Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 182 of 202
Found at i:56199242 original size:50 final size:50
Alignment explanation
Indices: 56199083--56199294 Score: 180
Period size: 50 Copynumber: 4.3 Consensus size: 50
56199073 GCAGCGGAGC
* *
56199083 AGATTGAAGCTATAACGGCGAATCTCACTTCCCTGACATTGCAATTT-AA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAATTTAAA
* * * * **** **
56199132 AGATTGAAGCCACAACGGTGAATCTTAC-TCCCAGGCGA-TGCAGCGGAGC
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAATTTAAA
* *
56199181 AGATTGAAGCTACAACGGCAAATCTCACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAATTTAAA
* * * * * ** *
56199231 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTCAC-TTCCCAGACATTGCAATTTAAA
56199281 AGATTGAAGCTACA
1 AGATTGAAGCTACA
56199295 GCAACGGATC
Statistics
Matches: 124, Mismatches: 34, Indels: 9
0.74 0.20 0.05
Matches are distributed among these distances:
48 10 0.08
49 50 0.40
50 59 0.48
51 5 0.04
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAATTTAAA
Found at i:56199330 original size:45 final size:45
Alignment explanation
Indices: 56199219--56199681 Score: 413
Period size: 45 Copynumber: 9.8 Consensus size: 45
56199209 TTCCCCGACA
* * *
56199219 TTGCAATTTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGC-TTCC---C
** * * *
56199268 ATTGCAGTGGAACAGATTGAAGCTACAGCAACGGATCTTGCTTCCC
1 -TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
** *
56199314 GGGCAGTTAAAAAGATTGAAGCTACAACAGGGGATCTTGCTTCCC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
** *
56199359 CGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGC--TTC---CC
* * *
56199409 TTGCAGTGAAACAGATTGAAGCTACAACAACGGATCTTGCTTCCC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
* * * ** *
56199454 TTGCAATTAAAAATATTGAAGCTACAACAGCGTATCTTATTTTCCTAGTG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTT-GCTTCC----C
* ** * *
56199504 TTGCAGTGAAACGGATTGAAGTTACAGCAGCGGATCTTGCTTCCC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
* * *
56199549 TTGCAATTAAAAATATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGC-TTCC---C
* * * * *
56199598 GTTGCAGTGAAACAGATTGAAGCTACAGCAGCGGATCTTACTTTCC
1 -TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
*
56199644 TAGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTT
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTT
56199682 ACTTTCCTAG
Statistics
Matches: 336, Mismatches: 62, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
45 174 0.52
46 10 0.03
47 3 0.01
48 3 0.01
49 12 0.04
50 134 0.40
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (45 bp):
TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
Found at i:56199415 original size:95 final size:95
Alignment explanation
Indices: 56199231--56199725 Score: 604
Period size: 95 Copynumber: 5.2 Consensus size: 95
56199221 GCAATTTAAA
* * ** * *
56199231 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTACAG
1 AGATTGAAGCTACAACAGCGGATCTTGC-TTCC---C-TTGCAATTAAAAAGATTGAAGCTACAA
* * * * *
56199296 CAACGGATCTTGC-TTCC---CG-GGCAGTTAAAA
61 CAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
* ** *
56199326 AGATTGAAGCTACAACAGGGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCTTGCAATTAAAAAGATTGAAGCTACAACAGCG
* *
56199391 GATCTTACTTTTCTAGCCTTGCAGTGAAAC
66 GATCTTACTTTCCTAGCGTTGCAGTGAAAC
* *
56199421 AGATTGAAGCTACAACAACGGATCTTGCTTCCCTTGCAATTAAAAATATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCTTGCAATTAAAAAGATTGAAGCTACAACAGCG
* * *
56199486 TATCTTATTTTCCTAGTGTTGCAGTGAAAC
66 GATCTTACTTTCCTAGCGTTGCAGTGAAAC
* * * *
56199516 GGATTGAAGTTACAGCAGCGGATCTTGCTTCCCTTGCAATTAAAAATATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCTTGCAATTAAAAAGATTGAAGCTACAACAGCG
56199581 GATCTTACTTTCCTAGCGTTGCAGTGAAAC
66 GATCTTACTTTCCTAGCGTTGCAGTGAAAC
* * * * *
56199611 AGATTGAAGCTACAGCAGCGGATCTTACTTTCCTAGCAGTTAAAAAGATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCTTGCAATTAAAAAGATTGAAGCTACAACAGCG
* * *
56199676 GATCTTACTTTCCTAGTGTTGCAGTGGAAT
66 GATCTTACTTTCCTAGCGTTGCAGTGAAAC
56199706 AGATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCG
56199726 ATTGAAGCTA
Statistics
Matches: 351, Mismatches: 44, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
90 32 0.09
91 4 0.01
94 5 0.01
95 310 0.88
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (95 bp):
AGATTGAAGCTACAACAGCGGATCTTGCTTCCCTTGCAATTAAAAAGATTGAAGCTACAACAGCG
GATCTTACTTTCCTAGCGTTGCAGTGAAAC
Found at i:56199440 original size:140 final size:140
Alignment explanation
Indices: 56199228--56199722 Score: 550
Period size: 140 Copynumber: 3.5 Consensus size: 140
56199218 ATTGCAATTT
* *
56199228 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCTTGCAGTGAAACAGATTGAAGCTA
* * * *
56199293 CAGCAACGGATCTTGCTTCCCGGGCAGTTAAAAAGATTGAAGCTACAACAGGGGATCTTGCTTCC
66 CAACAACGGATCTTGCTTCCCGTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCC
*
56199358 CCGGCAGTTA
131 CTGGCAGTTA
*
56199368 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCCTTGCAGTGAAACAGATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCTTGCAGTGAAACAGATTGAAGCTA
* * * * *
56199433 CAACAACGGATCTTGCTTCCCTTGCAATTAAAAATATTGAAGCTACAACAGCGTATCTTATTTTC
66 CAACAACGGATCTTGCTTCCCGTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTA-CTTC
* *
56199498 CTAGTGTTGCAGTGA
130 C--CTG--GCAGTTA
** * * * * * * *
56199513 AACGGATTGAAGTTACAGCAGCGGATCTTGC-TT-C---CCTTGCAATTAAAAATATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCTTGCAGTGAAACAGATTGAAGCTA
* * * * *
56199573 CAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAGCGGATCTTA
66 CAACAACGGATCTTGC-TTCC---CG-TGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTA
* *
56199638 CTTTCCTAGCAGTTA
126 CTTCCCTGGCAGTTA
** * *
56199653 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAATAGATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCTTGCAGTGAAACAGATTGAAGCTA
56199718 CAACA
66 CAACA
56199723 GCGATTGAAG
Statistics
Matches: 290, Mismatches: 50, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
140 182 0.63
141 10 0.03
142 2 0.01
143 2 0.01
144 6 0.02
145 88 0.30
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (140 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCTTGCAGTGAAACAGATTGAAGCTA
CAACAACGGATCTTGCTTCCCGTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCC
CTGGCAGTTA
Found at i:56199445 original size:190 final size:189
Alignment explanation
Indices: 56199231--56199893 Score: 664
Period size: 190 Copynumber: 3.4 Consensus size: 189
56199221 GCAATTTAAA
* * *
56199231 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTACAG
1 AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCATTGCA-T--AAAAGATTGAAGCTACAA
* * *
56199296 CAACGGATCTTGCTTCC-CG-GGCAGTTAAAAAGATTGAAGCTACAACAGGGGATCTTGCTTCCC
63 CAGCGGATCTTACTTCCTCGTGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCC
* *
56199359 CGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCCTTGCAGTGAAAC
128 CGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
* * * *
56199421 AGATTGAAGCTACAACAACGGATCTTGCTTCCCTTGCAATT--A-AAAATATTGAAGCTACAACA
1 AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGC-ATTGCATAAAAGATTGAAGCTACAACA
* * * * ** * *
56199483 GCGTATCTTATTTTCCTAGTGTTGCAGTGAAACGGATTGAAGTTACAGCAGCGGATCTTGCTTCC
65 GCGGATCTTA-CTTCCTCGTG--GCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCC
** * *
56199548 CTTGCAATTAAAAATATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
127 CCGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
* *
56199611 AGATTGAAGCTACAGCAGCGGATCTTACTTTCCTAGCAGTT--A-AAAAGATTGAAGCTACAACA
1 AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCA-TTGCATAAAAGATTGAAGCTACAACA
*
56199673 GCGGATCTTACTTTCCTAGTGTTGCAGTGGAATAGATTGAAGCTACAACAGCGATTGAAGCTACA
65 GCGGATCTTAC-TTCC------T-C-GTGG--CAG-TT--A---A-AA-A--GATTGAAGCTACA
* *
56199738 ACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGTATTTTACTTTCCT
109 ACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT
56199803 AGCGTTGCAGTGAAAC
174 AGCGTTGCAGTGAAAC
* * * * * *
56199819 AGATTGAAGCTACAGCAACGGATCTTGCTTCCCTGGCAGTT--A-AAAAGTTTGAAGCTGCAACA
1 AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCA-TTGCATAAAAGATTGAAGCTACAACA
56199881 GCGGATCTTACTT
65 GCGGATCTTACTT
56199894 TCCTAGCATT
Statistics
Matches: 394, Mismatches: 51, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
185 24 0.06
186 4 0.01
187 1 0.00
188 1 0.00
189 2 0.01
190 193 0.49
191 3 0.01
196 2 0.01
198 5 0.01
199 1 0.00
201 1 0.00
204 1 0.00
205 1 0.00
207 2 0.01
208 153 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (189 bp):
AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCATTGCATAAAAGATTGAAGCTACAACAG
CGGATCTTACTTCCTCGTGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGG
CAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
Found at i:56199730 original size:18 final size:18
Alignment explanation
Indices: 56199707--56199743 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56199697 CAGTGGAATA
56199707 GATTGAAGCTACAACAGC
1 GATTGAAGCTACAACAGC
56199725 GATTGAAGCTACAACAGC
1 GATTGAAGCTACAACAGC
56199743 G
1 G
56199744 GATCTTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (18 bp):
GATTGAAGCTACAACAGC
Found at i:56199764 original size:113 final size:113
Alignment explanation
Indices: 56199612--56199832 Score: 352
Period size: 113 Copynumber: 2.0 Consensus size: 113
56199602 CAGTGAAACA
* * *
56199612 GATTGAAGCTACAGCAGCGGATCTTACTTTCCTAGCAGTTAAAAAGATTGAAGCTACAACAGCGG
1 GATTGAAGCTACAACAGCGGATCTTACTTCCCCAGCAGTTAAAAAGATTGAAGCTACAACAGCGG
* * *
56199677 ATCTTACTTTCCTAGTGTTGCAGTGGAATAGATTGAAGCTACAACAGC
66 ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAACAGC
* * *
56199725 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGT
1 GATTGAAGCTACAACAGCGGATCTTACTTCCCCAGCAGTTAAAAAGATTGAAGCTACAACAGCGG
*
56199790 ATTTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACA
66 ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACA
56199833 GCAACGGATC
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
113 98 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (113 bp):
GATTGAAGCTACAACAGCGGATCTTACTTCCCCAGCAGTTAAAAAGATTGAAGCTACAACAGCGG
ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAACAGC
Found at i:56199832 original size:50 final size:49
Alignment explanation
Indices: 56199725--56199909 Score: 170
Period size: 45 Copynumber: 3.9 Consensus size: 49
56199715 CTACAACAGC
* ** *
56199725 GATTGAAGCTACAACAGCGGATCTTGC-TTCC---CCGGCAGTTAAAAA
1 GATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCTTGCAGTGAAAAA
* * *
56199770 GATTGAAGCTACAACAGCGTATTTTACTTTCCTAGCGTTGCAGTGAAACA
1 GATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-TTGCAGTGAAAAA
* * * * *
56199820 GATTGAAGCTACAGCAACGGATCTTGC-TTCC---CTGGCAGTTAAAAA
1 GATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCTTGCAGTGAAAAA
* *
56199865 GTTTGAAGCTGCAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
1 GATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-TTGCAGTG
56199910 GAATAGAATA
Statistics
Matches: 108, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
45 56 0.52
46 9 0.08
49 6 0.06
50 37 0.34
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (49 bp):
GATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCTTGCAGTGAAAAA
Found at i:56199871 original size:45 final size:45
Alignment explanation
Indices: 56199725--56199889 Score: 186
Period size: 45 Copynumber: 3.6 Consensus size: 45
56199715 CTACAACAGC
*
56199725 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAA
1 GATTGAAGCTACAACAGCGGATCTTGCTTCCCTGGCAGTTAAAAA
* * * * * *
56199770 GATTGAAGCTACAACAGCGTATTTTACTTTCCTAGCGTTGCAGTGAAACA
1 GATTGAAGCTACAACAGCGGATCTTGC-TTCC---C-TGGCAGTTAAAAA
* *
56199820 GATTGAAGCTACAGCAACGGATCTTGCTTCCCTGGCAGTTAAAAA
1 GATTGAAGCTACAACAGCGGATCTTGCTTCCCTGGCAGTTAAAAA
* *
56199865 GTTTGAAGCTGCAACAGCGGATCTT
1 GATTGAAGCTACAACAGCGGATCTT
56199890 ACTTTCCTAG
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 55 0.57
46 5 0.05
49 5 0.05
50 31 0.32
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (45 bp):
GATTGAAGCTACAACAGCGGATCTTGCTTCCCTGGCAGTTAAAAA
Found at i:56199882 original size:208 final size:208
Alignment explanation
Indices: 56199517--56199916 Score: 656
Period size: 208 Copynumber: 1.9 Consensus size: 208
56199507 CAGTGAAACG
* * ** *
56199517 GATTGAAGTTACAGCAGCGGATCTTGCTTCCCTTGCAATTAAAAATATTGAAGCTACAACAGCGG
1 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAATTAAAAAGATTGAAGCTACAACAGCGG
* *
56199582 ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAGCGGATCTTACTTTCCTAG
66 ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAACGGATCTTACTTCCCTAG
**
56199647 CAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAATAGATTG
131 CAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAGATTG
56199712 AAGCTACAACAGC
196 AAGCTACAACAGC
* *
56199725 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGT
1 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAATTAAAAAGATTGAAGCTACAACAGCGG
* * *
56199790 ATTTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAACGGATCTTGCTTCCCTGG
66 ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAACGGATCTTACTTCCCTAG
* *
56199855 CAGTTAAAAAGTTTGAAGCTGCAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAGA
131 CAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAGA
56199917 ATAAAACCAT
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
208 176 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (208 bp):
GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAATTAAAAAGATTGAAGCTACAACAGCGG
ATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTACAGCAACGGATCTTACTTCCCTAG
CAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAGATTG
AAGCTACAACAGC
Found at i:56199892 original size:95 final size:95
Alignment explanation
Indices: 56199725--56199909 Score: 298
Period size: 95 Copynumber: 1.9 Consensus size: 95
56199715 CTACAACAGC
* *
56199725 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGT
1 GATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGG
* *
56199790 ATTTTACTTTCCTAGCGTTGCAGTGAAACA
66 ATCTTACTTTCCTAGCATTGCAGTGAAACA
* * * *
56199820 GATTGAAGCTACAGCAACGGATCTTGCTTCCCTGGCAGTTAAAAAGTTTGAAGCTGCAACAGCGG
1 GATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGG
56199885 ATCTTACTTTCCTAGCATTGCAGTG
66 ATCTTACTTTCCTAGCATTGCAGTG
56199910 GAATAGAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (95 bp):
GATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGG
ATCTTACTTTCCTAGCATTGCAGTGAAACA
Found at i:56201386 original size:3 final size:3
Alignment explanation
Indices: 56201378--56201456 Score: 92
Period size: 3 Copynumber: 26.3 Consensus size: 3
56201368 TAATATTTTG
56201378 TTA TTA TTA TTA TCT- TTA TTA TTA TTA TTA TCT- TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* *
56201423 TTA TTA -TA TTTA TTA ATA TTA TTG TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
56201457 GTTTTTATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.06
3 58 0.88
4 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:56201401 original size:18 final size:17
Alignment explanation
Indices: 56201371--56201456 Score: 109
Period size: 18 Copynumber: 4.8 Consensus size: 17
56201361 GTAATTCTAA
*
56201371 TATTTTGTTATTATTAT
1 TATTTTATTATTATTAT
56201388 TATCTTTATTATTATTAT
1 TAT-TTTATTATTATTAT
56201406 TATCTTTATTATTATTAT
1 TAT-TTTATTATTATTAT
* *
56201424 TATTATATTTATTAATAT
1 TATTTTA-TTATTATTAT
56201442 TATTGTTATTATTAT
1 TATT-TTATTATTAT
56201457 GTTTTTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.10
18 53 0.87
19 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTTTATTATTATTAT
Found at i:56201628 original size:21 final size:21
Alignment explanation
Indices: 56201604--56201643 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56201594 CTATATATAT
* *
56201604 ATATATATTTTATATATTAAA
1 ATATATATATCATATATTAAA
*
56201625 ATATGTATATCATATATTA
1 ATATATATATCATATATTA
56201644 TTTTATGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATATATATCATATATTAAA
Found at i:56210779 original size:15 final size:15
Alignment explanation
Indices: 56210728--56210780 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
56210718 TAAAATATAT
56210728 ATTTATATTATTTTTA
1 ATTTATA-TATTTTTA
*
56210744 ATTTA-ATATTTAATA
1 ATTTATATATTT-TTA
*
56210759 ACTTTATATATTTTTT
1 A-TTTATATATTTTTA
56210775 ATTTAT
1 ATTTAT
56210781 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 11 0.35
17 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATATTTTTA
Found at i:56218328 original size:21 final size:22
Alignment explanation
Indices: 56218292--56218333 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
56218282 CTCCAAAACA
*
56218292 AGGGAAAATGAGTTA-CATTTT
1 AGGGAAAATGACTTACCATTTT
*
56218313 AGGGAAAATGTCTTACCATTT
1 AGGGAAAATGACTTACCATTT
56218334 CAATTTCCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (22 bp):
AGGGAAAATGACTTACCATTTT
Found at i:56218878 original size:33 final size:30
Alignment explanation
Indices: 56218841--56218900 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
56218831 CTAATTCAAA
56218841 TACAATCAATAAAAGTATAAGAACTTATTTGGG
1 TACAA-CAA-AAAA-TATAAGAACTTATTTGGG
* *
56218874 TACAACAAAAAATATAGGGACTTATTT
1 TACAACAAAAAATATAAGAACTTATTT
56218901 AATGAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.52
31 4 0.16
32 3 0.12
33 5 0.20
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (30 bp):
TACAACAAAAAATATAAGAACTTATTTGGG
Found at i:56219851 original size:26 final size:24
Alignment explanation
Indices: 56219817--56219865 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
56219807 AAAATTTTGT
*
56219817 TTAAATTAACTCATATTTATAAATAA
1 TTAAATTAAATC-TATTT-TAAATAA
*
56219843 TTAATTTAAATCTATTTTAAATA
1 TTAAATTAAATCTATTTTAAATA
56219866 TGCTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 5 0.24
26 10 0.48
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAATTAAATCTATTTTAAATAA
Found at i:56242222 original size:49 final size:49
Alignment explanation
Indices: 56242167--56242265 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
56242157 GTTCTTTGCA
56242167 TCAGGAAACTCAGAAATGGAAGTGTTATGCATACATTCAACTTTGAAGC
1 TCAGGAAACTCAGAAATGGAAGTGTTATGCATACATTCAACTTTGAAGC
56242216 TCAGGAAACTCAGAAATGGAAGTGTTATGCATACATTCAACTTTGAAGC
1 TCAGGAAACTCAGAAATGGAAGTGTTATGCATACATTCAACTTTGAAGC
56242265 T
1 T
56242266 TTCTCTTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (49 bp):
TCAGGAAACTCAGAAATGGAAGTGTTATGCATACATTCAACTTTGAAGC
Found at i:56245661 original size:6 final size:6
Alignment explanation
Indices: 56245652--56245686 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
56245642 GAGATGATGA
*
56245652 GATTGG GATTGG GATTGG CATTGG GATT-G GATTGG
1 GATTGG GATTGG GATTGG GATTGG GATTGG GATTGG
56245687 AGGGTTGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.17, C:0.03, G:0.46, T:0.34
Consensus pattern (6 bp):
GATTGG
Found at i:56262063 original size:5 final size:5
Alignment explanation
Indices: 56262053--56262088 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
56262043 AAACAAACAA
*
56262053 AAAAT AAAAT AAAAT AAAAT AGAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
56262089 GCAACGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:56262728 original size:48 final size:48
Alignment explanation
Indices: 56262659--56263028 Score: 278
Period size: 48 Copynumber: 7.6 Consensus size: 48
56262649 ATCGGGGAAA
*
56262659 TGAGATTCGCTGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
* * *** * **
56262707 TAAGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTGCAATGTCTGGGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAG
*
56262757 TGAGATTCGCTGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
* * *** * **
56262805 TAAGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTGCAATGTCTGGGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAG
* * * *
56262855 TGAGATTTGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
* * *** * **
56262903 TAAGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTGCAATGTCGGGGAAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAG
* * * ** * *
56262953 TGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCACTAGTAG
1 TGAGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
* * *
56263001 TGAGATTCGCCGCTGTGGCTTCGATCTT
1 TGAGATTCGCCGTTGTAGCTTCAATCTT
56263029 TTAAATTGCA
Statistics
Matches: 240, Mismatches: 70, Indels: 24
0.72 0.21 0.07
Matches are distributed among these distances:
47 5 0.02
48 125 0.52
49 6 0.03
50 100 0.42
51 4 0.02
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (48 bp):
TGAGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAG
Found at i:56262734 original size:98 final size:98
Alignment explanation
Indices: 56262618--56263063 Score: 703
Period size: 98 Copynumber: 4.6 Consensus size: 98
56262608 GTAAAATCTA
* * *
56262618 CCGTTGTGGCTTCGATCTTTTAAATTGCAATATCGGGGAAATGAGATTCGCTGTTGTAGCTTCAA
1 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
* * *
56262683 TCTTCTTCGCTGCATTGCCAGAAGTAAGATTCG
66 TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
*
56262716 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
1 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
* * *
56262781 TCTTCTTCGCTGCATTGCCAGAAGTAAGATTCG
66 TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
* * *
56262814 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGAAGTGAGATTTGCCGTTGTAGCTTCAA
1 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
56262879 TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
66 TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
56262912 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
1 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
* * * *
56262977 TCTGCTCCGCTGCATCACTAGTAGTGAGATTCG
66 TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
* * * *
56263010 CCGCTGTGGCTTCGATCTTTTAAATTGCAGTGTCGGGGAAGTGAGATCCGCTGT
1 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGT
56263064 CAGTGCAGGA
Statistics
Matches: 328, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 328 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (98 bp):
CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAA
TCTGCTCCGCTGCATCGCCAGAAGTAAGATTCG
Found at i:56278729 original size:13 final size:13
Alignment explanation
Indices: 56278711--56278774 Score: 101
Period size: 13 Copynumber: 4.9 Consensus size: 13
56278701 ACACTCAAAT
*
56278711 TTCTCAAAAGTAC
1 TTCTCAAAAGCAC
56278724 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
56278737 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
56278750 TTCTCAAAAGCAT
1 TTCTCAAAAGCAC
56278763 TTCTCAAAAGCA
1 TTCTCAAAAGCA
56278775 ATGAAGAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:56282570 original size:23 final size:24
Alignment explanation
Indices: 56282521--56282573 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
56282511 TGAAAGGTTC
56282521 AAAGTCAAATTGAACTATTTTTAA
1 AAAGTCAAATTGAACTATTTTTAA
56282545 AAAGTCAAATTGAACTATTTTTAA
1 AAAGTCAAATTGAACTATTTTTAA
56282569 AAAGT
1 AAAGT
56282574 TGAGAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (24 bp):
AAAGTCAAATTGAACTATTTTTAA
Found at i:56289585 original size:6 final size:6
Alignment explanation
Indices: 56289576--56289605 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
56289566 GAGATGATGA
56289576 GATTGG GATTGG GATTGG GATTGG GATTGG
1 GATTGG GATTGG GATTGG GATTGG GATTGG
56289606 AGGGTTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
GATTGG
Found at i:56290534 original size:8 final size:8
Alignment explanation
Indices: 56290523--56290567 Score: 90
Period size: 8 Copynumber: 5.6 Consensus size: 8
56290513 ATTAATTAAA
56290523 TTTTATTT
1 TTTTATTT
56290531 TTTTATTT
1 TTTTATTT
56290539 TTTTATTT
1 TTTTATTT
56290547 TTTTATTT
1 TTTTATTT
56290555 TTTTATTT
1 TTTTATTT
56290563 TTTTA
1 TTTTA
56290568 AAAGGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:56295764 original size:42 final size:42
Alignment explanation
Indices: 56295644--56295755 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
56295634 ATCGATGTCG
*
56295644 ATGCCATGTCCAAGACATGGTCTTACACGAGATCACACGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACGCCA
* *
56295686 ATGCCATGTCCCAAACATAGTCTTACACGAGATCACACGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACGCCA
* *
56295728 ATGTCATGTCCCAGTCATGGTCTTACAC
1 ATGCCATGTCCCAGACATGGTCTTACAC
56295756 TGGCTCACAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACGCCA
Found at i:56296412 original size:27 final size:26
Alignment explanation
Indices: 56296382--56296432 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
56296372 ATGTATTTTC
*
56296382 TATCATCAATTATCAAAATACACAATT
1 TATCAACAA-TATCAAAATACACAATT
* *
56296409 TATCAACAATGTCAAAATTCACAA
1 TATCAACAATATCAAAATACACAA
56296433 ACTTTAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (26 bp):
TATCAACAATATCAAAATACACAATT
Found at i:56298425 original size:25 final size:26
Alignment explanation
Indices: 56298372--56298426 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
56298362 AGATATATGA
56298372 CTCTTTGTGAGCTTCCTGATTAAAGG
1 CTCTTTGTGAGCTTCCTGATTAAAGG
*
56298398 CTCTTTGTGAGCTTCCTG-TTAATGG
1 CTCTTTGTGAGCTTCCTGATTAAAGG
56298423 CTCT
1 CTCT
56298427 CTGGTGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCTGATTAAAGG
Found at i:56298486 original size:25 final size:25
Alignment explanation
Indices: 56298354--56298486 Score: 76
Period size: 26 Copynumber: 5.3 Consensus size: 25
56298344 CAGCTCTTAT
* * * *
56298354 GAGCGTCCAGATATATGACTCTTTG
1 GAGCTTCCTGATATATGGCTCTCTG
* *
56298379 TGAGCTTCCTGAT-TAAAGGCTCTTTG
1 -GAGCTTCCTGATAT-ATGGCTCTCTG
*
56298405 TGAGCTTCCTGTTA-ATGGCTCTCTG
1 -GAGCTTCCTGATATATGGCTCTCTG
* * * *
56298430 GTGCTTCCTAATAT-TAGCT-TGCTT
1 GAGCTTCCTGATATATGGCTCT-CTG
** *
56298454 GAATTTCCTGATATATGGCTATCTG
1 GAGCTTCCTGATATATGGCTCTCTG
56298479 GAGCTTCC
1 GAGCTTCC
56298487 CGATTAATGG
Statistics
Matches: 81, Mismatches: 20, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
23 1 0.01
24 26 0.32
25 22 0.27
26 32 0.40
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (25 bp):
GAGCTTCCTGATATATGGCTCTCTG
Found at i:56304607 original size:15 final size:15
Alignment explanation
Indices: 56304587--56304619 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
56304577 ATAACATAAG
*
56304587 AGAAGAAAAAGAAGA
1 AGAAGAAAAAGAAAA
56304602 AGAAGAAAAAGAAAA
1 AGAAGAAAAAGAAAA
56304617 AGA
1 AGA
56304620 GATTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAGAAAA
Found at i:56311948 original size:15 final size:16
Alignment explanation
Indices: 56311928--56311966 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
56311918 AGAAAAAATC
*
56311928 ATTTTAT-AATATCAG
1 ATTTTATAAATATCAA
56311943 ATTTTATAAAATATCAA
1 ATTTTAT-AAATATCAA
56311960 ATTTTAT
1 ATTTTAT
56311967 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (16 bp):
ATTTTATAAATATCAA
Found at i:56312027 original size:18 final size:18
Alignment explanation
Indices: 56311974--56312030 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
56311964 TATGTATTTT
56311974 AAATTTAATAATA-ATATAA
1 AAATTTAA-AATATATA-AA
* * *
56311993 AAATATGATAATTTATAAA
1 AAAT-TTAAAATATATAAA
56312012 AAATTTAAAATATATAAA
1 AAATTTAAAATATATAAA
56312030 A
1 A
56312031 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 12 0.40
19 13 0.43
20 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAATTTAAAATATATAAA
Found at i:56312038 original size:18 final size:18
Alignment explanation
Indices: 56311973--56312039 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
56311963 TTATGTATTT
*
56311973 TAAATTTAATAATAATATA
1 TAAAATTAATAA-AATATA
* **
56311992 -AAAATATGATAATTTATA
1 TAAAAT-TAATAAAATATA
*
56312010 AAAAATT--TAAAATATA
1 TAAAATTAATAAAATATA
56312026 TAAAATTAATAAAA
1 TAAAATTAATAAAA
56312040 AAAAGTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
16 13 0.35
18 14 0.38
19 10 0.27
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
TAAAATTAATAAAATATA
Found at i:56312282 original size:22 final size:22
Alignment explanation
Indices: 56312222--56312278 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
56312212 TTGCCCACTC
**
56312222 ATATTATTTTTAAAATATATATTT
1 ATATTA-TTTTAATTTA-ATATTT
56312246 ATATTATTTTAATTTAATATTT
1 ATATTATTTTAATTTAATATTT
56312268 A-A-TATTTTAAT
1 ATATTATTTTAAT
56312279 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 1 0.03
22 7 0.23
23 8 0.26
24 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATTTTAATTTAATATTT
Found at i:56312288 original size:15 final size:15
Alignment explanation
Indices: 56312246--56312289 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56312236 ATATATATTT
*
56312246 ATATTATTTTAATTTA
1 ATATT-TTTTATTTTA
**
56312262 ATATTTAATATTTTA
1 ATATTTTTTATTTTA
56312277 ATATTTTTTATTT
1 ATATTTTTTATTT
56312290 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:56312299 original size:17 final size:17
Alignment explanation
Indices: 56312274--56312307 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56312264 ATTTAATATT
* *
56312274 TTAATATTTTTTATTTA
1 TTAAAATTTTATATTTA
56312291 TTAAAATTTTATATTTA
1 TTAAAATTTTATATTTA
56312308 GTTTTCTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAAAATTTTATATTTA
Found at i:56312906 original size:20 final size:19
Alignment explanation
Indices: 56312869--56312909 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
56312859 CCTATATGTT
* *
56312869 AAAAATTTATATATTTTTA
1 AAAAATTTAAATACTTTTA
56312888 AAAAATGTTAAATACTTTTA
1 AAAAAT-TTAAATACTTTTA
56312908 AA
1 AA
56312910 TATTTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAAATTTAAATACTTTTA
Found at i:56313593 original size:16 final size:16
Alignment explanation
Indices: 56313572--56313609 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
56313562 ACATAATGTA
56313572 TAATAATTATTAAAAT
1 TAATAATTATTAAAAT
56313588 TAATAATTATTAAAAT
1 TAATAATTATTAAAAT
*
56313604 TTATAA
1 TAATAA
56313610 AATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATAATTATTAAAAT
Found at i:56314114 original size:5 final size:5
Alignment explanation
Indices: 56314100--56314131 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
56314090 ATATATAAAC
56314100 TATT- TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
56314132 AGTAGGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:56316574 original size:43 final size:43
Alignment explanation
Indices: 56316512--56316758 Score: 372
Period size: 43 Copynumber: 5.8 Consensus size: 43
56316502 GTGTGGCTAA
* * *
56316512 CTTTAGCGGCGCTTGTCCCACAAACGCCGCTATAGACCGAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * *
56316555 CTTTAGTGGCGCTTATCCCACAAACGCCG--AAAGACCGAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
56316596 CTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * *
56316639 CTTTAGCGGCACTTCTCCCACAAACGCCGCTAAAGACCAAGAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
56316682 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
*
56316725 CTTTAGCGGCGCTTTTGCCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
56316759 AACATGATTT
Statistics
Matches: 185, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 36 0.19
43 149 0.81
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:56321473 original size:41 final size:41
Alignment explanation
Indices: 56321361--56321521 Score: 191
Period size: 41 Copynumber: 4.0 Consensus size: 41
56321351 AAATAAATTT
* *
56321361 TTAGCGGCGC-TTTCTCGAAAACGCCGCTAAAGACTCCAACA
1 TTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGACCCCAACA
* ** ** *
56321402 TTCGTTGCAATTTT-CAAAAACACCGCTAAAGACCCCAACA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAACA
*
56321442 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCATCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAACA
* * *
56321483 TTAGCGGCGCTTTTTCAAAAACGCCGCTACAGCCCCCAA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAA
56321522 AGGTAAGAAA
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 32 0.32
41 64 0.65
42 3 0.03
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAACA
Found at i:56321650 original size:41 final size:40
Alignment explanation
Indices: 56321552--56321657 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
56321542 TGGGCTTTGG
* * * * * *
56321552 TTTTTTGTGGCGTTTTTCCTAAAAAACGTCGCTAATGCTCA
1 TTTTTAGTGGCGTTTTT-TTGAAAAACGCCGCGAAGGCTCA
* *
56321593 TTTTTAGCGGCATTTTTTTGAAAAACGCCGCGAAGGCTCA
1 TTTTTAGTGGCGTTTTTTTGAAAAACGCCGCGAAGGCTCA
56321633 TTTTTAGTGGCG-TTTTTTGAAAAAC
1 TTTTTAGTGGCGTTTTTTTGAAAAAC
56321658 ACTGCTAATG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 13 0.24
40 28 0.51
41 14 0.25
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (40 bp):
TTTTTAGTGGCGTTTTTTTGAAAAACGCCGCGAAGGCTCA
Found at i:56321679 original size:15 final size:16
Alignment explanation
Indices: 56321650--56321682 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56321640 TGGCGTTTTT
*
56321650 TGAAAAACACTGCTAA
1 TGAAAAACACCGCTAA
56321666 TGAAAAAC-CCGCTAA
1 TGAAAAACACCGCTAA
56321681 TG
1 TG
56321683 CTCGATCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.18
Consensus pattern (16 bp):
TGAAAAACACCGCTAA
Found at i:56331547 original size:44 final size:44
Alignment explanation
Indices: 56331499--56331613 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
56331489 TTCGATCTGC
* *
56331499 TCCACTACTACT-TAGGGAGATAAGA-TCTCTAATCTTCAACCTAT
1 TCCACTACT-CTCCAGGGAGATAAGACT-TATAATCTTCAACCTAT
* *
56331543 TCCACTACTGTCCAGGGAGATAGGACTTATAATCTTCAACCTAT
1 TCCACTACTCTCCAGGGAGATAAGACTTATAATCTTCAACCTAT
* * * *
56331587 TCCACTGCTATCCAGGAAGATAGGACT
1 TCCACTACTCTCCAGGGAGATAAGACT
56331614 GGTATCTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.02
44 60 0.97
45 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
TCCACTACTCTCCAGGGAGATAAGACTTATAATCTTCAACCTAT
Found at i:56331763 original size:87 final size:87
Alignment explanation
Indices: 56331656--56331956 Score: 383
Period size: 87 Copynumber: 3.4 Consensus size: 87
56331646 GAATGCAAGG
* *
56331656 TCTGTTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGACCTGCTCC
1 TCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
56331721 AGTACTACTTAGGGAGATAAGA
66 AGTACTACTTAGGGAGATAAGA
* * * *
56331743 TCTGTAATTTTCAACCTACTCCACTGCAGCTCAGGGAGACAAGGTTGGGGTCTTCGATCTACTTC
1 TCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGC-TC
* * * * *
56331808 GCTGCCAATAC--AGGAAGACAAGA
65 -CAG-TACTACTTAGGGAGATAAGA
* * *
56331831 TCTGCT-ATTTTCAACCTACTCCACTGCTGCTCAAGGAGACAAAGCTGGGGACTTCAATCTGCTC
1 TCTG-TAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTC
* * *
56331895 CACTACTGCTTTGGGAGATAAGA
65 CAGTACTACTTAGGGAGATAAGA
*
56331918 TATGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 TCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
56331957 TAGGATTCAT
Statistics
Matches: 179, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
85 3 0.02
86 2 0.01
87 102 0.57
88 65 0.36
89 3 0.02
90 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (87 bp):
TCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
AGTACTACTTAGGGAGATAAGA
Found at i:56331779 original size:44 final size:44
Alignment explanation
Indices: 56331651--56332034 Score: 183
Period size: 44 Copynumber: 8.8 Consensus size: 44
56331641 TACAGGAATG
* *
56331651 CAAGGTCTGTTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 CAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* ** * * * * * * *
56331695 CAAG-GCTGGGGA-CTTCGACCTGCTCCAGTACTACTTAGGGAGA
1 CAAGATCT-GTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* *
56331738 TAAGATCTGTAATTTTCAACCTACTCCACTGCAGCTCAGGGAGA
1 CAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* *** * * * * * *** *
56331782 CAAGGT-TGGGGTCTTCGATCTACTTCGCTGCCAATACAGGAAGA
1 CAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT-CAGGGAGA
*
56331826 CAAGATCTGCT-ATTTTCAACCTACTCCACTGCTGCTCAAGGAGA
1 CAAGATCTG-TAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* ** * * * * **
56331870 CAA-AGCTGGGGA-CTTCAATCTGCTCCACTACTGCTTTGGGAGA
1 CAAGATCT-GTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* *
56331913 TAAGATATGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 CAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* * * * ** *
56331957 TAGGAT-TCATAATCTTCAGTCTATTCCACTGCTG-TCCAGGGAGA
1 CAAGATCT-GTAATTTTCAACCTACTCCACTGCTGCT-CAGGGAGA
* * ** *
56332001 TAGGA-CTCACAATTTTCAACCTATTCCACTGCTG
1 CAAGATCT-GTAATTTTCAACCTACTCCACTGCTG
56332035 TCCATGGAGA
Statistics
Matches: 248, Mismatches: 79, Indels: 26
0.70 0.22 0.07
Matches are distributed among these distances:
43 82 0.33
44 148 0.60
45 18 0.07
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
Found at i:56331800 original size:175 final size:175
Alignment explanation
Indices: 56331618--56331956 Score: 527
Period size: 175 Copynumber: 1.9 Consensus size: 175
56331608 AGGACTGGTA
* * * * *
56331618 TCTTCGATCTGCTTCGCCGTCAGTACAGGAATG-CAAGGTCTGTTATTTTCAACCTACTCCACTG
1 TCTTCGATCTACTTCGCCGCCAATACAGGAA-GACAAGATCTGCTATTTTCAACCTACTCCACTG
* * * * *
56331682 CTGCTCAGGGAGACAAGGCTGGGGACTTCGACCTGCTCCAGTACTACTTAGGGAGATAAGATCTG
65 CTGCTCAAGGAGACAAAGCTGGGGACTTCAACCTGCTCCACTACTACTTAGGGAGATAAGATATG
56331747 TAATTTTCAACCTACTCCACTGCAGCTCAGGGAGACAAGGTTGGGG
130 TAATTTTCAACCTACTCCACTGCAGCTCAGGGAGACAAGGTTGGGG
*
56331793 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCCGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* * *
56331858 TGCTCAAGGAGACAAAGCTGGGGACTTCAATCTGCTCCACTACTGCTTTGGGAGATAAGATATGT
66 TGCTCAAGGAGACAAAGCTGGGGACTTCAACCTGCTCCACTACTACTTAGGGAGATAAGATATGT
*
56331923 AATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
131 AATTTTCAACCTACTCCACTGCAGCTCAGGGAGA
56331957 TAGGATTCAT
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
174 1 0.01
175 147 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (175 bp):
TCTTCGATCTACTTCGCCGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAAGGAGACAAAGCTGGGGACTTCAACCTGCTCCACTACTACTTAGGGAGATAAGATATGT
AATTTTCAACCTACTCCACTGCAGCTCAGGGAGACAAGGTTGGGG
Found at i:56331856 original size:88 final size:86
Alignment explanation
Indices: 56331619--56331956 Score: 328
Period size: 87 Copynumber: 3.9 Consensus size: 86
56331609 GGACTGGTAT
* * *
56331619 CTTCGATCTGCTTCGCCGTCAGTACAGGAATG-CAAGGTCTGTTATTTTCAACCTACTCCACTGC
1 CTTCGATCTGCTTCGCAG-CAATACAGGAA-GACAAGATCTG-TATTTTCAACCTACTCCACTGC
56331683 TGCTCAGGGAGACAAGGCTGGGGA
63 TGCTCAGGGAGACAAGGCTGGGGA
* * * * *
56331707 CTTCGACCTGC-TC-CAGTACTACTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGC
1 CTTCGATCTGCTTCGCAGCAATAC--AGGAAGACAAGATCTGT-ATTTTCAACCTACTCCACTGC
* * *
56331770 AGCTCAGGGAGACAAGGTTGGGGT
63 TGCTCAGGGAGACAAGGCTGGGGA
* *
56331794 CTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCT
1 CTTCGATCTGCTTCGCAG-CAATACAGGAAGACAAGATCTG-TATTTTCAACCTACTCCACTGCT
* *
56331859 GCTCAAGGAGACAAAGCTGGGGA
64 GCTCAGGGAGACAAGGCTGGGGA
* * * * * * *
56331882 CTTCAATCTGC-TC-CA-CTACTGCTTTGGGAGATAAGATATGTAATTTTCAACCTACTCCACTG
1 CTTCGATCTGCTTCGCAGC-AATAC--AGGAAGACAAGATCTGT-ATTTTCAACCTACTCCACTG
56331944 CTGCTCAGGGAGA
62 CTGCTCAGGGAGA
56331957 TAGGATTCAT
Statistics
Matches: 206, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
84 1 0.00
85 7 0.03
86 6 0.03
87 110 0.53
88 75 0.36
89 3 0.01
90 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (86 bp):
CTTCGATCTGCTTCGCAGCAATACAGGAAGACAAGATCTGTATTTTCAACCTACTCCACTGCTGC
TCAGGGAGACAAGGCTGGGGA
Found at i:56332035 original size:44 final size:44
Alignment explanation
Indices: 56331927--56332183 Score: 347
Period size: 44 Copynumber: 5.8 Consensus size: 44
56331917 ATATGTAATT
* *
56331927 TTCAACCTACTCCACTGCTG-CTCAGGGAGATAGGATTCATAATC
1 TTCAACCTATTCCACTGCTGTC-CAGGGAGATAGGATTCACAATC
** * *
56331971 TTCAGTCTATTCCACTGCTGTCCAGGGAGATAGGACTCACAATT
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
*
56332015 TTCAACCTATTCCACTGCTGTCCATGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
* *
56332059 TT-AGACCTATTCCATTGCTGTCCAAGGAGATAGGATTCACAATC
1 TTCA-ACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
*
56332103 TTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
* * * **
56332147 TTCAACCTATTTCACTACTGTCTAAAGAGATAGGATT
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT
56332184 TATAACTTCA
Statistics
Matches: 189, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
43 1 0.01
44 186 0.98
45 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
Found at i:56334563 original size:3 final size:3
Alignment explanation
Indices: 56334557--56334614 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
56334547 TAATGTACAT
56334557 ATA ATA ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56334602 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
56334615 ACCAATTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56342109 original size:16 final size:16
Alignment explanation
Indices: 56342085--56342137 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
56342075 TGGTCTACTA
*
56342085 TAATAGAATAGGGCTG
1 TAATTGAATAGGGCTG
* * *
56342101 TAATTGAATAAGGTTC
1 TAATTGAATAGGGCTG
* *
56342117 TAATGGAATAGAGCTG
1 TAATTGAATAGGGCTG
56342133 TAATT
1 TAATT
56342138 AGTAATTCAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (16 bp):
TAATTGAATAGGGCTG
Found at i:56342350 original size:21 final size:21
Alignment explanation
Indices: 56342326--56342403 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
56342316 TTATTATTAA
56342326 AAATAATTTAATAAAAATAAT
1 AAATAATTTAATAAAAATAAT
* * **
56342347 AAATAATTTAAGCATATTTAA-
1 AAATAATTTAA-TAAAAATAAT
*
56342368 ACATAATTTAAT-AAAATAAT
1 AAATAATTTAATAAAAATAAT
*
56342388 ATATAATTTAATAAAA
1 AAATAATTTAATAAAA
56342404 TTCTTAATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.09
20 11 0.25
21 24 0.55
22 5 0.11
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAATTTAATAAAAATAAT
Found at i:56342417 original size:42 final size:42
Alignment explanation
Indices: 56342322--56342405 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
56342312 AAGATTATTA
* * *
56342322 TTAAAAATAATTTAATAAAAATAATAAATAATTTAAGCATAT
1 TTAAACATAATTTAATAAAAATAATAAATAATTTAAGAAAAT
* *
56342364 TTAAACATAATTTAAT-AAAATAATATATAATTTAATAAAAT
1 TTAAACATAATTTAATAAAAATAATAAATAATTTAAGAAAAT
56342405 T
1 T
56342406 CTTAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.59
42 15 0.41
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (42 bp):
TTAAACATAATTTAATAAAAATAATAAATAATTTAAGAAAAT
Found at i:56342898 original size:105 final size:103
Alignment explanation
Indices: 56342807--56343329 Score: 536
Period size: 108 Copynumber: 4.9 Consensus size: 103
56342797 AAAATTATTT
* * * * ****
56342807 TTTGGGTGCTGGCCAGTCCATGGCCGGCACCTAGTACAATTTTAAATTTTTTTTTCTTTTTTTTG
1 TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTT-TTTTTTTTG
56342872 TGTCAGAGTCAGATATCAGTATACGAAAAAAATAAAAAAA
65 TGTCAGAGTCAGATATCAGTATACGAAAAAAA-AAAAAAA
* * * * *
56342912 ATTGGGTGTTGGCCTGTTAATGGCCGACACCCAGTACAA-TTTAAAAAAAATTCTTTTTTTTTGT
1 TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTTTTTTTTTTGT
*
56342976 GTTAGAGTCAGATATCAGTATACGAAAAAAATAGAAAAAAAAA
66 GTCAGAGTCAGATATCAGTATACG---AAAA-A-AAAAAAAAA
* * * *
56343019 TTTGGATGTTGGTCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTTGT
1 TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTTTTTTTTTTGT
*
56343084 CTCAGAGTCAGATATCAGTATACGAAAAAAATAAAAATAAAAA
66 GTCAGAGTCAGATATCAGTATACG---AAAA-AAAAA-AAAAA
* * *
56343127 TTTTTTGGGTGTTGGCCTTTCAATGGCCGGCACCCAATACAATTTTTTTAAAAAAAATTCTTTTT
1 ---TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAA---TTTT-AAAAAAATTTTTTTT
* * *
56343192 TTTATGT-T-AGAATCAAATATCAGTATACGAAAAAAATAAAAAAA
59 TTTTTGTGTCAGAGTCAGATATCAGTATACGAAAAAAA-AAAAAAA
* * * * * *
56343236 TTTGGGTGCTGGCCTGTCAATTGCCGGCACCCAGTACAA-TTTAAAAAAA-ATTCTTTTTTTGGG
1 TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTTTTTTTTTTGT
*
56343299 GTCAGAATCAGATATCAGTATAC-AAAAAAAA
66 GTCAGAGTCAGATATCAGTATACGAAAAAAAA
56343330 TTTGGGTGCC
Statistics
Matches: 357, Mismatches: 44, Indels: 39
0.81 0.10 0.09
Matches are distributed among these distances:
100 9 0.03
101 15 0.04
102 22 0.06
103 33 0.09
104 9 0.03
105 32 0.09
106 39 0.11
107 46 0.13
108 59 0.17
109 8 0.02
110 6 0.02
111 35 0.10
113 19 0.05
114 4 0.01
115 21 0.06
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (103 bp):
TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTTTTTTTTTTGT
GTCAGAGTCAGATATCAGTATACGAAAAAAAAAAAAAA
Found at i:56343072 original size:107 final size:103
Alignment explanation
Indices: 56342860--56343330 Score: 622
Period size: 106 Copynumber: 4.4 Consensus size: 103
56342850 AAATTTTTTT
*
56342860 TTCTTTTTTTTGTGTCAGAGTCAGATATCAGTATACGAAAAAAATAAAAAAAA-TTGGGTGTTGG
1 TTCTTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAATAAAAAAAATTTGGGTGTTGG
* *
56342924 CCTGTTAATGGCCGACACCCAGTACAATTTAAAAAAAA
66 CCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
*
56342962 TTCTTTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAATAGAAAAAAAAATTTGGATG
1 TTC-TTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAAT---AAAAAAAATTTGGGTG
*
56343027 TTGGTCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
62 TTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
*
56343069 TTCTTTTTTTTTTGTCTCAGAGTCAGATATCAGTATACGAAAAAAATAAAAATAAAAATTTTTTG
1 TTCTTTTTTTTGTGT-T-AGAGTCAGATATCAGTATACGAAAAAAAT--AAA-AAAAA---TTTG
* *
56343134 GGTGTTGGCCTTTCAATGGCCGGCACCCAATACAATTTTTTTAAAAAAAA
58 GGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAA----TTTAAAAAAAA
* * * *
56343184 TTCTTTTTTTTATGTTAGAATCAAATATCAGTATACGAAAAAAAT-AAAAAAATTTGGGTGCTGG
1 TTCTTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAATAAAAAAAATTTGGGTGTTGG
*
56343248 CCTGTCAATTGCCGGCACCCAGTACAATTTAAAAAAAA
66 CCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
* * * * *
56343286 TTCTTTTTTTGGGGTCAGAATCAGATATCAGTATACAAAAAAAAT
1 TTCTTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAAT
56343331 TTGGGTGCCG
Statistics
Matches: 330, Mismatches: 24, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
102 53 0.16
103 41 0.12
106 54 0.16
107 53 0.16
108 34 0.10
109 5 0.02
110 2 0.01
111 35 0.11
113 27 0.08
114 1 0.00
115 25 0.08
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (103 bp):
TTCTTTTTTTTGTGTTAGAGTCAGATATCAGTATACGAAAAAAATAAAAAAAATTTGGGTGTTGG
CCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
Found at i:56343390 original size:77 final size:75
Alignment explanation
Indices: 56343267--56343407 Score: 219
Period size: 77 Copynumber: 1.9 Consensus size: 75
56343257 TGCCGGCACC
*
56343267 CAGTACAATTTAAAAAAAATTCTTTTTTTGGGGTCAGAATCAGATATCAGTATACAAAAAAAATT
1 CAGTACAAATTAAAAAAAATTCTTTTTTTGGGGTCAGAATCAGATATCAGTATACAAAAAAAATT
56343332 TGGGTGCCGG
66 TGGGTGCCGG
* * * *
56343342 CAGTACAAATTAAAAAAATTTCTTTTTTTTTTGTGTCAGAATCAGATATCAGTATACGAAAAAAA
1 CAGTACAAATTAAAAAAAATTC--TTTTTTTGGGGTCAGAATCAGATATCAGTATACAAAAAAAA
56343407 T
64 T
56343408 AAATTGTACT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 20 0.34
77 39 0.66
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (75 bp):
CAGTACAAATTAAAAAAAATTCTTTTTTTGGGGTCAGAATCAGATATCAGTATACAAAAAAAATT
TGGGTGCCGG
Found at i:56345369 original size:26 final size:27
Alignment explanation
Indices: 56345322--56345376 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
56345312 GAGAATATCT
*
56345322 GAAATATGGTAAGAGAGTTTGAGGGCA
1 GAAATATGGTAAGAGAGTTTGACGGCA
56345349 GAAATTAT-GTAA-AGAGTTTGACGGCA
1 GAAA-TATGGTAAGAGAGTTTGACGGCA
56345375 GA
1 GA
56345377 TGAAAGACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.58
27 8 0.31
28 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.24
Consensus pattern (27 bp):
GAAATATGGTAAGAGAGTTTGACGGCA
Found at i:56345673 original size:31 final size:31
Alignment explanation
Indices: 56345620--56345705 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
56345610 TTTATAAATT
* ***
56345620 GTGAATTATTTAAAAAAATTTATTTAAGTCA
1 GTGAATTATTTTAAAGTTTTTATTTAAGTCA
*
56345651 GTGAATTATTTTAAAGTTTTTATTTGAGTCA
1 GTGAATTATTTTAAAGTTTTTATTTAAGTCA
*
56345682 -TTAAGTTATTTTAAAGTTTTTATT
1 GTGAA-TTATTTTAAAGTTTTTATT
56345706 GGAGTCATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 3 0.06
31 45 0.94
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (31 bp):
GTGAATTATTTTAAAGTTTTTATTTAAGTCA
Found at i:56345711 original size:31 final size:31
Alignment explanation
Indices: 56345656--56345719 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
56345646 AGTCAGTGAA
*
56345656 TTATTTTAAAGTTTTTATTTGAGTCATTAAG
1 TTATTTTAAAGTTTTTATTGGAGTCATTAAG
*
56345687 TTATTTTAAAGTTTTTATTGGAGTCATTGAG
1 TTATTTTAAAGTTTTTATTGGAGTCATTAAG
56345718 TT
1 TT
56345720 GTTGAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.55
Consensus pattern (31 bp):
TTATTTTAAAGTTTTTATTGGAGTCATTAAG
Found at i:56346722 original size:21 final size:21
Alignment explanation
Indices: 56346696--56346753 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
56346686 ACCTCCATAA
* *
56346696 AAAATAAAAAAAATATATATT
1 AAAATAAAAAAAATATACATG
*
56346717 AAAATAATAAAAATA-ACATG
1 AAAATAAAAAAAATATACATG
**
56346737 CCAATAAAAAAAATATA
1 AAAATAAAAAAAATATA
56346754 ACAAAAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAATAAAAAAAATATACATG
Found at i:56347334 original size:27 final size:27
Alignment explanation
Indices: 56347296--56347347 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
56347286 AATGCTAGGT
* *
56347296 GTGCCGCCTATCAGGTAGGCACCACCA
1 GTGCCGCCTATCAGATAAGCACCACCA
*
56347323 GTGCCGCGTATCAGATAAGCACCAC
1 GTGCCGCCTATCAGATAAGCACCAC
56347348 ACCCCCGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (27 bp):
GTGCCGCCTATCAGATAAGCACCACCA
Found at i:56347716 original size:45 final size:44
Alignment explanation
Indices: 56347638--56347732 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 44
56347628 AAGAAAATTA
56347638 AAATAATTTAATCTCGATAAATTTAAATGTAAGTAAATAAAGAC
1 AAATAATTTAATCTCGATAAATTTAAATGTAAGTAAATAAAGAC
*
56347682 AAATAATTTAATCT-GAAATAAATTTAAATTTAAGTAAATAAAGAC
1 AAATAATTTAATCTCG--ATAAATTTAAATGTAAGTAAATAAAGAC
56347727 AAATAA
1 AAATAA
56347733 ATAACGACAG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 14 0.29
45 33 0.69
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (44 bp):
AAATAATTTAATCTCGATAAATTTAAATGTAAGTAAATAAAGAC
Found at i:56348497 original size:48 final size:48
Alignment explanation
Indices: 56348442--56348588 Score: 130
Period size: 48 Copynumber: 3.2 Consensus size: 48
56348432 TGTTTGTATT
56348442 TTTTTATATCTATAAATTTAATGTAGTTGTTTAGAATCTAAGGTTTCA
1 TTTTTATATCTATAAATTTAATGTAGTTGTTTAGAATCTAAGGTTTCA
*** * * * **
56348490 TTTTTATAT-T-TTCGTGT-AT-TAATT-TCTTAGAATGT-TTGTATT--
1 TTTTTATATCTATAAATTTAATGTAGTTGT-TTAGAATCTAAGGT-TTCA
* *
56348532 TTTTTATATCTATAAATTTAATGTAGTTGTTTAGGATTTAAGGTTTCA
1 TTTTTATATCTATAAATTTAATGTAGTTGTTTAGAATCTAAGGTTTCA
56348580 TTTTTATAT
1 TTTTTATAT
56348589 TTTCGTGTAT
Statistics
Matches: 72, Mismatches: 17, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
42 9 0.12
43 4 0.06
44 17 0.24
45 4 0.06
46 16 0.22
47 4 0.06
48 18 0.25
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (48 bp):
TTTTTATATCTATAAATTTAATGTAGTTGTTTAGAATCTAAGGTTTCA
Found at i:56348574 original size:90 final size:91
Alignment explanation
Indices: 56348415--56348643 Score: 392
Period size: 90 Copynumber: 2.5 Consensus size: 91
56348405 CAAAATAATA
56348415 GTATT-ATTTCTTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATGTAGTTGTTTAGAAT
1 GTATTAATTTCTTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATGTAGTTGTTTAGAAT
56348479 CTAAGGTTTCATTTTTATATTTTCGT
66 CTAAGGTTTCATTTTTATATTTTCGT
*
56348505 GTATTAATTTC-TTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATGTAGTTGTTTAGGAT
1 GTATTAATTTCTTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATGTAGTTGTTTAGAAT
*
56348569 TTAAGGTTTCATTTTTATATTTTCGT
66 CTAAGGTTTCATTTTTATATTTTCGT
* * *
56348595 GTATTAATTTCTTTA-AATGTTTGTATTTTTTTGTATTTGTAAATTTAAT
1 GTATTAATTTCTTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAAT
56348644 TTAATTCGTA
Statistics
Matches: 132, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
90 124 0.94
91 8 0.06
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (91 bp):
GTATTAATTTCTTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATGTAGTTGTTTAGAAT
CTAAGGTTTCATTTTTATATTTTCGT
Found at i:56348812 original size:87 final size:87
Alignment explanation
Indices: 56348611--56348819 Score: 210
Period size: 87 Copynumber: 2.4 Consensus size: 87
56348601 ATTTCTTTAA
* * *
56348611 ATGTTTGTATTTTTTTGTATTTGTAAATTTAATTTAATTCGTATTATATGTAGTTTGAATTTAAA
1 ATGTTTGTATTTTATTGTGTTTGTAAATTTAATTTAATACGTATTATATGTAGTTTGAATTTAAA
56348676 ATTTGTGTGTATTAATTTTACC
66 ATTTGTGTGTATTAATTTTACC
* * * * * * * *
56348698 ATCCGTTTGTA--GTGTTGGGTTTTTAAATTTAATTTAGTACGTATTAT-TTTTGTTTGAATTTT
1 AT--GTTTGTATTTTATTGTGTTTGTAAATTTAATTTAATACGTATTATATGTAGTTTGAATTTA
* * **
56348760 ATATTT-TTTGTATTAATATTGTAGG
64 AAATTTGTGTGTATTAAT-TT-TACC
*
56348785 ATGTTTGTATTTTATTGTGTCTGTAAATTTAATTT
1 ATGTTTGTATTTTATTGTGTTTGTAAATTTAATTT
56348820 GTCGTGTACT
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
85 17 0.18
86 19 0.20
87 54 0.56
89 7 0.07
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (87 bp):
ATGTTTGTATTTTATTGTGTTTGTAAATTTAATTTAATACGTATTATATGTAGTTTGAATTTAAA
ATTTGTGTGTATTAATTTTACC
Found at i:56348966 original size:20 final size:20
Alignment explanation
Indices: 56348920--56348966 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
56348910 AAATTAATAT
56348920 TAAAAACAGAATAATTACAA
1 TAAAAACAGAATAATTACAA
* *
56348940 AATAAAACA-AATATTTACATA
1 TA-AAAACAGAATAATTACA-A
56348961 TAAAAA
1 TAAAAA
56348967 TTAAAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAAACAGAATAATTACAA
Found at i:56358728 original size:2 final size:2
Alignment explanation
Indices: 56358721--56358769 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
56358711 GGTGATAGTC
56358721 AT AT AT AT AT AT 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 AT AT AT
56358763 AT AT AT A
1 AT AT AT A
56358770 CNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56367536 original size:15 final size:15
Alignment explanation
Indices: 56367516--56367546 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56367506 ATTAGCTTAG
*
56367516 TATTTTTAATATGTT
1 TATTTTTAATAAGTT
56367531 TATTTTTAATAAGTT
1 TATTTTTAATAAGTT
56367546 T
1 T
56367547 TAAATATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATTTTTAATAAGTT
Found at i:56369136 original size:15 final size:15
Alignment explanation
Indices: 56369106--56369134 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56369096 TCATCTTACG
56369106 TGAAATAATTTAAAA
1 TGAAATAATTTAAAA
56369121 TGAAA-AATTTAAAA
1 TGAAATAATTTAAAA
56369135 ATAGATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
TGAAATAATTTAAAA
Found at i:56369554 original size:20 final size:20
Alignment explanation
Indices: 56369529--56369591 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
56369519 TTGCTGCACC
*
56369529 ATGCTGTTGTTGTCCTTTCA
1 ATGCTGTTGTTGTCCCTTCA
56369549 ATGCTGTTGTTGTCCCTTCA
1 ATGCTGTTGTTGTCCCTTCA
* * *
56369569 ATGTTGCTGCTGTCCCTTCA
1 ATGCTGTTGTTGTCCCTTCA
56369589 ATG
1 ATG
56369592 GGAAAAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (20 bp):
ATGCTGTTGTTGTCCCTTCA
Found at i:56369683 original size:3 final size:3
Alignment explanation
Indices: 56369675--56369707 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
56369665 GAGAGAAAGG
*
56369675 AGA AGA AG- AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
56369708 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:56369685 original size:17 final size:17
Alignment explanation
Indices: 56369658--56369707 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
56369648 GGAAGAGAGA
56369658 AAGAA-AAGAG-AGAAAG
1 AAGAAGAAGAGAAG-AAG
*
56369674 GAGAAGAAGAGAAGAAG
1 AAGAAGAAGAGAAGAAG
56369691 AAGAAGAA-A-AAGAAG
1 AAGAAGAAGAGAAGAAG
56369706 AA
1 AA
56369708 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 15 0.50
18 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAGAAGAAG
Found at i:56370040 original size:21 final size:22
Alignment explanation
Indices: 56370002--56370043 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56369992 TTTTATTTGA
*
56370002 TTTTATTTATTTATTTAAAATT
1 TTTTATTGATTTATTTAAAATT
56370024 TTTTATTGATTTA-TTAAAAT
1 TTTTATTGATTTATTTAAAAT
56370044 GTTGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATTGATTTATTTAAAATT
Found at i:56370764 original size:23 final size:23
Alignment explanation
Indices: 56370738--56370786 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
56370728 TGCGGTCACA
56370738 GGCGTAAGCTCAACCTCTAGGTC
1 GGCGTAAGCTCAACCTCTAGGTC
*
56370761 GGCGTAAGCTCAATCTCTAGGTC
1 GGCGTAAGCTCAACCTCTAGGTC
56370784 GGC
1 GGC
56370787 TACCTTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (23 bp):
GGCGTAAGCTCAACCTCTAGGTC
Found at i:56372123 original size:33 final size:33
Alignment explanation
Indices: 56372038--56372150 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
56372028 CAGCCCACTA
* * * *
56372038 CCACCTCAGTACTCCAGTCATCCTAGCTCGTAT
1 CCACCTCAGTACTCCACTCCTTCTGGCTCGTAT
56372071 CCACCTCAGTACTCCACTCCTTCTGGCTCGTAT
1 CCACCTCAGTACTCCACTCCTTCTGGCTCGTAT
*
56372104 CCACCTCAGTACTCCACTCCTTCCGGC-CGTAT
1 CCACCTCAGTACTCCACTCCTTCTGGCTCGTAT
* *
56372136 CCACCGCCGTACTCC
1 CCACCTCAGTACTCC
56372151 GTTCCTCCCG
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 18 0.25
33 55 0.75
ACGTcount: A:0.17, C:0.45, G:0.12, T:0.26
Consensus pattern (33 bp):
CCACCTCAGTACTCCACTCCTTCTGGCTCGTAT
Found at i:56372524 original size:27 final size:27
Alignment explanation
Indices: 56372444--56372526 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 27
56372434 ACCCCACCAT
* * *
56372444 TCGCGCCTCTGAGTTAGGCACAACTAC
1 TCGCGCCTCTGAGATAGGCTCAACTAG
* * *
56372471 TCGTGCCTGTCAGATAGGCTCAACTAG
1 TCGCGCCTCTGAGATAGGCTCAACTAG
56372498 TCGCGCCTCTGAGATAGGCTCAACTAG
1 TCGCGCCTCTGAGATAGGCTCAACTAG
56372525 TC
1 TC
56372527 AACTTGTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (27 bp):
TCGCGCCTCTGAGATAGGCTCAACTAG
Found at i:56395091 original size:31 final size:31
Alignment explanation
Indices: 56395055--56395122 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
56395045 TTACAAAATT
56395055 ATCACTGAACTATTCAAAAGCTTTCATTTAA
1 ATCACTGAACTATTCAAAAGCTTTCATTTAA
* * * *
56395086 CTCACTGAATTATTCAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAGCTTTCATTTAA
56395117 ATCACT
1 ATCACT
56395123 TAAGTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.40
Consensus pattern (31 bp):
ATCACTGAACTATTCAAAAGCTTTCATTTAA
Found at i:56398107 original size:27 final size:27
Alignment explanation
Indices: 56398069--56398138 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
56398059 TAGTGGAGGG
56398069 TAACTGATTGGCGGCACCAAAGGTGCC
1 TAACTGATTGGCGGCACCAAAGGTGCC
* *
56398096 TAACTGATTGGCGGCACCGATGGTGCC
1 TAACTGATTGGCGGCACCAAAGGTGCC
56398123 -ATACTGATTGGCGGCA
1 TA-ACTGATTGGCGGCA
56398139 TCGAATCGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.21
Consensus pattern (27 bp):
TAACTGATTGGCGGCACCAAAGGTGCC
Found at i:56398816 original size:27 final size:27
Alignment explanation
Indices: 56398778--56398849 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
56398768 AACACGATTT
56398778 GGTGCCGCCAATCAG-TATGGCACCATC
1 GGTGCCGCCAATCAGTTA-GGCACCATC
* *
56398805 GGTGCCGCCAATCAGTTAGGCACCTTT
1 GGTGCCGCCAATCAGTTAGGCACCATC
56398832 GGTGCCGCCAATCAGTTA
1 GGTGCCGCCAATCAGTTA
56398850 CCCTCCACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 40 0.95
28 2 0.05
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.22
Consensus pattern (27 bp):
GGTGCCGCCAATCAGTTAGGCACCATC
Found at i:56405746 original size:7 final size:7
Alignment explanation
Indices: 56405734--56405767 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
56405724 TGTGAAATAT
56405734 AAATTTA
1 AAATTTA
*
56405741 AAATTTT
1 AAATTTA
56405748 AAATTTA
1 AAATTTA
56405755 AAATTTA
1 AAATTTA
56405762 AAATTT
1 AAATTT
56405768 TATATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AAATTTA
Found at i:56405760 original size:21 final size:21
Alignment explanation
Indices: 56405734--56405801 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 21
56405724 TGTGAAATAT
56405734 AAATTTAAAATTTTAAATTTA
1 AAATTTAAAATTTTAAATTTA
*
56405755 AAATTTAAAATTTTATATTATA
1 AAATTTAAAATTTTAAATT-TA
* *
56405777 ATATTATAAATTATTTTAGATTTA
1 AAATT-TAAA--ATTTTAAATTTA
56405801 A
1 A
56405802 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 18 0.45
22 6 0.15
23 4 0.10
24 3 0.08
25 9 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
AAATTTAAAATTTTAAATTTA
Found at i:56408459 original size:3 final size:3
Alignment explanation
Indices: 56408451--56408482 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56408441 ATACCTTTAA
56408451 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
56408483 AAACTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:56409348 original size:31 final size:31
Alignment explanation
Indices: 56409308--56409367 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
56409298 AAAATTTTAA
56409308 AATTAAAAAAGTATAA-AGACTAAAATTGACC
1 AATTAAAAAAGTATAAGA-ACTAAAATTGACC
*
56409339 AATTTAAAAAGTATAAGAACTAAAATTGA
1 AATTAAAAAAGTATAAGAACTAAAATTGA
56409368 TCAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (31 bp):
AATTAAAAAAGTATAAGAACTAAAATTGACC
Found at i:56409378 original size:31 final size:31
Alignment explanation
Indices: 56409313--56409378 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
56409303 TTTAAAATTA
**
56409313 AAAAAGTATAAAGACTAAAATTGACCAATTT
1 AAAAAGTATAAAGACTAAAATTGACCAAAAT
*
56409344 AAAAAGTAT-AAGAACTAAAATTGATCAAAAT
1 AAAAAGTATAAAG-ACTAAAATTGACCAAAAT
56409375 AAAA
1 AAAA
56409379 TATAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.23
Consensus pattern (31 bp):
AAAAAGTATAAAGACTAAAATTGACCAAAAT
Found at i:56409597 original size:23 final size:23
Alignment explanation
Indices: 56409571--56409614 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56409561 TTTAGTCATA
*
56409571 TTTTTATTTTTAAGAATTTAATG
1 TTTTTACTTTTAAGAATTTAATG
* *
56409594 TTTTTACTTTTCAGATTTTAA
1 TTTTTACTTTTAAGAATTTAA
56409615 AATTCAGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTTACTTTTAAGAATTTAATG
Found at i:56413622 original size:19 final size:19
Alignment explanation
Indices: 56413600--56413667 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
56413590 GAGGATATGT
56413600 AATCTTAGATATGATATAC
1 AATCTTAGATATGATATAC
56413619 AATCTTAGATATGATATATGC
1 AATCTTAGATATGATATA--C
* **
56413640 AATCTTAAATATGATATGT
1 AATCTTAGATATGATATAC
56413659 AATCTTAGA
1 AATCTTAGA
56413668 AGATATGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 26 0.60
21 17 0.40
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCTTAGATATGATATAC
Found at i:56413642 original size:21 final size:21
Alignment explanation
Indices: 56413594--56413656 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
56413584 ATCTTCGAGG
*
56413594 ATATGTAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56413615 ATA--CAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
56413634 ATATGCAATCTTAAATATGAT
1 ATATGCAATCTTAGATATGAT
56413655 AT
1 AT
56413657 GTAATCTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.47
21 20 0.53
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:56413685 original size:23 final size:22
Alignment explanation
Indices: 56413593--56413690 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 22
56413583 AATCTTCGAG
56413593 GATATGTAATCTT---AGATAT
1 GATATGTAATCTTAGAAGATAT
** *
56413612 GATATACAATCTTAG-ATATGAT
1 GATATGTAATCTTAGAAGAT-AT
*
56413634 -ATATGCAATCTT--AA-ATAT
1 GATATGTAATCTTAGAAGATAT
56413652 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTTAGAAGATAT
*
56413674 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
56413691 GATTTAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.03
19 24 0.38
20 1 0.02
21 16 0.25
22 8 0.12
23 13 0.20
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
GATATGTAATCTTAGAAGATAT
Found at i:56413700 original size:22 final size:23
Alignment explanation
Indices: 56413656--56413700 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56413646 AAATATGATA
*
56413656 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
56413679 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
56413701 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:56414377 original size:22 final size:22
Alignment explanation
Indices: 56414312--56414372 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 22
56414302 TATAATATAA
*
56414312 TAATTATTTTTATTTATTTATATG
1 TAATTA-TTTT-TTTATCTATATG
56414336 TAATTATTTTTTTATCTATATG
1 TAATTATTTTTTTATCTATATG
56414358 T-ATATATTTATTTTA
1 TAAT-TATTT-TTTTA
56414373 GTATACATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 9 0.26
24 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
TAATTATTTTTTTATCTATATG
Found at i:56414488 original size:15 final size:17
Alignment explanation
Indices: 56414456--56414493 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
56414446 AATGCAAATA
56414456 TATTTTTTTATATACTT
1 TATTTTTTTATATACTT
*
56414473 TATTTTTTT-T-TCCTT
1 TATTTTTTTATATACTT
56414488 TATTTT
1 TATTTT
56414494 CATAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTTATATACTT
Found at i:56417920 original size:2 final size:2
Alignment explanation
Indices: 56417915--56417944 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56417905 CCAAATACTT
56417915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
56417945 TTACCTTTGC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56422154 original size:34 final size:32
Alignment explanation
Indices: 56422116--56422183 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
56422106 GAATTATACT
56422116 AGGTTATAACCTTTTTTTTATAATATGTAAATTA
1 AGGTTATAACC--TTTTTTATAATATGTAAATTA
*
56422150 AGGTTATAGCCTTTTTTATAATATGTAAATTA
1 AGGTTATAACCTTTTTTATAATATGTAAATTA
56422182 AG
1 AG
56422184 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 23 0.70
34 10 0.30
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (32 bp):
AGGTTATAACCTTTTTTATAATATGTAAATTA
Found at i:56423000 original size:35 final size:34
Alignment explanation
Indices: 56422936--56423001 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
56422926 ACAAATTATT
* * *
56422936 TGTTACTGATATTGAGATGGGCTAAGGCCCAAAC
1 TGTTACTGATACTGAAAAGGGCTAAGGCCCAAAC
*
56422970 TGTTACTGATACTGAAAAAGGGCTTAGGCCCA
1 TGTTACTGATACTG-AAAAGGGCTAAGGCCCA
56423002 GGACTACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 13 0.48
35 14 0.52
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (34 bp):
TGTTACTGATACTGAAAAGGGCTAAGGCCCAAAC
Found at i:56431044 original size:27 final size:27
Alignment explanation
Indices: 56430688--56431033 Score: 383
Period size: 27 Copynumber: 12.9 Consensus size: 27
56430678 AAAATAACTA
* *
56430688 AAATACCCCCATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
** * *
56430715 AAATACCCTTAGAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGATCG
* * * *
56430742 AAATACCCTCATAGTGTAAAATAACCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
56430769 AAATACCCCCATAGGGTAGAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
56430796 AAATACCCCTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
56430823 AAATACCCCCATAGGGTAAATTGACTC-
1 AAATACCCCCATAGGGTAAAATGA-TCG
* * *
56430850 AAATA-CCCCTTAAGGT-AAATGACCG
1 AAATACCCCCATAGGGTAAAATGATCG
* *
56430875 AAATACCCCCATAGGGTAGAATAATCG
1 AAATACCCCCATAGGGTAAAATGATCG
* * *
56430902 AAATACCCTCATAGGGTAAAATGAACA
1 AAATACCCCCATAGGGTAAAATGATCG
* * * **
56430929 AAATACTCCAATAGGGTAGAATGGCCG
1 AAATACCCCCATAGGGTAAAATGATCG
* *
56430956 AAATACCCCCATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
* *
56430983 AAATACCCTCTTAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
56431010 AAATACCCTCATAGGGTAAAATGA
1 AAATACCCCCATAGGGTAAAATGA
56431034 CTATTATACC
Statistics
Matches: 267, Mismatches: 48, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
24 1 0.00
25 10 0.04
26 18 0.07
27 236 0.88
28 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:56431115 original size:72 final size:71
Alignment explanation
Indices: 56431002--56431138 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
56430992 CTTAGGGTAA
* * *
56431002 AATGATCGAAATACCCTCATAGGGTAAAATGACTATTATACCCC-TAGGAGATGAAATAACTGTT
1 AATGATCGAAATACCCTCATAGGGTAAAATGACGATAATACCCCATAGG-G-TAAAATAACTGTT
56431066 ATGGCTAG
64 ATGGCTAG
* * * *
56431074 AATGATTGGAATACCTTCATAGGGTAAAATGACCGA-AATACCCCATAGGGTAAAATGACTGTTA
1 AATGATCGAAATACCCTCATAGGGTAAAATGA-CGATAATACCCCATAGGGTAAAATAACTGTTA
56431138 T
65 T
56431139 ACCCCTAGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
71 13 0.23
72 37 0.66
73 6 0.11
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (71 bp):
AATGATCGAAATACCCTCATAGGGTAAAATGACGATAATACCCCATAGGGTAAAATAACTGTTAT
GGCTAG
Found at i:56431140 original size:26 final size:26
Alignment explanation
Indices: 56431091--56431165 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
56431081 GGAATACCTT
* **
56431091 CATAGGGTAAAATGACCGAAATACCC
1 CATAGGGTAAAATGACTGTTATACCC
56431117 CATAGGGTAAAATGACTGTTATACCC
1 CATAGGGTAAAATGACTGTTATACCC
*
56431143 C-TAGGAGATGAAATGACTGTTAT
1 CATAGG-G-TAAAATGACTGTTAT
56431166 GACTTTATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 4 0.09
26 25 0.58
27 14 0.33
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (26 bp):
CATAGGGTAAAATGACTGTTATACCC
Found at i:56431162 original size:98 final size:99
Alignment explanation
Indices: 56430984--56431166 Score: 314
Period size: 98 Copynumber: 1.9 Consensus size: 99
56430974 AAATGACCAA
* *
56430984 AATACCCTCTTAGGGTAAAATGATCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
1 AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
56431049 GAGATGAAATAACTGTTATGGCTAGAATGATTGG
66 GAGATGAAATAACTGTTATGGCTAGAATGATTGG
* *
56431083 AATACCTTCATAGGGTAAAATGACCGAAATACCC-CATAGGGTAAAATGACTGTTATACCCCTAG
1 AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
*
56431147 GAGATGAAATGACTGTTATG
66 GAGATGAAATAACTGTTATG
56431167 ACTTTATGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 48 0.61
99 31 0.39
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (99 bp):
AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
GAGATGAAATAACTGTTATGGCTAGAATGATTGG
Found at i:56435149 original size:107 final size:107
Alignment explanation
Indices: 56434963--56435159 Score: 304
Period size: 107 Copynumber: 1.8 Consensus size: 107
56434953 CAAAAAATTA
* * *
56434963 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGTTTGGGTTGTCATCCCACTTCGCGTTAAAAGGG
1 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
56435028 CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
66 CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
* * * *
56435070 AGTGTGTTGGGCTTAGTAACCGGGGTGGGGTGCTTGGGTTGCCATTCCACTTTGCGTCAAAAGGG
1 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
* **
56435135 CCAATACATTCTTAAGTAAAAAAAA
66 CCAAAACATTCTTAACCAAAAAAAA
56435160 AATGAAGGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 80 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (107 bp):
AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
Found at i:56442705 original size:123 final size:122
Alignment explanation
Indices: 56442538--56442789 Score: 375
Period size: 123 Copynumber: 2.1 Consensus size: 122
56442528 CTCAAAAACC
* *
56442538 GAAGTCAACCGAAATCGCACCCTCAATTCCCTGAAGGCGCACCAACCAACCCTTGGTCTCCACCC
1 GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
* * *
56442603 AACTA-ACGAAAGAATGTAGTGCAGTTTGGCAACACAAGAGAGAAC-GAATCGAAAAGAG
66 AAC-AGACAAAAGAACGTAGTGCAATTTGGCAACACAAGAGAGAACAG-ATCGAAAAG-G
* *
56442661 GAAGTCAACCAAAATCGTACCCTCAATTCCTTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
1 GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
**
56442726 AACAGACAAAAGAACGTAGTGCAATTTGGCAATGCAAGAGAGAACAGATCGAAAAGG
66 AACAGACAAAAGAACGTAGTGCAATTTGGCAACACAAGAGAGAACAGATCGAAAAGG
56442783 GAA-TCAA
1 GAAGTCAA
56442790 AGACTAGCAG
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
121 4 0.03
122 5 0.04
123 108 0.92
124 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (122 bp):
GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
AACAGACAAAAGAACGTAGTGCAATTTGGCAACACAAGAGAGAACAGATCGAAAAGG
Found at i:56443317 original size:3 final size:3
Alignment explanation
Indices: 56443309--56443410 Score: 195
Period size: 3 Copynumber: 34.0 Consensus size: 3
56443299 TGTACTGTAC
56443309 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
*
56443357 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT AAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
56443405 CAT CAT
1 CAT CAT
56443411 TATAATATTA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:56444112 original size:15 final size:16
Alignment explanation
Indices: 56444080--56444114 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
56444070 ACTTATACCG
56444080 AAAATGAAATATTAAA
1 AAAATGAAATATTAAA
56444096 AAAATGAAATATTAAA
1 AAAATGAAATATTAAA
56444112 AAA
1 AAA
56444115 GGCAAGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAATGAAATATTAAA
Found at i:56446570 original size:26 final size:26
Alignment explanation
Indices: 56446507--56446581 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
56446497 AACACACCAA
* *
56446507 TATCACAGCAAAACTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
*
56446533 TATCGCAACAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * * *
56446559 TATTGTAGCAAAGTTACCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
56446582 CAATATACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:56448189 original size:17 final size:17
Alignment explanation
Indices: 56448167--56448199 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56448157 CCCAAAACCG
56448167 AAATGAGAAGTATACCA
1 AAATGAGAAGTATACCA
*
56448184 AAATGAGCAGTATACC
1 AAATGAGAAGTATACC
56448200 CTTTTGGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGAGAAGTATACCA
Found at i:56450452 original size:50 final size:50
Alignment explanation
Indices: 56450377--56450612 Score: 313
Period size: 50 Copynumber: 4.8 Consensus size: 50
56450367 ATATGGGTAA
56450377 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
56450427 AGAGGTCACATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
56450477 AAAGGTCCCATGTAAGACCATGTGTGGGACATAGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * *
56450527 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
56450577 AGA------ATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
56450613 TGTTATTATC
Statistics
Matches: 165, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
44 28 0.17
50 137 0.83
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:56453862 original size:3 final size:3
Alignment explanation
Indices: 56453854--56453895 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
56453844 TGTACTGCAC
56453854 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
56453896 AATATTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:56456355 original size:18 final size:17
Alignment explanation
Indices: 56456313--56456360 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
56456303 TGTCGTTCGT
56456313 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
56456330 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
56456349 TTTCAAAACATT
1 TTTCAAAACATT
56456361 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:56460177 original size:6 final size:6
Alignment explanation
Indices: 56460168--56460201 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
56460158 GAAAAGGAAA
56460168 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
56460202 TATATTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:56461653 original size:34 final size:36
Alignment explanation
Indices: 56461599--56461668 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
56461589 CCTCATTTTA
* *
56461599 CTTTCTTTTCCTTTTCTTTTTTCTTC-TGGCCGAAC
1 CTTTCTTCTCCTTCTCTTTTTTCTTCTTGGCCGAAC
56461634 CTTTCTTCT-CTTCTCTTTTTTCTTCTTTGGCCGAA
1 CTTTCTTCTCCTTCTCTTTTTTCTTC-TTGGCCGAA
56461669 TAATCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 15 0.48
35 8 0.26
36 8 0.26
ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57
Consensus pattern (36 bp):
CTTTCTTCTCCTTCTCTTTTTTCTTCTTGGCCGAAC
Found at i:56462463 original size:81 final size:79
Alignment explanation
Indices: 56462323--56462576 Score: 287
Period size: 81 Copynumber: 3.1 Consensus size: 79
56462313 GTAATGGGAC
* * * *
56462323 CGAAATACCCTCGAAGGGTAAAATTACCGAAATACCTTCGAAGGGTAAAATTACTGAAATACCCT
1 CGAAATACCCTTGAAAGGTAAAATTACCAAAATACC-TCGAAGGGTAAAATTAC-GAAATACCCC
** * *
56462388 TTAAAGTTAAAATTAGT
64 CGAAAGGTAAAATGA-T
56462405 -GAAATACCCTTGAAAGGTAAAATTACCAAAATACTCTCGAAGGGTAAAATTATCGAAATACCCC
1 CGAAATACCCTTGAAAGGTAAAATTACCAAAATAC-CTCGAAGGGTAAAATTA-CGAAATACCCC
56462469 CGAAAGGTAAAATGAT
64 CGAAAGGTAAAATGAT
* * *
56462485 CGAAATACCCTT-AAAGGGTAAAATTACAAAAATACCCCCGAAGGGTAAAATGACCGAAATACCC
1 CGAAATACCCTTGAAA-GGTAAAATTACCAAAATA-CCTCGAAGGGTAAAATTA-CGAAATACCC
* *
56462549 CTGTAAGGTAAAATGAT
63 CCGAAAGGTAAAATGAT
**
56462566 CGTTATACCCT
1 CGAAATACCCT
56462577 AGGAGATGAA
Statistics
Matches: 151, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
80 4 0.03
81 144 0.95
82 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (79 bp):
CGAAATACCCTTGAAAGGTAAAATTACCAAAATACCTCGAAGGGTAAAATTACGAAATACCCCCG
AAAGGTAAAATGAT
Found at i:56462549 original size:27 final size:27
Alignment explanation
Indices: 56462321--56462548 Score: 249
Period size: 27 Copynumber: 8.4 Consensus size: 27
56462311 CCGTAATGGG
56462321 ACCGAAATACCCTCGAAGGGTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
*
56462348 ACCGAAATACCTTCGAAGGGTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
* ** * *
56462375 ACTGAAATACCCTTTAAAGTTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
** * *
56462402 AGTGAAATACCCTTGAAAGGTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
* *
56462429 ACCAAAATACTCTCGAAGGGTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
* * * *
56462456 ATCGAAATACCCCCGAAAGGTAAAATG
1 ACCGAAATACCCTCGAAGGGTAAAATT
* **
56462483 ATCGAAATACCCTTAAAGGGTAAAATT
1 ACCGAAATACCCTCGAAGGGTAAAATT
** * *
56462510 ACAAAAATACCCCCGAAGGGTAAAATG
1 ACCGAAATACCCTCGAAGGGTAAAATT
56462537 ACCGAAATACCC
1 ACCGAAATACCC
56462549 CTGTAAGGTA
Statistics
Matches: 165, Mismatches: 36, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 165 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
ACCGAAATACCCTCGAAGGGTAAAATT
Found at i:56462789 original size:26 final size:26
Alignment explanation
Indices: 56462758--56462828 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
56462748 CCACATATAC
*
56462758 TGTTACTGGCAGCTTTGCTGTGTTAT
1 TGTTACTGGCAGCTTTGCTGAGTTAT
* * **
56462784 TGTTACTAGAAATTTTGCTGAGTTAT
1 TGTTACTGGCAGCTTTGCTGAGTTAT
* *
56462810 TATTACTGGCGGCTTTGCT
1 TGTTACTGGCAGCTTTGCT
56462829 ACGATATTGG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTGAGTTAT
Found at i:56462986 original size:28 final size:28
Alignment explanation
Indices: 56462937--56463024 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
56462927 ACTGCATTTT
* *
56462937 ACTGATTATTGTATTGGGCTAAAGCTCAC
1 ACTG-TTACTGTATTGGGCTAAAGCCCAC
* *
56462966 ATTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAAGCCCAC
* *
56462994 ACTGTTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAAGCCCAC
56463022 ACT
1 ACT
56463025 ATACTGATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 50 0.94
29 3 0.06
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAAGCCCAC
Found at i:56463045 original size:33 final size:28
Alignment explanation
Indices: 56462941--56463058 Score: 85
Period size: 28 Copynumber: 4.0 Consensus size: 28
56462931 CATTTTACTG
* * * * *
56462941 ATTATTGTATTGGGCTAAAGCTCACATT
1 ATTACTGTATAGGGCTAAGGCCCACACT
* *
56462969 GTTACTGTATTGGGCTAAGGCCCACACT
1 ATTACTGTATAGGGCTAAGGCCCACACT
*
56462997 GTTACTGTA-ATGGGCTAAGGCCCACACT
1 ATTACTGTATA-GGGCTAAGGCCCACACT
* *
56463025 ATACTGATTCTGTATAGGGCTCAGGCCCAGACT
1 AT--T-A--CTGTATAGGGCTAAGGCCCACACT
56463058 A
1 A
56463059 ATTCTGCATG
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
28 50 0.68
30 1 0.01
31 1 0.01
33 21 0.28
34 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (28 bp):
ATTACTGTATAGGGCTAAGGCCCACACT
Found at i:56463114 original size:40 final size:40
Alignment explanation
Indices: 56463059--56463135 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
56463049 GCCCAGACTA
*
56463059 ATTCTGCATGTTGCATAGTGAATAGCTAGTAGGGGATCTG
1 ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGATCTG
* *
56463099 ATTCTGCATGATGCATAGTGATTGGCTAGTAGGGGAT
1 ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGAT
56463136 TACACATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.32
Consensus pattern (40 bp):
ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGATCTG
Found at i:56465570 original size:3 final size:3
Alignment explanation
Indices: 56465562--56465662 Score: 67
Period size: 3 Copynumber: 33.0 Consensus size: 3
56465552 TTAGTTTAAG
* * * *
56465562 ATT ATT ATT GATTT AGT ATC ATT ATT ATT ATT ATT ATT ATT AGT AGT
1 ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * **
56465609 AGT AGT AGT AGT AGT AGT ATT ATT ATT ATT ATT ATT GGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
56465657 CTT ATT
1 ATT ATT
56465663 TTTTTATTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 80 0.95
4 2 0.02
5 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:56465968 original size:4 final size:4
Alignment explanation
Indices: 56465959--56466038 Score: 160
Period size: 4 Copynumber: 20.0 Consensus size: 4
56465949 ATATTAAATT
56465959 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
56466007 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
56466039 TCTATTGTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:56466120 original size:29 final size:28
Alignment explanation
Indices: 56466087--56466161 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
56466077 CTTTTTTAAA
*
56466087 TATTTTAATATCTTTAATCTATTTCAACT
1 TATTTTAATAT-TTTAATCTATTTAAACT
* * *
56466116 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTTAATATT-TTAATCTATTTAAACT
*
56466145 TATTTTAACATTTTAAT
1 TATTTTAATATTTTAAT
56466162 TTATATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.57
Consensus pattern (28 bp):
TATTTTAATATTTTAATCTATTTAAACT
Done.