Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 89 of 222
Found at i:27840165 original size:10 final size:10
Alignment explanation
Indices: 27840146--27840180 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
27840136 AAATATATCG
27840146 AAAA-TAATC
1 AAAATTAATC
27840155 AAAATTAATC
1 AAAATTAATC
*
27840165 AAAATTAATT
1 AAAATTAATC
27840175 AAAATT
1 AAAATT
27840181 CAACATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTAATC
Found at i:27847271 original size:16 final size:17
Alignment explanation
Indices: 27847252--27847283 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27847242 TTTTTAAATA
27847252 TTTTTATTTTT-CTCTC
1 TTTTTATTTTTACTCTC
27847268 TTTTTATTTTTACTCT
1 TTTTTATTTTTACTCT
27847284 GCCAAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTACTCTC
Found at i:27850717 original size:24 final size:24
Alignment explanation
Indices: 27850679--27850978 Score: 153
Period size: 24 Copynumber: 12.8 Consensus size: 24
27850669 TGAATTGGAT
* *
27850679 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
27850704 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
27850728 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* *
27850748 AATTCTAAAATAATCATAAATGATA
1 AATT-TAAAATAATAATATATGATA
** * *
27850773 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
27850797 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
27850818 AATTTGAAATAA-ATATACATGATA
1 AATTTAAAATAATA-ATATATGATA
** * *
27850842 AATTTAAAATAATGTTA-ACGATG
1 AATTTAAAATAATAATATATGATA
* *
27850865 AATTTAAATTAATAACAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
27850888 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* **
27850912 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * *
27850936 AACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
*
27850958 AATTTAATGATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
27850979 AACATTCAAA
Statistics
Matches: 207, Mismatches: 46, Indels: 43
0.70 0.16 0.15
Matches are distributed among these distances:
20 5 0.02
21 13 0.06
22 28 0.14
23 56 0.27
24 88 0.43
25 16 0.08
26 1 0.00
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:27850783 original size:69 final size:69
Alignment explanation
Indices: 27850710--27850964 Score: 189
Period size: 69 Copynumber: 3.7 Consensus size: 69
27850700 AATAAATTTG
* *
27850710 AAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCTAAAAT-AATCATAAATGAT
1 AAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TAAAATAAAT-ATAAATGAT
27850772 AAATCCA
63 AAATCCA
* * * *
27850779 AAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAAATATACATGATAAA
1 AAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAAATATAAATGATAAA
**
27850844 TTTA
66 TCCA
** ** * ** * *
27850848 AAATAATGTTA-ACGATGAATTTAAATTAATAACATTGATAAA-TTACAAAT-AATAAAACATGA
1 AAATAATAATACATAATAAATTTAAA--AATATTAATGATAAATTTA-AAATAAATATAA-ATGA
*
27850910 TAAATCTA
62 TAAATCCA
* * * * *
27850918 AAATAATAATATACAATAAACTTAGATAATATTAATGATTAATTTAA
1 AAATAATAATACATAATAAATTTA-AAAATATTAATGATAAATTTAA
27850965 TGATAATAAG
Statistics
Matches: 146, Mismatches: 30, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
68 11 0.08
69 65 0.45
70 57 0.39
71 12 0.08
72 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (69 bp):
AAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAAATATAAATGATAAA
TCCA
Found at i:27850898 original size:46 final size:47
Alignment explanation
Indices: 27850794--27850900 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 47
27850784 ATAGTATATA
* *
27850794 ATAAATTT-AAA-AATATTAATGATAAATTTGAAATAAATATACATG
1 ATAAATTTAAAATAATGTTAACGATAAATTTGAAATAAATATACATG
* *
27850839 ATAAATTTAAAATAATGTTAACGATGAATTT-AAATTAATA-ACATTG
1 ATAAATTTAAAATAATGTTAACGATAAATTTGAAATAAATATACA-TG
27850885 ATAAA-TTACAAATAAT
1 ATAAATTTA-AAATAAT
27850901 AAAACATGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
45 14 0.26
46 25 0.46
47 15 0.28
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (47 bp):
ATAAATTTAAAATAATGTTAACGATAAATTTGAAATAAATATACATG
Found at i:27850948 original size:70 final size:69
Alignment explanation
Indices: 27850767--27850948 Score: 170
Period size: 70 Copynumber: 2.6 Consensus size: 69
27850757 ATAATCATAA
* * * * ** **
27850767 ATGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAAAT
1 ATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAACAATGATAAATTACAAATAAAT
*
27850832 ATAC
66 AAAC
* ** * * *
27850836 ATGATAAATTTAAAATAATGTTA-ACGATGAATTTAAATTAATAACATTGATAAATTACAAAT-A
1 ATGATAAATCTAAAATAATAATATACAATAAATTT-AA-TAATAACAATGATAAATTACAAATAA
27850899 ATAAAAC
64 AT-AAAC
*
27850906 ATGATAAATCTAAAATAATAATATACAATAAACTTAGATAATA
1 ATGATAAATCTAAAATAATAATATACAATAAATTTA-ATAATA
27850949 TTAATGATTA
Statistics
Matches: 88, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
68 8 0.09
69 24 0.27
70 47 0.53
71 9 0.10
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (69 bp):
ATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAACAATGATAAATTACAAATAAAT
AAAC
Found at i:27851789 original size:19 final size:19
Alignment explanation
Indices: 27851737--27851806 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
27851727 TGATTTCTTT
27851737 TTTCCTCCCTTTACACTGA
1 TTTCCTCCCTTTACACTGA
** *
27851756 TTTTTTTCTCTTTACACTGA
1 -TTTCCTCCCTTTACACTGA
*
27851776 TTTCCCCCCTTTACACTGA
1 TTTCCTCCCTTTACACTGA
27851795 TTTCCTCCCTTT
1 TTTCCTCCCTTT
27851807 TTTATGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.13, C:0.34, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTCCTCCCTTTACACTGA
Found at i:27854070 original size:21 final size:21
Alignment explanation
Indices: 27854044--27854083 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27854034 TACATTTATG
27854044 GGCATTAAAACAAGCCTACGA
1 GGCATTAAAACAAGCCTACGA
* *
27854065 GGCATTCAAACGAGCCTAC
1 GGCATTAAAACAAGCCTAC
27854084 AATGCCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.15
Consensus pattern (21 bp):
GGCATTAAAACAAGCCTACGA
Found at i:27854934 original size:38 final size:38
Alignment explanation
Indices: 27854892--27855034 Score: 155
Period size: 38 Copynumber: 3.7 Consensus size: 38
27854882 ACACCAACAC
*
27854892 GAAGCTTGCTAGGCATC-AAGCCTGATAAACACCGGCAT
1 GAAGCCTGCTAGGC-TCAAAGCCTGATAAACACCGGCAT
* * * * *
27854930 GAAGCTTGCTAGGCATC-AAGCTTGATAAACATCGGAAC
1 GAAGCCTGCTAGGC-TCAAAGCCTGATAAACACCGGCAT
* * * *
27854968 AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCTCCGGCAT
1 GAAGCCTGCTAGGCTCAAAGCCTGATAA-ACACCGGCAT
27855007 GAAGCCTGCTAGGCTCAAAGCCTGATAA
1 GAAGCCTGCTAGGCTCAAAGCCTGATAA
27855035 GTCACTAGCA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
37 2 0.02
38 55 0.62
39 31 0.35
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (38 bp):
GAAGCCTGCTAGGCTCAAAGCCTGATAAACACCGGCAT
Found at i:27855019 original size:39 final size:38
Alignment explanation
Indices: 27854968--27855111 Score: 171
Period size: 39 Copynumber: 3.7 Consensus size: 38
27854958 ACATCGGAAC
* **
27854968 AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCTCCGGCA
1 AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACTAGCA
* *
27855006 TGAAGCCTGCTAGGCTCAAAGCCTGATAAGTCACTAGCA
1 -AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACTAGCA
* * *
27855045 CAAAGCTTGTTAGGCTCAAAGCTCGATAAGTCACTAGCA
1 -AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACTAGCA
* *
27855084 CAAGGCCTGCTAGGCTCAAAGCTCGATA
1 -AAAGCCTGCTAGGCTCAAAGCCCGATA
27855112 CAATACACCG
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (38 bp):
AAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACTAGCA
Found at i:27855074 original size:78 final size:77
Alignment explanation
Indices: 27854893--27855105 Score: 211
Period size: 78 Copynumber: 2.8 Consensus size: 77
27854883 CACCAACACG
* * * * *
27854893 AAGCTTGCTAGGCATC-AAGCCTGATAA-ACACCGGCATGAAGCTTGCTAGGCATC-AAGCTTGA
1 AAGCCTGCTAGGC-TCAAAGCCCGATAAGTCACCGGCATGAAGCCTGCTAGGC-TCAAAGCCTGA
*
27854955 TAAACATCGGAACA
64 TAAACATCAGAACA
*
27854969 AAGCCTGCTAGGCTCAAAGCCCGATAAGTCTCCGGCATGAAGCCTGCTAGGCTCAAAGCCTGATA
1 AAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCGGCATGAAGCCTGCTAGGCTCAAAGCCTGATA
* *
27855034 AGTCA-CTAGCACA
66 A-ACATC-AGAACA
* * * ** *
27855047 AAGCTTGTTAGGCTCAAAGCTCGATAAGTCACTAGCA-CAAGGCCTGCTAGGCTCAAAGC
1 AAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCGGCATGAA-GCCTGCTAGGCTCAAAGC
27855106 TCGATACAAT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
75 2 0.02
76 24 0.21
77 34 0.30
78 55 0.48
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.19
Consensus pattern (77 bp):
AAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCGGCATGAAGCCTGCTAGGCTCAAAGCCTGATA
AACATCAGAACA
Found at i:27856161 original size:21 final size:21
Alignment explanation
Indices: 27856137--27856187 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
27856127 TTCTTTTGAA
*
27856137 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
27856158 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
27856179 CCTCTGCTT
1 CCTCTGCTT
27856188 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:27856240 original size:87 final size:87
Alignment explanation
Indices: 27856072--27856231 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
27856062 TTCTGCTCTA
* * *
27856072 CTCTGCTTCTCTCGATGCCGCATCAGGTTTAAGTTGTAGCTAGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTGAA
** *
27856137 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
* * * *
27856159 CTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTGAA
27856224 CCTCAACT
66 CCTCAACT
27856232 GTGGTCGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.39
Consensus pattern (87 bp):
CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:27861761 original size:16 final size:16
Alignment explanation
Indices: 27861742--27861781 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
27861732 GAATGCAAGC
*
27861742 TATGTAAGTTGTATT-T
1 TATGTAAGTTAT-TTAT
27861758 TATGTAAGTTATTTAT
1 TATGTAAGTTATTTAT
27861774 TATGTAAG
1 TATGTAAG
27861782 CTAAGTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATTTAT
Found at i:27861783 original size:41 final size:41
Alignment explanation
Indices: 27861738--27861854 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 41
27861728 TGTAGAATGC
* *
27861738 AAGCTATGTAAGTTGTATTTTATGTAAGTTATTTATTATGT
1 AAGCTATGTAAGTTGTATATTATGTAAGTTATGTATTATGT
* *
27861779 AAGCTAAGTAAGTTG-AGTATTATGTAAGCTATGTATTATGT
1 AAGCTATGTAAGTTGTA-TATTATGTAAGTTATGTATTATGT
* * * * *
27861820 TAGTTATGTAAGTTATGTATTATGTATGTTATGTA
1 AAGCTATGTAAGTTGTATATTATGTAAGTTATGTA
27861855 AGTTCTGTAG
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.02
41 62 0.98
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.47
Consensus pattern (41 bp):
AAGCTATGTAAGTTGTATATTATGTAAGTTATGTATTATGT
Found at i:27861789 original size:25 final size:25
Alignment explanation
Indices: 27861761--27861831 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
27861751 TGTATTTTAT
27861761 GTAAGTTATTTATTATGTAAGCTAA
1 GTAAGTTATTTATTATGTAAGCTAA
* *
27861786 GTAAGTTGA-GTATTATGTAAGCTAT
1 GTAAGTT-ATTTATTATGTAAGCTAA
27861811 GT-A-TTATGTTAGTTATGTAAG
1 GTAAGTTAT-TTA-TTATGTAAG
27861832 TTATGTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 3 0.08
25 32 0.82
26 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (25 bp):
GTAAGTTATTTATTATGTAAGCTAA
Found at i:27861836 original size:25 final size:25
Alignment explanation
Indices: 27861798--27861863 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
27861788 AAGTTGAGTA
*
27861798 TTATGTAAGCTATGTATTATGT-TAG
1 TTATGTAAGTTATGTATTATGTAT-G
27861823 TTATGTAAGTTATGTATTATGTATG
1 TTATGTAAGTTATGTATTATGTATG
*
27861848 TTATGTAAGTTCTGTA
1 TTATGTAAGTTATGTA
27861864 GAATGTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTATG
Found at i:27861842 original size:16 final size:16
Alignment explanation
Indices: 27861786--27861876 Score: 71
Period size: 16 Copynumber: 5.6 Consensus size: 16
27861776 TGTAAGCTAA
27861786 GTAAGTTGA-GTATTAT
1 GTAAGTT-ATGTATTAT
*
27861802 GTAAGCTATGTATTAT
1 GTAAGTTATGTATTAT
*
27861818 GTTAGTTATGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
27861836 GT-A-TTATGTATGTTAT
1 GTAAGTTATGTA--TTAT
* **
27861852 GTAAGTTCTGTAGAAT
1 GTAAGTTATGTATTAT
27861868 GTAAGTTAT
1 GTAAGTTAT
27861877 CTTAATATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
15 2 0.03
16 45 0.73
17 3 0.05
18 12 0.19
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:27861869 original size:25 final size:25
Alignment explanation
Indices: 27861798--27861876 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
27861788 AAGTTGAGTA
* ** *
27861798 TTATGTAAGCTATGTATTATGTTAG
1 TTATGTAAGTTATGTAGAATGTAAG
** *
27861823 TTATGTAAGTTATGTATTATGTATG
1 TTATGTAAGTTATGTAGAATGTAAG
*
27861848 TTATGTAAGTTCTGTAGAATGTAAG
1 TTATGTAAGTTATGTAGAATGTAAG
27861873 TTAT
1 TTAT
27861877 CTTAATATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTAGAATGTAAG
Found at i:27861870 original size:66 final size:66
Alignment explanation
Indices: 27861676--27861872 Score: 218
Period size: 66 Copynumber: 3.0 Consensus size: 66
27861666 TTCACTTTTT
* * * * * *
27861676 TATGTAAGTTGTATTTTATGTAAGCTATTTATTATGTAAACTACGTAAATTGTGTAGAATGCAAG
1 TATGTAAGTTGTATGTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
27861741 C
66 C
* * **
27861742 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGAGTATTATGTAAG
1 TATGTAAGTTGTATGTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
27861807 C
66 C
* * * * * *
27861808 TATGT-ATTATGT-TAGTTATGTAAGTTATGTATTATGTATGTTATGTAAGTTCTGTAGAATGTA
1 TATGTAAGT-TGTAT-GTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTA
27861871 AG
64 AG
27861873 TTATCTTAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
65 3 0.03
66 108 0.97
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (66 bp):
TATGTAAGTTGTATGTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
C
Found at i:27861915 original size:20 final size:20
Alignment explanation
Indices: 27861866--27861916 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
27861856 GTTCTGTAGA
27861866 ATGTAAGTTATCTTAATATT
1 ATGTAAGTTATCTTAATATT
* *
27861886 ATATAAGTTATCTTAATTTT
1 ATGTAAGTTATCTTAATATT
*
27861906 ATGTAGGTTAT
1 ATGTAAGTTAT
27861917 ACAAGTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (20 bp):
ATGTAAGTTATCTTAATATT
Found at i:27863134 original size:27 final size:29
Alignment explanation
Indices: 27863080--27863134 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
27863070 TAATTATCAC
*
27863080 AACAATCAACTTAATAATAATTGATAAAGT
1 AACAATCAACTTAATAATAAAT-ATAAAGT
27863110 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATCAACTTAATAATAAATATAAA
27863135 TCAAAAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.21
30 15 0.62
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATCAACTTAATAATAAATATAAAGT
Found at i:27864942 original size:7 final size:7
Alignment explanation
Indices: 27864922--27864975 Score: 92
Period size: 7 Copynumber: 7.7 Consensus size: 7
27864912 ATTAACTATA
27864922 AACCCCT
1 AACCCCT
27864929 AAACCCCT
1 -AACCCCT
27864937 AACCCCT
1 AACCCCT
27864944 AACCCCT
1 AACCCCT
27864951 AACCCCT
1 AACCCCT
27864958 AACCCCT
1 AACCCCT
27864965 AA-CCCT
1 AACCCCT
27864971 AACCC
1 AACCC
27864976 TTAAACCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.13
7 32 0.71
8 7 0.16
ACGTcount: A:0.31, C:0.56, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCCT
Found at i:27864982 original size:14 final size:14
Alignment explanation
Indices: 27864920--27864982 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
27864910 ACATTAACTA
27864920 TAAACCCCTAAACCCC
1 TAAA-CCCT-AACCCC
*
27864936 TAACCCCTAACCCC
1 TAAACCCTAACCCC
*
27864950 TAACCCCTAACCCC
1 TAAACCCTAACCCC
*
27864964 T-AACCCTAACCCT
1 TAAACCCTAACCCC
27864977 TAAACC
1 TAAACC
27864983 ATAATCCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
13 11 0.26
14 25 0.58
15 4 0.09
16 3 0.07
ACGTcount: A:0.33, C:0.51, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAACCCTAACCCC
Found at i:27865162 original size:8 final size:7
Alignment explanation
Indices: 27865147--27865209 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
27865137 ATTAACTATA
27865147 AACCCCT
1 AACCCCT
27865154 AAGCCCCT
1 AA-CCCCT
27865162 AACCCC-
1 AACCCCT
* *
27865168 AGCCCTT
1 AACCCCT
*
27865175 AACCCTT
1 AACCCCT
27865182 AACCCCT
1 AACCCCT
*
27865189 ACACCCTT
1 A-ACCCCT
*
27865197 AACCCTT
1 AACCCCT
27865204 AACCCC
1 AACCCC
27865210 AATCCTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 4 0.09
7 30 0.64
8 13 0.28
ACGTcount: A:0.27, C:0.52, G:0.03, T:0.17
Consensus pattern (7 bp):
AACCCCT
Found at i:27865167 original size:15 final size:14
Alignment explanation
Indices: 27865147--27865209 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
27865137 ATTAACTATA
27865147 AACCCCTAAGCCCCT
1 AACCCCTAA-CCCCT
* *
27865162 AACCCC-AGCCCTT
1 AACCCCTAACCCCT
*
27865175 AACCCTTAACCCCT
1 AACCCCTAACCCCT
* *
27865189 ACACCCTTAACCCTT
1 A-ACCCCTAACCCCT
27865204 AACCCC
1 AACCCC
27865210 AATCCTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.23
14 11 0.28
15 19 0.49
ACGTcount: A:0.27, C:0.52, G:0.03, T:0.17
Consensus pattern (14 bp):
AACCCCTAACCCCT
Found at i:27865180 original size:7 final size:7
Alignment explanation
Indices: 27865170--27865208 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
27865160 CTAACCCCAG
27865170 CCCTTAA
1 CCCTTAA
27865177 CCCTTAA
1 CCCTTAA
*
27865184 CCCCTACA
1 CCCTTA-A
27865192 CCCTTAA
1 CCCTTAA
27865199 CCCTTAA
1 CCCTTAA
27865206 CCC
1 CCC
27865209 CAATCCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.26, C:0.51, G:0.00, T:0.23
Consensus pattern (7 bp):
CCCTTAA
Found at i:27865246 original size:21 final size:21
Alignment explanation
Indices: 27865218--27865257 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
27865208 CCAATCCTTA
27865218 AACCATAT-CCATAAACCCCT
1 AACCATATCCCATAAACCCCT
*
27865238 AACCTATATCCCTTAAACCC
1 AACC-ATATCCCATAAACCC
27865258 TAAATTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCATATCCCATAAACCCCT
Found at i:27866026 original size:114 final size:114
Alignment explanation
Indices: 27865863--27866157 Score: 253
Period size: 114 Copynumber: 2.6 Consensus size: 114
27865853 CTATATTTTG
* * * * * *
27865863 CGGCGTTTTTAGACAAGCGCCACTAAAGTCTCTAAAACCTAAATTAAAAATGACATCG-TTCTCT
1 CGGCGTTTTTAGAAAAGCGCCACTAAAGTCTCGAAAACATAAATGAAAAACGACAACGATT-TCT
* * *
27865927 TAACAGTTTTGCATCACTTGTGATAAAGCGCGACTAAAGCTTCGCTAATA
65 TAACAATTTTGCAGCACTTATGATAAAGCGCGACTAAAGCTTCGCTAATA
* * * *
27865977 CGGCGTTTTCT-GAAAATCGCCACTAACGTCTCGAAAAGATAAATGAAAAACGGCAACGATTTCT
1 CGGCGTTTT-TAGAAAAGCGCCACTAAAGTCTCGAAAACATAAATGAAAAACGACAACGATTTCT
* * **
27866041 TAACAATTTTGCGGCGCTTATGATAAAGCGCCG-CTAATTCTT-GACT-ATAA
65 TAACAATTTTGCAGCACTTATGATAAAGCG-CGACTAAAGCTTCG-CTAAT-A
* * * * * * * *
27866091 CGGCATTTTTA-AGTAAGCGCCACTAAAGTCCCCAAAACCTAAACTG-AAAACGGCAGCGTTTTC
1 CGGCGTTTTTAGA-AAAGCGCCACTAAAGTCTCGAAAACATAAA-TGAAAAACGACAACGATTTC
27866154 TTAA
64 TTAA
27866158 TAGTTTTTGA
Statistics
Matches: 146, Mismatches: 27, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
113 5 0.03
114 134 0.92
115 7 0.05
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (114 bp):
CGGCGTTTTTAGAAAAGCGCCACTAAAGTCTCGAAAACATAAATGAAAAACGACAACGATTTCTT
AACAATTTTGCAGCACTTATGATAAAGCGCGACTAAAGCTTCGCTAATA
Found at i:27872014 original size:22 final size:23
Alignment explanation
Indices: 27871986--27872034 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
27871976 CTCTAGTTAA
27871986 CTTAATTGATTGATTGATATTC-
1 CTTAATTGATTGATTGATATTCG
27872008 CTTAATTGATTGATTGATATTCG
1 CTTAATTGATTGATTGATATTCG
27872031 CTTA
1 CTTA
27872035 TCCTCCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (23 bp):
CTTAATTGATTGATTGATATTCG
Found at i:27875876 original size:17 final size:19
Alignment explanation
Indices: 27875830--27875865 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27875820 ATATATAAAA
27875830 AATC-AGAAAAATATATAT
1 AATCTAGAAAAATATATAT
*
27875848 TATCTAGAAAAATATATA
1 AATCTAGAAAAATATATA
27875866 AATTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AATCTAGAAAAATATATAT
Found at i:27875982 original size:27 final size:30
Alignment explanation
Indices: 27875929--27875989 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 30
27875919 AAATTTGTTG
27875929 AAATTTATAATATTATTAAAAAATGTAAAA
1 AAATTTATAATATTATTAAAAAATGTAAAA
**
27875959 AAATTTA-AA-ATTA-TAAAAGTTGTAAAA
1 AAATTTATAATATTATTAAAAAATGTAAAA
27875986 AAAT
1 AAAT
27875990 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 16 0.55
28 4 0.14
29 2 0.07
30 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATTTATAATATTATTAAAAAATGTAAAA
Found at i:27881437 original size:41 final size:41
Alignment explanation
Indices: 27881379--27881460 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
27881369 AACCTAATTG
*
27881379 GGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCCCTTATTCTAATAAAATACTAAAAGATAA
*
27881420 GGAAAATAATTCTCTTATTCTAATAAAATACTAAAAGATAA
1 GGAAAATAATTCCCTTATTCTAATAAAATACTAAAAGATAA
27881461 AATAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (41 bp):
GGAAAATAATTCCCTTATTCTAATAAAATACTAAAAGATAA
Found at i:27884951 original size:40 final size:40
Alignment explanation
Indices: 27884904--27884983 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
27884894 AATATCAATT
27884904 AACTAAATATCTCAAATTATAATTAATCATGTTCAATTTA
1 AACTAAATATCTCAAATTATAATTAATCATGTTCAATTTA
27884944 AACTAAATATCTCAAATTATAATTAATCATGTTCAATTTA
1 AACTAAATATCTCAAATTATAATTAATCATGTTCAATTTA
27884984 TCAGTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (40 bp):
AACTAAATATCTCAAATTATAATTAATCATGTTCAATTTA
Found at i:27884979 original size:21 final size:21
Alignment explanation
Indices: 27884915--27884984 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
27884905 ACTAAATATC
27884915 TCAAATTATAATTAATCATGT
1 TCAAATTATAATTAATCATGT
* * *
27884936 TCAATTTA-AACTAAAT-AT-C
1 TCAAATTATAA-TTAATCATGT
27884955 TCAAATTATAATTAATCATGT
1 TCAAATTATAATTAATCATGT
*
27884976 TCAATTTAT
1 TCAAATTAT
27884985 CAGTTAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 11 0.29
20 8 0.21
21 19 0.50
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (21 bp):
TCAAATTATAATTAATCATGT
Found at i:27886246 original size:45 final size:45
Alignment explanation
Indices: 27886195--27886311 Score: 173
Period size: 45 Copynumber: 2.6 Consensus size: 45
27886185 ACACTGTTCA
27886195 ATTGGTTTGACTCTCTTCTTGATTGGTTAGTTGGGAGTCAACCAG
1 ATTGGTTTGACTCTCTTCTTGATTGGTTAGTTGGGAGTCAACCAG
*
27886240 ATTGGTTTGACTCTCTTCTTGACTT-GTTAGTTGGGAGTTAACCAG
1 ATTGGTTTGACTCTCTTCTTGA-TTGGTTAGTTGGGAGTCAACCAG
* * * *
27886285 ATTGATTTGGCTCTATTCTTGACTGGT
1 ATTGGTTTGACTCTCTTCTTGATTGGT
27886312 CTACCACAAC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.02
45 62 0.95
46 2 0.03
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (45 bp):
ATTGGTTTGACTCTCTTCTTGATTGGTTAGTTGGGAGTCAACCAG
Found at i:27888144 original size:22 final size:21
Alignment explanation
Indices: 27888119--27888163 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27888109 ACACGGCTGA
*
27888119 GTGCCTTATTTTATACGGGCGT
1 GTGCC-TATTTGATACGGGCGT
* *
27888141 GTGCCTCTTTGATATGGGCGT
1 GTGCCTATTTGATACGGGCGT
27888162 GT
1 GT
27888164 TGACCCTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.11, C:0.18, G:0.31, T:0.40
Consensus pattern (21 bp):
GTGCCTATTTGATACGGGCGT
Found at i:27889847 original size:25 final size:25
Alignment explanation
Indices: 27889813--27889880 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
27889803 ACATATTAGT
* *
27889813 TGAAAAGCCTTTGTGGCGAGATACC
1 TGAAAAGCCTTTGTGGCGAAATAAC
**
27889838 TGAAAAGCCTTTGTGGAAAAATAAC
1 TGAAAAGCCTTTGTGGCGAAATAAC
27889863 TGAAAAGCCTTTGTGGCG
1 TGAAAAGCCTTTGTGGCG
27889881 TATTACAGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (25 bp):
TGAAAAGCCTTTGTGGCGAAATAAC
Found at i:27903441 original size:14 final size:14
Alignment explanation
Indices: 27903422--27903450 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27903412 GAGATAATAG
27903422 ACATGATTTAGTAA
1 ACATGATTTAGTAA
27903436 ACATGATTTAGTAA
1 ACATGATTTAGTAA
27903450 A
1 A
27903451 GTATGCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
ACATGATTTAGTAA
Found at i:27904974 original size:16 final size:17
Alignment explanation
Indices: 27904949--27904981 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27904939 TTCATCACAC
*
27904949 TTAGGTTAA-TTTGCAT
1 TTAGGATAATTTTGCAT
27904965 TTAGGATAATTTTGCAT
1 TTAGGATAATTTTGCAT
27904982 CTAGTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (17 bp):
TTAGGATAATTTTGCAT
Found at i:27906662 original size:39 final size:40
Alignment explanation
Indices: 27906600--27906703 Score: 149
Period size: 39 Copynumber: 2.6 Consensus size: 40
27906590 ATTGTATGAT
27906600 TGCACAT-CGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
* * * *
27906639 TGTATATACGTGCCCC-GTTTGTACTTCGGTACCCCTGAT
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
*
27906678 TGCACATACGTGCCCCTGTTTATACT
1 TGCACATACGTGCCCCTGTTTGTACT
27906704 CTAGTAACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
39 40 0.71
40 16 0.29
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (40 bp):
TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
Found at i:27906695 original size:20 final size:20
Alignment explanation
Indices: 27906596--27906695 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 20
27906586 AATTATTGTA
*
27906596 TGATTGCACAT-CGTGCCCC
1 TGATTGTACATACGTGCCCC
* * *
27906615 TGTTTGTAC-TTCAGTACCCC
1 TGATTGTACATAC-GTGCCCC
* *
27906635 TGAATGTATATACGTGCCCC
1 TGATTGTACATACGTGCCCC
* * *
27906655 -GTTTGTAC-TTCGGTACCCC
1 TGATTGTACATAC-GTGCCCC
*
27906674 TGATTGCACATACGTGCCCC
1 TGATTGTACATACGTGCCCC
27906694 TG
1 TG
27906696 TTTATACTCT
Statistics
Matches: 58, Mismatches: 17, Indels: 11
0.67 0.20 0.13
Matches are distributed among these distances:
18 3 0.05
19 19 0.33
20 32 0.55
21 4 0.07
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (20 bp):
TGATTGTACATACGTGCCCC
Found at i:27907686 original size:73 final size:73
Alignment explanation
Indices: 27907583--27907725 Score: 277
Period size: 73 Copynumber: 2.0 Consensus size: 73
27907573 ATGATTTGCT
27907583 TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGATTT
1 TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGATTT
27907648 ATGATATA
66 ATGATATA
*
27907656 TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGGTTT
1 TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGATTT
27907721 ATGAT
66 ATGAT
27907726 TGTAGGGTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (73 bp):
TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGATTT
ATGATATA
Found at i:27912528 original size:16 final size:16
Alignment explanation
Indices: 27912485--27912531 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
27912475 ATGATAATTT
27912485 TTAAATGTTAATTAAG
1 TTAAATGTTAATTAAG
*
27912501 -T-AATTTAATAATTAAG
1 TTAAATGT--TAATTAAG
27912517 TTAAATGTTAATTAA
1 TTAAATGTTAATTAA
27912532 ACAAAAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 4 0.16
15 1 0.04
16 15 0.60
17 1 0.04
18 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
TTAAATGTTAATTAAG
Found at i:27916962 original size:40 final size:39
Alignment explanation
Indices: 27916878--27917101 Score: 240
Period size: 39 Copynumber: 5.6 Consensus size: 39
27916868 TTGAATGATG
* *
27916878 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
27916917 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAT
27916958 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
* * *
27916997 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
* * * *
27917036 TCCAGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAAT
* *
27917075 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGT-CCGAAGGCATTTG
27917102 AACGAGTATC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 74 0.46
40 74 0.46
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:27916978 original size:39 final size:40
Alignment explanation
Indices: 27916878--27917101 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
27916868 TTGAATGATG
* *
27916878 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
27916917 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
27916958 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27916997 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * * *
27917036 TCCAGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27917075 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
27917102 AACGAGTATC
Statistics
Matches: 162, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 74 0.46
40 75 0.46
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:27917123 original size:79 final size:78
Alignment explanation
Indices: 27916931--27917134 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 78
27916921 GGACTAAGAT
* * *
27916931 CCGAAGGCATTTGTGCGAG-ATACTAATTCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGTATACTAA-TCCAGGTTAAGTCCGAAGGCAATTGTGCGAGATACTA
*
27916995 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
*
27917009 CCGAAGGCATTTGTGCGAGT-TACTAAATCCAGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 CCGAAGGCATTTGTGCGAGTATACT-AATCCAGGTTAAGT-CCGAAGGCAATTGTGCGAGATACT
*
27917073 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAG-C
** *
27917089 CCGAAGGCATTTGAACGAGTAT-CTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTGCGAGTATACTA-ATCCAGGTT-AAGTCCGAAGG
27917135 TACGTGATTT
Statistics
Matches: 109, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
78 35 0.32
79 45 0.41
80 28 0.26
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTATACTAATCCAGGTTAAGTCCGAAGGCAATTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:27938242 original size:39 final size:40
Alignment explanation
Indices: 27938195--27938371 Score: 207
Period size: 39 Copynumber: 4.5 Consensus size: 40
27938185 AGACTAAGAT
27938195 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGTC
* *
27938234 CTGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGTC
* * * * *
27938273 CCGAAGGCATTTGTAAGAGTTACTAAATCCAGGTTAAGTC
1 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGTC
* * * * *
27938313 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTACGAGATACTAAT-TCCGGGCTAAGTC
*
27938353 CCGAAGGCATTTGAACGAG
1 CCGAAGGCATTTGTACGAG
27938372 TAGCTATATC
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
39 69 0.59
40 47 0.41
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGTC
Found at i:27938331 original size:79 final size:78
Alignment explanation
Indices: 27938195--27938398 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 78
27938185 AGACTAAGAT
* * * * *
27938195 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAG-CCTGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTAAGAG-TACTAAATCC-GGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
27938259 -ATTCCGGGCTAAG-C
64 TA-ACCGGGCTAAGTC
*
27938273 CCGAAGGCATTTGTAAGAGTTACTAAATCCAGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTA
1 CCGAAGGCATTTGTAAGAG-TACTAAATCC-GGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
27938338 TAACCGGGCTATGTC
64 TAACCGGGCTAAGTC
* * *
27938353 CCGAAGGCATTTG-AACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTAA-GAGTA-CTAAATCCGGTTAAGTCCCGAAGG
27938399 TACGTGATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
78 33 0.31
79 50 0.46
80 25 0.23
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTAAGAGTACTAAATCCGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTATA
ACCGGGCTAAGTC
Found at i:27951564 original size:262 final size:263
Alignment explanation
Indices: 27951068--27951611 Score: 700
Period size: 262 Copynumber: 2.1 Consensus size: 263
27951058 TTTAGAGTTC
* * * *
27951068 GTATCAAAATGTTTGATTTTTCAACAAGTGAAAGCCGAGCATCAAGTACCTTCTAGACTATTATA
1 GTATCAAAATGTTTGATTTGTCAACAAGTCAAAGCCGAACATCAAGTACCTTCTAGACTATTACA
** * * * * *
27951133 GCCTGTGATGATTCCAGAGTGGAAATGAGAACGGGTTACAATGGATTTTGTATCAGGATTGCCTT
66 AACTATGATGATTCCAAAGTAGAAATGAGAACGGGTTACAATGGATTTTGTATCAAGATTACCTT
** * * *
27951198 TGTTTCCGTGGAAGAAATATGTTAACTGGGTTATTGTGGATCGTTTGACTAAATCTGCACATTTC
131 TGTTTCCACGAAAGAAAGATGTTAACTGGGTTATTCTGGATCGTTTGACTAAATCTGCACATTTC
* **
27951263 ATTCCAGTTCGTACAAACTACTCGCTTAAGAGGTTAGCAGAATTATAGGTTTCTGAGATTGTACA
196 ATTCCAGTACGTACAAACTACTCGCTTAAGAAATTAGCAGAATTATAGGTTTCTGAGATTGTACA
27951328 TTT
261 TTT
* ** * * * *
27951331 GTATCGAAATGTTTGATTTGTCAGGAATTCAAAGCCGAACATCAGGTACCTTTTGGACTATTACA
1 GTATCAAAATGTTTGATTTGTCAACAAGTCAAAGCCGAACATCAAGTACCTTCTAGACTATTACA
** *
27951396 AACTATGATGATTCCAAAGTAGAAAT-AGGAATTGGTTACGATGGATTTTGTATCAAGA-TACCT
66 AACTATGATGATTCCAAAGTAGAAATGA-GAACGGGTTACAATGGATTTTGTATCAAGATTACCT
*
27951459 TTGTTTCCACGAAAGAAAGATGTTATCTGGGTTATTCTGGATCGTTTGACTAAAT-T-CACATAT
130 TTGTTTCCACGAAAGAAAGATGTTAACTGGGTTATTCTGGATCGTTTGACTAAATCTGCAC--AT
* * * * * *
27951522 TTCATTCCTGTACGTATAGATTACTCGCTTGAGAAATTAGCAGAATTATAGGTTTCTTAGATTGT
193 TTCATTCCAGTACGTACAAACTACTCGCTTAAGAAATTAGCAGAATTATAGGTTTCTGAGATTGT
*
27951587 ACGTTT
258 ACATTT
27951593 GTATCAAAATGTTTGATTT
1 GTATCAAAATGTTTGATTT
27951612 ATCATGTAAC
Statistics
Matches: 240, Mismatches: 38, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
260 3 0.01
261 1 0.00
262 135 0.56
263 101 0.42
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (263 bp):
GTATCAAAATGTTTGATTTGTCAACAAGTCAAAGCCGAACATCAAGTACCTTCTAGACTATTACA
AACTATGATGATTCCAAAGTAGAAATGAGAACGGGTTACAATGGATTTTGTATCAAGATTACCTT
TGTTTCCACGAAAGAAAGATGTTAACTGGGTTATTCTGGATCGTTTGACTAAATCTGCACATTTC
ATTCCAGTACGTACAAACTACTCGCTTAAGAAATTAGCAGAATTATAGGTTTCTGAGATTGTACA
TTT
Found at i:27952396 original size:42 final size:42
Alignment explanation
Indices: 27952347--27952460 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
27952337 GGTGTGATTT
**
27952347 CATGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATGT
1 CATGTAAGACCATGTCTGGGACA-TGGCATCGATATATGATAA
* * * * *
27952389 CGTGTAAGACCCTGTTTGGAACAGTGGCATCGATATATTATAA
1 CATGTAAGACCATGTCTGGGACA-TGGCATCGATATATGATAA
* *
27952432 CATGTAAGACCATATCTGGGATATGGCAT
1 CATGTAAGACCATGTCTGGGACATGGCAT
27952461 TGTACGAGCT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 33 0.58
43 24 0.42
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
CATGTAAGACCATGTCTGGGACATGGCATCGATATATGATAA
Found at i:27953081 original size:48 final size:48
Alignment explanation
Indices: 27953006--27953281 Score: 329
Period size: 48 Copynumber: 5.7 Consensus size: 48
27952996 GATAAGATGT
* *
27953006 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTGAA-GC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATT-AATGC
* * * *
27953054 TGTCCAAGTTAGTGCTTAAAGGTTGTCCATTTTTTAGCATATTAATGT
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* *
27953102 TGTCTAAATTAGTGCTTAAATGCTGTCCATTTTTAAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* *
27953150 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTGAGCATATTAATGT
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA-TTTTTT-AGCATATTAATGC
* * * * ** * *
27953200 TGTCAAAATTAATGCTTAATTGCTATCCATTTTTGCGTATATTGATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* * *
27953248 TGTCCAAATTGGTGCTTAACTACTGTCCATTTTT
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTT
27953282 GTACAAATCA
Statistics
Matches: 193, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
47 2 0.01
48 145 0.75
49 10 0.05
50 36 0.19
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (48 bp):
TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
Found at i:27953103 original size:25 final size:25
Alignment explanation
Indices: 27953075--27953203 Score: 72
Period size: 23 Copynumber: 5.2 Consensus size: 25
27953065 GTGCTTAAAG
27953075 GTTGTCCATTTTTTAGCATATTAAT
1 GTTGTCCATTTTTTAGCATATTAAT
* * ** *
27953100 GTTGTCTAAATTAGT-GC-T-TAAAT
1 GTTGTC-CATTTTTTAGCATATTAAT
* *
27953123 GCTGTCCATTTTTAAGCATATTAAT
1 GTTGTCCATTTTTTAGCATATTAAT
* * ** *
27953148 GCTGTCCAAATTAGT-GC-T-TAAAT
1 GTTGTCC-ATTTTTTAGCATATTAAT
27953171 GTTGTCCATTTTTTTGAGCATATTAAT
1 GTTGTCCA-TTTTTT-AGCATATTAAT
27953198 GTTGTC
1 GTTGTC
27953204 AAAATTAATG
Statistics
Matches: 72, Mismatches: 22, Indels: 18
0.64 0.20 0.16
Matches are distributed among these distances:
22 4 0.06
23 24 0.33
24 3 0.04
25 23 0.32
26 8 0.11
27 10 0.14
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (25 bp):
GTTGTCCATTTTTTAGCATATTAAT
Found at i:27953232 original size:98 final size:97
Alignment explanation
Indices: 27953002--27953298 Score: 375
Period size: 96 Copynumber: 3.1 Consensus size: 97
27952992 TGATGATAAG
* * * *
27953002 ATGTTGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTGAA-GCTGTCCAAGTTAG
1 ATGTTGTCAAAATTAGTGCTTAATTGCTGTCCATTTTTAAGCATATT-AATGCTGTCCAAATTAG
*
27953066 TGCTTAAAGGTTGTCCA-TTTTTTAGCATATTA
65 TGCTTAAATGTTGTCCATTTTTTTAGCATATTA
* *
27953098 ATGTTGTCTAAATTAGTGCTTAAATGCTGTCCATTTTTAAGCATATTAATGCTGTCCAAATTAGT
1 ATGTTGTCAAAATTAGTGCTTAATTGCTGTCCATTTTTAAGCATATTAATGCTGTCCAAATTAGT
27953163 GCTTAAATGTTGTCCATTTTTTTGAGCATATTA
66 GCTTAAATGTTGTCCATTTTTTT-AGCATATTA
* * ** * * *
27953196 ATGTTGTCAAAATTAATGCTTAATTGCTATCCATTTTTGCGTATATTGATGCTGTCCAAATTGGT
1 ATGTTGTCAAAATTAGTGCTTAATTGCTGTCCATTTTTAAGCATATTAATGCTGTCCAAATTAGT
* ** * * *
27953261 GCTTAACTACTGTCCATTTTTGTA-CAAATCA
66 GCTTAAATGTTGTCCATTTTTTTAGCATATTA
27953292 ATGTTGT
1 ATGTTGT
27953299 TCGAATATTG
Statistics
Matches: 177, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
95 2 0.01
96 84 0.47
97 7 0.04
98 84 0.47
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (97 bp):
ATGTTGTCAAAATTAGTGCTTAATTGCTGTCCATTTTTAAGCATATTAATGCTGTCCAAATTAGT
GCTTAAATGTTGTCCATTTTTTTAGCATATTA
Found at i:27960213 original size:20 final size:20
Alignment explanation
Indices: 27960188--27960226 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
27960178 TACTTTCTTC
27960188 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
27960208 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
27960227 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:27962688 original size:42 final size:43
Alignment explanation
Indices: 27962642--27962751 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 43
27962632 TTCTAAGGTG
27962642 TGATTTCATGTAAGACCATGTCTAGAACATTGGCATC-ATATA
1 TGATTTCATGTAAGACCATGTCTAGAACATTGGCATCGATATA
** * * * *
27962684 TGATTTTGTGTAAAACCCTGTCTGGGACATTGGCATCGATATA
1 TGATTTCATGTAAGACCATGTCTAGAACATTGGCATCGATATA
* ** *
27962727 TTATAACATGTAAGACCATATCTAG
1 TGATTTCATGTAAGACCATGTCTAG
27962752 GATATGACAT
Statistics
Matches: 52, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
42 31 0.60
43 21 0.40
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (43 bp):
TGATTTCATGTAAGACCATGTCTAGAACATTGGCATCGATATA
Found at i:27963355 original size:25 final size:25
Alignment explanation
Indices: 27963321--27963407 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
27963311 AAATTGGTGT
27963321 TTAATTGCTGTCCATTTTTGAGCATA
1 TTAA-TGCTGTCCATTTTTGAGCATA
** * *
27963347 TTAATGCTGTCCAAATTAGTGC-T-
1 TTAATGCTGTCCATTTTTGAGCATA
* * *
27963370 TAAATGTTGTCCATTTTTAAGCATA
1 TTAATGCTGTCCATTTTTGAGCATA
*
27963395 TTAATGTTGTCCA
1 TTAATGCTGTCCA
27963408 AATTAGTGCT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
23 15 0.32
24 2 0.04
25 26 0.55
26 4 0.09
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTGAGCATA
Found at i:27963380 original size:23 final size:23
Alignment explanation
Indices: 27963349--27963428 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
27963339 TGAGCATATT
27963349 AATGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
* ** * *
27963372 AATGTTGTCCATTTTTA-AGCATATT
1 AATGCTGTCCA-AATTAGTGC-T-TA
*
27963397 AATGTTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
27963420 AATGCTGTC
1 AATGCTGTC
27963429 TGTTTTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
23 21 0.49
24 8 0.19
25 14 0.33
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (23 bp):
AATGCTGTCCAAATTAGTGCTTA
Found at i:27963462 original size:51 final size:48
Alignment explanation
Indices: 27963308--27963534 Score: 285
Period size: 48 Copynumber: 4.7 Consensus size: 48
27963298 TAAGATGCTA
* * * * *
27963308 TCCAAATTGGTGTTTAATTGCTGTCCATTTTTGAGCATATTAATGCTG
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTTAAGCATATTAATGTTG
*
27963356 TCCAAATTAGTGCTTAAATGTTGTCCATTTTTAAGCATATTAATGTTG
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTTAAGCATATTAATGTTG
** *
27963404 TCCAAATTAGTGCTTAAATGCTGTCTGTTTTTTTTTAGCATATTAATGTTG
1 TCCAAATTAGTGCTTAAATGCTGTC---CATTTTTAAGCATATTAATGTTG
* * * * *
27963455 TCTAAATT-GATGCTTAATTGCTATCCATTTTTAAGTATATTAATGGTG
1 TCCAAATTAG-TGCTTAAATGCTGTCCATTTTTAAGCATATTAATGTTG
27963503 TCCAAATTAGTGCTTAAATGCTGTCCATTTTT
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTT
27963535 GTACAAATCA
Statistics
Matches: 153, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
48 111 0.73
49 1 0.01
50 1 0.01
51 40 0.26
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (48 bp):
TCCAAATTAGTGCTTAAATGCTGTCCATTTTTAAGCATATTAATGTTG
Found at i:27963534 original size:99 final size:99
Alignment explanation
Indices: 27963308--27963534 Score: 300
Period size: 99 Copynumber: 2.3 Consensus size: 99
27963298 TAAGATGCTA
* * *
27963308 TCCAAATTGGTGTTTAATTGCTGTCCA---TTTTTGAGCATATTAATGCTGTCCAAATTAGTGCT
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCATATTAATGCTGTCCAAATTAGTGCT
* * *
27963370 TAAATGTTGTCCATTTTTAAGCATATTAATGTTG
66 TAAATGCTATCCATTTTTAAGCATATTAATGGTG
** * * *
27963404 TCCAAATTAGTGCTTAAATGCTGTCTGTTTTTTTTTAGCATATTAATGTTGTCTAAATT-GATGC
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCATATTAATGCTGTCCAAATTAG-TGC
* *
27963468 TTAATTGCTATCCATTTTTAAGTATATTAATGGTG
65 TTAAATGCTATCCATTTTTAAGCATATTAATGGTG
27963503 TCCAAATTAGTGCTTAAATGCTGTCCATTTTT
1 TCCAAATTAGTGCTTAAATGCTGTCCATTTTT
27963535 GTACAAATCA
Statistics
Matches: 112, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
96 22 0.20
98 1 0.01
99 89 0.79
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (99 bp):
TCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCATATTAATGCTGTCCAAATTAGTGCT
TAAATGCTATCCATTTTTAAGCATATTAATGGTG
Found at i:27970709 original size:19 final size:19
Alignment explanation
Indices: 27970677--27970715 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27970667 AAATATAATT
*
27970677 TTAATTTTAATTTATTTGA
1 TTAATTTTAATTTACTTGA
27970696 TTAA-TTTAATTTTACTTGA
1 TTAATTTTAA-TTTACTTGA
27970715 T
1 T
27970716 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTAATTTTAATTTACTTGA
Found at i:27971706 original size:16 final size:16
Alignment explanation
Indices: 27971685--27971715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27971675 GTTATGCATG
*
27971685 AAAAATATAAAAGACA
1 AAAAATAAAAAAGACA
27971701 AAAAATAAAAAAGAC
1 AAAAATAAAAAAGAC
27971716 GTAATAGTGA
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:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAATAAAAAAGACA
Found at i:27977063 original size:31 final size:31
Alignment explanation
Indices: 27976999--27977063 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
27976989 TCTAAGGCCA
* *
27976999 TGTGGACATTCGAAATAGGGATACACAGTCG
1 TGTGGACATTCGAAATAGGCATACACAGCCG
27977030 TGTGGACATTCGAAATAGGCATACAC-GACCG
1 TGTGGACATTCGAAATAGGCATACACAG-CCG
27977061 TGT
1 TGT
27977064 CCAAACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (31 bp):
TGTGGACATTCGAAATAGGCATACACAGCCG
Found at i:27979208 original size:24 final size:24
Alignment explanation
Indices: 27979133--27979210 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
27979123 AGCTTATAAG
* *
27979133 AGCCA-TAATCGGGAAGCTCATGCT
1 AGCCATTAA-CGGGAAGCTCAGGAT
* * * * *
27979157 AGCCAATAACGGGTAGCTCTGAAA
1 AGCCATTAACGGGAAGCTCAGGAT
*
27979181 AGCCATTAACGGGAAGCTCCGGAT
1 AGCCATTAACGGGAAGCTCAGGAT
27979205 AGCCAT
1 AGCCAT
27979211 ATATTGGGAT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 39 0.93
25 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCAGGAT
Found at i:27979287 original size:26 final size:26
Alignment explanation
Indices: 27979251--27979310 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
27979241 GAAGCTCTGG
*
27979251 AGAGCCATTAATCAGGAAGCTTACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* *
27979277 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
27979303 AGAGCCAT
1 AGAGCCAT
27979311 ATATCGAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:27982376 original size:34 final size:34
Alignment explanation
Indices: 27982333--27982400 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
27982323 TTTCACACTT
27982333 GTGAACTTAATCAATATAAATCTTATGAATTCCA
1 GTGAACTTAATCAATATAAATCTTATGAATTCCA
*
27982367 GTGAACTTAATCAATATAGATCTTATGAATTCCA
1 GTGAACTTAATCAATATAAATCTTATGAATTCCA
27982401 TTGTATAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (34 bp):
GTGAACTTAATCAATATAAATCTTATGAATTCCA
Found at i:27989031 original size:17 final size:18
Alignment explanation
Indices: 27989002--27989036 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27988992 TTCTCCTAAA
*
27989002 TTTCAATTTTATTTAATT
1 TTTCAATTTTATTAAATT
27989020 TTTCAA-TTTATTAAATT
1 TTTCAATTTTATTAAATT
27989037 ATTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCAATTTTATTAAATT
Found at i:27992819 original size:20 final size:18
Alignment explanation
Indices: 27992786--27992822 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27992776 TGTGATGTTG
27992786 ATATGCTTAATTTAATTA
1 ATATGCTTAATTTAATTA
27992804 ATATGGCTTAAATTTAATT
1 ATAT-GCTT-AATTTAATT
27992823 CGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATGCTTAATTTAATTA
Found at i:27994570 original size:3 final size:3
Alignment explanation
Indices: 27994556--27994597 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
27994546 TGTTATTAAG
*
27994556 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27994598 CTATATATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27995071 original size:17 final size:17
Alignment explanation
Indices: 27995025--27995071 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
27995015 TGTACATGTA
27995025 TATATTTATATATTTTTT
1 TATATTTATATA-TTTTT
* * *
27995043 TCTAATGA-ATATTTTT
1 TATATTTATATATTTTT
27995059 TATATTTATATAT
1 TATATTTATATAT
27995072 ATACATATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TATATTTATATATTTTT
Found at i:27999922 original size:26 final size:26
Alignment explanation
Indices: 27999890--27999967 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 26
27999880 AATGGAGAAA
*
27999890 TAGGTTTTCAAAAATGAAAATGAATG
1 TAGGTTTCCAAAAATGAAAATGAATG
27999916 TAGGTTTCCAAAAATTTGGAAAA-GAATG
1 TAGGTTTCCAAAAA--T-GAAAATGAATG
*
27999944 TAGGTTTCCAAAAATGGAAATGAA
1 TAGGTTTCCAAAAATGAAAATGAA
27999968 AATGGAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.09
26 17 0.37
28 20 0.43
29 5 0.11
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (26 bp):
TAGGTTTCCAAAAATGAAAATGAATG
Found at i:28004637 original size:62 final size:62
Alignment explanation
Indices: 28004507--28004626 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
28004497 GGTACACACC
* * * * * *
28004507 CGTGTCCCTGACCGTGTGGTTTTATACCACAAATAGTGAGTTACACAGCCAAGGCACATGCC
1 CGTGTCCCTGACCGTGTGGTCTCATACCACAAACAGTGAGTTACACAGACAAGACACATGCA
* *
28004569 CGTGTCCCTGGCTGTGTGGTCTCATACCACAAACAGTGAGTTACAC-GACATAGACACA
1 CGTGTCCCTGACCGTGTGGTCTCATACCACAAACAGTGAGTTACACAGACA-AGACACA
28004627 CTCATGTGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 3 0.06
62 47 0.94
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (62 bp):
CGTGTCCCTGACCGTGTGGTCTCATACCACAAACAGTGAGTTACACAGACAAGACACATGCA
Found at i:28009797 original size:27 final size:27
Alignment explanation
Indices: 28009741--28009799 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
28009731 TTCTCAAAAT
**
28009741 TAAT-AAATATTAATTTATCGATAATT
1 TAATAAAATATTAATTTATCGATAAAG
*
28009767 TAATAAAATA-TACATTTATCGGTAAAG
1 TAATAAAATATTA-ATTTATCGATAAAG
28009794 TAATAA
1 TAATAA
28009800 CCTCGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (27 bp):
TAATAAAATATTAATTTATCGATAAAG
Found at i:28010406 original size:20 final size:19
Alignment explanation
Indices: 28010383--28010439 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
28010373 GGGAGCACCG
28010383 ATGTGCTAAGCAGGGCACAA
1 ATGTGC-AAGCAGGGCACAA
* *
28010403 ATGTGCATAGAAGAGCACCAA
1 ATGTGCA-AGCAGGGCA-CAA
28010424 A-GTGCAAGCAGGGCAC
1 ATGTGCAAGCAGGGCAC
28010440 CAGAGTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 8 0.26
20 18 0.58
21 4 0.13
ACGTcount: A:0.37, C:0.21, G:0.30, T:0.12
Consensus pattern (19 bp):
ATGTGCAAGCAGGGCACAA
Found at i:28010441 original size:19 final size:19
Alignment explanation
Indices: 28010385--28010448 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
28010375 GAGCACCGAT
28010385 GTGCTAAGCAGGGCA-CAAA
1 GTGC-AAGCAGGGCACCAAA
* *
28010404 TGTGCATAGAAGAGCACCAAA
1 -GTGCA-AGCAGGGCACCAAA
*
28010425 GTGCAAGCAGGGCACCAGA
1 GTGCAAGCAGGGCACCAAA
28010444 GTGCA
1 GTGCA
28010449 TAACAAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 17 0.46
20 16 0.43
21 4 0.11
ACGTcount: A:0.36, C:0.22, G:0.31, T:0.11
Consensus pattern (19 bp):
GTGCAAGCAGGGCACCAAA
Found at i:28010487 original size:20 final size:19
Alignment explanation
Indices: 28010452--28010512 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
28010442 GAGTGCATAA
* *
28010452 CAAGGAACACATGTGCAAT
1 CAAGGCACATATGTGCAAT
*
28010471 CAGAGGCATCATA-GTGCAAA
1 CA-AGGCA-CATATGTGCAAT
28010491 CAAGGCACATATGTGCAAT
1 CAAGGCACATATGTGCAAT
28010510 CAA
1 CAA
28010513 AAGTAATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 4 0.11
19 16 0.46
20 12 0.34
21 3 0.09
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
CAAGGCACATATGTGCAAT
Found at i:28010506 original size:19 final size:19
Alignment explanation
Indices: 28010444--28010508 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
28010434 GGGCACCAGA
* *
28010444 GTGCATAACAAGGAACACAT
1 GTGCA-AACAAGGCACATAT
*
28010464 GTGCAATCAGAGGCATCATA-
1 GTGCAAACA-AGGCA-CATAT
28010484 GTGCAAACAAGGCACATAT
1 GTGCAAACAAGGCACATAT
28010503 GTGCAA
1 GTGCAA
28010509 TCAAAAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.11
19 14 0.37
20 17 0.45
21 3 0.08
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (19 bp):
GTGCAAACAAGGCACATAT
Found at i:28010509 original size:39 final size:39
Alignment explanation
Indices: 28010425--28010511 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
28010415 GAGCACCAAA
*
28010425 GTGCAAGCAGGGCACCAGAGTGCATAACAAGGAACACAT
1 GTGCAATCAGGGCACCAGAGTGCATAACAAGGAACACAT
* * * *
28010464 GTGCAATCAGAGGCATCATAGTGCA-AACAAGGCACATAT
1 GTGCAATCAG-GGCACCAGAGTGCATAACAAGGAACACAT
28010503 GTGCAATCA
1 GTGCAATCA
28010512 AAAGTAATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 30 0.71
40 12 0.29
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (39 bp):
GTGCAATCAGGGCACCAGAGTGCATAACAAGGAACACAT
Found at i:28024656 original size:19 final size:20
Alignment explanation
Indices: 28024632--28024673 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
28024622 GTATTAAGGA
*
28024632 GCACCAACGTGCA-AACAGG
1 GCACCAAAGTGCATAACAGG
28024651 GCACCAAAGTGCATAACAGG
1 GCACCAAAGTGCATAACAGG
28024671 GCA
1 GCA
28024674 TAGATTAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.38, C:0.29, G:0.26, T:0.07
Consensus pattern (20 bp):
GCACCAAAGTGCATAACAGG
Found at i:28026673 original size:10 final size:10
Alignment explanation
Indices: 28026660--28026710 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
28026650 TTTATACATA
*
28026660 TTTAATTAAT
1 TTTAATTATT
28026670 TTT-A-TATT
1 TTTAATTATT
**
28026678 TTTAACAATT
1 TTTAATTATT
28026688 TTT-ATTATT
1 TTTAATTATT
28026697 TTTAATTATT
1 TTTAATTATT
28026707 TTTA
1 TTTA
28026711 TAAATTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.18
9 9 0.26
10 19 0.56
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTATT
Found at i:28026698 original size:19 final size:19
Alignment explanation
Indices: 28026669--28026711 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28026659 ATTTAATTAA
28026669 TTTTA-TATTTTTAACAAT
1 TTTTATTATTTTTAACAAT
**
28026687 TTTTATTATTTTTAATTAT
1 TTTTATTATTTTTAACAAT
28026706 TTTTAT
1 TTTTAT
28026712 AAATTTCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTATTTTTAACAAT
Found at i:28031705 original size:16 final size:17
Alignment explanation
Indices: 28031696--28031727 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28031686 TTCAAGACAA
28031696 ATGTTGTTCAAGAATAG
1 ATGTTGTTCAAGAATAG
28031713 ATGTTGTTC-AGAATA
1 ATGTTGTTCAAGAATA
28031728 ACCTCTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (17 bp):
ATGTTGTTCAAGAATAG
Found at i:28035442 original size:67 final size:65
Alignment explanation
Indices: 28035327--28035458 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 65
28035317 TTCGAAACTC
* *
28035327 AATCAAGAAAAATACTAAACTGTAATTATGACAAAAAGTCATATAAATCTTACACTCACATTTTC
1 AATCAAGAAAAATACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACA--CACATTTTC
28035392 TT
64 TT
* *
28035394 AATCAAGAAAAATACTAAACTGTAATTTTGGCAAAAAGCCATACAAATCTTACACACATTTTCTT
1 AATCAAGAAAAATACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACACACATTTTCTT
28035459 TCTGCAAGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 11 0.18
67 50 0.82
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (65 bp):
AATCAAGAAAAATACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACACACATTTTCTT
Found at i:28041285 original size:41 final size:41
Alignment explanation
Indices: 28041223--28041331 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 41
28041213 TGATCGAATG
* * *
28041223 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAA
*
28041264 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAA
* * * * *
28041305 CATTTCGGACTATAGGTCTAGCAGGCT
1 TAATTCAGACTTTACGTCTAGCAGGCT
28041332 AAAAGCCGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAA
Found at i:28041729 original size:25 final size:24
Alignment explanation
Indices: 28041698--28041772 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 24
28041688 TGTATATATA
28041698 TATTCGAATTTATGTATTAGCTATG
1 TATTCGAA-TTATGTATTAGCTATG
*
28041723 TATTCGAA-TATGTA-TA--TATA
1 TATTCGAATTATGTATTAGCTATG
*
28041743 TATTCGAATGTAGGTATTAGCTATG
1 TATTCGAAT-TATGTATTAGCTATG
28041768 TATTC
1 TATTC
28041773 AGGTATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 11 0.26
22 7 0.17
23 8 0.19
25 16 0.38
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (24 bp):
TATTCGAATTATGTATTAGCTATG
Found at i:28041732 original size:45 final size:45
Alignment explanation
Indices: 28041683--28041772 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
28041673 TGTATATGAT
* *
28041683 GAATATGTATATATATATTCGAATTTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
28041728 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
28041773 AGGTATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (45 bp):
GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
Found at i:28042982 original size:20 final size:19
Alignment explanation
Indices: 28042959--28042997 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
28042949 GAAGAAATGA
*
28042959 AAATGAGAGATGAGATGATG
1 AAATGAGAGAAGAGA-GATG
28042979 AAATGAGAGAAGAGAGATG
1 AAATGAGAGAAGAGAGATG
28042998 CTTGAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.36, T:0.15
Consensus pattern (19 bp):
AAATGAGAGAAGAGAGATG
Found at i:28044421 original size:51 final size:50
Alignment explanation
Indices: 28044239--28044582 Score: 309
Period size: 51 Copynumber: 6.8 Consensus size: 50
28044229 ACTTTTATCA
* * *
28044239 TTCGATACACGTAGTAGGCTTCACATAGTACTACACACGTGATC-AAGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * *
28044288 TTACAGTTCATGTAGTAGCCTTCACATAGTACTACACACGTG-TC-AAGTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * *
28044337 TTACAGTTCACATAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * **
28044389 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
** * * * * *
28044439 TATCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTTACTAAAACTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGTT
* * * * * *
28044491 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* * *
28044541 TATCGATACACGTAGTAGCCTTCATACAGTACTACACACGTG
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
28044583 TTCATCGATA
Statistics
Matches: 239, Mismatches: 48, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
49 48 0.20
50 41 0.17
51 143 0.60
52 7 0.03
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:28044474 original size:102 final size:102
Alignment explanation
Indices: 28044246--28044582 Score: 398
Period size: 102 Copynumber: 3.3 Consensus size: 102
28044236 TCATTCGATA
* * * * * **
28044246 CACGTAGTAGGCTTCACATAGTACTACACACGTGATC-AAG-TTTTACAGTTCATGTAGTAGCCT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGTAGCCT
* * * *
28044309 TCACATAGTACTACACACGTG-TCA-AGTTT-TACAGTT
65 TCACTTAGTACTACACATGTGACCATAGTTTAT-CAATT
* * *
28044345 CACATAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTT
*
28044410 CACTTAGTACTACACATGTGACCATCGTTTATCAATT
66 CACTTAGTACTACACATGTGACCATAGTTTATCAATT
* * * * *
28044447 CACGTAGTAGCCTTCACACAGTACTACACACGTTACTAAAACTTCTCGGTACACATTGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTT
* *
28044512 CACTTAGTACTACACATGTGACCATTA-TTTATCGATA
66 CACTTAGTACTACACATGTGACCA-TAGTTTATCAATT
*
28044549 CACGTAGTAGCCTTCATACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACACAGTACTACACACGTG
28044583 TTCATCGATA
Statistics
Matches: 206, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
99 33 0.16
100 36 0.17
101 6 0.03
102 129 0.63
103 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTT
CACTTAGTACTACACATGTGACCATAGTTTATCAATT
Found at i:28044589 original size:153 final size:150
Alignment explanation
Indices: 28044239--28044589 Score: 390
Period size: 153 Copynumber: 2.3 Consensus size: 150
28044229 ACTTTTATCA
* * * * *
28044239 TTCGATACACGTAGTAGGCTTCACATAGTACTACACACGTGATCA-AGTTTTACAGTTCATGTAG
1 TTCGATACACGTAGTAGCCTTCATATAGTACTACACACGTGATCATCGTTTTACAATTCACGTAG
* * * *
28044303 TAGCCTTCACATAGTACTACACACGTGTCAAGTTTTACAGTTCACATAGTAGCCTTCACATAGTA
66 TAGCCTTCACACAGTACTACACACGTGTCAACTTCTACAGTACACATAGTAGCCTTCACATAGTA
*
28044368 CTACATACGTGACCAAAGCTT
131 CTACACACGTGACCAAA-CTT
* * * *
28044389 TTCGGTACACATAGTAGCCTTCACT-TAGTACTACACATGTGACCATCG-TTTATCAATTCACGT
1 TTCGATACACGTAGTAGCCTTCA-TATAGTACTACACACGTGATCATCGTTTTA-CAATTCACGT
* *
28044452 AGTAGCCTTCACACAGTACTACACACGT-TACTAAAACTTCT-CGGTACACATTGTAGCCTTCAC
64 AGTAGCCTTCACACAGTACTACACACGTGT-C---AACTTCTACAGTACACATAGTAGCCTTCAC
* * *
28044515 TTAGTACTACACATGTGACCATTA-TT
125 ATAGTACTACACACGTGACCA-AACTT
* *
28044541 TATCGATACACGTAGTAGCCTTCATACAGTACTACACACGTGTTCATCG
1 T-TCGATACACGTAGTAGCCTTCATATAGTACTACACACGTGATCATCG
28044590 ATACCTTATT
Statistics
Matches: 166, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
150 43 0.26
151 37 0.22
152 4 0.02
153 76 0.46
154 6 0.04
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (150 bp):
TTCGATACACGTAGTAGCCTTCATATAGTACTACACACGTGATCATCGTTTTACAATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGTCAACTTCTACAGTACACATAGTAGCCTTCACATAGTA
CTACACACGTGACCAAACTT
Found at i:28047533 original size:22 final size:22
Alignment explanation
Indices: 28047508--28047556 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28047498 AGGCAAAAAC
28047508 CATGTAGAAAGAGACACACAGT
1 CATGTAGAAAGAGACACACAGT
* * *
28047530 CATGTTGGAGGAGACACACAGT
1 CATGTAGAAAGAGACACACAGT
28047552 CATGT
1 CATGT
28047557 TCTAAGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
CATGTAGAAAGAGACACACAGT
Found at i:28051592 original size:18 final size:18
Alignment explanation
Indices: 28051569--28051671 Score: 54
Period size: 17 Copynumber: 5.9 Consensus size: 18
28051559 ATAGCTCACT
28051569 AGAACTGCGAGCTCACCA
1 AGAACTGCGAGCTCACCA
***
28051587 AGAACTATAAGCTCACCA
1 AGAACTGCGAGCTCACCA
*
28051605 A-AA-TGTACGAGCTCACAA
1 AGAACTG--CGAGCTCACCA
* *
28051623 AG-ATTGTGAGCTCACCA
1 AGAACTGCGAGCTCACCA
* * *
28051640 A-CACTGCAAACTCACCA
1 AGAACTGCGAGCTCACCA
* *
28051657 AGCA-TGAGAGCTCAC
1 AGAACTGCGAGCTCAC
28051672 TTGCGAGCTC
Statistics
Matches: 63, Mismatches: 16, Indels: 13
0.68 0.17 0.14
Matches are distributed among these distances:
16 1 0.02
17 32 0.51
18 28 0.44
19 2 0.03
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.16
Consensus pattern (18 bp):
AGAACTGCGAGCTCACCA
Found at i:28057674 original size:19 final size:17
Alignment explanation
Indices: 28057650--28057704 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
28057640 TTTCAATTTA
28057650 ACCCAAAATATTTATTTTT
1 ACCCAAAA-A-TTATTTTT
*
28057669 ACCCAAAAATTATTTTA
1 ACCCAAAAATTATTTTT
*
28057686 AACCATAAAATTAATTTTT
1 ACCCA-AAAATT-ATTTTT
28057705 TATTTTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 11 0.35
18 7 0.23
19 13 0.42
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
ACCCAAAAATTATTTTT
Found at i:28059421 original size:17 final size:17
Alignment explanation
Indices: 28059399--28059480 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
28059389 AACTGCGAGC
28059399 TGCGAGCTCACCAAATG
1 TGCGAGCTCACCAAATG
* * **
28059416 TGCGAGTTCACCTAACC
1 TGCGAGCTCACCAAATG
* * *
28059433 TGCAAGTTCACCAAATA
1 TGCGAGCTCACCAAATG
*
28059450 TGCGAGCTCTACAAAATAG
1 TGCGAGCTC-ACCAAAT-G
28059469 T--GAGCTCACCAA
1 TGCGAGCTCACCAA
28059481 GATTACGAGC
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
16 4 0.08
17 39 0.78
18 6 0.12
19 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (17 bp):
TGCGAGCTCACCAAATG
Found at i:28059490 original size:17 final size:17
Alignment explanation
Indices: 28059470--28059601 Score: 77
Period size: 17 Copynumber: 7.5 Consensus size: 17
28059460 ACAAAATAGT
28059470 GAGCTCACCAAGATTAC
1 GAGCTCACCAAGATTAC
* ** **
28059487 GAGCTCGCCTGCGAACAGC
1 GAGCTCACC-AAGATTA-C
*
28059506 GAGCTCACCAAGAACTAC
1 GAGCTCACCAAG-ATTAC
* *
28059524 GAGCTCACTAAAATGTAC
1 GAGCTCACCAAGAT-TAC
* * *
28059542 GAGCTCACTAAGATAAT
1 GAGCTCACCAAGATTAC
* *
28059559 GAGCTCACCAACAGTAC
1 GAGCTCACCAAGATTAC
* *
28059576 AAGCTCACCAAGCATGA-
1 GAGCTCACCAAG-ATTAC
28059593 GAGCTCACC
1 GAGCTCACC
28059602 TGCAAGCTCT
Statistics
Matches: 84, Mismatches: 26, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
17 40 0.48
18 33 0.39
19 11 0.13
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (17 bp):
GAGCTCACCAAGATTAC
Found at i:28059526 original size:18 final size:18
Alignment explanation
Indices: 28059470--28059554 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 18
28059460 ACAAAATAGT
*
28059470 GAGCTCACCAAG-ATTAC
1 GAGCTCACCAAGAACTAC
* **
28059487 GAGCTCGCCTGCGAAC-AGC
1 GAGCTCACC-AAGAACTA-C
28059506 GAGCTCACCAAGAACTAC
1 GAGCTCACCAAGAACTAC
* *
28059524 GAGCTCACTAA-AATGTAC
1 GAGCTCACCAAGAA-CTAC
*
28059542 GAGCTCACTAAGA
1 GAGCTCACCAAGA
28059555 TAATGAGCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 10 0.19
18 31 0.58
19 12 0.23
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.15
Consensus pattern (18 bp):
GAGCTCACCAAGAACTAC
Found at i:28059597 original size:34 final size:34
Alignment explanation
Indices: 28059507--28059601 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 34
28059497 GCGAACAGCG
* *
28059507 AGCTCACCAAGAACTACGAGCTCACTAAAATGTACG
1 AGCTCACCAAG-A-TACGAGCTCACCAAAATGTACA
* * *
28059543 AGCTCACTAAGATAATGAGCTCACCAACA-GTACA
1 AGCTCACCAAGAT-ACGAGCTCACCAAAATGTACA
28059577 AGCTCACCAAGCATGA-GAGCTCACC
1 AGCTCACCAAG-AT-ACGAGCTCACC
28059602 TGCAAGCTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 24 0.48
35 16 0.32
36 10 0.20
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.16
Consensus pattern (34 bp):
AGCTCACCAAGATACGAGCTCACCAAAATGTACA
Found at i:28059760 original size:3 final size:3
Alignment explanation
Indices: 28059752--28059789 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28059742 AGCCAAGTTG
28059752 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28059790 GCTTATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28069254 original size:13 final size:13
Alignment explanation
Indices: 28069219--28069256 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
28069209 GAGTTTTCAT
*
28069219 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
28069232 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
28069245 TGCTTTTGAGAA
1 TGCTTTTGAGAA
28069257 ATTTGAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:28069508 original size:19 final size:19
Alignment explanation
Indices: 28069484--28069541 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
28069474 AATTATTTAT
28069484 TAAATT-TAATTAGAATATA
1 TAAATTATAATTA-AATATA
* *
28069503 TAAATTATATTTAAATATT
1 TAAATTATAATTAAATATA
*
28069522 TAAATATAAAAGTTAAATAT
1 TAAAT-TATAA-TTAAATAT
28069542 TTGTAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.50
20 8 0.25
21 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TAAATTATAATTAAATATA
Found at i:28069781 original size:8 final size:8
Alignment explanation
Indices: 28069768--28069794 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28069758 TATATAAACT
28069768 ATATTTAA
1 ATATTTAA
28069776 ATATTTAA
1 ATATTTAA
28069784 ATATTTAA
1 ATATTTAA
28069792 ATA
1 ATA
28069795 CAAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTTAA
Found at i:28070076 original size:30 final size:30
Alignment explanation
Indices: 28070059--28070183 Score: 144
Period size: 30 Copynumber: 4.2 Consensus size: 30
28070049 ACTTTTTTTG
28070059 AAATTATATTTTAACCCCTAAACTTTCTTA
1 AAATTATATTTTAACCCCTAAACTTTCTTA
* *
28070089 AAATTATATTTCAACCCCTAAACTTTCTCA
1 AAATTATATTTTAACCCCTAAACTTTCTTA
* * * *
28070119 AAATTATGTTTTGACCCCTAAAATTTCTTG
1 AAATTATATTTTAACCCCTAAACTTTCTTA
* * * * *
28070149 AAATTAAATTTTGA-TCCTAAATTTTCTCA
1 AAATTATATTTTAACCCCTAAACTTTCTTA
28070178 AAATTA
1 AAATTA
28070184 CACTTTGGCC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 17 0.21
30 64 0.79
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
AAATTATATTTTAACCCCTAAACTTTCTTA
Found at i:28070125 original size:60 final size:59
Alignment explanation
Indices: 28070059--28070183 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 59
28070049 ACTTTTTTTG
* *
28070059 AAATTATATTTTAACCCCTAAACTTTCTTAAAATTATATTTCAACCCCTAAACTTTCTCA
1 AAATTATATTTTAACCCCTAAAATTTCTTAAAATTAAATTTCAA-CCCTAAACTTTCTCA
* * * ** * *
28070119 AAATTATGTTTTGACCCCTAAAATTTCTTGAAATTAAATTTTGATCCTAAATTTTCTCA
1 AAATTATATTTTAACCCCTAAAATTTCTTAAAATTAAATTTCAACCCTAAACTTTCTCA
28070178 AAATTA
1 AAATTA
28070184 CACTTTGGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 19 0.34
60 37 0.66
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (59 bp):
AAATTATATTTTAACCCCTAAAATTTCTTAAAATTAAATTTCAACCCTAAACTTTCTCA
Found at i:28070415 original size:24 final size:24
Alignment explanation
Indices: 28070388--28070447 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
28070378 ACGAAATTCA
28070388 AAAAAAAAGAGAGAAAAGCTTCGG
1 AAAAAAAAGAGAGAAAAGCTTCGG
* *
28070412 AAAAAAAAAAGAGAAAAGCTTTGG
1 AAAAAAAAGAGAGAAAAGCTTCGG
*
28070436 GAAAAAAAGAGA
1 AAAAAAAAGAGA
28070448 AGAGGAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.63, C:0.05, G:0.23, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGAGAGAAAAGCTTCGG
Found at i:28070920 original size:15 final size:14
Alignment explanation
Indices: 28070889--28070931 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
28070879 GCAGGCCAGA
* *
28070889 AAAAAAAGAAGAGG
1 AAAAAAAGAAAAAG
28070903 AAAAAAAGATAAAAG
1 AAAAAAAGA-AAAAG
28070918 AAAAAAAGGAAAAA
1 AAAAAAA-GAAAAA
28070932 AAACCCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.36
15 14 0.56
16 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:28072366 original size:11 final size:11
Alignment explanation
Indices: 28072350--28072454 Score: 58
Period size: 11 Copynumber: 9.7 Consensus size: 11
28072340 TATTTTTTAA
28072350 TTTTAAAATAT
1 TTTTAAAATAT
28072361 TTTTAAAATACT
1 TTTTAAAATA-T
****
28072373 TTTTTTTTTAT
1 TTTTAAAATAT
**
28072384 TTTT-TTA-AT
1 TTTTAAAATAT
28072393 -TTTAAAATAT
1 TTTTAAAATAT
*
28072403 TTCTAAAATACT
1 TTTTAAAATA-T
** *
28072415 TTTT--TTTAA
1 TTTTAAAATAT
28072424 TTTTAAAATAT
1 TTTTAAAATAT
28072435 TTTTAAAATACT
1 TTTTAAAATA-T
28072447 TTTTAAAA
1 TTTTAAAA
28072455 AAAATTTTTA
Statistics
Matches: 71, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
8 3 0.04
9 7 0.10
10 6 0.08
11 35 0.49
12 20 0.28
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28072398 original size:42 final size:42
Alignment explanation
Indices: 28072342--28072421 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
28072332 TAAATATATA
*
28072342 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTTAT
1 TTTTTTAATTTTAAAATATTTCTAAAATACTTTTTTTTTTAT
28072384 TTTTTTAATTTTAAAATATTTCTAAAATACTTTTTTTT
1 TTTTTTAATTTTAAAATATTTCTAAAATACTTTTTTTT
28072422 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (42 bp):
TTTTTTAATTTTAAAATATTTCTAAAATACTTTTTTTTTTAT
Found at i:28072419 original size:32 final size:32
Alignment explanation
Indices: 28072383--28072450 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
28072373 TTTTTTTTTA
28072383 TTTTTTTAATTTTAAAATATTTCTAAAATACT
1 TTTTTTTAATTTTAAAATATTTCTAAAATACT
*
28072415 TTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTTAATTTTAAAATATTTCTAAAATACT
28072447 TTTT
1 TTTT
28072451 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTTTTAATTTTAAAATATTTCTAAAATACT
Found at i:28072437 original size:42 final size:42
Alignment explanation
Indices: 28072348--28072454 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
28072338 TATATTTTTT
* ***
28072348 AATTTTAAAATATTTTTAAAATACTTTTTTTTTTATTTTTTT
1 AATTTTAAAATATTTTTAAAATACTTTTTTTTTAATTTTAAA
*
28072390 AATTTTAAAATATTTCTAAAATAC-TTTTTTTTAATTTTAAA
1 AATTTTAAAATATTTTTAAAATACTTTTTTTTTAATTTTAAA
28072431 ATATTTTTAAAATACTTTTTAAAA
1 A-A-TTTTAAAATA-TTTTTAAAA
28072455 AAAATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 14 0.25
42 24 0.43
43 10 0.18
44 8 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (42 bp):
AATTTTAAAATATTTTTAAAATACTTTTTTTTTAATTTTAAA
Found at i:28073847 original size:50 final size:49
Alignment explanation
Indices: 28073658--28073852 Score: 167
Period size: 50 Copynumber: 3.9 Consensus size: 49
28073648 GATAATAACA
* ** * * * *
28073658 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGTAC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATAG
* * * * * ** *
28073707 TGCCAATGCCATATTCCAGATATGGTTTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATA-TAG
** *
28073757 TGCTC-ATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGC-CAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAT-AG
* * *
28073807 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATA
28073853 ATCTCAATGA
Statistics
Matches: 112, Mismatches: 30, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
49 37 0.33
50 74 0.66
51 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATAG
Found at i:28073850 original size:100 final size:99
Alignment explanation
Indices: 28073665--28073852 Score: 223
Period size: 100 Copynumber: 1.9 Consensus size: 99
28073655 ACATGCCAAA
* ** * * * * * *
28073665 GCCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGCCATATTCCAGATAT
1 GCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTACTGCCAACGCCATATCCCAGACAT
* * **
28073730 GGTTTTACATGGGAGTTCTCATATTGGTGCTCAT
66 GGTCTTACATGGAACCTCTCATATTGGTGCTCAT
* * *
28073764 GCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAGACA
1 GCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCT-ACTGCCAACGCCATATCCCAGACA
28073829 TGGTCTTACATGGAACCTCTCATA
65 TGGTCTTACATGGAACCTCTCATA
28073853 ATCTCAATGA
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
99 33 0.46
100 39 0.54
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (99 bp):
GCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTACTGCCAACGCCATATCCCAGACAT
GGTCTTACATGGAACCTCTCATATTGGTGCTCAT
Found at i:28075131 original size:50 final size:50
Alignment explanation
Indices: 28075056--28075297 Score: 240
Period size: 50 Copynumber: 4.9 Consensus size: 50
28075046 CATTTGGGTA
* * *
28075056 AAGAGGTCTCATGTAAGACCATGTCTTGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
28075106 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
28075156 GAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCAATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
28075206 GAGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGTAC-AGGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GAT
* * *
28075257 AACA--TCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28075298 TGTTATTATT
Statistics
Matches: 161, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
49 32 0.20
50 124 0.77
51 3 0.02
52 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:28079479 original size:71 final size:72
Alignment explanation
Indices: 28079387--28079519 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
28079377 CCAAAATCAT
* **
28079387 ATATAAACAACTATTGATAAAACTA-ATTTA-GTATAAATAAGTAAAACATAAATTCAATATCCA
1 ATATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAAAACATAAATTCAATATCCA
28079450 AAGACTAA
65 AAGACTAA
28079458 ATATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAAAACATAAATTCAATATC
1 ATATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAAAACATAAATTCAATATC
28079520 TATTGACAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
71 27 0.47
72 30 0.53
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.28
Consensus pattern (72 bp):
ATATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAAAACATAAATTCAATATCCAA
AGACTAA
Found at i:28079983 original size:18 final size:18
Alignment explanation
Indices: 28079962--28080009 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
28079952 TCCATTAATT
*
28079962 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATG
28079980 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
*
28079998 TGAACATTATTT
1 TGAACATCATTT
28080010 CTCATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:28083534 original size:16 final size:15
Alignment explanation
Indices: 28083509--28083542 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
28083499 ATGATTTCAG
28083509 TTTTAGAGATGTGAT
1 TTTTAGAGATGTGAT
28083524 TTTTCAGAGATGTGAT
1 TTTT-AGAGATGTGAT
28083540 TTT
1 TTT
28083543 GAATAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.50
Consensus pattern (15 bp):
TTTTAGAGATGTGAT
Found at i:28085418 original size:19 final size:19
Alignment explanation
Indices: 28085371--28085412 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28085361 ATGGCAAAGT
* *
28085371 TGAGAAATG-ATTATGAGA
1 TGAGAAATGAAATATGAAA
28085389 TGAGAAATGAAATATGAAA
1 TGAGAAATGAAATATGAAA
28085408 TGAGA
1 TGAGA
28085413 TGTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (19 bp):
TGAGAAATGAAATATGAAA
Found at i:28096407 original size:14 final size:15
Alignment explanation
Indices: 28096390--28096418 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28096380 GAGATGAGAG
28096390 ATGAAAT-ATGAAAT
1 ATGAAATAATGAAAT
28096404 ATGAAATAATGAAAT
1 ATGAAATAATGAAAT
28096419 GAGATGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (15 bp):
ATGAAATAATGAAAT
Found at i:28098755 original size:24 final size:24
Alignment explanation
Indices: 28098699--28098756 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
28098689 TCGTATATAG
28098699 CATAAGTTCGCATAGAAGAATACAA
1 CATAAGTTCGCATA-AAGAATACAA
* *
28098724 CATGAGTTCGCAT-AAGACATACAG
1 CATAAGTTCGCATAAAGA-ATACAA
*
28098748 TATAAGTTC
1 CATAAGTTC
28098757 ACACAAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.14
24 12 0.43
25 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
CATAAGTTCGCATAAAGAATACAA
Found at i:28105260 original size:23 final size:23
Alignment explanation
Indices: 28105234--28105374 Score: 185
Period size: 23 Copynumber: 6.2 Consensus size: 23
28105224 AGTGTTATTG
28105234 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
28105257 ATCAGTGATAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
28105280 TTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
**
28105303 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
28105326 TTCAGTGGTAGCTACGGCTAC-T
1 ATCAGTGGTAGCTACGGCTACAT
* * *
28105348 ATCAGTGGCAGCTTCAGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
28105371 ATCA
1 ATCA
28105375 ATGTGGCACT
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 18 0.18
23 82 0.82
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:28105302 original size:46 final size:46
Alignment explanation
Indices: 28105235--28105370 Score: 220
Period size: 46 Copynumber: 3.0 Consensus size: 46
28105225 GTGTTATTGA
*
28105235 TCAGTGGTAGCTACGGCTACATATCAGTGATAGCTTCGGCTACATT
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACATT
* *
28105281 TCAGTGGTAGCTACGACTACATATCAGTGGTAGCTTTGGCTACATT
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACATT
* *
28105327 TCAGTGGTAGCTACGGCTAC-TATCAGTGGCAGCTTCAGCTACAT
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
28105371 ATCAATGTGG
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 21 0.25
46 62 0.75
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (46 bp):
TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACATT
Done.