Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 167 of 290
Found at i:54193026 original size:28 final size:28
Alignment explanation
Indices: 54192958--54193139 Score: 285
Period size: 28 Copynumber: 6.5 Consensus size: 28
54192948 CATGAGATTG
* * * *
54192958 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
54192987 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54193015 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54193043 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
54193071 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54193099 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54193126 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54193140 GACTTAATAT
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 23 0.16
28 103 0.72
29 18 0.12
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54205191 original size:79 final size:81
Alignment explanation
Indices: 54205055--54205237 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
54205045 TTGAATGATG
* *
54205055 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
54205119 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
54205134 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
54205196 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
54205214 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
54205238 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:54205253 original size:40 final size:40
Alignment explanation
Indices: 54205056--54205239 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
54205046 TGAATGATGT
* * * *
54205056 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
54205096 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
54205136 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54205174 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54205215 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54205240 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54205261 original size:79 final size:79
Alignment explanation
Indices: 54205108--54205272 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
54205098 GGACTAAGAT
* **
54205108 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
54205173 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
54205187 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
54205250 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
54205266 CCGAAGG
1 CCGAAGG
54205273 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54213078 original size:40 final size:39
Alignment explanation
Indices: 54212994--54213215 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 39
54212984 TTGAATGATG
* * * *
54212994 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
54213034 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
54213074 TCCGGGCTAAGCCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
54213112 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
54213151 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
54213192 -CC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
54213216 AATGAGGAGC
Statistics
Matches: 162, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 34 0.21
39 58 0.36
40 60 0.37
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54213095 original size:39 final size:40
Alignment explanation
Indices: 54212994--54213215 Score: 253
Period size: 39 Copynumber: 5.7 Consensus size: 40
54212984 TTGAATGATG
* * *
54212994 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
54213033 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
54213074 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54213112 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
54213151 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54213190 AACC-GGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54213216 AATGAGGAGC
Statistics
Matches: 161, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
38 34 0.21
39 59 0.37
40 58 0.36
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:54213206 original size:117 final size:118
Alignment explanation
Indices: 54212994--54213213 Score: 279
Period size: 117 Copynumber: 1.9 Consensus size: 118
54212984 TTGAATGATG
*
54212994 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
54213059 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAA
* * * * **
54213112 TCCGGGTTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
54213174 TTGTGCGAGTTACT-ATAACC-GGCTATGTCCCGAAGGCATT
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
54213214 TGAATGAGGA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
116 9 0.10
117 61 0.69
118 18 0.20
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:54213233 original size:79 final size:78
Alignment explanation
Indices: 54212994--54213248 Score: 225
Period size: 79 Copynumber: 3.3 Consensus size: 78
54212984 TTGAATGATG
* * * * * * *
54212994 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATTT
** *
54213059 GTGCGAGAT-ACTAAT
64 GAACGAG-TGACTAAA
* * *
54213074 TCCGGGCTAAG-CCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGA
* *
54213138 GCGAGTTACTAAA
66 ACGAGTGACTAAA
*
54213151 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC-GGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
* *
54213214 TGAATGAG-GAGCTATA
63 TGAACGAGTGA-CTAAA
* *
54213230 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54213249 TACGTGATTT
Statistics
Matches: 151, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
76 1 0.01
77 35 0.23
78 47 0.31
79 55 0.36
80 13 0.09
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGA
ACGAGTGACTAAA
Found at i:54216142 original size:27 final size:28
Alignment explanation
Indices: 54216096--54216153 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
54216086 TACCTAGACC
54216096 CCCTATATATGATAAAATGACTATTTTG
1 CCCTATATATGATAAAATGACTATTTTG
* * *
54216124 CCCT-TATATGTTAAGATGACTGTTTTG
1 CCCTATATATGATAAAATGACTATTTTG
54216151 CCC
1 CCC
54216154 CTATGTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (28 bp):
CCCTATATATGATAAAATGACTATTTTG
Found at i:54218027 original size:93 final size:93
Alignment explanation
Indices: 54217914--54218085 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
54217904 GCCCATAAGT
* * *
54217914 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTTAGACTCAACTCA
1 GAACTAGGACTCAACTCAACGAG-TCAGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
54217978 ACGAGCTCGAATGCCTAGTTACATCTCTC
65 ACGAGCTCGAATGCCTAGTTACATCTCTC
** *
54218007 GAACTAGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACTCAACGAGTCAGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
54218072 CGAGTTCGGATGCC
66 CGAGCTCGAATGCC
54218086 CAAATATCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
92 3 0.04
93 67 0.96
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTAGGACTCAACTCAACGAGTCAGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGAATGCCTAGTTACATCTCTC
Found at i:54218077 original size:46 final size:46
Alignment explanation
Indices: 54217906--54218076 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 46
54217896 TGTAACCCGC
* *
54217906 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TCTGGACATTCGCAT
** * *
54217952 CCATAAGTGAACTTAGACTCAACTCAACGAG-CTCGA-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTCTGGACATTCGC-A--T
* *** * *
54217998 ACATCTCTCGAACTAGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTCTGGACATTCGCAT
54218045 CCATAAGTGAACTCGGACTCAACTCAACGAGT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGT
54218077 TCGGATGCCC
Statistics
Matches: 97, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
43 1 0.01
44 5 0.05
46 57 0.59
47 26 0.27
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTCTGGACATTCGCAT
Found at i:54221978 original size:46 final size:45
Alignment explanation
Indices: 54221832--54222001 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
54221822 GGTTGAGCAT
* * *
54221832 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AACGC
* * * * *
54221877 CCGAACTCGTTG-GTTGAGTCCGAGTTC-GTGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACAACGC
54221921 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AACGC
*
54221969 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54222002 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
44 17 0.17
45 13 0.13
46 52 0.50
47 17 0.17
48 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAACGC
Found at i:54225004 original size:47 final size:47
Alignment explanation
Indices: 54224872--54225329 Score: 720
Period size: 47 Copynumber: 9.6 Consensus size: 47
54224862 TATTTGAATA
*
54224872 AATGTGAAAGTGTATATATGTGATAAGGCCTGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
54224920 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54224969 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54225016 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54225065 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54225114 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54225160 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54225209 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
54225256 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54225303 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54225330 TCCCGAAGGG
Statistics
Matches: 386, Mismatches: 17, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
46 20 0.05
47 169 0.44
48 37 0.10
49 141 0.37
50 19 0.05
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54228950 original size:46 final size:46
Alignment explanation
Indices: 54228828--54228952 Score: 205
Period size: 46 Copynumber: 2.7 Consensus size: 46
54228818 GGTTGAGCAT
* * *
54228828 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
54228874 CCGAACTCGTTGTGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
54228920 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54228953 GGGGCGGGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:54233784 original size:46 final size:46
Alignment explanation
Indices: 54233717--54233883 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 46
54233707 TGTAACCCGC
*
54233717 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
54233763 CCATAAGTGAACTCAGACTCAACTCAACAAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * *
54233813 CTC-T---TGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
54233856 CCATAAGTGAACTCGAACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
54233884 AAGTTCGGAT
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
46 52 0.54
47 25 0.26
48 1 0.01
49 1 0.01
50 5 0.05
51 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:54233832 original size:93 final size:93
Alignment explanation
Indices: 54233724--54233896 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
54233714 CGCCCATAAG
* * *
54233724 TGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTC-AGACTCAACTC
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGA-ACTCAACTC
54233788 AACAAGCTCGGATGCCTAGTTACATCTCT
65 AACAAGCTCGGATGCCTAGTTACATCTCT
* *
54233817 TGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
54233882 ACAAGTTCGGATGCC
66 ACAAGCTCGGATGCC
54233897 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACAAGCTCGGATGCCTAGTTACATCTCT
Found at i:54238366 original size:46 final size:45
Alignment explanation
Indices: 54238270--54238433 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 45
54238260 GTGCTGATAC
* *
54238270 CATGTCCC-AACATGGTCTTACACT-GACACCTCTCATAGCCGATG
1 CATGTCCCAAACATGGTCTTACACTGGATACGTCTCA-AGCCGATG
*
54238314 CATGTCCCAGACAT-GTCTTACACTGGATTACGTCTCAAGGCCGATG
1 CATGTCCCAAACATGGTCTTACACTGGA-TACGTCTCAA-GCCGATG
* *
54238360 CATGTCCCAAACAT-GTCTTACACTAGCA-ATCGTCTCAATGTCGATG
1 CATGTCCCAAACATGGTCTTACACT-GGATA-CGTCTCAA-GCCGATG
54238406 CCATGTCCCAAACATGGTCTTACACTGG
1 -CATGTCCCAAACATGGTCTTACACTGG
54238434 CTCTCATAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
44 18 0.17
45 8 0.08
46 51 0.49
47 17 0.16
48 10 0.10
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (45 bp):
CATGTCCCAAACATGGTCTTACACTGGATACGTCTCAAGCCGATG
Found at i:54238457 original size:94 final size:93
Alignment explanation
Indices: 54238215--54238480 Score: 266
Period size: 94 Copynumber: 2.8 Consensus size: 93
54238205 CTCAAACATT
** *
54238215 GATGTCATGTCCCAAACATGGTCTTACACAAGTTCTAGCATATATGT-GCTGATACCATGTCCC-
1 GATG-CATGTCCCAAACATGGTCTTACACTGGTTCT--CATA-ATGTGGCTGAT-GCATGTCCCA
54238278 AACATGGTCTTACACT-G-ACACCTCTCATAGCC
61 AACAT-GTCTTACACTAGCACACCTCTCATAGCC
* *
54238310 GATGCATGTCCCAGACAT-GTCTTACACTGGATTACGTC-TCAA---GGCCGATGCATGTCCCAA
1 GATGCATGTCCCAAACATGGTCTTACACTGG-TT-C-TCAT-AATGTGGCTGATGCATGTCCCAA
* *
54238370 ACATGTCTTACACTAGCA-ATCGTCTCA-ATGTC
62 ACATGTCTTACACTAGCACA-CCTCTCATA-GCC
*
54238402 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAAACA
1 GATG-CATGTCCCAAACATGGTCTTACACTGGTTCTCATAATGTGGCTGATGCATGTCCCAAACA
54238467 TGTCTTACACTAGC
65 TGTCTTACACTAGC
54238481 TCACTCAAGT
Statistics
Matches: 145, Mismatches: 10, Indels: 33
0.77 0.05 0.18
Matches are distributed among these distances:
90 18 0.12
91 17 0.12
92 15 0.10
93 26 0.18
94 63 0.43
95 5 0.03
96 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (93 bp):
GATGCATGTCCCAAACATGGTCTTACACTGGTTCTCATAATGTGGCTGATGCATGTCCCAAACAT
GTCTTACACTAGCACACCTCTCATAGCC
Found at i:54247113 original size:119 final size:120
Alignment explanation
Indices: 54246937--54247159 Score: 310
Period size: 119 Copynumber: 1.9 Consensus size: 120
54246927 TACTCGTTCA
* *
54246937 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
54247002 ATAGT-AAATCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCATACC
66 ATAGTCAAATAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCATACC
* *
54247057 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* ** *
54247119 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTCAAATAGCACAAAGCCTTCGGGACTTAACCCGGA
54247160 CATCATTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 21 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTCAAATAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCATACC
Found at i:54247119 original size:79 final size:80
Alignment explanation
Indices: 54246935--54247159 Score: 255
Period size: 79 Copynumber: 2.8 Consensus size: 80
54246925 GCTACTCGTT
* * *
54246935 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTC-TACCAATGCCTTCGGGACTTAGCCCG
*
54246999 G-TTATAGTAAATCGCA
64 GAATATAGTAAATCGCA
*
54247015 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCATACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTC-TACCAATGCCTTCGGGACTTAGCCCGG
*
54247079 AAT-TAGTAACTCGCA
65 AATATAGTAAATCGCA
* * * * *
54247094 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACT-TAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCTA-C-CAATGCCTTCGGGACTTAGCCC
54247157 GGA
63 GGA
54247160 CATCATTCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 60 0.48
80 58 0.46
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCTACCAATGCCTTCGGGACTTAGCCCGGA
ATATAGTAAATCGCA
Found at i:54247159 original size:40 final size:40
Alignment explanation
Indices: 54246916--54247159 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
54246906 CGGAATTTAA
** *
54246916 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
54246956 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54246996 CCGGTTATAGTAAATCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* ** *
54247036 CCGGATTTAGTAACTCATACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54247075 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54247115 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54247155 CCGGA
1 CCGGA
54247160 CATCATTCGA
Statistics
Matches: 175, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 31 0.18
40 130 0.74
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54249314 original size:46 final size:46
Alignment explanation
Indices: 54249255--54249378 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
54249245 CTCTTGTAGT
* *
54249255 CGATGCATATCCCAGACATGTCTTACACTGGCTTA-T-GTCTCCACAC
1 CGATGCATATCCCAGACATGTCTTACACT-AC-TACTCGTCTCAACAC
* * **
54249301 CGATGCATGTCCCAGACATGTCTTATACTACTACTCGTCTCAATGC
1 CGATGCATATCCCAGACATGTCTTACACTACTACTCGTCTCAACAC
54249347 CGATGCCATATCCCAGACATAGTCTTACACTA
1 CGATG-CATATCCCAGACAT-GTCTTACACTA
54249379 GCTCTCATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 39 0.59
47 13 0.20
48 10 0.15
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (46 bp):
CGATGCATATCCCAGACATGTCTTACACTACTACTCGTCTCAACAC
Found at i:54249892 original size:42 final size:42
Alignment explanation
Indices: 54249841--54250127 Score: 434
Period size: 42 Copynumber: 6.8 Consensus size: 42
54249831 GTTTACAAAC
* *
54249841 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
54249883 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
54249925 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
54249967 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AA
* * * **
54250009 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGGC
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
54250051 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A
*
54250093 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
54250128 TTTTTTTTCT
Statistics
Matches: 225, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
41 3 0.01
42 219 0.97
43 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:54250183 original size:84 final size:82
Alignment explanation
Indices: 54249841--54250229 Score: 345
Period size: 84 Copynumber: 4.6 Consensus size: 82
54249831 GTTTACAAAC
* * * * *
54249841 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCG-CTTAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTA-AACAAAACGCCGCTAAAGAACATG
* **
54249905 TTCTTTAGCGGCGCTTAGAA
65 TTCTTTAGCGGC-ATT-TTA
* *
54249925 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTAGAAAAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTA-AACAAAACGCCGCTAAAGAACATG
*
54249989 TTCTTTAGCGGCGTTTGTAA
65 TTCTTTAGCGGCATTT-T-A
* * * * **
54250009 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCG-CTTAGGCAAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTAAAC-AAAACGCCGCTAAAGAACATG
**
54250073 TTCTTTAGCGGC-GCTTA
65 TTCTTTAGCGGCATTTTA
*** * *
54250090 AGGGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTCTAATCGCCGCTAAAGAAC
1 A---AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTTAAACAAAACGCCGCTAAAGAAC
* *
54250155 ATGTTCTTTAGTGGCATTTTTT
62 ATGTTCTTTAGCGGCA-TTTTA
* * * * *
54250177 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATACAAAAACGCC
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTTAAAC-AAAACGCC
54250230 ACTATTTTGG
Statistics
Matches: 258, Mismatches: 36, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
81 2 0.01
82 1 0.00
83 3 0.01
84 210 0.81
85 36 0.14
86 3 0.01
87 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTAAACAAAACGCCGCTAAAGAACATGT
TCTTTAGCGGCATTTTA
Found at i:54250183 original size:126 final size:126
Alignment explanation
Indices: 54249841--54250214 Score: 430
Period size: 126 Copynumber: 3.0 Consensus size: 126
54249831 GTTTACAAAC
* * * * * *
54249841 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAAAAAAATGCCACTAAAGAACATG
* ** *
54249905 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
65 TTCTTTAGCGGCGATTAGGCAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
54249967 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGACCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGAACATGT
* *
54250032 TCTTTAGCGGCGCTTAGGCAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
66 TCTTTAGCGGCGATTAGGCAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-A
* * * ***** *
54250093 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTCTAATCGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT-GCCACTAAAGAACATG
* **** * * *
54250158 TTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
65 TTCTTTAGCGGCGATTAGGCAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
54250215 TTATACAAAA
Statistics
Matches: 216, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
125 4 0.02
126 187 0.87
127 25 0.12
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (126 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGAACATGT
TCTTTAGCGGCGATTAGGCAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:54250607 original size:21 final size:21
Alignment explanation
Indices: 54250539--54250609 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
54250529 TTTTGCTCTG
* *
54250539 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
54250560 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
54250581 CGCTGCTTCCCTCGCTTCTGC
1 CTCTGCTTCCCTCGCTGCAGC
54250602 CTCTGCTT
1 CTCTGCTT
54250610 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.44, G:0.18, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:54256105 original size:11 final size:9
Alignment explanation
Indices: 54256057--54256366 Score: 84
Period size: 7 Copynumber: 36.0 Consensus size: 9
54256047 AATTGCAATG
54256057 GTAAGTTAT
1 GTAAGTTAT
54256066 GTAAGTTAT
1 GTAAGTTAT
54256075 GTAAGTTAAAT
1 GTAAGTT--AT
54256086 GT-A-TTAT
1 GTAAGTTAT
54256093 GTAAGTTAAAT
1 GTAAGTT--AT
54256104 GTAAG-T-T
1 GTAAGTTAT
54256111 GTAAGTTAT
1 GTAAGTTAT
*
54256120 -TATGTATTAT
1 GTAAG--TTAT
54256130 GTAAG-T-T
1 GTAAGTTAT
54256137 GTAAGTTAAAT
1 GTAAGTT--AT
*
54256148 GT-A-TTGT
1 GTAAGTTAT
54256155 GTAAG-T-T
1 GTAAGTTAT
54256162 GTAAGTTAAAT
1 GTAAGTT--AT
54256173 GT-A-TTAT
1 GTAAGTTAT
54256180 GTAAG-T-T
1 GTAAGTTAT
54256187 GTAAGTTAT
1 GTAAGTTAT
*
54256196 -TATGTATTAT
1 GTAAG--TTAT
54256206 GTAAG-T-T
1 GTAAGTTAT
54256213 GTAAGTTAT
1 GTAAGTTAT
* *
54256222 -TATGTATTGT
1 GTAAG--TTAT
54256232 GTAAG-T-T
1 GTAAGTTAT
54256239 GTAAGTTAAAT
1 GTAAGTT--AT
54256250 GT-A-TTAT
1 GTAAGTTAT
54256257 GTAAGTTAAAT
1 GTAAGTT--AT
54256268 GT-A-TTAT
1 GTAAGTTAT
54256275 GTAAG-T-T
1 GTAAGTTAT
54256282 GTAAGTTACAT
1 GTAAGTT--AT
54256293 GT-A-TTAT
1 GTAAGTTAT
54256300 GTAAG-T-T
1 GTAAGTTAT
54256307 GTAAGTTAAAT
1 GTAAGTT--AT
54256318 GT-A-TTAT
1 GTAAGTTAT
54256325 GTAAG-T-T
1 GTAAGTTAT
54256332 GTAAGTTAT
1 GTAAGTTAT
*
54256341 -TATGTATTAT
1 GTAAG--TTAT
54256351 GTAAG-T-T
1 GTAAGTTAT
54256358 GTAAGTTAT
1 GTAAGTTAT
54256367 TATGTATTGT
Statistics
Matches: 229, Mismatches: 10, Indels: 124
0.63 0.03 0.34
Matches are distributed among these distances:
7 87 0.38
8 38 0.17
9 39 0.17
10 23 0.10
11 42 0.18
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:54256157 original size:25 final size:25
Alignment explanation
Indices: 54256102--54256509 Score: 538
Period size: 26 Copynumber: 16.6 Consensus size: 25
54256092 TGTAAGTTAA
*
54256102 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
54256128 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
*
54256153 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
*
54256178 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
*
54256204 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
*
54256230 GTGTAAGTTGTAAGTTAAATG---T
1 ATGTAAGTTGTAAGTTAAATGTATT
54256252 AT-T-A--TGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
*
54256273 ATGTAAGTTGTAAGTTACATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
54256298 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
*
54256323 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
*
54256349 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
* *
54256375 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
*
54256401 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATT
*
54256427 GTGTAAGTTGTAAGTTAAATG---T
1 ATGTAAGTTGTAAGTTAAATGTATT
*
54256449 AT-T-A--TGTCAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
54256470 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT
54256495 ATGTAAGTTGTAAGT
1 ATGTAAGTTGTAAGT
54256510 AATATAATTA
Statistics
Matches: 349, Mismatches: 17, Indels: 33
0.87 0.04 0.08
Matches are distributed among these distances:
18 25 0.07
20 2 0.01
21 8 0.02
22 6 0.02
23 2 0.01
25 141 0.40
26 165 0.47
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (25 bp):
ATGTAAGTTGTAAGTTAAATGTATT
Found at i:54256408 original size:197 final size:196
Alignment explanation
Indices: 54256102--54256522 Score: 729
Period size: 197 Copynumber: 2.1 Consensus size: 196
54256092 TGTAAGTTAA
* *
54256102 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATTGTGTAAGTTGTAAG
1 ATGTAAGTTGTAAGTTATAATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAG
54256167 TTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGT
66 TTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGT
*
54256232 GTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTACATGTAT
131 GTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTAT
54256297 T
196 T
*
54256298 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAA
1 ATGTAAGTTGTAAGTTATAATGTATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAA
* *
54256362 GTTATTATGTATTGTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
65 GTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
54256427 GTGTAAGTTGTAAGTTAAATGTATTATGTCAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGT
129 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGT
54256492 ATT
194 ATT
54256495 ATGTAAGTTGTAAGTAATATAAT-TATTA
1 ATGTAAGTTGTAAGT--TATAATGTATTA
54256523 ATAATATTTA
Statistics
Matches: 213, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
195 24 0.11
196 40 0.19
197 139 0.65
199 7 0.03
200 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (196 bp):
ATGTAAGTTGTAAGTTATAATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAG
TTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGT
GTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTAT
T
Found at i:54256503 original size:18 final size:18
Alignment explanation
Indices: 54256435--54256478 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
54256425 TTGTGTAAGT
54256435 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
*
54256453 TGTCAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
54256471 TGTAAGTT
1 TGTAAGTT
54256479 GTAAGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:54256697 original size:72 final size:72
Alignment explanation
Indices: 54256512--54256801 Score: 562
Period size: 72 Copynumber: 4.0 Consensus size: 72
54256502 TTGTAAGTAA
54256512 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
54256577 TATTTTTT
66 TA-TTTTT
54256585 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
54256650 TATTTTT
66 TATTTTT
54256657 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
54256722 TATTTTT
66 TATTTTT
*
54256729 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAGTATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
54256794 TATTTTT
66 TATTTTT
54256801 T
1 T
54256802 TATATTTTAT
Statistics
Matches: 216, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
72 149 0.69
73 67 0.31
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (72 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTT
Found at i:54256970 original size:13 final size:13
Alignment explanation
Indices: 54256952--54257022 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
54256942 ATTTATAATT
54256952 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
54256965 ATTTAAGTAACAT
1 ATTTAAGTAATAA
54256978 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
54256991 ATTTAAGTAACAT
1 ATTTAAGTAATAA
54257004 ATTTAAGTAATAA
1 ATTTAAGTAATAA
54257017 ATTTAA
1 ATTTAA
54257023 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:54256981 original size:26 final size:26
Alignment explanation
Indices: 54256951--54257022 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
54256941 TATTTATAAT
54256951 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
54256977 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
54257003 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
54257023 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:54257049 original size:17 final size:17
Alignment explanation
Indices: 54257027--54257167 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
54257017 ATTTAAACAA
54257027 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
54257044 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
54257061 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
54257084 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
54257101 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
54257118 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
54257141 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
54257158 ATTTTAGTAA
1 ATTTTAGTAA
54257168 TAAATTTAAC
Statistics
Matches: 104, Mismatches: 4, Indels: 32
0.74 0.03 0.23
Matches are distributed among these distances:
16 2 0.02
17 71 0.68
23 29 0.28
24 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.45
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:54257053 original size:40 final size:40
Alignment explanation
Indices: 54256994--54257093 Score: 173
Period size: 40 Copynumber: 2.5 Consensus size: 40
54256984 GTAATAAATT
** *
54256994 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
54257034 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
54257074 TAAGTAATGTATTTTAGTAA
1 TAAGTAATGTATTTTAGTAA
54257094 GTAATGTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (40 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
Found at i:54257060 original size:13 final size:13
Alignment explanation
Indices: 54256952--54257174 Score: 95
Period size: 17 Copynumber: 16.3 Consensus size: 13
54256942 ATTTATAATT
*
54256952 ATTTAAGTAATAA
1 ATTTTAGTAATAA
* * *
54256965 ATTTAAGTAACAT
1 ATTTTAGTAATAA
*
54256978 ATTTAAGTAATAA
1 ATTTTAGTAATAA
* * *
54256991 ATTTAAGTAACAT
1 ATTTTAGTAATAA
*
54257004 ATTTAAGTAATAA
1 ATTTTAGTAATAA
*
54257017 A-TTTA--AACAA
1 ATTTTAGTAATAA
54257027 ATTTTAGTAAGTAA
1 ATTTTAGTAA-TAA
54257041 TGTATTTTAGTAATAA
1 ---ATTTTAGTAATAA
*
54257057 A-TTTA--AACAA
1 ATTTTAGTAATAA
54257067 ATTTTAGTAAGTAA
1 ATTTTAGTAA-TAA
54257081 TGTATTTTAGTAAGTAA
1 ---ATTTTAGTAA-TAA
54257098 TGTATTTTAGTAATAA
1 ---ATTTTAGTAATAA
*
54257114 A-TTTA--AACAA
1 ATTTTAGTAATAA
54257124 ATTTTAGTAAGTAA
1 ATTTTAGTAA-TAA
54257138 TTTATTTTAGTAAGTAA
1 ---ATTTTAGTAA-TAA
54257155 TGTATTTTAGTAATAA
1 ---ATTTTAGTAATAA
54257171 ATTT
1 ATTT
54257175 AACATTCAAT
Statistics
Matches: 173, Mismatches: 16, Indels: 42
0.75 0.07 0.18
Matches are distributed among these distances:
10 15 0.09
11 12 0.07
12 11 0.06
13 57 0.33
14 6 0.03
16 9 0.05
17 63 0.36
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (13 bp):
ATTTTAGTAATAA
Found at i:54257099 original size:57 final size:57
Alignment explanation
Indices: 54257027--54257176 Score: 291
Period size: 57 Copynumber: 2.6 Consensus size: 57
54257017 ATTTAAACAA
54257027 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
*
54257084 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
54257141 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAA
54257177 CATTCAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (57 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
Found at i:54258525 original size:11 final size:11
Alignment explanation
Indices: 54258509--54258548 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
54258499 GATGATAATA
54258509 CATTAGTTACC
1 CATTAGTTACC
54258520 CATTAGTTACC
1 CATTAGTTACC
*
54258531 CACTAGTTACC
1 CATTAGTTACC
54258542 CA-TAGTT
1 CATTAGTT
54258549 TGAGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:54259636 original size:84 final size:83
Alignment explanation
Indices: 54259529--54259729 Score: 330
Period size: 84 Copynumber: 2.4 Consensus size: 83
54259519 ATTAACACCG
54259529 TTTTGTGGCGTTTTTGGTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
1 TTTTGTGGCGTTTTT-G-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
54259594 TCGTGGTCTGGAATTGCATT
64 TCGTGGTCTGGAATTGCATT
*
54259614 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTT-GAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTT
54259679 CGTGGTCTGGAATTGCATT
65 CGTGGTCTGGAATTGCATT
* * *
54259698 ATTTGTGGCATTTTCTTAAAAACGCCACTAAA
1 TTTTGTGGCGTTTT-TGAAAAACGCCACTAAA
54259730 AGTTTAACTA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 93 0.85
85 17 0.15
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTTGTGGCGTTTTTGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTTC
GTGGTCTGGAATTGCATT
Found at i:54260134 original size:12 final size:12
Alignment explanation
Indices: 54260117--54260142 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54260107 TTAAAATAGC
54260117 ACGACCTCTTTT
1 ACGACCTCTTTT
54260129 ACGACCTCTTTT
1 ACGACCTCTTTT
54260141 AC
1 AC
54260143 AGTTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (12 bp):
ACGACCTCTTTT
Found at i:54260969 original size:112 final size:112
Alignment explanation
Indices: 54260755--54261344 Score: 941
Period size: 112 Copynumber: 5.3 Consensus size: 112
54260745 AACACCTAGA
* * *
54260755 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCAAAGGACACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * * * * ** *
54260819 GAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCGGC-GTTATCTATAAACGCCACTAATGCTCACTCT
54260867 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
54260932 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
** *
54260979 TTAGCGGCGCTTCGCAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAATGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* *
54261043 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
* *
54261090 TTAGCGGCGCTTTACAATAAATGCCACGAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
54261155 GTGTATTATTTGCGGCGTTATCTATAAATGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
*
54261202 TTAGCGGCGCTTTACAATAAAGGCCACTAAGTCCCCCCCCAAAGGCCACAAAACGGCACCGTCTG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCCAAAGGCCACAAAACGGCACCGTCTG
54261267 GGTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
65 GGTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
* **
54261315 TTAGCGGCGCTTTTCCTTAAACGCCACTAA
1 TTAGCGGCGCTTTACAATAAACGCCACTAA
54261345 TGCTCACTCT
Statistics
Matches: 444, Mismatches: 31, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
111 104 0.23
112 188 0.42
113 152 0.34
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
Found at i:54261151 original size:223 final size:224
Alignment explanation
Indices: 54260755--54261341 Score: 953
Period size: 223 Copynumber: 2.6 Consensus size: 224
54260745 AACACCTAGA
* * *
54260755 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCAAAGGACACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * * * * *
54260819 GAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCTTTAGCGGCGCTTTACAA
66 GTGTATTATTTGCGGC-GTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAA
*
54260884 TAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCG
130 TAAACGCCACGAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCG
54260949 TTATCTATAAACGCCACTAATGCTCACTCT
195 TTATCTATAAACGCCACTAATGCTCACTCT
** *
54260979 TTAGCGGCGCTTCGCAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAATGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
54261043 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
66 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
*
54261108 AAATGCCACGAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
131 AAACGCCACGAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
*
54261173 TATCTATAAATGCCACTAATGCTCACTCT
196 TATCTATAAACGCCACTAATGCTCACTCT
*
54261202 TTAGCGGCGCTTTACAATAAAGGCCACTAAGTCCCCCCCCAAAGGCCACAAAACGGCACCGTCTG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCCAAAGGCCACAAAACGGCACCGTCTG
* * * **
54261267 GGTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
65 GGTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAA
54261332 TAAACGCCAC
130 TAAACGCCAC
54261342 TAATGCTCAC
Statistics
Matches: 336, Mismatches: 24, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
223 164 0.49
224 72 0.21
225 100 0.30
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (224 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
AAACGCCACGAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
TATCTATAAACGCCACTAATGCTCACTCT
Found at i:54261337 original size:40 final size:40
Alignment explanation
Indices: 54261292--54261408 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
54261282 GCGTTATCTA
**
54261292 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
54261332 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
* *
54261372 TAAACGCCGCTATTGCTCACTCTTTAGCGGCGCTTTT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTT
54261409 GCTCCAAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (40 bp):
TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
Found at i:54264207 original size:26 final size:26
Alignment explanation
Indices: 54264169--54264220 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
54264159 ATCATAATAC
54264169 GATGCCAGCGTCCTAGACATGGTCTT
1 GATGCCAGCGTCCTAGACATGGTCTT
*
54264195 GATGCCAGTGTCCTAGACATGGTCTT
1 GATGCCAGCGTCCTAGACATGGTCTT
54264221 ACACGTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (26 bp):
GATGCCAGCGTCCTAGACATGGTCTT
Found at i:54272104 original size:28 final size:28
Alignment explanation
Indices: 54272041--54272194 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
54272031 ATATTAAGTC
*
54272041 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
54272068 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
54272096 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
54272124 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54272152 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54272181 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54272195 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.18
28 76 0.66
29 19 0.16
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54699792 original size:22 final size:21
Alignment explanation
Indices: 54699763--54699803 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
54699753 TAGATAGAAG
54699763 GAATTGGTTTAGGATTGGTCA
1 GAATTGGTTTAGGATTGGTCA
*
54699784 GAATATGGTTTAGGTTTGGT
1 GAAT-TGGTTTAGGATTGGT
54699804 TATGGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.41
Consensus pattern (21 bp):
GAATTGGTTTAGGATTGGTCA
Found at i:54706513 original size:79 final size:81
Alignment explanation
Indices: 54706377--54706561 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
54706367 TTGAATGATG
* *
54706377 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
54706441 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
54706456 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
54706518 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
54706536 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54706562 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:54706575 original size:40 final size:40
Alignment explanation
Indices: 54706378--54706561 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
54706368 TGAATGATGT
* * * *
54706378 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
54706418 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
54706458 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54706496 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54706537 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54706562 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54706583 original size:79 final size:79
Alignment explanation
Indices: 54706430--54706594 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
54706420 GGACTAAGAT
* * **
54706430 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
54706495 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
54706509 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
54706572 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
54706588 CCGAAGG
1 CCGAAGG
54706595 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54710818 original size:39 final size:40
Alignment explanation
Indices: 54710701--54710883 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
54710691 GCTACTCATT
*
54710701 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
54710741 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
54710781 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
54710820 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
54710861 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
54710884 AACATCATTC
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:54710845 original size:79 final size:80
Alignment explanation
Indices: 54710703--54710883 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
54710693 TACTCATTCA
* *
54710703 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
54710768 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
* **
54710783 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
54710845 ATATGGTCACTTAGCAC
64 ATATAGTAACTTAGCAC
*
54710862 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
54710884 AACATCATTC
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 58 0.67
80 25 0.29
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:54717635 original size:22 final size:22
Alignment explanation
Indices: 54717584--54717647 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
54717574 AACAGGATGG
*
54717584 CTCAACGCCGTAGACAGGACAA
1 CTCAACGTCGTAGACAGGACAA
*
54717606 CTCAACGTCGTAGACAGGACTA
1 CTCAACGTCGTAGACAGGACAA
* *
54717628 CTCAACGTCATAGGCAGGAC
1 CTCAACGTCGTAGACAGGAC
54717648 GGCTAAAGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (22 bp):
CTCAACGTCGTAGACAGGACAA
Found at i:54717953 original size:27 final size:27
Alignment explanation
Indices: 54717905--54717957 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
54717895 CATTCTACCA
*
54717905 TACAGGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGGTCATTTTACAC
** *
54717932 TACAAGGGTATTTTGGTGATTTTACA
1 TACAAGGGTATTACGGTCATTTTACA
54717958 AATCTGGTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTACGGTCATTTTACAC
Found at i:54720874 original size:23 final size:23
Alignment explanation
Indices: 54720848--54721059 Score: 216
Period size: 23 Copynumber: 9.2 Consensus size: 23
54720838 AGAATCTGTA
* *
54720848 GGCTACATCTTAGTGGTAGCTTT
1 GGCTACATCTCAGTGGTAGCTTC
* *
54720871 GGCTGCATCTCAGTGCTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTC
* *
54720894 AGCTACAAT-ACAGTGGTAGCTTC
1 GGCTAC-ATCTCAGTGGTAGCTTC
* *
54720917 GACTACATCTCATTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTC
* *
54720940 GGCTACAAT-ACAGTGGTAGCTTT
1 GGCTAC-ATCTCAGTGGTAGCTTC
*
54720963 GGCTACATCTCAGTTGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTC
*
54720986 AGCTACATCTCAGTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTC
* *
54721009 GGCTACAAT-ACAGTGGTAGCTTT
1 GGCTAC-ATCTCAGTGGTAGCTTC
* *
54721032 AGCTACAT-TACAGTGATAGCTTC
1 GGCTACATCT-CAGTGGTAGCTTC
54721055 GGCTA
1 GGCTA
54721060 TATTACAGTG
Statistics
Matches: 154, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
22 6 0.04
23 142 0.92
24 6 0.04
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (23 bp):
GGCTACATCTCAGTGGTAGCTTC
Found at i:54721069 original size:46 final size:46
Alignment explanation
Indices: 54720859--54721059 Score: 253
Period size: 46 Copynumber: 4.4 Consensus size: 46
54720849 GCTACATCTT
* * *
54720859 AGTGGTAGCTTTGGCTGCATCTCAGTGCTAGCTTCAGCTACAATAC
1 AGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATAC
* * *
54720905 AGTGGTAGCTTCGACTACATCTCATTGGTAGCTTCGGCTACAATAC
1 AGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATAC
* * *
54720951 AGTGGTAGCTTTGGCTACATCTCAGTTGTAGCTTCAGCTAC-ATCTC
1 AGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAAT-AC
* * *
54720997 AGTGGTAGCTTCGGCTACAAT-ACAGTGGTAGCTTTAGCTACATTAC
1 AGTGGTAGCTTCGGCTAC-ATCTCAGTGGTAGCTTCAGCTACAATAC
*
54721043 AGTGATAGCTTCGGCTA
1 AGTGGTAGCTTCGGCTA
54721060 TATTACAGTG
Statistics
Matches: 133, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
45 2 0.02
46 128 0.96
47 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (46 bp):
AGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATAC
Found at i:54721069 original size:69 final size:68
Alignment explanation
Indices: 54720848--54721059 Score: 266
Period size: 69 Copynumber: 3.1 Consensus size: 68
54720838 AGAATCTGTA
* * * * * * *
54720848 GGCTACATCTTAGTGGTAGCTTTGGCTGC-ATCTCAGTGCTAGCTTCAGCTACAATACAGTGGTA
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAAT-ACAGTGGTAGCTTTAGCTACATTACAGT-GTA
54720912 GCTTC
64 GCTTC
* * *
54720917 GACTACATCTCATTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTACATCT-CAGTTGTA
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTAGCTACAT-TACAG-TGTA
54720981 GCTTC
64 GCTTC
*
54720986 AGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTAGCTACATTACAGTGATAG
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTAGCTACATTACAGTG-TAG
54721051 CTTC
65 CTTC
54721055 GGCTA
1 GGCTA
54721060 TATTACAGTG
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
68 3 0.02
69 116 0.94
70 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (68 bp):
GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTAGCTACATTACAGTGTAGC
TTC
Found at i:54724712 original size:27 final size:26
Alignment explanation
Indices: 54724664--54724723 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
54724654 GTGAGGCTAC
*
54724664 CAGATATTGTGACGAAGTCACCAAATA
1 CAGATATTGTGACGAAGCCACCAAA-A
* * * *
54724691 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAAAA
54724717 CAGATAT
1 CAGATAT
54724724 ATATATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAAAA
Found at i:54728525 original size:46 final size:48
Alignment explanation
Indices: 54728453--54728555 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
54728443 GACAGGACAG
* * * *
54728453 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-CATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATACATATGGCATTGGA
* *
54728499 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATACATATGGCATTGGA
54728547 GACAGGAAT
1 GACAGGAAT
54728556 AATTCATGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 27 0.55
47 1 0.02
48 21 0.43
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATACATATGGCATTGGA
Found at i:54734853 original size:40 final size:40
Alignment explanation
Indices: 54734798--54734942 Score: 272
Period size: 40 Copynumber: 3.6 Consensus size: 40
54734788 CGGATGATAA
*
54734798 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54734838 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54734878 CCGGGGTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54734918 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54734943 AGCGGGTAGC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54742724 original size:40 final size:40
Alignment explanation
Indices: 54742669--54742846 Score: 270
Period size: 40 Copynumber: 4.5 Consensus size: 40
54742659 CGGATGATAA
*
54742669 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54742709 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54742749 CCGGGGTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
54742789 CCGGGCTAAGTCCCAAAGGCATTTGAGCG-GGTAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
54742829 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54742847 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
39 17 0.13
40 111 0.87
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54746101 original size:46 final size:48
Alignment explanation
Indices: 54746029--54746131 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
54746019 GACAGGACAG
* * * *
54746029 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
54746075 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
54746123 GACAGGAAT
1 GACAGGAAT
54746132 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:54756987 original size:26 final size:26
Alignment explanation
Indices: 54756958--54757010 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
54756948 TCCAACATGC
54756958 ATTTAGGCCAATTTA-CTCCTAGGGGT
1 ATTTAGG-CAATTTATCTCCTAGGGGT
* * *
54756984 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGCAATTTATCTCCTAGGGGT
54757010 A
1 A
54757011 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGCAATTTATCTCCTAGGGGT
Found at i:54758294 original size:24 final size:24
Alignment explanation
Indices: 54758262--54758383 Score: 199
Period size: 24 Copynumber: 5.0 Consensus size: 24
54758252 AATTCCTGCT
*
54758262 CCTTGATCAGCTCCTAAATCTTCTC
1 CCTT-ATCAGCTCCTAAATCCTCTC
* *
54758287 CTTTATCAGTTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
54758311 CCTTATCAGCTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
54758335 CCTTATCAGCTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
*
54758359 CCTTATCAGCTCCTAAATCTTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
54758383 C
1 C
54758384 TAACAGCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 88 0.97
25 3 0.03
ACGTcount: A:0.20, C:0.39, G:0.05, T:0.36
Consensus pattern (24 bp):
CCTTATCAGCTCCTAAATCCTCTC
Found at i:54758335 original size:12 final size:12
Alignment explanation
Indices: 54758267--54758386 Score: 50
Period size: 12 Copynumber: 10.0 Consensus size: 12
54758257 CTGCTCCTTG
*
54758267 ATCAGCTCCTAA
1 ATCATCTCCTAA
* **
54758279 ATCTTCTCCTTT
1 ATCATCTCCTAA
54758291 ATCAGT-TCCTAA
1 ATCA-TCTCCTAA
* *
54758303 ATCCTCTCCCT-T
1 ATCATCT-CCTAA
*
54758315 ATCAGCTCCTAA
1 ATCATCTCCTAA
* *
54758327 ATCCTCTCCCT-T
1 ATCATCT-CCTAA
*
54758339 ATCAGCTCCTAA
1 ATCATCTCCTAA
* *
54758351 ATCCTCTCCCT-T
1 ATCATCT-CCTAA
*
54758363 ATCAGCTCCTAA
1 ATCATCTCCTAA
*
54758375 ATCTTCTCCTAA
1 ATCATCTCCTAA
54758387 CAGCCTTTCA
Statistics
Matches: 74, Mismatches: 26, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
11 10 0.14
12 54 0.73
13 10 0.14
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (12 bp):
ATCATCTCCTAA
Found at i:54763451 original size:18 final size:18
Alignment explanation
Indices: 54763430--54763465 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54763420 TACTTTAGCC
54763430 ATTTACTTTTACTGCAAT
1 ATTTACTTTTACTGCAAT
54763448 ATTTACTTTTACTGCAAT
1 ATTTACTTTTACTGCAAT
54763466 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTACTTTTACTGCAAT
Found at i:54763476 original size:17 final size:18
Alignment explanation
Indices: 54763436--54763477 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54763426 AGCCATTTAC
* *
54763436 TTTTACTGCAATATTTAC
1 TTTTACTGCAATATTAAA
54763454 TTTTACTGCAAT-TTAAA
1 TTTTACTGCAATATTAAA
54763471 TTTTACT
1 TTTTACT
54763478 CTAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTTACTGCAATATTAAA
Found at i:54766348 original size:31 final size:31
Alignment explanation
Indices: 54766313--54766414 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 31
54766303 TGAGAATTAC
54766313 AATCAGAATCAGGTGACAGAATCAGAATCAA
1 AATCAGAATCAGGTGACAGAATCAGAATCAA
* *
54766344 AATCAGAATCAGAATTTGGTGACAGAATTAGAATCAG
1 AATCAGAATC---A---GGTGACAGAATCAGAATCAA
* * *
54766381 AATCAGTATCAGGTAATAGAATCA-ATATCAA
1 AATCAGAATCAGGTGACAGAATCAGA-ATCAA
54766412 AAT
1 AAT
54766415 GTGAATGCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
30 1 0.02
31 27 0.47
34 2 0.04
37 27 0.47
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
AATCAGAATCAGGTGACAGAATCAGAATCAA
Found at i:54766354 original size:37 final size:37
Alignment explanation
Indices: 54766313--54766392 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
54766303 TGAGAATTAC
54766313 AATCAGAATCAGGTGACAGAATCAGAATCAAAATCAG
1 AATCAGAATCAGGTGACAGAATCAGAATCAAAATCAG
** * *
54766350 AATCAGAATTTGGTGACAGAATTAGAATCAGAATCAG
1 AATCAGAATCAGGTGACAGAATCAGAATCAAAATCAG
*
54766387 TATCAG
1 AATCAG
54766393 GTAATAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (37 bp):
AATCAGAATCAGGTGACAGAATCAGAATCAAAATCAG
Found at i:54766377 original size:6 final size:6
Alignment explanation
Indices: 54766284--54766358 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
54766274 AAGAAACATT
* * * * *
54766284 ATCAGA A-CTAGA ATCAAA ATGAGA ATTACA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
*
54766333 ATCAGA ATCAAA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
54766359 TTGGTGACAG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
5 2 0.04
6 46 0.87
7 4 0.08
8 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54766881 original size:27 final size:27
Alignment explanation
Indices: 54766851--54767044 Score: 244
Period size: 27 Copynumber: 7.2 Consensus size: 27
54766841 AACACCCTAG
* * *
54766851 GGGTAAAATGGTAATTTTTTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
*
54766878 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* *
54766905 GGGCAAAATAGTAATTCTATAAATTGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* *
54766932 GGGTAAAACAGTAATTCTATAAATCAA
1 GGGTAAAATAGTAATTCTATAAATCGA
* * *
54766959 GGATAAAATAGTAATTTTTTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* * *
54766986 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* *
54767013 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
54767040 GGGTA
1 GGGTA
54767045 GTTTGGTAAT
Statistics
Matches: 148, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (27 bp):
GGGTAAAATAGTAATTCTATAAATCGA
Found at i:54766937 original size:54 final size:54
Alignment explanation
Indices: 54766851--54767044 Score: 271
Period size: 54 Copynumber: 3.6 Consensus size: 54
54766841 AACACCCTAG
* * *
54766851 GGGTAAAATGGTAATTTTTTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* * * * *
54766905 GGGCAAAATAGTAATTCTATAAATTGAGGGTAAAACAGTAATTCTATAAATCAA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* * *
54766959 GGATAAAATAGTAATTTTTTAAATCGAGGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* *
54767013 GGGTAAAACAGTAATTCTGTAAATCGAGGGTA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTA
54767045 GTTTGGTAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (54 bp):
GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
Found at i:54767054 original size:81 final size:81
Alignment explanation
Indices: 54766851--54767071 Score: 253
Period size: 81 Copynumber: 2.7 Consensus size: 81
54766841 AACACCCTAG
** * * * * * *
54766851 GGGTAAAATGGTAATTTTTTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGCAAAATAG
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAG
*
54766916 TAATTCTATAAATTGA
66 TAATTCTATAAATCGA
* * *
54766932 GGGTAAAACAGTAATTCTATAAATCAAGGATAAAATAGTAATTTTTTAAATCGAGGGTAAAACAG
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAG
* *
54766997 TAATTTTGTAAATCGA
66 TAATTCTATAAATCGA
* *** * * *
54767013 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAGTTTGGTAATTTTACAAGTCGAGGGTA
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTA
54767072 TTTCAGTAAT
Statistics
Matches: 117, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 117 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (81 bp):
GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAG
TAATTCTATAAATCGA
Found at i:54767179 original size:81 final size:82
Alignment explanation
Indices: 54767033--54767217 Score: 191
Period size: 81 Copynumber: 2.3 Consensus size: 82
54767023 GTAATTCTGT
* * ***
54767033 AAATC-GAGGGTAGTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTACAGGTCGATGG
1 AAATCAGAGGGTATTTTGGTAATTTTACAAGACGAGGGTATTTCAGTAATTTTACAAACCGATGG
54767097 TATTTCAGTAATTTCAC
66 TATTTCAGTAATTTCAC
* **
54767114 AAATCAGA-GGTATTTTGGTAATTTTACAA-ACTAGTGGTATTTTGGTAATTTTACAAACC-AGT
1 AAATCAGAGGGTATTTTGGTAATTTTACAAGACGAG-GGTATTTCAGTAATTTTACAAACCGA-T
** * *
54767176 GGTATTTTGGTAATTTTAT
64 GGTATTTCAGTAATTTCAC
* *
54767195 AAACCA-AGGGTATTTTGTTAATT
1 AAATCAGAGGGTATTTTGGTAATT
54767218 CTACCGTACA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
80 5 0.06
81 79 0.92
82 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (82 bp):
AAATCAGAGGGTATTTTGGTAATTTTACAAGACGAGGGTATTTCAGTAATTTTACAAACCGATGG
TATTTCAGTAATTTCAC
Found at i:54767198 original size:27 final size:27
Alignment explanation
Indices: 54767041--54767217 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
54767031 GTAAATCGAG
* * *
54767041 GGTAGTTTGGTAATTTTACAAGTCGAG-
1 GGTATTTTGGTAATTTTACAA-ACCAGT
** ***
54767068 GGTATTTCAGTAATTTTACAGGTC-GAT
1 GGTATTTTGGTAATTTTACAAACCAG-T
** * * *
54767095 GGTATTTCAGTAATTTCACAAATCAGA
1 GGTATTTTGGTAATTTTACAAACCAGT
*
54767122 GGTATTTTGGTAATTTTACAAACTAGT
1 GGTATTTTGGTAATTTTACAAACCAGT
54767149 GGTATTTTGGTAATTTTACAAACCAGT
1 GGTATTTTGGTAATTTTACAAACCAGT
*
54767176 GGTATTTTGGTAATTTTATAAACCAAG-
1 GGTATTTTGGTAATTTTACAAACC-AGT
*
54767203 GGTATTTTGTTAATT
1 GGTATTTTGGTAATT
54767218 CTACCGTACA
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
25 1 0.01
27 122 0.97
28 3 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACCAGT
Found at i:54767265 original size:27 final size:27
Alignment explanation
Indices: 54767213--54767279 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
54767203 GGTATTTTGT
* * *
54767213 TAATTCTACCGTACAGGGGCATTTCAG
1 TAATTCTACCCTACAAGGGCAGTTCAG
*
54767240 TAATTCTACCCTACAAGGGTAGTTCAG
1 TAATTCTACCCTACAAGGGCAGTTCAG
* *
54767267 TAATGCTAGCCTA
1 TAATTCTACCCTA
54767280 TAGATATGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
TAATTCTACCCTACAAGGGCAGTTCAG
Found at i:54769157 original size:6 final size:6
Alignment explanation
Indices: 54769139--54769232 Score: 61
Period size: 6 Copynumber: 15.3 Consensus size: 6
54769129 AAGAAACATT
* * *
54769139 ATCAGA A-CTAGA ATCAGA ATCAAA ATCAGA ATCAGA ATTATGTG A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* *
54769188 ATTAGA ATCAGA ATCAGT ATCAGGTA AT-AGA ATCA-A TATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA -ATCAGA AT
54769233 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
5 6 0.09
6 53 0.78
7 6 0.09
8 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (6 bp):
ATCAGA
Found at i:54769229 original size:31 final size:30
Alignment explanation
Indices: 54769153--54769232 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
54769143 GAACTAGAAT
* * *
54769153 CAGAATCAAAATCAGAATCAGAATTATGTGA
1 CAGAATC-AAATCAGAATCAGAATCAGGTAA
* *
54769184 CAGAATTAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCA-AATCAGAATCAGAATCAGGTAA
*
54769215 TAGAATCAATATCAGAAT
1 CAGAATCAA-ATCAGAAT
54769233 GTGAATGCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 2 0.05
31 38 0.95
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.24
Consensus pattern (30 bp):
CAGAATCAAATCAGAATCAGAATCAGGTAA
Found at i:54769695 original size:27 final size:27
Alignment explanation
Indices: 54769665--54769885 Score: 230
Period size: 27 Copynumber: 8.2 Consensus size: 27
54769655 AACACCCTAG
* *
54769665 GGGTAAAAT-GATAATTTTTTAAATCGA
1 GGGTAAAATAG-TAATTCTATAAATCGA
* *
54769692 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* *
54769719 GGGCAAAATAGTAATTCTATAAATTGA
1 GGGTAAAATAGTAATTCTATAAATCGA
*
54769746 GGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAATAGTAATTCTATAAATCGA
* * *
54769773 GGATAAAATAGTAATTTTTTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
*
54769800 GGGTAAAACAGTAATTC-AGTAAATCGA
1 GGGTAAAATAGTAATTCTA-TAAATCGA
* * *
54769827 GCGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
*** * * *
54769854 GGGTAGTTTAGTAATTTTACAAGTCGA
1 GGGTAAAATAGTAATTCTATAAATCGA
54769881 GGGTA
1 GGGTA
54769886 TTTCAATAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
27 163 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (27 bp):
GGGTAAAATAGTAATTCTATAAATCGA
Found at i:54769734 original size:54 final size:54
Alignment explanation
Indices: 54769665--54769858 Score: 255
Period size: 54 Copynumber: 3.6 Consensus size: 54
54769655 AACACCCTAG
*
54769665 GGGTAAAAT-GATAATTTTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAATAG-TAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* * * * * *
54769719 GGGCAAAATAGTAATTCTATAAATTGAGGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* * *
54769773 GGATAAAATAGTAATTTTTTAAATCGAGGGTAAAACAGTAATTCAGTAAATCGA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
* * *
54769827 GCGTAAAACAGTAATTCTGTAAATCGAGGGTA
1 GGGTAAAATAGTAATTCTTTAAATCGAGGGTA
54769859 GTTTAGTAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
54 117 0.99
55 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (54 bp):
GGGTAAAATAGTAATTCTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGA
Found at i:54769895 original size:27 final size:27
Alignment explanation
Indices: 54769850--54769924 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
54769840 ATTCTGTAAA
*
54769850 TCGAGGGTAGTTT-AGTAATTTTACAAG
1 TCGAGGGTA-TTTCAATAATTTTACAAG
*
54769877 TCGAGGGTATTTCAATAATTTTACAGG
1 TCGAGGGTATTTCAATAATTTTACAAG
*
54769904 TCGATGGTATTTCAATAATTT
1 TCGAGGGTATTTCAATAATTT
54769925 CATAAAACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
TCGAGGGTATTTCAATAATTTTACAAG
Found at i:54769949 original size:27 final size:27
Alignment explanation
Indices: 54769919--54770030 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
54769909 GGTATTTCAA
*
54769919 TAATTTCATAAAACAGAGGTATTTTGG
1 TAATTTTATAAAACAGAGGTATTTTGG
*
54769946 TAATTTTA-CAAACTAG-GGTATTTTGG
1 TAATTTTATAAAAC-AGAGGTATTTTGG
* * *
54769972 TAATTTTACAAACCAGTGGTATTTTGG
1 TAATTTTATAAAACAGAGGTATTTTGG
* *
54769999 TAATTTTATAAACCA-AGGGTATTTTGT
1 TAATTTTATAAAACAGA-GGTATTTTGG
54770026 TAATT
1 TAATT
54770031 CTACCCTACA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
26 24 0.32
27 50 0.68
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (27 bp):
TAATTTTATAAAACAGAGGTATTTTGG
Found at i:54769965 original size:26 final size:26
Alignment explanation
Indices: 54769936--54770049 Score: 138
Period size: 27 Copynumber: 4.3 Consensus size: 26
54769926 ATAAAACAGA
*
54769936 GGTATTTTGGTAATTTTACAAACTAG
1 GGTATTTTGGTAATTTTACAAACAAG
*
54769962 GGTATTTTGGTAATTTTACAAACCAG
1 GGTATTTTGGTAATTTTACAAACAAG
*
54769988 TGGTATTTTGGTAATTTTATAAACCAAG
1 -GGTATTTTGGTAATTTTACAAA-CAAG
* * **
54770016 GGTATTTTGTTAATTCTACCCTACAAG
1 GGTATTTTGGTAATTTTA-CAAACAAG
54770043 GGTATTT
1 GGTATTT
54770050 CAGTAGTGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
26 25 0.32
27 48 0.62
28 4 0.05
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTACAAACAAG
Found at i:54783513 original size:49 final size:49
Alignment explanation
Indices: 54783441--54783668 Score: 226
Period size: 49 Copynumber: 4.8 Consensus size: 49
54783431 TGAGGTCACG
54783441 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
*** * *
54783490 TGTGTAGTACTAAGTGCAGGCTACTATACGTACCTGATAACT--TCGATCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCG--CA
* * ** * *
54783539 CGTGT-G---T-A--G-AGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
54783581 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATTGGTCGCA
* *
54783630 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
54783669 GCTTCGGCTA
Statistics
Matches: 140, Mismatches: 24, Indels: 30
0.72 0.12 0.15
Matches are distributed among these distances:
41 17 0.12
42 6 0.04
43 1 0.01
44 3 0.02
45 1 0.01
46 1 0.01
47 4 0.03
48 1 0.01
49 85 0.61
50 21 0.15
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:54786037 original size:6 final size:6
Alignment explanation
Indices: 54786019--54786108 Score: 53
Period size: 6 Copynumber: 14.7 Consensus size: 6
54786009 AAGGAACATT
* *
54786019 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAGGTG AT-AGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * *
54786068 ATCAAA ATCA-A TATTATGTG A-CAGA ATCAGA ATCAGA ATCA
1 ATCAGA ATCAGA -ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA
54786109 ATATCAGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
5 5 0.08
6 54 0.82
7 4 0.06
8 3 0.05
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (6 bp):
ATCAGA
Found at i:54786063 original size:31 final size:31
Alignment explanation
Indices: 54786027--54786169 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
54786017 TTATCAGAAC
54786027 TAGAATCAGAATCAGAATCAGA-ATTAGGTGA
1 TAGAATCAGAATCAGAATCA-ATATTAGGTGA
* *
54786058 TAGAATCAGAATCAAAATCAATATTATGTGA
1 TAGAATCAGAATCAGAATCAATATTAGGTGA
* * *
54786089 CAGAATCAGAATCAGAATCAATATCAGGTAA
1 TAGAATCAGAATCAGAATCAATATTAGGTGA
* * * * * * *
54786120 CAGAATCAAAATAAGAATTAGTATCAGGTAA
1 TAGAATCAGAATCAGAATCAATATTAGGTGA
* *
54786151 AAGAATCAAAAATCAGAAT
1 TAGAATC-AGAATCAGAAT
54786170 GTGAATGAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
30 1 0.01
31 86 0.89
32 10 0.10
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.22
Consensus pattern (31 bp):
TAGAATCAGAATCAGAATCAATATTAGGTGA
Found at i:54786354 original size:27 final size:27
Alignment explanation
Indices: 54786316--54786746 Score: 603
Period size: 27 Copynumber: 16.0 Consensus size: 27
54786306 CAGAGGTATT
* *
54786316 TACCCTACAGGGGTATTCCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
54786343 TACCCTACAGGGGTATTCCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
54786370 TACCCTACAAGGGTA-TTCTAGTAATTC
1 TACCCTACAGGGGTATTTC-GGTAATTC
54786397 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * *
54786424 CACCCTACAGGGGTATTTAGGTATTTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
54786451 TACCCTACAAGGGTATTTCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
54786478 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * *
54786505 TACCCTACACGGGTATTCCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
54786532 TACCCTACAGTGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
54786559 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * *
54786586 TACCCTACAGAGGTATTGCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
54786613 TACCATACAGGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * *
54786640 TACCCTATAGGGGTATTGCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
54786667 TACCCTACAGGGCTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
54786694 CACCCTACAGGGGTATTTCGGTATTTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
54786721 TACCCTACAAGGGTATTTCGGTAATT
1 TACCCTACAGGGGTATTTCGGTAATT
54786747 TTATAAATCG
Statistics
Matches: 353, Mismatches: 49, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 348 0.99
28 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCGGTAATTC
Found at i:54787105 original size:27 final size:27
Alignment explanation
Indices: 54786728--54787098 Score: 348
Period size: 27 Copynumber: 13.7 Consensus size: 27
54786718 TTCTACCCTA
* * *
54786728 CAAGGGTATTTCGGTAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** * ** *
54786755 CGAGGGTAAAATGGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
54786782 CAAGGGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** **
54786809 CGAGGGTATTTCAATAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* ** * *
54786836 CGAGGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
54786863 C-AGAGGTATTTTGGTAATTTCACAAAT
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* *
54786890 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
54786917 TAAGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
54786944 AAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
54786971 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
54786998 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * *
54787025 CAGGGGTATTTTGGTGATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
54787052 CAAGGGTATTTTAGTGATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
54787079 CAAGGGTATTTTGATAATTT
1 CAAGGGTATTTTGGTAATTT
54787099 GGTAAACTAA
Statistics
Matches: 291, Mismatches: 51, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
26 2 0.01
27 288 0.99
28 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:54796807 original size:3 final size:3
Alignment explanation
Indices: 54796799--54796824 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54796789 TTACACATAA
54796799 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
54796825 TAAGTCTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:54801642 original size:34 final size:34
Alignment explanation
Indices: 54801593--54801691 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
54801583 TCCCAGTTAG
* * *
54801593 GGCCTTAGCCCATTTCAGTAACAGTAGCAGTCTG
1 GGCCTGAGCCCATTTCAGTAATAGTAGCAGTCTA
*
54801627 GGGCTGAGCCCATTTCAGTAATAGTAGCAGTCTA
1 GGCCTGAGCCCATTTCAGTAATAGTAGCAGTCTA
*
54801661 GGCCTGAGCCCATTTCAGTAATAGTATCAGT
1 GGCCTGAGCCCATTTCAGTAATAGTAGCAGT
54801692 ACCGTATGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (34 bp):
GGCCTGAGCCCATTTCAGTAATAGTAGCAGTCTA
Found at i:54802072 original size:18 final size:18
Alignment explanation
Indices: 54802049--54802084 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54802039 GCCTTAGTCG
54802049 TGCGAACTACACAGCCTA
1 TGCGAACTACACAGCCTA
54802067 TGCGAACTACACAGCCTA
1 TGCGAACTACACAGCCTA
54802085 ACCCAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (18 bp):
TGCGAACTACACAGCCTA
Found at i:54804946 original size:18 final size:18
Alignment explanation
Indices: 54804925--54804967 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
54804915 AAGTGTTTCT
54804925 GAAAGTATCTCC-TTGGAA
1 GAAAGTA-CTCCATTGGAA
54804943 GAAAGTACTCCGATTTGGAA
1 GAAAGTACTCC-A-TTGGAA
54804963 GAAAG
1 GAAAG
54804968 GGCAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
20 11 0.50
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (18 bp):
GAAAGTACTCCATTGGAA
Found at i:54813758 original size:33 final size:33
Alignment explanation
Indices: 54813721--54813792 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
54813711 CCCACAATGC
* *
54813721 TACTGTATAGGGCTAAGGCCCTGACTGTACTGT
1 TACTGTATAGGGCTAAGGCCCAGACTGTACTGA
* **
54813754 TACTGAATAGGGCTTTGGCCCAGACTGTACTGA
1 TACTGTATAGGGCTAAGGCCCAGACTGTACTGA
54813787 TACTGT
1 TACTGT
54813793 GTTGTTTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (33 bp):
TACTGTATAGGGCTAAGGCCCAGACTGTACTGA
Found at i:54815200 original size:42 final size:43
Alignment explanation
Indices: 54815123--54815244 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
54815113 CATTGACTTA
* *
54815123 TGATTTACGTGTAAGGCCATGTCTTGGACATTGGCATC-ATACT
1 TGATTT-CGTGTAAGACCATGTCTTGGACAGTGGCATCGATACT
* * *
54815166 TGATTTCGTGTAAGACCCTGT-TTGGGATAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCATGTCTT-GGACAGTGGCATCGATACT
* * * *
54815209 TGATTACATGTAAGACCACGTCTTGGACATTGGCAT
1 TGATTTCGTGTAAGACCATGTCTTGGACAGTGGCAT
54815245 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 24 0.37
43 37 0.57
44 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTCTTGGACAGTGGCATCGATACT
Found at i:54822228 original size:79 final size:82
Alignment explanation
Indices: 54822110--54822294 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
54822100 GCTACTCGTT
* * * *
54822110 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTTGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCC-TTCGGATCTTAACCC
* *
54822173 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
54822190 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54822253 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
54822270 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54822295 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 5 0.06
79 51 0.57
80 34 0.38
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:54822294 original size:40 final size:40
Alignment explanation
Indices: 54822091--54822294 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
54822081 CGGAATTTAA
** *
54822091 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
54822131 CCGGTTATAGTAACTCGCACAATTGCCTTTGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54822171 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54822210 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54822250 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54822290 CCGGA
1 CCGGA
54822295 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54830250 original size:40 final size:39
Alignment explanation
Indices: 54830202--54830305 Score: 154
Period size: 39 Copynumber: 2.6 Consensus size: 39
54830192 AGCCCGGTTA
* *
54830202 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCAGGATT
1 TAGTAACTCGCACAAATGCCTTCGGG-CTTAACCAGGAAT
* *
54830242 TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGCTTAACCAGGAAT
*
54830281 TAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
54830306 ATCTTAGTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGGCTTAACCAGGAAT
Found at i:54830274 original size:79 final size:80
Alignment explanation
Indices: 54830175--54830358 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 80
54830165 GCTACTCGTT
* * * *
54830175 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCAG
1 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCAG
* *
54830238 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* ** *
54830254 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCAGGA
* *
54830319 TATGGTCACTTAGCA
66 TATAGTAACTTAGCA
54830334 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
54830359 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
78 3 0.03
79 66 0.74
80 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCAGGA
TATAGTAACTTAGCA
Found at i:54830295 original size:39 final size:39
Alignment explanation
Indices: 54830175--54830358 Score: 183
Period size: 40 Copynumber: 4.6 Consensus size: 39
54830165 GCTACTCGTT
* *
54830175 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATT-TAGTAACTCGCA
* * *
54830214 CAATTGCCTTCGGGACTTAACCAGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCGCA
* *
54830254 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
* * * * * * *
54830293 CAAATGCCTTCGGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGATTTAGTAAC-TCGCA
54830334 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
54830359 CATCATTCAA
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
39 46 0.39
40 62 0.53
41 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
Found at i:54832982 original size:43 final size:42
Alignment explanation
Indices: 54832884--54832988 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
54832874 AAGACCATGC
* *
54832884 CTGGGACGTTGGCATCGTACTTGATTTCGTGTAAAACCCTGT
1 CTGGGACGTTGGCATCGTACTTGATTACGTGTAAAACCCTAT
* * * *
54832926 CTGGGATAG-TGGCATCGATATTTGATTACTTGTAAGACCAC-AT
1 CTGGGA-CGTTGGCATCG-TACTTGATTACGTGTAAAACC-CTAT
54832969 CTGGGACGTTGGCATCGTAC
1 CTGGGACGTTGGCATCGTAC
54832989 GAGCTTTCCG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
42 17 0.33
43 33 0.65
44 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (42 bp):
CTGGGACGTTGGCATCGTACTTGATTACGTGTAAAACCCTAT
Found at i:54837260 original size:51 final size:51
Alignment explanation
Indices: 54837175--54837374 Score: 321
Period size: 51 Copynumber: 3.9 Consensus size: 51
54837165 ACGGATACAC
*
54837175 AGTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAA
* * *
54837226 AGTGGCCTTCACATAGTACTACATTTGTGTCCAAAGCTATTTTATTAACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
* *
54837277 AATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
*
54837328 AGTGGCCTTCACATAGTACCACACTTGTGTCTAAAGCTATTTTATTC
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
54837375 CTCAGGTTCA
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 1 0.01
51 135 0.99
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
Found at i:54837444 original size:28 final size:27
Alignment explanation
Indices: 54837401--54837489 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
54837391 AAAATTCTCG
54837401 CTTAGCACAATGCCATGGACTTATTTCA
1 CTTAGCAC-ATGCCATGGACTTATTTCA
* *
54837429 CTTAGCACATTACCATTGACTTATTTCA
1 CTTAGCACA-TGCCATGGACTTATTTCA
* *
54837457 CCTAG---ATGCCATGGTCTTATTTCA
1 CTTAGCACATGCCATGGACTTATTTCA
*
54837481 CATAGCACA
1 CTTAGCACA
54837490 ATGTCATATC
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
24 19 0.38
25 1 0.02
27 2 0.04
28 28 0.56
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (27 bp):
CTTAGCACATGCCATGGACTTATTTCA
Found at i:54839501 original size:25 final size:25
Alignment explanation
Indices: 54839473--54839521 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
54839463 GAGATAGAAG
*
54839473 CTTTAATTACTTAAACGATGGGTAT
1 CTTTAATTACTTAAACGACGGGTAT
*
54839498 CTTTAATTACTTACACGACGGGTA
1 CTTTAATTACTTAAACGACGGGTA
54839522 CATTAATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (25 bp):
CTTTAATTACTTAAACGACGGGTAT
Found at i:54839670 original size:14 final size:14
Alignment explanation
Indices: 54839651--54839683 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54839641 ATTTAATTGG
54839651 AAAATTAA-TTAATT
1 AAAATTAATTTAA-T
54839665 AAAATTAATTTAAT
1 AAAATTAATTTAAT
54839679 AAAAT
1 AAAAT
54839684 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTAATTTAAT
Found at i:54843365 original size:13 final size:13
Alignment explanation
Indices: 54843347--54843371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54843337 ATCTTATCAA
54843347 TTGGAATTTTTAT
1 TTGGAATTTTTAT
54843360 TTGGAATTTTTA
1 TTGGAATTTTTA
54843372 GTTTTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
TTGGAATTTTTAT
Found at i:54848950 original size:28 final size:29
Alignment explanation
Indices: 54848917--54849009 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 29
54848907 ACTGCATCTA
*
54848917 ATTTATATTACAATGTTTGTA-ATTTTGC
1 ATTTATATTACAAAGTTTGTATATTTTGC
* * *
54848945 ATTTATATTATAAAGTTTGTATTTTTTTC
1 ATTTATATTACAAAGTTTGTATATTTTGC
* *
54848974 ATTTATATTACCAAA-TATATAT-TTTTGC
1 ATTTATATTA-CAAAGTTTGTATATTTTGC
*
54849002 ATGTATAT
1 ATTTATAT
54849010 AAGTTGATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 31 0.57
29 20 0.37
30 3 0.06
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (29 bp):
ATTTATATTACAAAGTTTGTATATTTTGC
Found at i:54851979 original size:37 final size:37
Alignment explanation
Indices: 54851929--54852007 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54851919 TTATTACGAA
* * *
54851929 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54851966 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54852003 GTCTT
1 GTCTT
54852008 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54852300 original size:49 final size:49
Alignment explanation
Indices: 54852126--54852609 Score: 765
Period size: 49 Copynumber: 10.1 Consensus size: 49
54852116 CCCTTCGGGA
* * * *
54852126 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
54852173 CCTGTCACATATATAT--ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54852220 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54852267 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54852316 CCTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54852365 CTTATCTC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54852412 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54852461 CTTATCACATATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54852510 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
54852559 CTTATCAC--ATATATACACTTTCATGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54852606 CTTA
1 CTTA
54852610 CTATCATTTC
Statistics
Matches: 410, Mismatches: 18, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
45 6 0.01
46 2 0.00
47 162 0.40
48 1 0.00
49 239 0.58
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54852323 original size:96 final size:97
Alignment explanation
Indices: 54852126--54852609 Score: 743
Period size: 96 Copynumber: 5.0 Consensus size: 97
54852116 CCCTTCGGGA
* * * * * * *
54852126 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GCCCTGTCACATATATAT
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATATAT
54852189 --ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
54852220 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
54852284 CACTTTCACATTCATCACATCGGCCATTAGGC
66 CACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54852316 CCTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCTC--ATATAT
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
54852379 ACACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
54852412 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
54852477 GCACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
54852510 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
**
54852573 ACACTTTCATGTTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
54852606 CTTA
1 CTTA
54852610 CTATCATTTC
Statistics
Matches: 366, Mismatches: 17, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
93 2 0.01
94 54 0.15
96 171 0.47
98 139 0.38
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (97 bp):
CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
CACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54852398 original size:145 final size:144
Alignment explanation
Indices: 54852126--54852606 Score: 776
Period size: 145 Copynumber: 3.3 Consensus size: 144
54852116 CCCTTCGGGA
* * * * *
54852126 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCA-GCCCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCCTATCACATATATA
54852188 T-ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
65 TCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
54852252 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
*
54852267 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
* *
54852332 ACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCTCATATATACACTTTCACATTCATCA
66 -CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
54852397 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
*
54852412 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
54852477 GCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
66 -CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
54852542 CACATCGGCCATTAGGC
128 CACATCGGCCATTAGGC
**
54852559 CTTATCAC--ATATATACACTTTCATGTTCATCACATCGGCCATTAGGCC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
54852607 TTACTATCAT
Statistics
Matches: 318, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
141 9 0.03
142 3 0.01
143 44 0.14
145 215 0.68
147 47 0.15
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (144 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGC
Found at i:54857251 original size:40 final size:40
Alignment explanation
Indices: 54857214--54857396 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
54857204 GCTACTCGTT
*
54857214 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
54857254 CAATTGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
54857294 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
54857333 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
54857374 CAAA-GCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54857397 ACATCATTCA
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.02
39 40 0.33
40 69 0.57
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:54857325 original size:79 final size:81
Alignment explanation
Indices: 54857214--54857397 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
54857204 GCTACTCGTT
* * *
54857214 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
54857277 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
54857294 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
54857358 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
*
54857374 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
54857398 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 3 0.03
79 64 0.71
80 23 0.26
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:54861072 original size:38 final size:38
Alignment explanation
Indices: 54861026--54861101 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54861016 TGCTAAACAT
54861026 TTCACAATCATACTATAAATCACATTCCATCATTCAAC
1 TTCACAATCATACTATAAATCACATTCCATCATTCAAC
54861064 TTCACAATCATACTATAAATCACATTCCATCATTCAAC
1 TTCACAATCATACTATAAATCACATTCCATCATTCAAC
54861102 AAGCATACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (38 bp):
TTCACAATCATACTATAAATCACATTCCATCATTCAAC
Found at i:54863318 original size:33 final size:32
Alignment explanation
Indices: 54863259--54863322 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
54863249 ACGAAGTCAC
* *
54863259 CAGATATAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATAGATATTGTGGCGAAGCCACCAGAA
*
54863291 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATATAGATAT-TGTGGCGAAGCCACCAGA
54863323 TTGCAGCGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (32 bp):
CAGATATAGATATTGTGGCGAAGCCACCAGAA
Found at i:54864148 original size:26 final size:26
Alignment explanation
Indices: 54864042--54864185 Score: 155
Period size: 27 Copynumber: 5.4 Consensus size: 26
54864032 GGGGCAAAAT
* * *
54864042 GGTAATTTTACCCCACCAGGGTATCTC
1 GGTAATTCTACCCTA-CAGGGTATTTC
*
54864069 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGTATTTC
* * *
54864096 GGTATTTCTACCCAACAAGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGTATTTC
*
54864123 GGTAATTCTATCCTACAGGGTATTTTC
1 GGTAATTCTACCCTACAGGGTA-TTTC
* *
54864150 -ATAATTCTACCTTACAGGGTATTTC
1 GGTAATTCTACCCTACAGGGTATTTC
54864175 GGTAATTCTAC
1 GGTAATTCTAC
54864186 AACTTATCCA
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
25 4 0.04
26 35 0.36
27 57 0.59
28 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (26 bp):
GGTAATTCTACCCTACAGGGTATTTC
Found at i:54870849 original size:27 final size:26
Alignment explanation
Indices: 54870801--54870860 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
54870791 GCGAGGCTGC
*
54870801 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
54870828 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
54870854 CATATAT
1 CAGATAT
54870861 ATATGTGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:54871744 original size:27 final size:27
Alignment explanation
Indices: 54871602--54871747 Score: 170
Period size: 27 Copynumber: 5.4 Consensus size: 27
54871592 GGGGCAAAAT
* * *
54871602 GGTAATTTTAGCCC-ACAAGGGTATCTC
1 GGTAATTCTA-CCCTACAGGGGTATTTC
*
54871629 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
54871656 GGTATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
54871683 GGTAATTCTATCCTACAGGGGTATTTTC
1 GGTAATTCTACCCTACAGGGGTA-TTTC
* *
54871711 -ATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
54871737 GGTAATTCTAC
1 GGTAATTCTAC
54871748 AACTTATCCA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 7 0.07
27 90 0.90
28 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:54878093 original size:20 final size:20
Alignment explanation
Indices: 54878068--54878111 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
54878058 GAGTCAGGCT
54878068 TTATCAATGGTATTATTGAA
1 TTATCAATGGTATTATTGAA
54878088 TTATCAATGGTATTATTGAA
1 TTATCAATGGTATTATTGAA
54878108 TTAT
1 TTAT
54878112 AAAATTAAAA
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:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (20 bp):
TTATCAATGGTATTATTGAA
Found at i:54883932 original size:43 final size:43
Alignment explanation
Indices: 54883876--54883973 Score: 169
Period size: 43 Copynumber: 2.3 Consensus size: 43
54883866 TCAGAATCAC
54883876 ATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAT
1 ATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAT
* *
54883919 ATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACAT
1 ATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAT
*
54883962 ATATCAATGCCA
1 ATATCGATGCCA
54883974 TGGTCTTACT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (43 bp):
ATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAT
Found at i:54887781 original size:28 final size:29
Alignment explanation
Indices: 54887749--54887803 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
54887739 ATCCGAAAAA
*
54887749 CTGATAT-CATGGCCCAAAGGCAAATCAG
1 CTGATATGCATGGCCCAAAGCCAAATCAG
*
54887777 CTGATATGCATGGCCCGAAGCCAAATC
1 CTGATATGCATGGCCCAAAGCCAAATC
54887804 GGTTTATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (29 bp):
CTGATATGCATGGCCCAAAGCCAAATCAG
Found at i:54889720 original size:35 final size:35
Alignment explanation
Indices: 54889645--54889723 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
54889635 CCCATCACAG
* * * *
54889645 ATACAAATGCATATTCGGGCTTAAGCCCATTTCAG
1 ATACAGATACATATTCGGGCCTAAGCCCATTTCAA
* *
54889680 ATACAGATACATATTTGGGCCTAAGCCTATTTCAA
1 ATACAGATACATATTCGGGCCTAAGCCCATTTCAA
54889715 ATACAGATA
1 ATACAGATA
54889724 TAGATATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (35 bp):
ATACAGATACATATTCGGGCCTAAGCCCATTTCAA
Done.