTTAAGATAA
18711695 A
1 A
18711696 TTTTTTTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (65 bp):
AAGGTATCAACTATACGAGTTAATTTTGATATCTCAAGCTTTTGATATAACAACATTTAAGATAA
Found at i:18720107 original size:27 final size:27
Alignment explanation
Indices: 18720069--18720121 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
18720059 TTGAATATAA
*
18720069 AAGGGGTTGCTAAGTGCTGATTCCCCC
1 AAGGGGTTGCTAAGTGCTAATTCCCCC
18720096 AAGGGGTTGCTAAGTGCTAATTCCCC
1 AAGGGGTTGCTAAGTGCTAATTCCCC
18720122 GATTCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (27 bp):
AAGGGGTTGCTAAGTGCTAATTCCCCC
Found at i:18720138 original size:33 final size:33
Alignment explanation
Indices: 18720073--18720336 Score: 138
Period size: 33 Copynumber: 7.8 Consensus size: 33
18720063 ATATAAAAGG
*
18720073 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
18720100 GGTTGCTAAGTGCTAATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
18720133 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
18720175 GGTTGCTAAGTGCTGATT-CCC---TCA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
18720202 GGTTGCTATGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
18720235 GGTTGCTAAGTGCTGATTCCACTATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCCCGAT-TC-----AT-TG---GT
* *
18720278 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
18720311 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
18720337 AACGGTTAAT
Statistics
Matches: 182, Mismatches: 23, Indels: 57
0.69 0.09 0.22
Matches are distributed among these distances:
27 38 0.21
28 5 0.03
31 5 0.03
32 4 0.02
33 60 0.33
34 10 0.05
35 1 0.01
36 2 0.01
37 3 0.02
38 2 0.01
39 3 0.02
40 4 0.02
41 1 0.01
42 21 0.12
43 23 0.13
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:18720159 original size:102 final size:102
Alignment explanation
Indices: 18719960--18720299 Score: 491
Period size: 102 Copynumber: 3.3 Consensus size: 102
18719950 AAGTATTTTA
* * * * *
18719960 AATGTGAAGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGCTGCTAAGTGTTGATTCCCCGACTC
1 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATC
* * *
18720025 ATTGGTGGTTACTAAGTGTTGATTCCATCGTATCTTG
66 ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTG
* * * *
18720062 AATATAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTAATTCCCCGATTC
1 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATC
* * *
18720127 ATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTA
66 ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTG
* * *
18720164 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTATGTGCTGATTCCCCGAATC
1 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATC
**
18720229 ATTGGTGGTTGCTAAGTGCTGATTCCACTATATCTTTG
66 ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC-TTG
18720267 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
1 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
18720300 GAATCACTGG
Statistics
Matches: 209, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
102 176 0.84
103 33 0.16
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (102 bp):
AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATC
ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTG
Found at i:18720209 original size:27 final size:29
Alignment explanation
Indices: 18720173--18720254 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 29
18720163 AAATGTGAAG
18720173 GGGGTTGCTAAGTGCTGATTCCC-TCA-A
1 GGGGTTGCTAAGTGCTGATTCCCATCATA
* *
18720200 GGGGTTGCTATGTGCTGATTCCCCGAATCATT
1 GGGGTTGCTAAGTGCTGATT-CCC--ATCATA
18720232 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
18720255 ACTATATCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 19 0.41
28 3 0.07
31 3 0.07
32 4 0.09
33 17 0.37
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGGTTGCTAAGTGCTGATTCCCATCATA
Found at i:18722853 original size:16 final size:17
Alignment explanation
Indices: 18722826--18722870 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
18722816 TTAATAGTTT
* *
18722826 TTAAAAGGTTAATTTAG
1 TTAAAAGATTAATTAAG
*
18722843 -TAAATGATTAATTAAG
1 TTAAAAGATTAATTAAG
18722859 TTAAAAGATTAA
1 TTAAAAGATTAA
18722871 ATAAAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (17 bp):
TTAAAAGATTAATTAAG
Found at i:18729379 original size:4 final size:4
Alignment explanation
Indices: 18729370--18729409 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
18729360 TCAGTGACAC
18729370 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18729410 CACCTCAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:18730329 original size:18 final size:19
Alignment explanation
Indices: 18730307--18730354 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
18730297 TTGTTCGGAA
18730307 ATATTTATTTTGATGT-TT
1 ATATTTATTTTGATGTATT
*
18730325 TTA-TTATTTTTGATGTATT
1 ATATTTA-TTTTGATGTATT
*
18730344 ATATGTATTTT
1 ATATTTATTTT
18730355 AAAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 8 0.33
20 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
ATATTTATTTTGATGTATT
Found at i:18733601 original size:7 final size:7
Alignment explanation
Indices: 18733589--18733633 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
18733579 AGATAGACAT
18733589 GCAGATA
1 GCAGATA
18733596 GCAGATA
1 GCAGATA
18733603 GCAGATA
1 GCAGATA
18733610 GCAGATA
1 GCAGATA
18733617 GCAGATA
1 GCAGATA
18733624 GCAGATA
1 GCAGATA
18733631 GCA
1 GCA
18733634 ATAATAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.29, T:0.13
Consensus pattern (7 bp):
GCAGATA
Found at i:18742061 original size:40 final size:40
Alignment explanation
Indices: 18742006--18742085 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
18741996 AGCCCGTAGG
18742006 CATAAAATGTATATACATATACAAATATATCACTACACCA
1 CATAAAATGTATATACATATACAAATATATCACTACACCA
* *
18742046 CATAAAATGTATATACATTTACAAATATATCCCTACACCA
1 CATAAAATGTATATACATATACAAATATATCACTACACCA
18742086 TACCAAGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (40 bp):
CATAAAATGTATATACATATACAAATATATCACTACACCA
Found at i:18747197 original size:42 final size:42
Alignment explanation
Indices: 18747061--18747269 Score: 244
Period size: 42 Copynumber: 5.0 Consensus size: 42
18747051 TACTGAAGTA
* *
18747061 CACCGGCATGAAGCCTGCCAGACA-ATAAGTCTG-AAATAATT
1 CACCGGCATCAAGCCTGCTAGACATA-AAGTCTGAAAATAATT
* *
18747102 TACCGGCATCAAGCCTGCTAGACATAAAGTCTG-AAGTAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
*
18747143 CACTGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
* * * * *
18747185 CACCGGCATCAAGCTTGCTAGGCATTAAGCCTAAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
* * * * *
18747227 CACTGGCATCAAGCCTACTAGGCATTAAGCCTGAAAATCAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAAT-AATT
18747270 ATATTCCAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 66 0.45
42 78 0.53
43 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (42 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
Found at i:18755775 original size:42 final size:42
Alignment explanation
Indices: 18755701--18755848 Score: 181
Period size: 42 Copynumber: 3.5 Consensus size: 42
18755691 ATAATTCACC
* * *
18755701 GGCATAAAGTCTG-AAGTAATTCACCGGTATCAAGCCTGCTA
1 GGCATAAAGCCTGAAAATAATTCACCGGCATCAAGCCTGCTA
* * * *
18755742 GACATAAAGTCTGAAAATAATTTACCGGCATCAAGCTTGCTA
1 GGCATAAAGCCTGAAAATAATTCACCGGCATCAAGCCTGCTA
* * *
18755784 GGCATTAAGCCTAAAAATAATTCACCGGCATCAAGCCTACTA
1 GGCATAAAGCCTGAAAATAATTCACCGGCATCAAGCCTGCTA
*
18755826 GGCATTAAGCCTGAAAATCAATT
1 GGCATAAAGCCTGAAAAT-AATT
18755849 ATATTCCAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 12 0.13
42 76 0.83
43 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (42 bp):
GGCATAAAGCCTGAAAATAATTCACCGGCATCAAGCCTGCTA
Found at i:18755958 original size:2 final size:2
Alignment explanation
Indices: 18755951--18755975 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18755941 AGTCATTATC
18755951 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
18755976 TTCTTATACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18756857 original size:30 final size:30
Alignment explanation
Indices: 18756817--18756883 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
18756807 AGAGACCATG
18756817 GATGAGTTCCCTTACACATTCGGCTTTCAAA
1 GATGA-TTCCCTTACACATTCGGCTTTCAAA
18756848 GATGATTCCCTTACACATTCGGCTTTCAAA
1 GATGATTCCCTTACACATTCGGCTTTCAAA
18756878 GATGAT
1 GATGAT
18756884 AAAAATCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (30 bp):
GATGATTCCCTTACACATTCGGCTTTCAAA
Done.