Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 135 of 378
Found at i:38412225 original size:40 final size:40
Alignment explanation
Indices: 38412063--38412227 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
38412053 AAATTGAATG
* * **
38412063 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * *
38412102 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG--G
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
* *
38412140 CTATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATT
* *
38412180 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
38412220 ATATCCGG
1 ATATCCGG
38412228 TTATATTCCG
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 3 0.03
38 29 0.28
39 14 0.13
40 56 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:38420149 original size:38 final size:40
Alignment explanation
Indices: 38420098--38420206 Score: 143
Period size: 38 Copynumber: 2.8 Consensus size: 40
38420088 CTGGAAATTA
* *
38420098 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-T-GGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTAGGC
**
38420136 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTAGGC
*
38420176 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
38420207 ACGTGATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 3 0.05
38 28 0.45
39 1 0.02
40 28 0.45
41 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTAGGC
Found at i:38420220 original size:40 final size:40
Alignment explanation
Indices: 38420058--38420222 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
38420048 AAATTGAATG
* * **
38420058 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * *
38420097 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG--G
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
* *
38420135 CTATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATT
* *
38420175 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
38420215 ATATCCGG
1 ATATCCGG
38420223 TTATATTCCG
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 3 0.03
38 29 0.28
39 14 0.13
40 56 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:38422199 original size:93 final size:93
Alignment explanation
Indices: 38422087--38422257 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
38422077 GCCCATAAGT
* *
38422087 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38422152 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
38422180 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38422245 CGAGTTCGGATGC
66 CGAGTTCGGATGC
38422258 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:38422273 original size:46 final size:46
Alignment explanation
Indices: 38422079--38422259 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
38422069 TGTAACCCGC
* * *
38422079 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
38422125 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
38422175 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
38422218 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
38422260 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:38424667 original size:30 final size:30
Alignment explanation
Indices: 38424623--38424711 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
38424613 CAAAGATAAC
38424623 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
38424652 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
38424682 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
38424712 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:38424671 original size:15 final size:15
Alignment explanation
Indices: 38424623--38424702 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
38424613 CAAAGATAAC
*
38424623 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
38424637 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
38424652 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
38424667 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
38424682 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
38424697 AAGAAA
1 AAGAAA
38424703 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:38424711 original size:15 final size:15
Alignment explanation
Indices: 38424634--38424711 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
38424624 AGAAAACCGA
38424634 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
38424649 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
38424663 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
38424678 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
38424694 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
38424709 ATA
1 ATA
38424712 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:38433752 original size:40 final size:39
Alignment explanation
Indices: 38433707--38433836 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
38433697 CGGAATATAA
38433707 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
38433747 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38433787 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
38433827 CCGGATATAA
1 CCGGATATAA
38433837 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:38433851 original size:40 final size:40
Alignment explanation
Indices: 38433723--38433874 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
38433713 ATAACCATGT
* * *
38433723 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
38433763 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
38433803 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
38433843 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
38433875 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:38433857 original size:80 final size:80
Alignment explanation
Indices: 38433723--38433872 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
38433713 ATAACCATGT
*
38433723 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
38433787 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
38433803 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
38433866 CCCGGAT
64 CCCGGAT
38433873 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:38436824 original size:40 final size:40
Alignment explanation
Indices: 38436779--38436946 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
38436769 CGGAATACAA
38436779 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
38436819 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
38436859 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTATTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
38436899 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
38436939 CCGGATAT
1 CCGGATAT
38436947 CATTCAATTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 100 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:38439054 original size:185 final size:186
Alignment explanation
Indices: 38438715--38439063 Score: 506
Period size: 185 Copynumber: 1.9 Consensus size: 186
38438705 GTCACAGTAT
* ***
38438715 GTCTCAGTTGTATGTCCCCTATAGGTTTTAAAGGCATTCAAGTTTGGCAGTTACATGGCCTAGCA
1 GTCTCAGTCGTATGTCCCCTATAGGTTTTAAAGGCATTCAAGTTCAACAGTTACATGGCCTAGCA
* * **
38438780 CACAGCCTGGCTCACGGGCGTGTGGCTTGGCCGTGTGACCCAAGTCAGAGAGTTACACGAGCATG
66 CACAGCCTAGCTCACGGGCGTGTGGCTTGGCCGTGTGACCCAAGTCAAAGAGTTACACGAGCACA
* *
38438845 GACATGGCAGTGTGCCCCTACTTCGAATGTCCACGCGACCTATGACACAGGCATGC
131 GACACGGCAGTGTGCCCATACTTCGAATGTCCACGCGACCTATGACACAGGCATGC
* * *
38438901 GTCTCAGTCGTGTGTCCCCTGTAGGTTTTTAAGGCATTCAAG-TCAACAGTTACATGGCCTAGCA
1 GTCTCAGTCGTATGTCCCCTATAGGTTTTAAAGGCATTCAAGTTCAACAGTTACATGGCCTAGCA
* * *
38438965 CATAGCCTAGCTCACGGGTGTGTGGCTTGGCCGTGTGACCCAAGTCAAAGAGTTACAC-AGGTAC
66 CACAGCCTAGCTCACGGGCGTGTGGCTTGGCCGTGTGACCCAAGTCAAAGAGTTACACGA-GCAC
*
38439029 AGACACGGCCA-TGTGTCCATACTTCGAATGTCCAC
130 AGACACGG-CAGTGTGCCCATACTTCGAATGTCCAC
38439064 ACAGCCTGAG
Statistics
Matches: 144, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
184 1 0.01
185 103 0.72
186 40 0.28
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (186 bp):
GTCTCAGTCGTATGTCCCCTATAGGTTTTAAAGGCATTCAAGTTCAACAGTTACATGGCCTAGCA
CACAGCCTAGCTCACGGGCGTGTGGCTTGGCCGTGTGACCCAAGTCAAAGAGTTACACGAGCACA
GACACGGCAGTGTGCCCATACTTCGAATGTCCACGCGACCTATGACACAGGCATGC
Found at i:38442526 original size:93 final size:93
Alignment explanation
Indices: 38442414--38442585 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
38442404 GCCCATAAGT
* *
38442414 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38442479 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
38442507 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38442572 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
38442586 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:38442581 original size:46 final size:46
Alignment explanation
Indices: 38442406--38442581 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
38442396 TGTAACCCGC
* * *
38442406 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
38442452 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
38442502 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
38442545 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
38442582 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:38444495 original size:44 final size:43
Alignment explanation
Indices: 38444442--38444587 Score: 184
Period size: 43 Copynumber: 3.4 Consensus size: 43
38444432 CTTTTGGGTA
* * **
38444442 TATCTGATGATGCACTGTGTGTGCCAGTATAGTAGCTTCAGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCAGTT
** *
38444485 TCATCCGATGATGCACTGTGTGCACTAGTATATTTTCTTCAGTT
1 T-ATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCAGTT
* * * *
38444529 TATTCGATGATGCACTATGTGTGCCAATATATTTTCTTCGGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCAGTT
38444572 TATCCGATGATGCACT
1 TATCCGATGATGCACT
38444588 TACGTGCCAA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 51 0.59
44 36 0.41
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (43 bp):
TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCAGTT
Found at i:38444560 original size:43 final size:42
Alignment explanation
Indices: 38444442--38444606 Score: 179
Period size: 43 Copynumber: 3.8 Consensus size: 42
38444432 CTTTTGGGTA
* * * **
38444442 TATCTGATGATGCACTGTGTGTGCCAGTATAGTAGCTTCAGTT
1 TATCCGATGATGCACT-TGTGTGCCAATATATTTTCTTCAGTT
*
38444485 TCATCCGATGATGCAC-TGTGTGCACTAGTATATTTTCTTCAGTT
1 T-ATCCGATGATGCACTTGTGTGC-C-AATATATTTTCTTCAGTT
* *
38444529 TATTCGATGATGCACTATGTGTGCCAATATATTTTCTTCGGTT
1 TATCCGATGATGCACT-TGTGTGCCAATATATTTTCTTCAGTT
** *
38444572 TATCCGATGATGCACTTACGTGCCAATATAATTTC
1 TATCCGATGATGCACTTGTGTGCCAATATATTTTC
38444607 ATAGGTTCAT
Statistics
Matches: 106, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
42 23 0.22
43 46 0.43
44 30 0.28
45 7 0.07
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (42 bp):
TATCCGATGATGCACTTGTGTGCCAATATATTTTCTTCAGTT
Found at i:38453885 original size:48 final size:48
Alignment explanation
Indices: 38453824--38454111 Score: 317
Period size: 48 Copynumber: 6.0 Consensus size: 48
38453814 ATACTAAGGT
* *
38453824 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTA
* * * * * *
38453872 TATAAGAGCTAGTGTAAGACCATGACTAGGACATGGCATCAGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTA
* * * * * *
38453920 TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTA
* * *
38453968 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTA
* * * * *
38454016 TATGTG-GCTAGTGTAATACCATGTTTGGAACATGGCATCGGCACCGATA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC--TA
* * * *
38454065 TATGAGAGCCAATGTAAGACCATGTTTGGGACATGGCATCAGCATCT
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCT
38454112 TACCCTTTTG
Statistics
Matches: 193, Mismatches: 44, Indels: 6
0.79 0.18 0.02
Matches are distributed among these distances:
47 33 0.17
48 121 0.63
49 6 0.03
50 33 0.17
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTA
Found at i:38453988 original size:96 final size:96
Alignment explanation
Indices: 38453824--38454107 Score: 408
Period size: 96 Copynumber: 2.9 Consensus size: 96
38453814 ATACTAAGGT
* * * *
38453824 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTTATATAAGAGCTAGTGTAA
1 TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTAA
* *
38453889 GACCATGACTAGGACATGGCATCAGCCTCGA
66 GACCATGTCTGGGACATGGCATCAGCCTCGA
*
38453920 TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCATTTATATGAGAGCTAGTGTAA
1 TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTAA
* *
38453985 GACCATGTCTGGGACATGGCGTCGGCCTCGA
66 GACCATGTCTGGGACATGGCATCAGCCTCGA
* ** * *
38454016 TATGT-GGCTAGTGTAATACCATGTTTGGAACATGGCATCGGCACCGATATATGAGAGCCAATGT
1 TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCA--TTTATATGAGAGCTAGTGT
*
38454080 AAGACCATGTTTGGGACATGGCATCAGC
64 AAGACCATGTCTGGGACATGGCATCAGC
38454108 ATCTTACCCT
Statistics
Matches: 168, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
95 36 0.21
96 92 0.55
97 40 0.24
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (96 bp):
TATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCAGCCTCGA
Found at i:38465709 original size:37 final size:37
Alignment explanation
Indices: 38465656--38465777 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
38465646 TATAAAAGAA
*
38465656 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38465693 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38465730 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
38465767 GTCTCACCCGG
1 GTCTTACCCGG
38465778 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:38465934 original size:49 final size:49
Alignment explanation
Indices: 38465879--38466141 Score: 447
Period size: 49 Copynumber: 5.4 Consensus size: 49
38465869 TTTTACATTA
*
38465879 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38465928 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38465977 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38466026 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * * *
38466075 GCCATTAGGCCTCATCACATATACATCCACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
38466124 G-CATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38466142 CATATATGTA
Statistics
Matches: 207, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
48 15 0.07
49 192 0.93
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.28
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38469476 original size:29 final size:29
Alignment explanation
Indices: 38469439--38469747 Score: 582
Period size: 29 Copynumber: 10.7 Consensus size: 29
38469429 TGTTGAAAAA
* * *
38469439 CTCGTACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469468 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469497 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469526 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
38469555 CTCGCACACATGGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469584 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469613 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469642 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469671 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469700 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38469729 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
38469748 AATCATTCGC
Statistics
Matches: 275, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 275 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:38471887 original size:37 final size:37
Alignment explanation
Indices: 38471834--38471955 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
38471824 TATAAAAGAA
*
38471834 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38471871 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38471908 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
38471945 GTCTCACCCGG
1 GTCTTACCCGG
38471956 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:38472112 original size:49 final size:49
Alignment explanation
Indices: 38472057--38472320 Score: 456
Period size: 49 Copynumber: 5.4 Consensus size: 49
38472047 TTTTACATTA
*
38472057 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38472106 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38472155 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38472204 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * *
38472253 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
38472302 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38472321 CATATATGTA
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 209 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38475767 original size:29 final size:29
Alignment explanation
Indices: 38475685--38475911 Score: 398
Period size: 29 Copynumber: 8.1 Consensus size: 29
38475675 GACTCACACA
38475685 CTCG-TTACTGATCTCGCACAC--AGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475711 CTCGATTACTGATCT-GCACAC--A-T-C
1 CTCGATTACTGATCTCGCACACATAGTGC
38475735 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475764 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475793 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475822 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475851 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475880 CTCGATTACTGATCTCGCACACATAGTGC
1 CTCGATTACTGATCTCGCACACATAGTGC
38475909 CTC
1 CTC
38475912 AATCATTCGC
Statistics
Matches: 195, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.08
25 7 0.04
26 11 0.06
27 11 0.06
28 1 0.01
29 149 0.76
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (29 bp):
CTCGATTACTGATCTCGCACACATAGTGC
Found at i:38478057 original size:37 final size:37
Alignment explanation
Indices: 38478004--38478094 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
38477994 TATAAAAGAA
38478004 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
38478041 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
38478078 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
38478095 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:38478338 original size:49 final size:49
Alignment explanation
Indices: 38478189--38478495 Score: 500
Period size: 49 Copynumber: 6.4 Consensus size: 49
38478179 TTTTACATTA
*
38478189 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACAT--
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38478236 GCCATTAGGCCT-ATCACATATACAT-CACTTTCACATTCA-CACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38478282 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38478331 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38478380 GCCATTAGGCCTCATCACATATACAT-CACTTTCACATTCATCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * * *
38478428 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
38478477 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38478496 CATATATGTA
Statistics
Matches: 249, Mismatches: 5, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
44 5 0.02
45 14 0.06
46 25 0.10
47 25 0.10
48 60 0.24
49 120 0.48
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38478425 original size:97 final size:96
Alignment explanation
Indices: 38478189--38478495 Score: 496
Period size: 97 Copynumber: 3.2 Consensus size: 96
38478179 TTTTACATTA
*
38478189 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACAT--GCCATTAGGCCTATCA
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTATCA
38478252 CATATACAT-CACTTTCACATTCACACATCG
66 CATATACATACACTTTCACATTCACACATCG
38478282 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATC
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCT-ATC
38478347 ACATATACATACACTTTCACATTCACCACATCG
65 ACATATACATACACTTTCACATTCA-CACATCG
*
38478380 GCCATTAGGCCTCATCACATATACAT-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCC-TATC
* *
38478444 ACATATACATACACTTTCACATTCATCGCATTG
65 ACATATACATACACTTTCACATTCA-CACATCG
* *
38478477 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38478496 CATATATGTA
Statistics
Matches: 201, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
93 46 0.23
95 12 0.06
96 13 0.06
97 96 0.48
98 34 0.17
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.29
Consensus pattern (96 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTATCA
CATATACATACACTTTCACATTCACACATCG
Found at i:38478462 original size:146 final size:142
Alignment explanation
Indices: 38478189--38478495 Score: 524
Period size: 146 Copynumber: 2.1 Consensus size: 142
38478179 TTTTACATTA
38478189 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATGCCATTAGGCCTATCACA
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATGCCATTAGGCCTATCACA
38478254 TATACATCACTTTCACATTCACACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACA
66 TATACATCACTTTCACATTCACACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACA
38478319 TTCACCACATCG
131 TTCACCACATCG
*
38478331 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACAT--GCCATTAGGCCT-ATC
*
38478396 ACATATACATCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTT
63 ACATATACATCACTTTCACATTCA-CACATCGGCCATTAGGCCTCATCACATATACATACACTTT
* * *
38478461 CACATTCATCGCATTG
127 CACATTCACCACATCG
*
38478477 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
38478496 CATATATGTA
Statistics
Matches: 154, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
142 46 0.30
144 12 0.08
145 27 0.18
146 69 0.45
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.29
Consensus pattern (142 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATGCCATTAGGCCTATCACA
TATACATCACTTTCACATTCACACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACA
TTCACCACATCG
Found at i:38481834 original size:29 final size:29
Alignment explanation
Indices: 38481797--38482134 Score: 631
Period size: 29 Copynumber: 11.7 Consensus size: 29
38481787 TGTTGAAAAA
* * *
38481797 CTCGTACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38481826 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38481855 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
38481884 CTCGCACACATGGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
38481913 CTCGCACACATGGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38481942 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38481971 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38482000 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38482029 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38482058 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38482087 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38482116 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
38482135 AATCATTCGC
Statistics
Matches: 304, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 304 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:38484275 original size:37 final size:37
Alignment explanation
Indices: 38484222--38484343 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
38484212 TATAAAAGAA
*
38484222 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38484259 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
38484296 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
38484333 GTCTCACCCGG
1 GTCTTACCCGG
38484344 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:38484500 original size:49 final size:49
Alignment explanation
Indices: 38484445--38484708 Score: 456
Period size: 49 Copynumber: 5.4 Consensus size: 49
38484435 TTTTACATTA
*
38484445 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38484494 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38484543 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38484592 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * * *
38484641 GCCATTAGGCCTCATCACATATACATCCACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
38484690 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38484709 CATATATGTA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 208 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.28
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38488189 original size:39 final size:39
Alignment explanation
Indices: 38488121--38488196 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
38488111 AACAGGTTTG
*
38488121 CATATAGGGTTCACACATAGGGTTCGCATATACGGTTCA
1 CATATAGGGTTCACACATAGAGTTCGCATATACGGTTCA
* * *
38488160 CATATAGGGTTCACATATAGAGTTTGCATATAGGGTT
1 CATATAGGGTTCACACATAGAGTTCGCATATACGGTT
38488197 TGTGTACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (39 bp):
CATATAGGGTTCACACATAGAGTTCGCATATACGGTTCA
Found at i:38488198 original size:13 final size:13
Alignment explanation
Indices: 38488115--38488196 Score: 92
Period size: 13 Copynumber: 6.3 Consensus size: 13
38488105 ATACATAACA
*
38488115 GGTTTGCATATAG
1 GGTTCGCATATAG
* *
38488128 GGTTCACACATAG
1 GGTTCGCATATAG
*
38488141 GGTTCGCATATAC
1 GGTTCGCATATAG
*
38488154 GGTTCACATATAG
1 GGTTCGCATATAG
*
38488167 GGTTCACATATAG
1 GGTTCGCATATAG
* *
38488180 AGTTTGCATATAG
1 GGTTCGCATATAG
38488193 GGTT
1 GGTT
38488197 TGTGTACTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (13 bp):
GGTTCGCATATAG
Found at i:38488367 original size:24 final size:24
Alignment explanation
Indices: 38488339--38488393 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
38488329 TAAAAGAATC
*
38488339 CGCATACCTATGTACAT-AAGTGTT
1 CGCATACATATGTACATAAAGT-TT
* *
38488363 CGCATACATATTTACCTAAAGTTT
1 CGCATACATATGTACATAAAGTTT
38488387 CGCATAC
1 CGCATAC
38488394 TTACTCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (24 bp):
CGCATACATATGTACATAAAGTTT
Found at i:38488410 original size:24 final size:23
Alignment explanation
Indices: 38488352--38488411 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
38488342 ATACCTATGT
* *
38488352 ACATAAGTGTTCGCATACATATTT
1 ACATAAGT-TTCGCATACATACTC
* *
38488376 ACCTAAAGTTTCGCATACTTACTC
1 ACAT-AAGTTTCGCATACATACTC
38488400 ACATAAGGTTTC
1 ACATAA-GTTTC
38488412 AAATGTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.07
24 23 0.79
25 4 0.14
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (23 bp):
ACATAAGTTTCGCATACATACTC
Found at i:38490689 original size:29 final size:29
Alignment explanation
Indices: 38490657--38490720 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
38490647 AACTGCATTC
* *
38490657 ATAT-AATCATATGTATATATATTAGAGCA
1 ATATGAAT-ATATATATATATATTAGAGAA
*
38490686 ATATGAATATATATATATATATTATAGAA
1 ATATGAATATATATATATATATTAGAGAA
38490715 ATATGA
1 ATATGA
38490721 GATTAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (29 bp):
ATATGAATATATATATATATATTAGAGAA
Found at i:38491902 original size:2 final size:2
Alignment explanation
Indices: 38491895--38491924 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38491885 TATAAATCAC
38491895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38491925 GCTATAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38493563 original size:47 final size:47
Alignment explanation
Indices: 38493511--38493633 Score: 156
Period size: 47 Copynumber: 2.6 Consensus size: 47
38493501 AATTCATCTA
* ** *
38493511 CTCGACTAATGGTTTATCCACAACGTATTCTAGTCGGCAGTCATCTG
1 CTCGACTAGTGGTTTATCCACAACGTATTCTAGTCAACAGTCATATG
* * * * *
38493558 TTCGACCAGTGGTTTATCCACAACATATTTTAGTCAACGGTCATATG
1 CTCGACTAGTGGTTTATCCACAACGTATTCTAGTCAACAGTCATATG
*
38493605 CTCGACTAGTGGTTCATCCACAACGTATT
1 CTCGACTAGTGGTTTATCCACAACGTATT
38493634 AGCAGCTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (47 bp):
CTCGACTAGTGGTTTATCCACAACGTATTCTAGTCAACAGTCATATG
Found at i:38497977 original size:19 final size:19
Alignment explanation
Indices: 38497953--38498016 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
38497943 AATAACATTA
38497953 ATACTTAATAACCATTGTG
1 ATACTTAATAACCATTGTG
* * * *
38497972 ATACTTACTTACC-TTATTA
1 ATACTTAATAACCATT-GTG
38497991 ATACTTAATAACCATTGTG
1 ATACTTAATAACCATTGTG
38498010 ATACTTA
1 ATACTTA
38498017 CTTACCTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.06
19 31 0.89
20 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (19 bp):
ATACTTAATAACCATTGTG
Found at i:38497991 original size:38 final size:38
Alignment explanation
Indices: 38497949--38498027 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
38497939 GCACAATAAC
38497949 ATTAATACTTAATAACCATTGTGATACTTACTTACCTT
1 ATTAATACTTAATAACCATTGTGATACTTACTTACCTT
38497987 ATTAATACTTAATAACCATTGTGATACTTACTTACCTT
1 ATTAATACTTAATAACCATTGTGATACTTACTTACCTT
38498025 ATT
1 ATT
38498028 TCTTAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (38 bp):
ATTAATACTTAATAACCATTGTGATACTTACTTACCTT
Found at i:38498073 original size:46 final size:48
Alignment explanation
Indices: 38498020--38498117 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 48
38498010 ATACTTACTT
*
38498020 ACCTTATTTCTTAAT-T-ATAGGATTTCGATCCCCACTCATAAAAATA
1 ACCTTATTTCTTAATATGATAGGACTTCGATCCCCACTCATAAAAATA
38498066 ACCTTATTTCTTAATCATAGGATAGGACTTCGATCCCCACTCATAAAAATA
1 ACCTTATTTCTTAAT-AT--GATAGGACTTCGATCCCCACTCATAAAAATA
38498117 A
1 A
38498118 AATACATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 15 0.33
48 1 0.02
51 30 0.65
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (48 bp):
ACCTTATTTCTTAATATGATAGGACTTCGATCCCCACTCATAAAAATA
Found at i:38500223 original size:20 final size:20
Alignment explanation
Indices: 38500198--38500238 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
38500188 TTACCTTTAG
38500198 GGGAGTAAGCCGCCCAACAT
1 GGGAGTAAGCCGCCCAACAT
*
38500218 GGGAGTAAGCCGCCCACCAT
1 GGGAGTAAGCCGCCCAACAT
38500238 G
1 G
38500239 AATGTGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.32, T:0.10
Consensus pattern (20 bp):
GGGAGTAAGCCGCCCAACAT
Found at i:38503924 original size:2 final size:2
Alignment explanation
Indices: 38503912--38503947 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
38503902 AAATGAATCA
*
38503912 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38503948 TAATTATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38504242 original size:9 final size:9
Alignment explanation
Indices: 38504228--38504254 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38504218 AATTAAACAG
38504228 TTTGAGTTA
1 TTTGAGTTA
38504237 TTTGAGTTA
1 TTTGAGTTA
38504246 TTTGAGTTA
1 TTTGAGTTA
38504255 ATCAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (9 bp):
TTTGAGTTA
Found at i:38504499 original size:14 final size:14
Alignment explanation
Indices: 38504480--38504507 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38504470 AAAGAAAAAA
38504480 TCATTATATTGTTT
1 TCATTATATTGTTT
38504494 TCATTATATTGTTT
1 TCATTATATTGTTT
38504508 ATGTAGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
TCATTATATTGTTT
Found at i:38509145 original size:93 final size:93
Alignment explanation
Indices: 38508986--38509157 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
38508976 AGGATATTTG
* * * *
38508986 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATTGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
38509051 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
38509079 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
38509144 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
38509158 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:38509164 original size:46 final size:46
Alignment explanation
Indices: 38508996--38509165 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
38508986 GGCATTCGAA
* * * *
38508996 CTCGTTGAGTTGAGTCCGAGTTCACTTATTGATGCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
*** * * * *
38509042 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGCATCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC--CCGAG
38509089 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
38509135 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38509166 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
45 2 0.02
46 65 0.64
47 32 0.31
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
Found at i:38509296 original size:21 final size:21
Alignment explanation
Indices: 38509271--38509314 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
38509261 CTACTCAAAT
38509271 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
38509292 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
38509313 GG
1 GG
38509315 GACGTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.36, T:0.14
Consensus pattern (21 bp):
GGAGGAATACTCGAGATGAAA
Found at i:38514505 original size:46 final size:45
Alignment explanation
Indices: 38514452--38514627 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
38514442 TATTTGGGCA
38514452 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
38514498 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
38514545 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
38514591 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38514628 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:38514607 original size:93 final size:93
Alignment explanation
Indices: 38514448--38514619 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
38514438 TAGATATTTG
* *
38514448 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
38514513 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
38514541 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
38514606 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
38514620 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:38517773 original size:49 final size:50
Alignment explanation
Indices: 38517701--38517925 Score: 301
Period size: 49 Copynumber: 4.5 Consensus size: 50
38517691 TGAGGTTACC
*
38517701 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTCGGTCACA
*** * * *
38517750 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAA-TTCGGTCACA
* ** *
38517801 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCGGATGGTTCGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTCGGTCACA
* * *
38517851 TATGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATT-GGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTCGGTCACA
38517900 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
38517926 TGCGTACTAG
Statistics
Matches: 150, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
49 66 0.44
50 47 0.31
51 37 0.25
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTCGGTCACA
Found at i:38522919 original size:5 final size:5
Alignment explanation
Indices: 38522909--38522945 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
38522899 GATGCCAACC
38522909 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
38522946 TTTTTGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:38525929 original size:80 final size:80
Alignment explanation
Indices: 38525791--38526009 Score: 228
Period size: 80 Copynumber: 2.7 Consensus size: 80
38525781 GAATCACGTA
* * * ** * * *
38525791 CCTTC-GGAATTTAACCGGATATAGCGACTCGCTCGATTGTCTTCGGGACATT-GCCCGGTTATA
1 CCTTCGGGAATTGACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGAC-TTAGCCCGGTTATA
* * *
38525854 GTGATTCGCACAATTG
65 GTAACTCGCACAAATG
* * *
38525870 CCTTCGGGAATT-AGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTG
1 CCTTCGGGAATTGA-CCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATA
38525934 GTAACTCGCACAAATG
65 GTAACTCGCACAAATG
* * * *
38525950 CCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGAATTGACCCGGATTTAGTAAC-TCGCACGAATGCCTTCGGGACTTAGCCCGG
38526010 ACACCATTCG
Statistics
Matches: 117, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
79 8 0.07
80 82 0.70
81 27 0.23
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (80 bp):
CCTTCGGGAATTGACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:38526009 original size:41 final size:40
Alignment explanation
Indices: 38525831--38526010 Score: 195
Period size: 40 Copynumber: 4.5 Consensus size: 40
38525821 GCTCGATTGT
* * *
38525831 CTTCGGGACATT-GCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGATT-TAGTAACTCGCACAAATGC
* *
38525871 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
38525911 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
38525951 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
38525992 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
38526011 CACCATTCGA
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 86 0.74
41 28 0.24
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:38533999 original size:80 final size:80
Alignment explanation
Indices: 38533861--38534079 Score: 228
Period size: 80 Copynumber: 2.7 Consensus size: 80
38533851 GAATCACGTA
* * * ** * * *
38533861 CCTTC-GGAATTTAACCGGATATAGCGACTCGCTCGATTGTCTTCGGGACATT-GCCCGGTTATA
1 CCTTCGGGAATTGACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGAC-TTAGCCCGGTTATA
* * *
38533924 GTGATTCGCACAATTG
65 GTAACTCGCACAAATG
* * *
38533940 CCTTCGGGAATT-AGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTG
1 CCTTCGGGAATTGA-CCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATA
38534004 GTAACTCGCACAAATG
65 GTAACTCGCACAAATG
* * * *
38534020 CCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGAATTGACCCGGATTTAGTAAC-TCGCACGAATGCCTTCGGGACTTAGCCCGG
38534080 ACACCATTCG
Statistics
Matches: 117, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
79 8 0.07
80 82 0.70
81 27 0.23
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (80 bp):
CCTTCGGGAATTGACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:38534079 original size:41 final size:40
Alignment explanation
Indices: 38533901--38534080 Score: 195
Period size: 40 Copynumber: 4.5 Consensus size: 40
38533891 GCTCGATTGT
* * *
38533901 CTTCGGGACATT-GCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGATT-TAGTAACTCGCACAAATGC
* *
38533941 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
38533981 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
38534021 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
38534062 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
38534081 CACCATTCGA
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 86 0.74
41 28 0.24
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:38539196 original size:27 final size:27
Alignment explanation
Indices: 38539166--38539220 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
38539156 ACGGTTGGAC
* * * *
38539166 CACATGCCCATGAGACAGGCCGTGTGT
1 CACACGCCCAAGACACACGCCGTGTGT
*
38539193 CACACGGCCAAGACACACGCCGTGTGT
1 CACACGCCCAAGACACACGCCGTGTGT
38539220 C
1 C
38539221 TACCCCTGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.27, T:0.15
Consensus pattern (27 bp):
CACACGCCCAAGACACACGCCGTGTGT
Found at i:38545739 original size:13 final size:14
Alignment explanation
Indices: 38545721--38545766 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
38545711 CTAGTCTCTC
38545721 TTAATTTTTAATT-
1 TTAATTTTTAATTA
*
38545734 TTAA-TTTTATTTA
1 TTAATTTTTAATTA
38545747 TTAATTTTTTAATTAA
1 TTAA-TTTTTAATT-A
38545763 TTAA
1 TTAA
38545767 ATTATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.26
13 8 0.30
15 7 0.26
16 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAATTTTTAATTA
Found at i:38555565 original size:27 final size:28
Alignment explanation
Indices: 38555534--38555635 Score: 156
Period size: 27 Copynumber: 3.8 Consensus size: 28
38555524 TTGCCAGAAT
* *
38555534 AGATA-TTGTGACAGAGTCACCAGATAC
1 AGATATTTGTGGCAGAGCCACCAGATAC
*
38555561 AGATA-TTGTGGCAGAGCCACCAGAAAC
1 AGATATTTGTGGCAGAGCCACCAGATAC
38555588 AGATATTTGTGGCAGAGCCACCAGAT-C
1 AGATATTTGTGGCAGAGCCACCAGATAC
38555615 AGATATTTGTGGCAGAGCCAC
1 AGATATTTGTGGCAGAGCCAC
38555636 TAGAACGCTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 51 0.73
28 19 0.27
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (28 bp):
AGATATTTGTGGCAGAGCCACCAGATAC
Found at i:38555610 original size:55 final size:54
Alignment explanation
Indices: 38555534--38555640 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 54
38555524 TTGCCAGAAT
*
38555534 AGATATTGTGACAGAGTCACCAGATACAGATA-TTGTGGCAGAGCCACCAGAAAC
1 AGATATTGTGACAGAGCCACCAGAT-CAGATATTTGTGGCAGAGCCACCAGAAAC
* *
38555588 AGATATTTGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCACTAGAA
1 AGATA-TTGTGACAGAGCCACCAGATCAGATATTTGTGGCAGAGCCACCAGAA
38555641 CGCTTCCTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
54 11 0.23
55 37 0.77
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (54 bp):
AGATATTGTGACAGAGCCACCAGATCAGATATTTGTGGCAGAGCCACCAGAAAC
Found at i:38556910 original size:25 final size:23
Alignment explanation
Indices: 38556856--38556910 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
38556846 TTTCAGCCAG
38556856 GGAAGAAAAGAAGGAGAAAAGAA
1 GGAAGAAAAGAAGGAGAAAAGAA
* *
38556879 -AATAGAAGAAGAGAGGAGAAGAGAA
1 GGA-AGAA-AAGA-AGGAGAAAAGAA
38556904 GGAAGAA
1 GGAAGAA
38556911 TTCGGCACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
22 1 0.04
23 4 0.16
24 4 0.16
25 15 0.60
26 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (23 bp):
GGAAGAAAAGAAGGAGAAAAGAA
Found at i:38558304 original size:12 final size:12
Alignment explanation
Indices: 38558287--38558311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38558277 ATGTAAGTGA
38558287 TCTTGATGATTT
1 TCTTGATGATTT
38558299 TCTTGATGATTT
1 TCTTGATGATTT
38558311 T
1 T
38558312 TACATTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:38559118 original size:46 final size:45
Alignment explanation
Indices: 38559027--38559387 Score: 323
Period size: 46 Copynumber: 7.8 Consensus size: 45
38559017 GTAATTTGTG
* * * * *
38559027 TGCCAGTGTAAAACTAGGTCTGGGAGATGGCATCGGCATTGAGACGA
1 TGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* *
38559074 GTGCCAGTGTAAGACATGTCCGGGACATGCATCGACCTCGAGACGTA
1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* *
38559121 AGCCAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGAC-A
1 TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGA
* * * * ** *
38559165 TGTCAGTGTAAGACCATTTCTGGGTCATGGCATCGGCATTTAGATGA
1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* **
38559212 GTGCCAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGAGACGTA
1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* *
38559259 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGAC-A
1 TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
* * * *
38559303 TGTCAGTGTAAGACCATGCCTGGGACATGGCATTGGCCTCGATGAGGA
1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-GACGA
* *
38559351 TAGCCAGTGTAAGACCATATTTGGGACATGGCATCGG
1 T-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
38559388 TAACTTAACC
Statistics
Matches: 254, Mismatches: 46, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
44 24 0.09
45 27 0.11
46 119 0.47
47 27 0.11
48 27 0.11
49 30 0.12
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (45 bp):
TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:38559278 original size:138 final size:138
Alignment explanation
Indices: 38559046--38559335 Score: 465
Period size: 138 Copynumber: 2.1 Consensus size: 138
38559036 AAAACTAGGT
* * *
38559046 CTGGGAGATGGCATCGGCATTGAGACGAGTGCCAGTGTAAGACATGTCCGGGACATGCATCGACC
1 CTGGGACATGGCATCGGCATTGAGACGAGTGCCAGTGTAAGACATGTCCAGGACATGCATAGACC
38559111 TCGAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACATGTCAGTGTAA
66 TCGAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACATGTCAGTGTAA
**
38559176 GACCATTT
131 GACCATGC
* * * *
38559184 CTGGGTCATGGCATCGGCATTTAGATGAGTGCCAGTGTAAGACATGTCTAGGACATGCATTAG-C
1 CTGGGACATGGCATCGGCATTGAGACGAGTGCCAGTGTAAGACATGTCCAGGACATGCA-TAGAC
* *
38559248 CTCGAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGACATGTCAGTGTA
65 CTCGAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACATGTCAGTGTA
38559313 AGACCATGC
130 AGACCATGC
38559322 CTGGGACATGGCAT
1 CTGGGACATGGCAT
38559336 TGGCCTCGAT
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 137 0.99
139 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (138 bp):
CTGGGACATGGCATCGGCATTGAGACGAGTGCCAGTGTAAGACATGTCCAGGACATGCATAGACC
TCGAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACATGTCAGTGTAA
GACCATGC
Found at i:38560335 original size:13 final size:13
Alignment explanation
Indices: 38560317--38560342 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38560307 TGGCCATGTG
38560317 AAAGGACACGGGC
1 AAAGGACACGGGC
38560330 AAAGGACACGGGC
1 AAAGGACACGGGC
38560343 GTGTGTCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.38, T:0.00
Consensus pattern (13 bp):
AAAGGACACGGGC
Found at i:38570193 original size:35 final size:35
Alignment explanation
Indices: 38570154--38570224 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
38570144 GTTATGTGAA
38570154 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
1 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
38570189 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
1 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
38570224 T
1 T
38570225 TATAAACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.34, T:0.32
Consensus pattern (35 bp):
TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
Found at i:38571147 original size:2 final size:2
Alignment explanation
Indices: 38571140--38571164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38571130 ATGACATGTG
38571140 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38571165 GACTAGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38577315 original size:18 final size:18
Alignment explanation
Indices: 38577288--38577333 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
38577278 ACCAGTACCT
* *
38577288 GACACAAGTCGCGGCCAC
1 GACACTAGTCGCGCCCAC
* *
38577306 GACATTAGTCGTGCCCAC
1 GACACTAGTCGCGCCCAC
38577324 GACACTAGTC
1 GACACTAGTC
38577334 AAGATAGGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (18 bp):
GACACTAGTCGCGCCCAC
Found at i:38578876 original size:30 final size:30
Alignment explanation
Indices: 38578840--38578900 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
38578830 TAACCAGATG
*
38578840 TTAGAACGTTTAGCTGGAAAGTCTTATTAT
1 TTAGAACGTTTAGCTGGAAAGTCTCATTAT
38578870 TTAGAACGTTTAGCTGGAAAGTCTCATTAT
1 TTAGAACGTTTAGCTGGAAAGTCTCATTAT
38578900 T
1 T
38578901 GTTGTTTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (30 bp):
TTAGAACGTTTAGCTGGAAAGTCTCATTAT
Found at i:38585072 original size:7 final size:7
Alignment explanation
Indices: 38585060--38585096 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
38585050 ATTATTTTGT
38585060 TTTATTA
1 TTTATTA
38585067 TTTATTA
1 TTTATTA
38585074 TTTATTTA
1 TTTA-TTA
38585082 TTT-TTA
1 TTTATTA
38585088 TTT-TTA
1 TTTATTA
38585094 TTT
1 TTT
38585097 TATTTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTATTA
Found at i:38585080 original size:11 final size:11
Alignment explanation
Indices: 38585064--38585106 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
38585054 TTTTGTTTTA
38585064 TTATTTATTAT
1 TTATTTATTAT
38585075 TTATTTATT-T
1 TTATTTATTAT
38585085 TTATTT-TTATT
1 TTATTTATTA-T
38585096 TTATTTTATTA
1 TTA-TTTATTA
38585107 ATTTGGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.25
11 13 0.46
12 3 0.11
13 3 0.11
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:38585103 original size:16 final size:17
Alignment explanation
Indices: 38585060--38585106 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
38585050 ATTATTTTGT
38585060 TTTATTATTTATTATTTA
1 TTTATT-TTTATTATTTA
38585078 TTTATTTTTATT-TTTA
1 TTTATTTTTATTATTTA
38585094 TTT-TATTTTATTA
1 TTTAT-TTTTATTA
38585107 ATTTGGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.04
16 14 0.52
17 6 0.22
18 6 0.22
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTATTTA
Found at i:38593848 original size:18 final size:18
Alignment explanation
Indices: 38593807--38593858 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
38593797 TTCAGCGTAT
* **
38593807 TTGAAATTGAATCTGTTA
1 TTGAATTTGAATCTGAAA
38593825 TCTGAATTTGAATCTGAAA
1 T-TGAATTTGAATCTGAAA
*
38593844 TTGAATTTGTATCTG
1 TTGAATTTGAATCTG
38593859 TATCTGACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
TTGAATTTGAATCTGAAA
Found at i:38596552 original size:29 final size:29
Alignment explanation
Indices: 38596519--38596679 Score: 259
Period size: 29 Copynumber: 5.6 Consensus size: 29
38596509 CCTCCGAACT
** * * *
38596519 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
38596548 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
38596577 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
38596606 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
38596635 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
38596664 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
38596680 ATCTCGTCAC
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 123 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:38596581 original size:87 final size:87
Alignment explanation
Indices: 38596461--38596679 Score: 244
Period size: 87 Copynumber: 2.5 Consensus size: 87
38596451 TACTCGATTT
** * * ** * *
38596461 CGCACACTTAGTGCCACGTAATTT-AAGCTCGCACACACAGTGCCATA-CCCTCCGAACTCGCAC
1 CGCACACTTAGTGCCAAAT-ATTTCCAGCACGCACACTTAGTGCCATATACCTCC-AACACGCAC
* * *
38596524 ACCCAGTGCCGTATTTTTCCAGCT
64 ACCCAGTGCCATATATTTCCAGCA
* ** *
38596548 TGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACAC
1 CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATACCTCCAACACGCACAC
**
38596613 TTAGTGCCATATATTTCCAGCA
66 CCAGTGCCATATATTTCCAGCA
*
38596635 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCA
1 CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCA
38596680 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
86 4 0.04
87 104 0.94
88 3 0.03
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.25
Consensus pattern (87 bp):
CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATACCTCCAACACGCACAC
CCAGTGCCATATATTTCCAGCA
Found at i:38604414 original size:28 final size:28
Alignment explanation
Indices: 38604350--38604449 Score: 130
Period size: 27 Copynumber: 3.5 Consensus size: 28
38604340 CATGAAATTG
* * *
38604350 GCACTAAGTGTGCGGGTTTAAAATTTGTACA
1 GCACTAAGTGTGCGAGTTT--GA-TTGTATA
38604381 GCACTAAGTGTGCGAGTTTGATTGTATA
1 GCACTAAGTGTGCGAGTTTGATTGTATA
*
38604409 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTGTATA
38604436 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38604450 GACTCACTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 24 0.37
28 22 0.34
29 1 0.02
31 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTGTATA
Found at i:38604460 original size:27 final size:27
Alignment explanation
Indices: 38604380--38604461 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
38604370 AAATTTGTAC
* * * *
38604380 AGCACTAAGTGTGCGAGTTTGATTGTAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
38604408 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
38604435 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
38604462 GTTTTGAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 31 0.63
28 17 0.35
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:38612208 original size:31 final size:28
Alignment explanation
Indices: 38612170--38612269 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 28
38612160 CATGAAATTG
*
38612170 GCACTAAGTGTGCGGGTTTAAAATTTGTACA
1 GCACTAAGTGTGCGAGTTT--AA-TTGTACA
* * *
38612201 GCACTAAGTGTGCAAGTTTGATTGTATA
1 GCACTAAGTGTGCGAGTTTAATTGTACA
* * *
38612229 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTGTACA
*
38612256 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
38612270 GACTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.37
28 21 0.34
29 1 0.02
31 17 0.27
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTGTACA
Found at i:38612234 original size:28 final size:27
Alignment explanation
Indices: 38612194--38612268 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
38612184 GGTTTAAAAT
*
38612194 TTGTACAGCACTAAGTGTGCAAGTTTGA
1 TTGTATAGCACTAAGTGTGCAAG-TTGA
*
38612222 TTGTATAGCACTAAGTGTGCGAGTTGA
1 TTGTATAGCACTAAGTGTGCAAGTTGA
* *
38612249 TTATATAACACTAAGTGTGC
1 TTGTATAGCACTAAGTGTGC
38612269 GGACTCACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (27 bp):
TTGTATAGCACTAAGTGTGCAAGTTGA
Found at i:38613989 original size:25 final size:25
Alignment explanation
Indices: 38613961--38614039 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
38613951 CGAATGGCCA
38613961 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * * *
38613986 ATGTGGT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
38614008 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
38614033 ATGTGAT
1 ATGTGAT
38614040 AAGGCCGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 7 0.18
23 9 0.23
24 9 0.23
25 14 0.36
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:38614110 original size:25 final size:25
Alignment explanation
Indices: 38614035--38614110 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
38614025 ATGCATATAT
38614035 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
38614060 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
38614082 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
38614107 GTGA
1 GTGA
38614111 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:38614153 original size:47 final size:47
Alignment explanation
Indices: 38613914--38614146 Score: 367
Period size: 47 Copynumber: 5.0 Consensus size: 47
38613904 TTAGGATTTT
** * *
38613914 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
38613961 ATGTGATGAATGTGAACATGCATATATGTGGTAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
38614008 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38614055 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
38614102 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
38614147 TGATGTGAAA
Statistics
Matches: 172, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 172 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:38614280 original size:98 final size:96
Alignment explanation
Indices: 38614125--38614308 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 96
38614115 GAACATGCAT
* * * *
38614125 ATATGTGGTAAAGCCGAATGGCTGATGTGAAATGTGTATGAGATATGTATATGTGGTAAAGCTGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
38614190 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
38614221 ATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGC
*
38614285 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
38614309 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 26 0.32
97 2 0.03
98 51 0.64
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:38614324 original size:50 final size:48
Alignment explanation
Indices: 38614124--38614308 Score: 282
Period size: 48 Copynumber: 3.8 Consensus size: 48
38614114 TGAACATGCA
* *
38614124 TATATGTGGTAAAGCCGAATGGCTGATGTGAAATGTGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
38614172 TATATGTGGTAAAGCTGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
38614220 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
38614270 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
38614309 GGCGATGTGC
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 77 0.62
49 4 0.03
50 41 0.33
51 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:38614562 original size:37 final size:37
Alignment explanation
Indices: 38614454--38614562 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
38614444 GGAAATATAT
*
38614454 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
38614491 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
38614528 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
38614563 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:38616553 original size:51 final size:51
Alignment explanation
Indices: 38616413--38616633 Score: 185
Period size: 51 Copynumber: 4.4 Consensus size: 51
38616403 CGGATGCCTG
* * * * * ** * *
38616413 GTGGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACAAA
1 GTGGCCTGCACTTAGTACCACACATGTGA-CCAAAGCTATCTGGTACACATA
* * * * **
38616464 GTGGCCTTCACATGGTACCACACTTGTGACCAAAGCTATCTTTTACACATA
1 GTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGGTACACATA
* * *
38616515 GTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGTACACATA
1 GTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGGTACACATA
* * * * ** *
38616566 GTAGCCTACAGTTAGTACTACACATACGACCTAA-CTATCTGGTACACATA
1 GTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGGTACACATA
*
38616616 GTAGCCTGCACTTAGTAC
1 GTGGCCTGCACTTAGTAC
38616634 TACGCACGTG
Statistics
Matches: 141, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 31 0.22
51 109 0.77
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (51 bp):
GTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGGTACACATA
Found at i:38616618 original size:50 final size:51
Alignment explanation
Indices: 38616507--38616636 Score: 172
Period size: 50 Copynumber: 2.6 Consensus size: 51
38616497 AGCTATCTTT
* * ** *
38616507 TACACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATACGACCGAAGCTATCGGG
* * * *
38616558 TACACATAGTAGCCTACAGTTAGTACTACACATACGACCTAA-CTATCTGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATACGACCGAAGCTATCGGG
38616608 TACACATAGTAGCCTGCACTTAGTACTAC
1 TACACATAGTAGCCTGCACTTAGTACTAC
38616637 GCACGTGACC
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 34 0.50
51 34 0.50
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACTTAGTACTACACATACGACCGAAGCTATCGGG
Found at i:38616647 original size:50 final size:51
Alignment explanation
Indices: 38616478--38616649 Score: 193
Period size: 51 Copynumber: 3.4 Consensus size: 51
38616468 CCTTCACATG
* * * ** *
38616478 GTACCACACTTGTGACCAAAGCTATCTTTTACACATAGTGGCCTGCACTTA
1 GTACTACACATGTGACCTAAGCTATCTGGTACACATAGTAGCCTGCACTTA
* * * * * *
38616529 GTACCACACATGTGATCGAAGCTATCGGGTACACATAGTAGCCTACAGTTA
1 GTACTACACATGTGACCTAAGCTATCTGGTACACATAGTAGCCTGCACTTA
**
38616580 GTACTACACATACGACCTAA-CTATCTGGTACACATAGTAGCCTGCACTTA
1 GTACTACACATGTGACCTAAGCTATCTGGTACACATAGTAGCCTGCACTTA
* *
38616630 GTACTACGCACGTGACCTAA
1 GTACTACACATGTGACCTAA
38616650 AACCTTTTTA
Statistics
Matches: 100, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 43 0.43
51 57 0.57
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (51 bp):
GTACTACACATGTGACCTAAGCTATCTGGTACACATAGTAGCCTGCACTTA
Found at i:38618703 original size:79 final size:81
Alignment explanation
Indices: 38618601--38618785 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 81
38618591 GCTACTCATT
* * *
38618601 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCATAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
38618664 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
**
38618681 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
*
38618745 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
38618761 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38618786 CATCATTCGA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.60
80 34 0.37
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:38618785 original size:40 final size:40
Alignment explanation
Indices: 38618601--38618785 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
38618591 GCTACTCATT
* *
38618601 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
38618641 TAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
38618681 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * *
38618720 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
38618761 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38618786 CATCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 80 0.63
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:38629676 original size:14 final size:14
Alignment explanation
Indices: 38629657--38629687 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38629647 TTTGAATTAT
38629657 AATGCCACTAATCC
1 AATGCCACTAATCC
*
38629671 AATGCCGCTAATCC
1 AATGCCACTAATCC
38629685 AAT
1 AAT
38629688 AGTTTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGCCACTAATCC
Found at i:38637200 original size:15 final size:16
Alignment explanation
Indices: 38637182--38637211 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38637172 AAAATAAAAA
38637182 TAACA-AAATTTAAAT
1 TAACACAAATTTAAAT
38637197 TAACACAAATTTAAA
1 TAACACAAATTTAAA
38637212 ATTGAAGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (16 bp):
TAACACAAATTTAAAT
Found at i:38637213 original size:17 final size:16
Alignment explanation
Indices: 38637176--38637214 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
38637166 ATAATAAAAA
*
38637176 TAAAAATAACAAAATT
1 TAAAATTAACAAAATT
38637192 T-AAATTAACACAAATT
1 TAAAATTAACA-AAATT
38637208 TAAAATT
1 TAAAATT
38637215 GAAGTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATTAACAAAATT
Found at i:38640089 original size:23 final size:23
Alignment explanation
Indices: 38640058--38640103 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
38640048 CACCAATTGT
38640058 CATTATTAATATTTTGCACACTA
1 CATTATTAATATTTTGCACACTA
*
38640081 CATTCTTAATATTTTGCACACTA
1 CATTATTAATATTTTGCACACTA
38640104 AGTGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (23 bp):
CATTATTAATATTTTGCACACTA
Found at i:38640195 original size:40 final size:40
Alignment explanation
Indices: 38640115--38640197 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 40
38640105 GTGCCATATA
* *
38640115 CATATATAGCCGAAGCTATCTCCAATCGCACACCAGGTGC
1 CATATATAGCCGAAGCTATCTCCAACCGCACACCAAGTGC
* * * * **
38640155 CATATTTAGCCGAAGCTATTTCGAACCGTACAGTAAGTGC
1 CATATATAGCCGAAGCTATCTCCAACCGCACACCAAGTGC
38640195 CAT
1 CAT
38640198 TTTTTTTAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (40 bp):
CATATATAGCCGAAGCTATCTCCAACCGCACACCAAGTGC
Found at i:38641786 original size:31 final size:31
Alignment explanation
Indices: 38641748--38641811 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
38641738 GTGCTGACTA
38641748 CCTATATTTACAATCAATAATTTATATACTC
1 CCTATATTTACAATCAATAATTTATATACTC
38641779 CCTATATTTACAATCAATAATTTATATACTC
1 CCTATATTTACAATCAATAATTTATATACTC
38641810 CC
1 CC
38641812 CCTCAAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (31 bp):
CCTATATTTACAATCAATAATTTATATACTC
Found at i:38642022 original size:14 final size:14
Alignment explanation
Indices: 38642003--38642029 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38641993 GCTTTGTTCT
38642003 TTCATGAAACATGC
1 TTCATGAAACATGC
38642017 TTCATGAAACATG
1 TTCATGAAACATG
38642030 AGATTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (14 bp):
TTCATGAAACATGC
Found at i:38645190 original size:13 final size:13
Alignment explanation
Indices: 38645172--38645197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38645162 CAGATATAAT
38645172 ATGATTTAGGAAG
1 ATGATTTAGGAAG
38645185 ATGATTTAGGAAG
1 ATGATTTAGGAAG
38645198 GAAAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
ATGATTTAGGAAG
Found at i:38648038 original size:2 final size:2
Alignment explanation
Indices: 38648031--38648073 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38648021 AGTTACTTTT
38648031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38648073 T
1 T
38648074 TTAATTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38649114 original size:16 final size:16
Alignment explanation
Indices: 38649093--38649125 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38649083 TTGACAATGT
38649093 GATAATATCTTTGACG
1 GATAATATCTTTGACG
38649109 GATAATATCTTTGACG
1 GATAATATCTTTGACG
38649125 G
1 G
38649126 CCTCCAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (16 bp):
GATAATATCTTTGACG
Found at i:38650314 original size:26 final size:26
Alignment explanation
Indices: 38650285--38650344 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
38650275 TCCCTTTGAA
* * *
38650285 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
38650311 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
38650339 CCATTC
1 TCATTC
38650345 TTAATGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:38655416 original size:47 final size:48
Alignment explanation
Indices: 38655343--38655571 Score: 219
Period size: 46 Copynumber: 4.9 Consensus size: 48
38655333 GTGGGTAAGG
*
38655343 TGCCGATGCCAT-TCCCAGACACGGTCTTACACTAGCTCAT-ATCTCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCA
*
38655389 TGTCGATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTCA
* * * * *
38655436 TAGCCGATG-CATGTCCCAAACAT-GTCTCACACTAGCTTA-CGTCTTGA
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATC-TCA
* * * * *
38655483 GGCCAATG-CATGTCCCAAACAT-GTCTTACACTAGCAC-TCGTCTCGA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-A
* *
38655529 TGCCGATGCCATGTCCAAGACATGGTCTTAAACTAGCTC-TCAT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCAT
38655572 AATGTGGTTG
Statistics
Matches: 152, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 71 0.47
47 58 0.38
48 22 0.14
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCA
Found at i:38655525 original size:46 final size:45
Alignment explanation
Indices: 38655438--38655612 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 45
38655428 TCATCTCATA
* *
38655438 GCCGATGCATGTCCCAAACATGTCTCACACTAGCTTACGTCTTGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCCT-CGTCTTGAG
* * *
38655484 GCCAATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCGAT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGC-CTCGTCTTGAG
* * ** *
38655530 GCCGATGCCATGT-CCAAGACATGGTCTTAAACTAGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAA-ACAT-GTCTTACACTAGC-CTCGTCTTGAG
** * *
38655578 GTTGATGCATGTCTCAGACATGTCTTACACTAGCC
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCC
38655613 CACAATAACC
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 61 0.58
47 19 0.18
48 24 0.23
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCCTCGTCTTGAG
Found at i:38663113 original size:47 final size:49
Alignment explanation
Indices: 38663044--38663168 Score: 145
Period size: 47 Copynumber: 2.7 Consensus size: 49
38663034 AAAGTGCCGG
* * * *
38663044 TGCCATGTCCCAGACACGGTCTTACGCTAGCTCAT-ATCTCAT-GTCGA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCTCATCATCTCATAATCGA
*
38663091 TGCCATGTCCCAAACATGGTCTTACACT-GAC-CATCATCTCGTAATCGA
1 TGCCATGTCCCAAACATGGTCTTACACTAG-CTCATCATCTCATAATCGA
*
38663139 TG-CATGTCCCAAACAT-GTCTCACACTAGCT
1 TGCCATGTCCCAAACATGGTCTTACACTAGCT
38663169 TACGTCTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
46 14 0.21
47 47 0.70
48 6 0.09
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (49 bp):
TGCCATGTCCCAAACATGGTCTTACACTAGCTCATCATCTCATAATCGA
Found at i:38663221 original size:46 final size:44
Alignment explanation
Indices: 38663138--38663308 Score: 139
Period size: 46 Copynumber: 3.7 Consensus size: 44
38663128 CTCGTAATCG
* * *
38663138 ATGCATGTCCCAAACATGTCTCACACTAGCTTACGTCTTGAGACCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCCT-CGTCTTGAG-CCA
*
38663184 ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGATGCCGA
1 ATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTTGA-GCC-A
* * * * ***
38663231 TAT-CATGTCCAAGACATGGTCTTACACTGGCTCTCATAATGTG-GTTG
1 -ATGCATGTCCCAGACAT-GTCTTACACTAGC-CTCGT-CT-TGAGCCA
38663278 ATGCATGTCCCAGACATGTCTTACACTAGCC
1 ATGCATGTCCCAGACATGTCTTACACTAGCC
38663309 CACAATAACC
Statistics
Matches: 102, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
45 1 0.01
46 51 0.50
47 29 0.28
48 19 0.19
49 1 0.01
50 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCCTCGTCTTGAGCCA
Found at i:38665781 original size:56 final size:55
Alignment explanation
Indices: 38665720--38665826 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 55
38665710 CCATTGGAAG
**
38665720 ATAAATCATCACTTTTAATTTGAATAGTGCTTGTGAATAATTAAATTTGTAAGATT
1 ATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATT-AATTTGTAAGATT
38665776 ATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAA
1 ATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAA
38665827 TCTATAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 9 0.18
56 40 0.82
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.42
Consensus pattern (55 bp):
ATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAAGATT
Found at i:38669697 original size:16 final size:17
Alignment explanation
Indices: 38669662--38669703 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
38669652 GTCTTTTTAT
* *
38669662 TTTTTTTACTTTTTTGA
1 TTTTTTTACTTATTTCA
38669679 TTTTTTT-CTTATTTCA
1 TTTTTTTACTTATTTCA
38669695 TTTTGTTTA
1 TTTT-TTTA
38669704 TTTTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTTACTTATTTCA
Found at i:38669698 original size:24 final size:24
Alignment explanation
Indices: 38669671--38669716 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38669661 TTTTTTTTAC
*
38669671 TTTT-TTGATTTTTTTCTTATTTCA
1 TTTTGTTGATTTTGTT-TTATTTCA
*
38669695 TTTTGTTTATTTTGTTTTATTT
1 TTTTGTTGATTTTGTTTTATTT
38669717 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTGTTGATTTTGTTTTATTTCA
Found at i:38669724 original size:10 final size:9
Alignment explanation
Indices: 38669655--38669725 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
38669645 ATAAATTGTC
38669655 TTTTTATTT
1 TTTTTATTT
*
38669664 TTTTTACTT
1 TTTTTATTT
*
38669673 TTTTGA-TT
1 TTTTTATTT
*
38669681 TTTTT-CTT
1 TTTTTATTT
* *
38669689 ATTTCATTT
1 TTTTTATTT
*
38669698 TGTTTATTT
1 TTTTTATTT
38669707 TGTTTTATTT
1 T-TTTTATTT
38669717 TTTATTATT
1 TTT-TTATT
38669726 AACTTTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 11 0.23
9 24 0.50
10 13 0.27
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (9 bp):
TTTTTATTT
Found at i:38669780 original size:23 final size:22
Alignment explanation
Indices: 38669715--38669808 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
38669705 TTTGTTTTAT
* **
38669715 TTTTTATTATTAACTTTAAAAA
1 TTTTTATAATTATTTTTAAAAA
* * *
38669737 -ATTTGTAATGTATATTT-AAAA
1 TTTTTATAAT-TATTTTTAAAAA
38669758 TGTTTTATAA-TATTTTTTAAAAA
1 T-TTTTATAATTA-TTTTTAAAAA
* *
38669781 TTTTAATTATTATTTTTAAAAA
1 TTTTTATAATTATTTTTAAAAA
38669803 TATTTT
1 T-TTTT
38669809 TTTAACTTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
21 12 0.22
22 26 0.48
23 16 0.30
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTTTATAATTATTTTTAAAAA
Found at i:38669890 original size:36 final size:36
Alignment explanation
Indices: 38669833--38669908 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
38669823 TATATTTGTG
* * *
38669833 AAATTAATTTTTTATATATTTTAAAAATGTATTTTTT
1 AAATTAATTTTTGATAAATTTTAAAAAT-TAATTTTT
*
38669870 AAATTAATTTTTGA-AAATTTTAAATATTAATTTTT
1 AAATTAATTTTTGATAAATTTTAAAAATTAATTTTT
38669905 AAAT
1 AAAT
38669909 ATTAACCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 11 0.31
36 11 0.31
37 13 0.37
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
AAATTAATTTTTGATAAATTTTAAAAATTAATTTTT
Found at i:38669904 original size:14 final size:14
Alignment explanation
Indices: 38669887--38669913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38669877 TTTTTGAAAA
38669887 TTTTAAATATTAAT
1 TTTTAAATATTAAT
38669901 TTTTAAATATTAA
1 TTTTAAATATTAA
38669914 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:38669913 original size:37 final size:37
Alignment explanation
Indices: 38669833--38669913 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
38669823 TATATTTGTG
* * *
38669833 AAATTAATTTTTTATATATTTTAAAAATGTATTTTTT
1 AAATTAATTTTTGATAAATTTTAAAAATGTATTTTTA
*
38669870 AAATTAATTTTTGA-AAATTTTAAATAT-TAATTTTTA
1 AAATTAATTTTTGATAAATTTTAAAAATGT-ATTTTTA
38669906 AATATTAA
1 AA-ATTAA
38669914 CCATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 19 0.50
37 18 0.47
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (37 bp):
AAATTAATTTTTGATAAATTTTAAAAATGTATTTTTA
Found at i:38669920 original size:23 final size:22
Alignment explanation
Indices: 38669872--38669913 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
38669862 TATTTTTTAA
*
38669872 ATTAATTTTTGAAAATTTTAAAT
1 ATTAATTTTT-AAAATATTAAAT
38669895 ATTAATTTTT-AAATATTAA
1 ATTAATTTTTAAAATATTAA
38669914 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAATTTTTAAAATATTAAAT
Found at i:38669990 original size:21 final size:21
Alignment explanation
Indices: 38669965--38670012 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
38669955 TTGTAAATAC
38669965 AATTTCTTTAA-TTTCTTTTTA
1 AATTT-TTTAACTTTCTTTTTA
*
38669986 AATTTTTTAACTTT-TTTTTT
1 AATTTTTTAACTTTCTTTTTA
38670006 AATTTTT
1 AATTTTT
38670013 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTTTTAACTTTCTTTTTA
Found at i:38670152 original size:17 final size:17
Alignment explanation
Indices: 38670097--38670157 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 17
38670087 CACCCTTATT
*
38670097 ATTTTTTTACTTTTTT-
1 ATTTTTTTTCTTTTTTA
38670113 ATTTAATTTTGTCTTTTTCTTA
1 ATTT--TTTT-TC-TTTT-TTA
38670135 ATTTTTTTTCTTTTTTA
1 ATTTTTTTTCTTTTTTA
38670152 AGTTTT
1 A-TTTT
38670158 ACATTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 12 0.32
19 3 0.08
20 8 0.22
21 2 0.05
22 4 0.11
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (17 bp):
ATTTTTTTTCTTTTTTA
Found at i:38670287 original size:34 final size:33
Alignment explanation
Indices: 38670244--38670341 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 33
38670234 ATGTTTTACA
38670244 ATTTTTTTAAATTTTAAT-TATTATTATTAAAATT
1 ATTTTTTTAAATTTTAATATA-TATT-TTAAAATT
* *
38670278 ATTTTTTT-AACTTTAGATATATATTTGTGAAATT
1 ATTTTTTTAAATTTTA-ATATATATTT-TAAAATT
38670312 ATGTTTTTATAAATTTTAAATATATATTTT
1 AT-TTTTT-TAAATTTT-AATATATATTTT
38670342 TCAAATTAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
33 7 0.13
34 22 0.41
35 7 0.13
36 2 0.04
37 15 0.28
38 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (33 bp):
ATTTTTTTAAATTTTAATATATATTTTAAAATT
Found at i:38670348 original size:37 final size:36
Alignment explanation
Indices: 38670246--38670354 Score: 118
Period size: 37 Copynumber: 3.1 Consensus size: 36
38670236 GTTTTACAAT
* *
38670246 TTTTTTAAATTTTAATTAT-TATTATTAAAATTAT-
1 TTTTTTAAATTTTAAATATATATTTTTAAAATTATG
* * * *
38670280 TTTTTT-AACTTTAGATATATATTTGTGAAATTATG
1 TTTTTTAAATTTTAAATATATATTTTTAAAATTATG
*
38670315 TTTTTATAAATTTTAAATATATATTTTTCAAATTA-G
1 TTTTT-TAAATTTTAAATATATATTTTTAAAATTATG
38670351 TTTT
1 TTTT
38670355 GAAATTATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
33 9 0.15
34 18 0.30
35 5 0.08
36 6 0.10
37 23 0.38
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (36 bp):
TTTTTTAAATTTTAAATATATATTTTTAAAATTATG
Found at i:38670447 original size:18 final size:19
Alignment explanation
Indices: 38670426--38670464 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
38670416 AAATTTTAAA
38670426 TTATG-TTTAAAATTTACT
1 TTATGTTTTAAAATTTACT
38670444 TTATGTTTTTAAAATTTACT
1 TTATG-TTTTAAAATTTACT
38670464 T
1 T
38670465 CAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATGTTTTAAAATTTACT
Done.