Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 86 of 163
Found at i:27932048 original size:21 final size:21
Alignment explanation
Indices: 27932019--27932059 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27932009 ACACCAAAAC
* *
27932019 AGGCTTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
27932040 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
27932060 AAGCGCCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGCTTTTT
Found at i:27932166 original size:43 final size:42
Alignment explanation
Indices: 27932119--27932237 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 42
27932109 CGCCGCTAAA
* * * *
27932119 TTTAGCGGCGTTTATGTGAAAAAATCCGCTAAAGATCATGGCC
1 TTTAGCGGCGTTT-TATCAAAAAAGCCGCTAAAGATCATGACC
* * *
27932162 TTTAGCGGCACTTTTATCACAAACGCCGCTAAAGATCATGACC
1 TTTAGCGGC-GTTTTATCAAAAAAGCCGCTAAAGATCATGACC
* *
27932205 TTTAGCGGCGCTTCTCA-CAAAAATGCCGCTAAA
1 TTTAGCGGCG-TT-TTATCAAAAAAGCCGCTAAA
27932238 AACATACGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 57 0.92
44 5 0.08
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGTTTTATCAAAAAAGCCGCTAAAGATCATGACC
Found at i:27933924 original size:27 final size:27
Alignment explanation
Indices: 27933846--27933928 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
27933836 TGCTAAGTGG
27933846 TTTAGTTTTAGAATTTAAAATAATAAA
1 TTTAGTTTTAGAATTTAAAATAATAAA
* *** ** *
27933873 -TTAATAAAAGCAA-AAAAACACAATAAA
1 TTTAGTTTTAG-AATTTAAA-ATAATAAA
27933900 TTTAGTTTTAGAATTTAAAATAATAAA
1 TTTAGTTTTAGAATTTAAAATAATAAA
27933927 TT
1 TT
27933929 AATAAATTAA
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
26 9 0.24
27 20 0.53
28 9 0.24
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (27 bp):
TTTAGTTTTAGAATTTAAAATAATAAA
Found at i:27934071 original size:15 final size:15
Alignment explanation
Indices: 27934038--27934071 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
27934028 AATAAATTAA
27934038 CAAAATGCTTTTAGT
1 CAAAATGCTTTTAGT
27934053 CAAATATGCTTTTAG-
1 CAAA-ATGCTTTTAGT
27934068 CAAA
1 CAAA
27934072 CTAATATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (15 bp):
CAAAATGCTTTTAGT
Found at i:27935994 original size:23 final size:24
Alignment explanation
Indices: 27935959--27936003 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
27935949 CTTCAATCAT
*
27935959 TCTGCTTCAATTATCT-CAATTAAA
1 TCTGCATCAATTAT-TACAATTAAA
27935983 TCTGCATC-ATTATTACAATTA
1 TCTGCATCAATTATTACAATTA
27936004 TTGTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 11 0.58
24 7 0.37
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (24 bp):
TCTGCATCAATTATTACAATTAAA
Found at i:27936822 original size:73 final size:73
Alignment explanation
Indices: 27936723--27936867 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
27936713 AAAGCGCAGC
* * * *
27936723 AAAAAACCTAAGCCCAACGACGCCGTTTT-TCGGGCTTTTGGGAATTTAGCGGCGTTTTTGAGAA
1 AAAAAACATAAGCCCAACGACGCCGTTTTGT-GAGCTTTCGGGAATTTAGCGGCGTTTTTAAGAA
27936787 AACGCCGCA
65 AACGCCGCA
* * *
27936796 AAAAAACATAAGCGCAACGA-GACCGTTTTGTGAGCTTTCGGGGATTTAGCGGTGTTTTTAAGAA
1 AAAAAACATAAGCCCAACGACG-CCGTTTTGTGAGCTTTCGGGAATTTAGCGGCGTTTTTAAGAA
27936860 AACGCCGC
65 AACGCCGC
27936868 TAATGCTCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
72 1 0.02
73 61 0.97
74 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (73 bp):
AAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCTTTCGGGAATTTAGCGGCGTTTTTAAGAAA
ACGCCGCA
Found at i:27936981 original size:115 final size:114
Alignment explanation
Indices: 27936767--27937312 Score: 914
Period size: 114 Copynumber: 4.8 Consensus size: 114
27936757 CTTTTGGGAA
* *
27936767 TTTAGCGGCGTTTTTGAGAAAACGCCGCAAAAAAACATAAGCGCAACGA-GACCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACG-CCGTTTTGTGAGC
* * *
27936831 TTTCGGGGATTTAGCGGTGTTTTTAAGAAAACGCCGCTAATGCTCAAGTC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* * *
27936881 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAACACATAAGCCCCTACGACGCCATTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAG-CCCAACGACGCCGTTTTGTGAGC
*
27936946 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* * * * *
27936996 TTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAAATATAAACCCAATGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCT
27937061 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
*
27937110 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCT
*
27937175 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
27937224 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
27937289 TTTCGGGGATTTAGCGGCGTTTTT
65 TTTCGGGGATTTAGCGGCGTTTTT
27937313 GATAAAGTGC
Statistics
Matches: 403, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
114 224 0.56
115 178 0.44
116 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
Found at i:27937247 original size:229 final size:230
Alignment explanation
Indices: 27936767--27937312 Score: 920
Period size: 229 Copynumber: 2.4 Consensus size: 230
27936757 CTTTTGGGAA
* *
27936767 TTTAGCGGCG-TTTTTGAGAAAACGCCGCAAAAAAACATAAGCGCAACGA-GACCGTTTTGTGAG
1 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACG-CCGTTTTGTGAG
*
27936830 CTTTCGGGGATTTAGCGGTGTTTTTAAGAAAACGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTT
65 CTTTCGGGGATTTAGCGGCGTTTTTAAGAAAACGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTT
* * *
27936895 TGAGAAAGCGCCGCAAAAACACATAAGCCCCTACGACGCCATTTTGTGAGCTTTCGGGGATTTAG
130 TGAGAAAGCGCCACAAAAAAACATAAGCCCCAACGACGCCATTTTGTGAGCTTTCGGGGATTTAG
*
27936960 CGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
195 CGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
* * * *
27936996 TTTAGCGGCGTTTTTT-AGAAAGCGCCGCAAAAAAATATAAACCCAATGACGTCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
* *
27937060 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTT
66 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAACGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTT
*
27937125 GAGAAAGCGCCACAAAAAAACATAAG-CCCAACGACGCCGTTTTGTGAGCTTTCGGGGATTTAGC
131 GAGAAAGCGCCACAAAAAAACATAAGCCCCAACGACGCCATTTTGTGAGCTTTCGGGGATTTAGC
*
27937189 GGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGTC
196 GGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
27937224 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
27937289 TTTCGGGGATTTAGCGGCGTTTTT
66 TTTCGGGGATTTAGCGGCGTTTTT
27937313 GATAAAGTGC
Statistics
Matches: 295, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
228 85 0.29
229 204 0.69
230 6 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (230 bp):
TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
TTTCGGGGATTTAGCGGCGTTTTTAAGAAAACGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTT
GAGAAAGCGCCACAAAAAAACATAAGCCCCAACGACGCCATTTTGTGAGCTTTCGGGGATTTAGC
GGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
Found at i:27937345 original size:74 final size:74
Alignment explanation
Indices: 27937224--27937380 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
27937214 TGCTCAGGTC
*
27937224 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGC
27937289 TTTCGGGGA
66 TTTCGGGGA
* * * *
27937298 TTTAGCGGCG-TTTTTGATAAAGTGCCGCAAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAG
1 TTTAGCGGCGTTTTTTGAGAAAGCGCCGC-AAAAAAACATAAGCCCAACGACGCCGTTTTCTGAG
* *
27937362 CTTTCGTGGT
65 CTTTCGGGGA
27937372 TTTAGCGGC
1 TTTAGCGGC
27937381 CAAAAATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
73 16 0.21
74 59 0.79
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (74 bp):
TTTAGCGGCGTTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGC
TTTCGGGGA
Found at i:27937700 original size:28 final size:27
Alignment explanation
Indices: 27937653--27937728 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
27937643 TAAGGCCGGT
27937653 TTAGGGAGTATGGGTTTAAGGATTATGGA
1 TTAGGG-GT-TGGGTTTAAGGATTATGGA
* *
27937682 TTAGGGGTTGGGATTTAAGGTTTATGGG
1 TTAGGGGTTGGG-TTTAAGGATTATGGA
27937710 TTAGAGGGTTAGGGGTTTA
1 TTAG-GGGTT--GGGTTTA
27937729 GGGGTTAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.10
28 19 0.46
29 11 0.27
30 4 0.10
31 3 0.07
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (27 bp):
TTAGGGGTTGGGTTTAAGGATTATGGA
Found at i:27937718 original size:8 final size:7
Alignment explanation
Indices: 27937707--27937750 Score: 61
Period size: 8 Copynumber: 5.9 Consensus size: 7
27937697 TAAGGTTTAT
27937707 GGGTTAG
1 GGGTTAG
27937714 AGGGTTAG
1 -GGGTTAG
27937722 GGGTTTAG
1 GGG-TTAG
27937730 GGGTTAG
1 GGGTTAG
27937737 AGGGTTAG
1 -GGGTTAG
27937745 GGGTTA
1 GGGTTA
27937751 AAAGTTAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.18, C:0.00, G:0.52, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:27937727 original size:23 final size:23
Alignment explanation
Indices: 27937700--27937749 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
27937690 TGGGATTTAA
*
27937700 GGTTTATGGGTTAGAGGGTTAGG
1 GGTTTAGGGGTTAGAGGGTTAGG
27937723 GGTTTAGGGGTTAGAGGGTTAGG
1 GGTTTAGGGGTTAGAGGGTTAGG
27937746 GGTT
1 GGTT
27937750 AAAAGTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (23 bp):
GGTTTAGGGGTTAGAGGGTTAGG
Found at i:27937733 original size:15 final size:14
Alignment explanation
Indices: 27937707--27937750 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 14
27937697 TAAGGTTTAT
27937707 GGGTTAGAGGGTTAG
1 GGGTTAG-GGGTTAG
27937722 GGGTTTAGGGGTTAG
1 GGG-TTAGGGGTTAG
27937737 AGGGTTAGGGGTTA
1 -GGGTTAGGGGTTA
27937751 AAAGTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.52, T:0.30
Consensus pattern (14 bp):
GGGTTAGGGGTTAG
Found at i:27938748 original size:105 final size:98
Alignment explanation
Indices: 27938556--27938753 Score: 245
Period size: 105 Copynumber: 1.9 Consensus size: 98
27938546 GCAATAGAGG
* * *
27938556 CGTTTTTTATAAAAACGCCGCAAAAAAATCCATTTATAAAAAAATAAAATAATTTAGCATAGCAA
1 CGTTTTTTATAAAAACACCGCAAAAAAATCAATTTATAAAAAAATAAAATAATTTAGAATAGCAA
*
27938621 AACGACGTCATTTTGTTCAAAATGAAATAGCGA
66 AACGACGTCATTTTGTTCAAAATAAAATAGCGA
**
27938654 CGTTTTTTATAAAAACACCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGA
1 CGTTTTTTATAAAAACACCGC-AAAA-AAATCAATTTAT---AAA-AAAAT-AAAATAATTTAGA
**
27938719 ATAGCAAAACGGTGT-AGTTTTGTTCAAAATAAAAT
59 ATAGCAAAACGACGTCA-TTTTGTTCAAAATAAAAT
27938754 TTTTTTAAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
98 20 0.24
99 4 0.05
100 11 0.13
103 3 0.04
104 6 0.07
105 40 0.48
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (98 bp):
CGTTTTTTATAAAAACACCGCAAAAAAATCAATTTATAAAAAAATAAAATAATTTAGAATAGCAA
AACGACGTCATTTTGTTCAAAATAAAATAGCGA
Found at i:27939217 original size:203 final size:203
Alignment explanation
Indices: 27938759--27939505 Score: 1209
Period size: 203 Copynumber: 3.7 Consensus size: 203
27938749 AAAATTTTTT
*
27938759 TAAAGATTTATAAAAAAATTTAAAAAATTTAGCATAGCAAAACGACGTCATTTTGATCAAAATGA
1 TAAAGATTTATAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGA
* * *
27938824 AATAGCAGCGTTTTTATAAAAAAACGCCTCAAAAATAAATCAATTTATAAAAAACAAAATAAAAA
66 AATAGCGGCGTTTTT-TATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAA
* * * * * *
27938889 TTTTTTAGAATAGCAAAACAGCGTAGTTTTGTTCAAAATAAAAAAATTTGGCGGCGTTT-T--TA
130 TTCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAAT-AAAAAATTTTGCGGCGTTTCTCATA
*
27938951 AAAACGCCAC
194 AAAACGCCGC
**** * *
27938961 TAAAGATTTATAAATTTTTTTTAAAATTTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGA
1 TAAAGATTTATAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGA
* *
27939026 AATAACGGCGTTTTTTATAAAAACGTCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAAT
66 AATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAAT
27939091 TCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTCTCATAAA
131 TCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTCTCATAAA
27939156 AACGCCGC
196 AACGCCGC
27939164 TAAAGATTT-TAAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATG
1 TAAAGATTTAT-AAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATG
*
27939228 AAATAGCGGCGTTTTTTATAAAAATGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAA
65 AAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAA
27939293 TTCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTCTCATAA
130 TTCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTCTCATAA
27939358 AAACGCCGC
195 AAACGCCGC
27939367 TAAAGATTT-TAAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATG
1 TAAAGATTTAT-AAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATG
* *
27939431 AAATAGCGGCGTTTTTCATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAA-AAAAAAAAAA
65 AAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAA
*
27939495 TTTTTTAGAAT
130 TTCTTTAGAAT
27939506 AACAANNNNN
Statistics
Matches: 509, Mismatches: 32, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
200 18 0.04
201 81 0.16
202 91 0.18
203 319 0.63
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (203 bp):
TAAAGATTTATAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGA
AATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAAT
TCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTCTCATAAA
AACGCCGC
Found at i:27940180 original size:105 final size:102
Alignment explanation
Indices: 27940048--27940782 Score: 555
Period size: 105 Copynumber: 7.4 Consensus size: 102
27940038 ATTTAAAAAA
* *
27940048 TTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAGCGGCGTTTTTTATAAAAATGCC
1 TTTAGAATAGCAAAACGGCGTCATTTTGATCAAAATGAAATA-CGGCGTTTTTTATAAAAACGCC
27940113 GCAAAAATAAATCAATTTATAAAAAACAAAATAAAATTTT
65 GCAAAAATAAATCAATTTATAAAAAACAAAATAAAA--TT
* ***** **
27940153 TTTAGAATAGCAAAACGGCGT-AGTTTTGTTCAAAAT-AAA-A-AAAAATTTGCATAAAAACGCC
1 TTTAGAATAGCAAAACGGCGTCA-TTTTGATCAAAATGAAATACGGCGTTTTTTATAAAAACGCC
*
27940214 GC-----TAAA--GATTTATAAAAAA-ATTAAA-AAAA--
65 GCAAAAATAAATCAATTTATAAAAAACA--AAATAAAATT
* *
27940243 TTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAACGGCGTTTTTTATAAAAACGTC
1 TTTAGAATAGCAAAACGGCGTCATTTTGATCAAAATGAAAT-ACGGCGTTTTTTATAAAAACGCC
27940308 GCAAAAATAAATCAATTTATAAAAAACAAAATAAAAATT
65 GCAAAAATAAATCAATTTATAAAAAACAAAAT-AAAATT
* * * * * * *
27940347 CTTTAGAATCGTAAAACGGAGT-AGTTTTGTTCAAAATAAAAAATTTTGCGGCGTTTTCTCAT-A
1 -TTTAGAATAGCAAAACGGCGTCA-TTTTGATCAAAAT--GAAA---TACGGCGTTTT-TTATAA
* ** **
27940410 AAACGCCGC-----TAAA--GATTT-TAAAAAA-AATTTAAAAAA
58 AAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAATT
* * *
27940446 TTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAGCGGCCTTTTTTATAAAAATGCC
1 TTTAGAATAGCAAAACGGCGTCATTTTGATCAAAATGAAATA-CGGCGTTTTTTATAAAAACGCC
27940511 GCAAAAATAAATCAATTTATAAAAAACAAAATAAAATTTT
65 GCAAAAATAAATCAATTTATAAAAAACAAAATAAAA--TT
* ***** **
27940551 TTTAGAATAGCAAAACGGCGT-AGTTTTGTTCAAAAT-AAA-A-AAAAATTTGCATAAAAACGCC
1 TTTAGAATAGCAAAACGGCGTCA-TTTTGATCAAAATGAAATACGGCGTTTTTTATAAAAACGCC
*
27940612 GC-----TAAA--GATTTATAAAAAA-ATTAAA-AAAA--
65 GCAAAAATAAATCAATTTATAAAAAACA--AAATAAAATT
* *
27940641 TTTAGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAGCGGCGTTTTTATAAAAAAACGC
1 TTTAGAATAGCAAAACGGCGTCATTTTGATCAAAATGAAATA-CGGCGTTTTT-TATAAAAACGC
*
27940706 CGCAAAAATAAATCAATTTATAAAAAAGAAAATAAAATTGT
64 CGCAAAAATAAATCAATTTATAAAAAACAAAATAAAA-T-T
* *
27940747 TTTAAAATAGCAAAACGGCGT-AGTTTTGTTCAAAAT
1 TTTAGAATAGCAAAACGGCGTCA-TTTTGATCAAAAT
27940783 AAAAACAATT
Statistics
Matches: 489, Mismatches: 76, Indels: 129
0.70 0.11 0.19
Matches are distributed among these distances:
90 64 0.13
91 8 0.02
92 1 0.00
93 7 0.01
94 67 0.14
95 18 0.04
96 11 0.02
98 29 0.06
99 13 0.03
100 10 0.02
101 56 0.11
102 32 0.07
103 10 0.02
104 13 0.03
105 94 0.19
106 31 0.06
107 3 0.01
109 18 0.04
110 4 0.01
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (102 bp):
TTTAGAATAGCAAAACGGCGTCATTTTGATCAAAATGAAATACGGCGTTTTTTATAAAAACGCCG
CAAAAATAAATCAATTTATAAAAAACAAAATAAAATT
Found at i:27940319 original size:195 final size:195
Alignment explanation
Indices: 27940017--27940796 Score: 1251
Period size: 195 Copynumber: 4.0 Consensus size: 195
27940007 AATTTTTGCA
*
27940017 CCGCTAAAGATTTATAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
1 CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
*
27940082 ATGAAATAGCGGCGTTTTTTATAAAAATGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAA
66 ATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAA
27940147 AATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGCATAAAAACG
131 AATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGCATAAAAACG
27940212 CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
1 CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
* *
27940277 ATGAAATAACGGCGTTTTTTATAAAAACGTCGCAAAAATAAATCAATTTATAAAAAACAAAATAA
66 ATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAA
* * * * * * *
27940342 AAATTCTTTAGAATCGTAAAACGGAGTAGTTTTGTTCAAAAT--AAAAAATTTTGCGGCGTTTTC
131 AATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTT---GC-----A
27940405 TCATAAAACG
188 T-A-AAAACG
*
27940415 CCGCTAAAGATTT-TAAAAAAAATTTAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAA
1 CCGCTAAAGATTTAT-AAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAA
* *
27940479 AATGAAATAGCGGCCTTTTTTATAAAAATGCCGCAAAAATAAATCAATTTATAAAAAACAAAATA
65 AATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATA
27940544 AAATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGCATAAAAAC
130 AAATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGCATAAAAAC
27940609 G
195 G
27940610 CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
1 CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
* *
27940675 ATGAAATAGCGGCGTTTTTATAAAAAAACGCCGCAAAAATAAATCAATTTATAAAAAAGAAAATA
66 ATGAAATAGCGGCGTTTTT-TATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATA
* * * *
27940740 AAATTGTTTTAAAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAACAATTTTGC
130 AAATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGC
27940797 GGCGTTTTAA
Statistics
Matches: 538, Mismatches: 32, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
193 9 0.02
195 249 0.46
196 99 0.18
197 1 0.00
201 1 0.00
202 4 0.01
203 166 0.31
205 9 0.02
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (195 bp):
CCGCTAAAGATTTATAAAAAAATTAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTGATCAAA
ATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAA
AATTTTTTTAGAATAGCAAAACGGCGTAGTTTTGTTCAAAATAAAAAAAAATTTGCATAAAAACG
Found at i:27942804 original size:6 final size:6
Alignment explanation
Indices: 27942793--27942821 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27942783 ATGGTATTCC
27942793 TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
27942822 CCACGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:27944532 original size:43 final size:43
Alignment explanation
Indices: 27944465--27944728 Score: 277
Period size: 43 Copynumber: 6.2 Consensus size: 43
27944455 TATTTTTAGT
* * *
27944465 GGCGTTTTTGCA-AGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTTTG-AGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * *
27944507 GGCGTTTTCTGATAAAAGCGCCGCTAAAGGTCTTGATCTACAGT
1 GGCGTTTT-TGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * * *
27944551 GGCGTTTGTG-GAAAAATCCCCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTTTGAG-AAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * * *
27944594 GGCATTTGTTG-TAAAAGCGCCGCTAAAGATCCTGATCTATAGC
1 GGCGTTT-TTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* *
27944637 GGCGTTTATG-GAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * * *
27944679 GGCGTTTGTGAGGAAAGCGCCGCTAAAGGTCATGGTCTATAGC
1 GGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
27944722 GGCGTTT
1 GGCGTTT
27944729 ATTTCCACAA
Statistics
Matches: 188, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
42 50 0.27
43 120 0.64
44 18 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
GGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
Found at i:27944702 original size:85 final size:83
Alignment explanation
Indices: 27944465--27944730 Score: 291
Period size: 85 Copynumber: 3.1 Consensus size: 83
27944455 TATTTTTAGT
* * * * *
27944465 GGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTTCTGATAAAAGCGCC
1 GGCGTTTATGGAA-AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG-TTTGTG--AAAAGCGCC
* * *
27944529 GCTAAAGGTCTTGATCTACAGT
62 GCTAAAGGTCATGATCTATAGC
* * * * *
27944551 GGCGTTTGTGGAAAAATCCCCGCTAAAGGTCTTGAGCTATAGCGGCATTTGTTGTAAAAGCGCCG
1 GGCGTTTATGG-AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTG-TG-AAAAGCGCCG
* *
27944616 CTAAAGATCCTGATCTATAGC
63 CTAAAGGTCATGATCTATAGC
*
27944637 GGCGTTTATGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGAGGAAAGCGCCGC
1 GGCGTTTATGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGA--AAAGCGCCGC
*
27944702 TAAAGGTCATGGTCTATAGC
64 TAAAGGTCATGATCTATAGC
27944722 GGCGTTTAT
1 GGCGTTTAT
27944731 TTCCACAAAC
Statistics
Matches: 153, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
83 1 0.01
84 2 0.01
85 70 0.46
86 63 0.41
87 17 0.11
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (83 bp):
GGCGTTTATGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAGCGCCGCTA
AAGGTCATGATCTATAGC
Found at i:27953030 original size:34 final size:32
Alignment explanation
Indices: 27952950--27953032 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 32
27952940 TCTCAAGGCT
*
27952950 GCAGCGCCTAATATATCCAACAGTTTCAAGATA
1 GCAG-GCCAAATATATCCAACAGTTTCAAGATA
*
27952983 TGGCATGCCAAATATATCCAACAGTTTCAAGATCA
1 --GCAGGCCAAATATATCCAACAGTTTCAAGAT-A
27953018 -CAAGGCCAAA-ATATC
1 GC-AGGCCAAATATATC
27953033 TGAAATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 6 0.14
33 7 0.16
34 26 0.60
35 4 0.09
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (32 bp):
GCAGGCCAAATATATCCAACAGTTTCAAGATA
Found at i:27962456 original size:14 final size:14
Alignment explanation
Indices: 27962437--27962472 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
27962427 TGACAATCAA
27962437 TAAAATCCCGATGT
1 TAAAATCCCGATGT
27962451 TAAAATCCCGATGT
1 TAAAATCCCGATGT
27962465 TAAAATCC
1 TAAAATCC
27962473 AGAAAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (14 bp):
TAAAATCCCGATGT
Found at i:27962753 original size:27 final size:27
Alignment explanation
Indices: 27962723--27962782 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
27962713 TTTAATAGTG
27962723 ACAGTA-CAATATGGGCCATAGCCCAA
1 ACAGTATCAATATGGGCCATAGCCCAA
* * * *
27962749 TACAGTATTAGTGTGGGCCTTAGCCCAA
1 -ACAGTATCAATATGGGCCATAGCCCAA
27962777 ACAGTA
1 ACAGTA
27962783 ACGGTGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (27 bp):
ACAGTATCAATATGGGCCATAGCCCAA
Found at i:27963176 original size:32 final size:32
Alignment explanation
Indices: 27963129--27963237 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 32
27963119 ATGTGATTGC
* *
27963129 CACAAAGCCAACAGTAGCAGTGACATGATCGA
1 CACAAAGCCATCAGTAACAGTGACATGATCGA
* * * *
27963161 TACACAA-CCATCAGTAACGGTGATATGATCGG
1 CACA-AAGCCATCAGTAACAGTGACATGATCGA
** * * *
27963193 CACAAAGCCATCAGTAATGGTAATATGATCGG
1 CACAAAGCCATCAGTAACAGTGACATGATCGA
*
27963225 CAGAAAGCCATCA
1 CACAAAGCCATCA
27963238 ATAGCATCGC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.03
32 61 0.94
33 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (32 bp):
CACAAAGCCATCAGTAACAGTGACATGATCGA
Found at i:27963267 original size:26 final size:26
Alignment explanation
Indices: 27963237--27963290 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
27963227 GAAAGCCATC
27963237 AATAGCATCGCAGCAAAGCTGCCAGT
1 AATAGCATCGCAGCAAAGCTGCCAGT
** *
27963263 AATAGTTTTGCAGCAAAGCTGCCAGT
1 AATAGCATCGCAGCAAAGCTGCCAGT
27963289 AA
1 AA
27963291 CAGTATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
AATAGCATCGCAGCAAAGCTGCCAGT
Found at i:27963316 original size:27 final size:27
Alignment explanation
Indices: 27963284--27963343 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
27963274 AGCAAAGCTG
27963284 CCAGTAACAGT-ATATGTTGCCA-AGCCA
1 CCAGTAACAGTGAT-TG-TGCCAGAGCCA
*
27963311 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGCCAGAGCCA
27963338 CCAGTA
1 CCAGTA
27963344 CAATACTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 24 0.80
28 2 0.07
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGCCAGAGCCA
Found at i:27963451 original size:24 final size:24
Alignment explanation
Indices: 27963415--27963545 Score: 156
Period size: 24 Copynumber: 5.5 Consensus size: 24
27963405 AGCACAGAAC
**
27963415 CAGTCATACAAATCACAGAAAAAT
1 CAGTCATTTAAATCACAGAAAAAT
*
27963439 TAGTCATTTAAATCACAGAAAAAT
1 CAGTCATTTAAATCACAGAAAAAT
* *
27963463 CAGTTATTTAAATCACAGACAAAT
1 CAGTCATTTAAATCACAGAAAAAT
* *
27963487 CAGTCATTTACATCTCAGAAAAAT
1 CAGTCATTTAAATCACAGAAAAAT
* **
27963511 CAGTCATTTACATCACAGGTAAAT
1 CAGTCATTTAAATCACAGAAAAAT
27963535 C-GATCATTTAA
1 CAG-TCATTTAA
27963546 CCTCGAGGGT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 1 0.01
24 91 0.99
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (24 bp):
CAGTCATTTAAATCACAGAAAAAT
Found at i:27963598 original size:27 final size:27
Alignment explanation
Indices: 27963562--27963921 Score: 368
Period size: 27 Copynumber: 13.4 Consensus size: 27
27963552 GGGTAAAATA
*
27963562 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * * *
27963589 GTTATCTTACCCTACAGGAGCATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* *
27963616 ATCATTTTACCCTACA-AGG-ACTTACG
1 GTCATTTTACCCTACAGGGGTA-TTACG
* *
27963642 GTTATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
27963669 GTTATTTTACCCTACAGGGGTATTGCT
1 GTCATTTTACCCTACAGGGGTATTACG
27963696 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * * *
27963723 GTTATTTTACCATATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGTATTACG
27963750 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
27963777 ATCATTTTACCATACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
27963804 GTTATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
** *
27963831 ACCATTTTATCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* ** **
27963858 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
27963885 GT-GTTCTACCCTAC-GGGGTAATTTCG
1 GTCATTTTACCCTACAGGGGT-ATTACG
*
27963911 ATCATTTTACC
1 GTCATTTTACC
27963922 TTATGGGGGC
Statistics
Matches: 273, Mismatches: 55, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
25 6 0.02
26 33 0.12
27 233 0.85
28 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:27963757 original size:81 final size:81
Alignment explanation
Indices: 27963565--27963881 Score: 406
Period size: 81 Copynumber: 3.9 Consensus size: 81
27963555 TAAAATAGTC
* * * * *
27963565 ATTTTACCCTACAGGGGCATTACGGTTATCTTACCCTACAGGAGCATTACAATCATTTTACCCTA
1 ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTA
*
27963630 CA-AGG-ACTTACGGTT
66 CAGGGGTA-TTACGGTT
* * * *
27963645 ATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTGCTG-TCATTTTACCCT
1 ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTAC-GATCATTTTACCCT
27963709 ACAGGGGTATTACGGTT
65 ACAGGGGTATTACGGTT
* * * *
27963726 ATTTTACCATATAGGGGCATTATGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCATA
1 ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTA
*
27963791 CAGGGGCATTACGGTT
66 CAGGGGTATTACGGTT
* ** *
27963807 ATTTTACCCTACAGGGGTATTACGACCATTTTATCCTACAGGGGTATTACGATCATTTTACCCTA
1 ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTA
**
27963872 TGGGGGTATT
66 CAGGGGTATT
27963882 TTGGTGTTCT
Statistics
Matches: 207, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
80 60 0.29
81 146 0.71
82 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (81 bp):
ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTA
CAGGGGTATTACGGTT
Found at i:27963929 original size:27 final size:26
Alignment explanation
Indices: 27963645--27963963 Score: 153
Period size: 27 Copynumber: 11.8 Consensus size: 26
27963635 ACTTACGGTT
* * *
27963645 ATTTTACCCTATAGGGGTATTACGGTT
1 ATTTTACCCTAT-GGGGTATTTCGATC
* *
27963672 ATTTTACCCTACAGGGGTATTGCTG-TC
1 ATTTTACCCTA-TGGGGTATTTC-GATC
* * * *
27963699 ATTTTACCCTACAGGGGTATTACGGTT
1 ATTTTACCCTA-TGGGGTATTTCGATC
* * *
27963726 ATTTTACCATATAGGGGCATTAT-GGTC
1 ATTTTACCCTAT-GGGGTATT-TCGATC
* *
27963753 ATTTTACCCTACAGGGGTATTACGATC
1 ATTTTACCCTA-TGGGGTATTTCGATC
* * * * * *
27963780 ATTTTACCATACAGGGGCATTACGGTT
1 ATTTTACCCTA-TGGGGTATTTCGATC
* * *
27963807 ATTTTACCCTACAGGGGTATTACGACC
1 ATTTTACCCTA-TGGGGTATTTCGATC
* * *
27963834 ATTTTATCCTACAGGGGTATTACGATC
1 ATTTTACCCTA-TGGGGTATTTCGATC
* *
27963861 ATTTTACCCTATGGGGGTATTTTGGT-
1 ATTTTACCCTAT-GGGGTATTTCGATC
* * *
27963887 GTTCTACCCTACGGGGTAATTTCGATC
1 ATTTTACCCTATGGGGT-ATTTCGATC
* * *
27963914 ATTTTACCTTATGGGGGCATTTC-AGTT
1 ATTTTACCCTAT-GGGGTATTTCGA-TC
27963941 ATTTTACCC-ATCGAGGGTATTTC
1 ATTTTACCCTAT-G-GGGTATTTC
27963964 AGTTATTTTA
Statistics
Matches: 234, Mismatches: 45, Indels: 26
0.77 0.15 0.09
Matches are distributed among these distances:
25 5 0.02
26 20 0.09
27 204 0.87
28 5 0.02
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGATC
Found at i:27963992 original size:38 final size:38
Alignment explanation
Indices: 27963936--27964012 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
27963926 GGGGGCATTT
* *
27963936 CAGTTATTTTACCCATCGAGGGTATTTCAGTTATTTTA
1 CAGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
27963974 CAGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
1 CAGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
27964012 C
1 C
27964013 CCTTTGAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (38 bp):
CAGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
Found at i:27964007 original size:27 final size:27
Alignment explanation
Indices: 27963974--27964028 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
27963964 AGTTATTTTA
27963974 CAGTCATTTTACCCATCGAGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
* *
27964001 CAGTCATTTTACCCTTTGAGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
27964028 C
1 C
27964029 GATCTAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCATCGAGGGTATTT
Found at i:27968602 original size:50 final size:50
Alignment explanation
Indices: 27968548--27968654 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
27968538 ACATAAGAGT
* * *
27968548 TCTCATATCGGTGCCCATGCCATCTCCCAGACATAGTCTTACGGGGGACC
1 TCTCATATCGGTGCCAACGCCATCTCCCAGACATAGTCTTACAGGGGACC
* * * * *
27968598 TCTCATCTCGGTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACC
1 TCTCATATCGGTGCCAACGCCATCTCCCAGACATAGTCTTACAGGGGACC
*
27968648 ACTCATA
1 TCTCATA
27968655 ACTTCAATGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATCTCCCAGACATAGTCTTACAGGGGACC
Found at i:27969325 original size:6 final size:6
Alignment explanation
Indices: 27969316--27969351 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27969306 ATAAAATCGA
*
27969316 TTTTGA TTTTG- TTTTGC TTTTGC TTTTGC TTTTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC T
27969352 CAAATTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.03, C:0.11, G:0.17, T:0.69
Consensus pattern (6 bp):
TTTTGC
Found at i:27969350 original size:18 final size:17
Alignment explanation
Indices: 27969316--27969351 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27969306 ATAAAATCGA
27969316 TTTTGATTTTGTTTTGC
1 TTTTGATTTTGTTTTGC
*
27969333 TTTTGCTTTTGCTTTTGC
1 TTTTGATTTTG-TTTTGC
27969351 T
1 T
27969352 CAAATTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.03, C:0.11, G:0.17, T:0.69
Consensus pattern (17 bp):
TTTTGATTTTGTTTTGC
Found at i:27971855 original size:51 final size:51
Alignment explanation
Indices: 27971783--27972117 Score: 312
Period size: 51 Copynumber: 6.6 Consensus size: 51
27971773 GATAAACACA
* * * * *
27971783 TGTGTAGTACTGTGTGGAGGCTACTACGTGTGCCGATAAA-TAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAACT-TTGGTCACG
* *
27971834 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGAG-CACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-CTTTG-GTCACG
* * * * * * *
27971885 TGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTATGGTTACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAACTTTGGTCACG
*
27971936 TGTGTAGTACTAAGTGAAGGCTACAATA-G-GTACCGA-AAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTAC--TACGTGTACCGATAAA-CTTTGGTCACG
* * * * *
27971987 TATGTAGTACTATATGAAGGCTACTACATGAACCG-TAAAAC-TTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAACTTTGGTCACG
* * * * *
27972037 TGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ATTGATTACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAACTTTGGTCACG
27972086 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
27972118 TCGAATGGAT
Statistics
Matches: 235, Mismatches: 36, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
49 44 0.19
50 47 0.20
51 133 0.57
52 9 0.04
53 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAACTTTGGTCACG
Found at i:27971959 original size:102 final size:102
Alignment explanation
Indices: 27971783--27972120 Score: 377
Period size: 102 Copynumber: 3.3 Consensus size: 102
27971773 GATAAACACA
* * ** *
27971783 TGTGTAGTACTGTGTGGAGGCTACTACGTGTGCCGATAAA-TAATGGTCACATGTGTAGTACTAA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTACTAA
27971847 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGAGCACG
65 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGAGCACG
* * *
27971885 TGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTACTAAG
*
27971950 TGAAGGCTACAATAG-GTACCGAAAAGCTTTG-GTCACG
66 TGAAGGCTACTAT-GTGTACCGAAAAGCTTTGAG-CACG
* * * * * * * *
27971987 TATGTAGTACTATATGAAGGCTACTACATG-AACCGTAAAACT-TGATCACGTGTGTAGTACTAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGTACTAA
* * * **
27972050 GTGAAGGCTACTACGTGAACTGTAAAA---TTGATTACG
65 GTGAAGGCTACTATGTGTACCG-AAAAGCTTTGAGCACG
27972086 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
27972121 AATGGATAAA
Statistics
Matches: 199, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
99 33 0.17
100 3 0.02
101 38 0.19
102 123 0.62
103 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTACTAAG
TGAAGGCTACTATGTGTACCGAAAAGCTTTGAGCACG
Found at i:27976231 original size:16 final size:15
Alignment explanation
Indices: 27976212--27976246 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
27976202 TCTTGAATTG
*
27976212 TTATTCATTTCTATCT
1 TTATTCATGTCTAT-T
27976228 TTATTCATGTCTATT
1 TTATTCATGTCTATT
27976243 TTAT
1 TTAT
27976247 ATATAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.14, G:0.03, T:0.63
Consensus pattern (15 bp):
TTATTCATGTCTATT
Found at i:27988170 original size:25 final size:25
Alignment explanation
Indices: 27988106--27988171 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
27988096 CAGGCCCATT
*
27988106 TTCACAGCTCGGGTGAGCATATTTA
1 TTCACAGCTCGTGTGAGCATATTTA
* *
27988131 TTCACAACTCATGTGAGCATATTTA
1 TTCACAGCTCGTGTGAGCATATTTA
27988156 GTT-ACAGCTCGTGTGA
1 -TTCACAGCTCGTGTGA
27988172 ACATTTATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATATTTA
Found at i:27996568 original size:43 final size:43
Alignment explanation
Indices: 27996521--27996625 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 43
27996511 AAATATAATG
*
27996521 GCACACATAGTGCATCATCGGGAA-AG-TCGAAGTAATTATACTA
1 GCACACATAGTGCATCATC--GAACAGACCGAAGTAATTATACTA
* * *
27996564 GCACACGA-AGGGCATCATCGAACAGACCGAAGTAATTATATTG
1 GCACAC-ATAGTGCATCATCGAACAGACCGAAGTAATTATACTA
27996607 GCACACATAGTGCATCATC
1 GCACACATAGTGCATCATC
27996626 AGATAAACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
41 3 0.06
42 3 0.06
43 46 0.87
44 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (43 bp):
GCACACATAGTGCATCATCGAACAGACCGAAGTAATTATACTA
Found at i:27998623 original size:10 final size:10
Alignment explanation
Indices: 27998601--27998631 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
27998591 CAATTTTAAC
27998601 ATGTTTGAAAA
1 ATGTTT-AAAA
27998612 ATGTTTAAAA
1 ATGTTTAAAA
27998622 ATGTTTAAAA
1 ATGTTTAAAA
27998632 GTTTGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (10 bp):
ATGTTTAAAA
Found at i:28001547 original size:31 final size:31
Alignment explanation
Indices: 28001510--28001577 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
28001500 CAAAGAGCTT
*
28001510 AATTGATTGAAAATTTGACATTTAGGGATTG
1 AATTGATTGAAAATTTGACATTTAGAGATTG
28001541 AATTGATTGAAAATTTGACATTTAGAGATTG
1 AATTGATTGAAAATTTGACATTTAGAGATTG
28001572 AATTGA
1 AATTGA
28001578 GTGTAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (31 bp):
AATTGATTGAAAATTTGACATTTAGAGATTG
Found at i:28008002 original size:42 final size:42
Alignment explanation
Indices: 28007944--28008028 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
28007934 GTTGATATAT
* * * *
28007944 TTTGTGAAAACGAATGTCATATCTTGCTTCTCTTGTGCCCTA
1 TTTGAGAAAACCAATGTCATATCTTGCCTCTCATGTGCCCTA
28007986 TTTGAGAAAACCAATGTCATATCTTGCCTCTCATGTGCCCTA
1 TTTGAGAAAACCAATGTCATATCTTGCCTCTCATGTGCCCTA
28008028 T
1 T
28008029 CTTTCTATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (42 bp):
TTTGAGAAAACCAATGTCATATCTTGCCTCTCATGTGCCCTA
Found at i:28010626 original size:12 final size:12
Alignment explanation
Indices: 28010609--28010633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28010599 CTTCTTGATG
28010609 AACCTCATTACA
1 AACCTCATTACA
28010621 AACCTCATTACA
1 AACCTCATTACA
28010633 A
1 A
28010634 CTATAGACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (12 bp):
AACCTCATTACA
Found at i:28016140 original size:12 final size:12
Alignment explanation
Indices: 28016123--28016148 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28016113 TCTCGTGCTT
28016123 TTGCCATAATAC
1 TTGCCATAATAC
28016135 TTGCCATAATAC
1 TTGCCATAATAC
28016147 TT
1 TT
28016149 TCACCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (12 bp):
TTGCCATAATAC
Found at i:28021966 original size:50 final size:50
Alignment explanation
Indices: 28021905--28022046 Score: 248
Period size: 50 Copynumber: 2.8 Consensus size: 50
28021895 GATAATAACA
* *
28021905 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
28021955 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
28022005 TGCCAACACCATGTCCCATACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
28022047 TTACCCAAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28024766 original size:16 final size:17
Alignment explanation
Indices: 28024740--28024772 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28024730 TATTATCATT
28024740 TTTTCAATTATATTATA
1 TTTTCAATTATATTATA
*
28024757 TTTT-AATTATTTTATA
1 TTTTCAATTATATTATA
28024773 AAGTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCAATTATATTATA
Found at i:28032227 original size:63 final size:64
Alignment explanation
Indices: 28032127--28032255 Score: 242
Period size: 63 Copynumber: 2.0 Consensus size: 64
28032117 CCCTTTGAGA
28032127 TTCTATGTGATGCTAGTGATAAAGCTGTTGGTGCGGCTTTAGGACAAAGGAATGGGAGAGAGTC
1 TTCTATGTGATGCTAGTGATAAAGCTGTTGGTGCGGCTTTAGGACAAAGGAATGGGAGAGAGTC
*
28032191 TTCTATGTGATG-TAGTGATAAAGCTGTTGGTGCGGCTTTATGACAAAGGAATGGGAGAGAGTC
1 TTCTATGTGATGCTAGTGATAAAGCTGTTGGTGCGGCTTTAGGACAAAGGAATGGGAGAGAGTC
28032254 TT
1 TT
28032256 ATATTATTAG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 52 0.81
64 12 0.19
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.30
Consensus pattern (64 bp):
TTCTATGTGATGCTAGTGATAAAGCTGTTGGTGCGGCTTTAGGACAAAGGAATGGGAGAGAGTC
Found at i:28033990 original size:26 final size:26
Alignment explanation
Indices: 28033954--28034005 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28033944 CTTGTGAGAG
28033954 GCAACCCACGTTTTCAGGGAAGTTTT
1 GCAACCCACGTTTTCAGGGAAGTTTT
28033980 GCAACCCACGTTTTCAGGGAAGTTTT
1 GCAACCCACGTTTTCAGGGAAGTTTT
28034006 CTTTCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (26 bp):
GCAACCCACGTTTTCAGGGAAGTTTT
Found at i:28034911 original size:20 final size:22
Alignment explanation
Indices: 28034882--28034931 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
28034872 TCTGCTTTCG
*
28034882 GAAAGAAAAAAGAGAA-A-AAA
1 GAAAGGAAAAAGAGAAGAGAAA
28034902 GAAAGGAAAAAGAGAAGAGAAA
1 GAAAGGAAAAAGAGAAGAGAAA
*
28034924 GAAGGGAA
1 GAAAGGAA
28034932 TTGATGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 1 0.04
22 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
GAAAGGAAAAAGAGAAGAGAAA
Found at i:28046463 original size:45 final size:45
Alignment explanation
Indices: 28046414--28046580 Score: 217
Period size: 45 Copynumber: 3.7 Consensus size: 45
28046404 TATAGGAATT
* * *
28046414 GAGTAAAACCATAGTTGAAAGACACTATGGCATCACAATTTAGAC
1 GAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTTAGAC
* *
28046459 GAGTAAGACCATAGCTAAAAGACACTATGGCATCATGATTTAGAC
1 GAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTTAGAC
* * * * * * *
28046504 AAGTAAGTCCATAGCTGAAAGACGCTATGACATCACGATTCAAAA
1 GAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTTAGAC
*
28046549 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GAGTAAGACCATAGCTGAAAGACACTATGGCA
28046581 ACATGACGGG
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 103 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTTAGAC
Found at i:28046525 original size:90 final size:90
Alignment explanation
Indices: 28046422--28046586 Score: 240
Period size: 90 Copynumber: 1.8 Consensus size: 90
28046412 TTGAGTAAAA
* * * * *
28046422 CCATAGTTGAAAGACACTATGGCATCACAATTTAGACGAGTAAGACCATAGCTAAAAGACACTAT
1 CCATAGCTGAAAGACACTATGACATCACAATTCAAAAGAGTAAGACCATAGCTAAAAGACACTAT
*
28046487 GGCATCATGATTTAGACAAGTAAGT
66 GGCAACATGATTTAGACAAGTAAGT
* * * *
28046512 CCATAGCTGAAAGACGCTATGACATCACGATTCAAAAGAGTAAGACCATAGTTGAAAGACACTAT
1 CCATAGCTGAAAGACACTATGACATCACAATTCAAAAGAGTAAGACCATAGCTAAAAGACACTAT
28046577 GGCAACATGA
66 GGCAACATGA
28046587 CGGGAAATGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (90 bp):
CCATAGCTGAAAGACACTATGACATCACAATTCAAAAGAGTAAGACCATAGCTAAAAGACACTAT
GGCAACATGATTTAGACAAGTAAGT
Found at i:28046614 original size:46 final size:46
Alignment explanation
Indices: 28046364--28046675 Score: 192
Period size: 45 Copynumber: 6.9 Consensus size: 46
28046354 GTTGGCTCGA
* * **
28046364 GAAATGAATAAGACCATAATTGAAAGACACTATAGC-ACTAT-ATAG
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAAC-ATGACGG
* * * * * ***
28046409 GAATTGAGTAAAACCATAGTTGAAAGACACTATGGCATCA-CAATT
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
* * * * * * * ***
28046454 TAGACGAGTAAGACCATAGCTAAAAGACACTATGGCATCATGATTTA
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGA-CGG
* * * * * * **
28046501 GACAA-G--TAAGTCCATAGCTGAAAGACGCTATGACATCACGA-TT
1 GA-AATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
* * *
28046544 CAAAAGAGTAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
* * * *
28046590 GAAATGGATAAGACGATGGTTGAAAGACACTATGGCAACATGCCGG
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
*
28046636 GAAATGAATAAGACCATAGTTGAAAG--ACTATGGCATCATG
1 GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATG
28046676 CTAAACATAA
Statistics
Matches: 211, Mismatches: 47, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
42 2 0.01
43 3 0.01
44 13 0.06
45 125 0.59
46 64 0.30
47 3 0.01
48 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (46 bp):
GAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGG
Found at i:28046867 original size:40 final size:40
Alignment explanation
Indices: 28046766--28046908 Score: 121
Period size: 40 Copynumber: 3.6 Consensus size: 40
28046756 ACGAATGGTT
* * *
28046766 ATATGAATTAGTTATACA-AAATGGATATATGAAATGATG
1 ATATGAATTAGTTATATAGAAATAGATATACGAAATGATG
* * * *
28046805 ATAAGAATTGGTTATATGGAAATAGATGTACGAAA-GAGTTG
1 ATATGAATTAGTTATATAGAAATAGATATACGAAATGA--TG
* * * *
28046846 -TATGAATTAGTTATATAGAAATAGATAAACAAAATAATT
1 ATATGAATTAGTTATATAGAAATAGATATACGAAATGATG
* * *
28046885 ATATGAATCAGATATATGGAAATA
1 ATATGAATTAGTTATATAGAAATA
28046909 ATTATATGAA
Statistics
Matches: 81, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 17 0.21
40 61 0.75
41 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (40 bp):
ATATGAATTAGTTATATAGAAATAGATATACGAAATGATG
Found at i:28048905 original size:21 final size:21
Alignment explanation
Indices: 28048881--28048932 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
28048871 CGTTCTCTTT
* *
28048881 TTTTTATTTCT-TTTTCTTTAC
1 TTTTT-TTTCTCTCTTCCTTAC
*
28048902 TTTTTTTTATCTCTTCCTTAC
1 TTTTTTTTCTCTCTTCCTTAC
28048923 TTTTTCTTTC
1 TTTTT-TTTC
28048933 ATCTTCCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTTCTCTCTTCCTTAC
Found at i:28048937 original size:21 final size:21
Alignment explanation
Indices: 28048898--28048939 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28048888 TTCTTTTTCT
*
28048898 TTACTTTTTTTTATCTCTTCC
1 TTACTTTTTCTTATCTCTTCC
28048919 TTACTTTTTCTT-TCATCTTCC
1 TTACTTTTTCTTATC-TCTTCC
28048940 CCTTTCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (21 bp):
TTACTTTTTCTTATCTCTTCC
Found at i:28049881 original size:19 final size:21
Alignment explanation
Indices: 28049839--28049883 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
28049829 TATCCATTAA
28049839 TAAAAATATAATTATATTATT
1 TAAAAATATAATTATATTATT
28049860 TAAAAATA-AATT-TA-TATCT
1 TAAAAATATAATTATATTAT-T
28049879 TAAAA
1 TAAAA
28049884 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 4 0.17
21 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATAATTATATTATT
Found at i:28050025 original size:166 final size:167
Alignment explanation
Indices: 28049738--28050072 Score: 645
Period size: 166 Copynumber: 2.0 Consensus size: 167
28049728 TAATATAAAA
28049738 TTTATATTATAGCTTTATAAACTTAATTTGCTATTAAGTCAGAATTTGTGTGAAATATTTGGATT
1 TTTATATTATAGCTTTATAAACTTAATTTGCTATTAAGTCAGAATTTGTGTGAAATATTTGGATT
*
28049803 TGATATATCCAATAGCAAAGTATTTTTATCCATTAATAAAAATATAATTATATTATTTAAAAATA
66 TGATATATCCAATAGCAAAGTATTTTTAACCATTAATAAAAATATAATTATATTATTTAAAAATA
28049868 AATTTATATCTTAAAATTTAAATATTTTATTATTTAT
131 AATTTATATCTTAAAATTTAAATATTTTATTATTTAT
28049905 TTTATATTATAG-TTTATAAACTTAATTTGCTATTAAGTCAGAATTTGTGTGAAATATTTGGATT
1 TTTATATTATAGCTTTATAAACTTAATTTGCTATTAAGTCAGAATTTGTGTGAAATATTTGGATT
*
28049969 TGATATATCCAATAGCAAAGTATTTTTAACCCTTAATAAAAATATAATTATATTATTTAAAAATA
66 TGATATATCCAATAGCAAAGTATTTTTAACCATTAATAAAAATATAATTATATTATTTAAAAATA
28050034 AATTTATATCTTAAAATTTAAATATTTTATTATTTAT
131 AATTTATATCTTAAAATTTAAATATTTTATTATTTAT
28050071 TT
1 TT
28050073 AACAAAAAAT
Statistics
Matches: 166, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
166 154 0.93
167 12 0.07
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (167 bp):
TTTATATTATAGCTTTATAAACTTAATTTGCTATTAAGTCAGAATTTGTGTGAAATATTTGGATT
TGATATATCCAATAGCAAAGTATTTTTAACCATTAATAAAAATATAATTATATTATTTAAAAATA
AATTTATATCTTAAAATTTAAATATTTTATTATTTAT
Found at i:28050047 original size:19 final size:21
Alignment explanation
Indices: 28050005--28050049 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
28049995 TAACCCTTAA
28050005 TAAAAATATAATTATATTATT
1 TAAAAATATAATTATATTATT
28050026 TAAAAATA-AATT-TA-TATCT
1 TAAAAATATAATTATATTAT-T
28050045 TAAAA
1 TAAAA
28050050 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 4 0.17
21 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATAATTATATTATT
Found at i:28052638 original size:21 final size:21
Alignment explanation
Indices: 28052614--28052665 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
28052604 CGTTCTCTTT
* *
28052614 TTTTTATTTCT-TTTTCTTTAC
1 TTTTT-TTTCTCTCTTCCTTAC
*
28052635 TTTTTTTTATCTCTTCCTTAC
1 TTTTTTTTCTCTCTTCCTTAC
28052656 TTTTTCTTTC
1 TTTTT-TTTC
28052666 ATCTTCCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTTCTCTCTTCCTTAC
Found at i:28052670 original size:21 final size:21
Alignment explanation
Indices: 28052631--28052672 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28052621 TTCTTTTTCT
*
28052631 TTACTTTTTTTTATCTCTTCC
1 TTACTTTTTCTTATCTCTTCC
28052652 TTACTTTTTCTT-TCATCTTCC
1 TTACTTTTTCTTATC-TCTTCC
28052673 CCTTTCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (21 bp):
TTACTTTTTCTTATCTCTTCC
Found at i:28053614 original size:19 final size:21
Alignment explanation
Indices: 28053572--28053616 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
28053562 TATCCATTAA
28053572 TAAAAATATAATTATATTATT
1 TAAAAATATAATTATATTATT
28053593 TAAAAATA-AATT-TA-TATCT
1 TAAAAATATAATTATATTAT-T
28053612 TAAAA
1 TAAAA
28053617 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 4 0.17
21 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATAATTATATTATT
Found at i:28065032 original size:70 final size:72
Alignment explanation
Indices: 28064904--28065048 Score: 215
Period size: 70 Copynumber: 2.0 Consensus size: 72
28064894 TTACTATCGC
* * *
28064904 TTGCTTATTGGATAGAGTTGACTATATGTTTTTTATAAGGAGGTGATTAGAACATCTCATTTTAT
1 TTGCTTATTGGATAGAGGTGACTATATGTTTTTTATAAGAAGGTGATTAAAACATCTCATTTTAT
28064969 TCAAA-A
66 TCAAATA
* *
28064975 TTGCTTATTGGATAGAGGT-ACTGTTTGTTTTTTATAAGAAGGT-ATTTAAAACATCTCATTTTA
1 TTGCTTATTGGATAGAGGTGACTATATGTTTTTTATAAGAAGGTGA-TTAAAACATCTCATTTTA
28065038 TTCAAATA
65 TTCAAATA
28065046 TTG
1 TTG
28065049 GAATTTTCTG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
69 1 0.01
70 44 0.66
71 22 0.33
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.44
Consensus pattern (72 bp):
TTGCTTATTGGATAGAGGTGACTATATGTTTTTTATAAGAAGGTGATTAAAACATCTCATTTTAT
TCAAATA
Found at i:28065903 original size:46 final size:46
Alignment explanation
Indices: 28065772--28065905 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 46
28065762 GTCTATGTGT
*
28065772 TAGGATATTATTATGAGATATTATCTCTTAGCAATTTGAGTT-TTAA
1 TAGGATATTATTATAAGATATTATCTCTTAGCAATTTGA-TTCTTAA
** * * *
28065818 TAGG--A-TAGCATAGGATATTATCTCTTAGCAATTTTATTCTTAG
1 TAGGATATTATTATAAGATATTATCTCTTAGCAATTTGATTCTTAA
*
28065861 TAGGATATTATTATAAGATATTATCT-TTAAGTAATTTGATTCTTA
1 TAGGATATTATTATAAGATATTATCTCTT-AGCAATTTGATTCTTA
28065906 CGTAACTACT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
42 2 0.03
43 33 0.46
44 1 0.01
45 3 0.04
46 33 0.46
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (46 bp):
TAGGATATTATTATAAGATATTATCTCTTAGCAATTTGATTCTTAA
Found at i:28065942 original size:56 final size:56
Alignment explanation
Indices: 28065880--28065994 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
28065870 ATTATAAGAT
* *
28065880 ATTATCTTTAAGTAATTTGATTCTTACGTAACTACTACTGTATAGATATATATATC
1 ATTATCTTTAAGTAATTTGATTCATACGTAACTACTACTGTATAGATATATATACC
*
28065936 ATTATCTTTTAGTAATTTGATTCATACGTAACTACTACTGTATAGATATATATACC
1 ATTATCTTTAAGTAATTTGATTCATACGTAACTACTACTGTATAGATATATATACC
28065992 ATT
1 ATT
28065995 TAGGTCTATC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (56 bp):
ATTATCTTTAAGTAATTTGATTCATACGTAACTACTACTGTATAGATATATATACC
Found at i:28066015 original size:56 final size:54
Alignment explanation
Indices: 28065899--28066015 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 54
28065889 AAGTAATTTG
* * * * * *
28065899 ATTCTTACGTAACTACTACTGTATAGATATATATATCATTATCTTTTAGTAATTTG
1 ATTCATACGTAACTACTACTGTATAGATATATATACCATTATCTATCAATAA--TA
28065955 ATTCATACGTAACTACTACTGTATAGATATATATACCATTTAGGTCTATCAATAA-A
1 ATTCATACGTAACTACTACTGTATAGATATATATACCA-TTA--TCTATCAATAATA
28066011 ATTCA
1 ATTCA
28066016 AGAGATTACC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
56 41 0.79
57 3 0.06
59 8 0.15
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (54 bp):
ATTCATACGTAACTACTACTGTATAGATATATATACCATTATCTATCAATAATA
Found at i:28071813 original size:41 final size:41
Alignment explanation
Indices: 28071754--28071908 Score: 152
Period size: 41 Copynumber: 3.8 Consensus size: 41
28071744 TGTACTGGAG
* * * * *
28071754 ATATTGTATTAGGTCTTGAACCTAGCAGGCTTTGTGCCTGT
1 ATATTGAATTAGGCCTTGAGCCTAGCAGGCTTTGTACCGGT
* *
28071795 ATATT-ATGTTAGGCCTTGAGCCTAGTAGGCTTTGTACCGGT
1 ATATTGA-ATTAGGCCTTGAGCCTAGCAGGCTTTGTACCGGT
* *
28071836 GTATTGAATTAGGCCTTGAGCCTAGCAAGCTTTG-AGCCGGT
1 ATATTGAATTAGGCCTTGAGCCTAGCAGGCTTTGTA-CCGGT
* * * * *
28071877 GTATTGCATCAAGCCTTCAGCCTAGCAGGCTT
1 ATATTGAATTAGGCCTTGAGCCTAGCAGGCTT
28071909 CTTGTCGGTG
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.01
41 93 0.98
42 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (41 bp):
ATATTGAATTAGGCCTTGAGCCTAGCAGGCTTTGTACCGGT
Found at i:28071918 original size:41 final size:40
Alignment explanation
Indices: 28071807--28071930 Score: 124
Period size: 41 Copynumber: 3.0 Consensus size: 40
28071797 ATTATGTTAG
* * *
28071807 GCCTTGAGCCTAGTAGGC-TTTGTACCGGTGTATTGAATTAG
1 GCCTTGAGCCTAGCAGGCTTTTGT--CGGTGTATTGAATCAA
* * * *
28071848 GCCTTGAGCCTAGCAAGCTTTGAGCCGGTGTATTGCATCAA
1 GCCTTGAGCCTAGCAGGCTTT-TGTCGGTGTATTGAATCAA
* *
28071889 GCCTTCAGCCTAGCAGGCTTCTTGTCGGTGTATTGTATCAA
1 GCCTTGAGCCTAGCAGGCTT-TTGTCGGTGTATTGAATCAA
28071930 G
1 G
28071931 TAACTTGTAC
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 64 0.94
42 3 0.04
43 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (40 bp):
GCCTTGAGCCTAGCAGGCTTTTGTCGGTGTATTGAATCAA
Found at i:28078261 original size:13 final size:13
Alignment explanation
Indices: 28078243--28078267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28078233 ATTGAGTTTT
28078243 AATTAATTAATTA
1 AATTAATTAATTA
28078256 AATTAATTAATT
1 AATTAATTAATT
28078268 GAAGTGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTAATTA
Found at i:28080208 original size:13 final size:13
Alignment explanation
Indices: 28080190--28080214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28080180 CGGCTGTGTG
28080190 CCACACATGGCCA
1 CCACACATGGCCA
28080203 CCACACATGGCC
1 CCACACATGGCC
28080215 GTGTGCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.48, G:0.16, T:0.08
Consensus pattern (13 bp):
CCACACATGGCCA
Found at i:28082556 original size:27 final size:27
Alignment explanation
Indices: 28082516--28082578 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28082506 TACAATTTTT
* * *
28082516 CCACAAAGGTAGTTCATTCAGAGTACG
1 CCACAAAGGCAGTTCATTCAAAGTACA
* *
28082543 CCACAAAGGCAGTTCTTTCAAAGTTCA
1 CCACAAAGGCAGTTCATTCAAAGTACA
28082570 CCACAAAGG
1 CCACAAAGG
28082579 TTATGCTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (27 bp):
CCACAAAGGCAGTTCATTCAAAGTACA
Found at i:28082587 original size:27 final size:27
Alignment explanation
Indices: 28082543--28082625 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
28082533 TCAGAGTACG
*
28082543 CCACAAAGGC-AGTTCTTTCAAAGTTCA
1 CCACAAAGGCTA-TGCTTTCAAAGTTCA
* * **
28082570 CCACAAAGGTTATGCTTTCATAGTTTG
1 CCACAAAGGCTATGCTTTCAAAGTTCA
* **
28082597 CCACAAAGGCTATTCTTTCAGGGTTCA
1 CCACAAAGGCTATGCTTTCAAAGTTCA
28082624 CC
1 CC
28082626 GTGAAGGCTC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (27 bp):
CCACAAAGGCTATGCTTTCAAAGTTCA
Found at i:28084764 original size:23 final size:22
Alignment explanation
Indices: 28084721--28084764 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
28084711 TTCTAAGTCG
28084721 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
28084744 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
28084765 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:28084928 original size:51 final size:50
Alignment explanation
Indices: 28084859--28084997 Score: 152
Period size: 51 Copynumber: 2.7 Consensus size: 50
28084849 ATGTCCGGTT
* *
28084859 CACATAATAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTACACATAGTACTACACATGTGACCA-AACCATCCGATA
* * * ** * * *
28084910 CACGTAGTAGCCTGCACATGGTACTACACACATGATCGAAACTATCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACATGTGA-CCAAACCATCCGATA
* *
28084961 CGCATAGTAGCCTACACATAGTACTACACATGCGACC
1 CACATAGTAGCCTACACATAGTACTACACATGTGACC
28084998 TATCATTTCG
Statistics
Matches: 69, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
50 1 0.01
51 66 0.96
52 2 0.03
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (50 bp):
CACATAGTAGCCTACACATAGTACTACACATGTGACCAAACCATCCGATA
Found at i:28093271 original size:42 final size:42
Alignment explanation
Indices: 28093212--28093300 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
28093202 ATAGCCTAGC
* *
28093212 ACACGGCCTAGAACACGGGTC-TGTGTGGCAACTTAGAGAGTT
1 ACACGGCCTAGAACACGGG-CATGTGGGGCAACTCAGAGAGTT
* *
28093254 ACACGGCCTAGCACACGGGCATGTGGGGCAACTCAGTGAGTT
1 ACACGGCCTAGAACACGGGCATGTGGGGCAACTCAGAGAGTT
28093296 ACACG
1 ACACG
28093301 AATGAAGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (42 bp):
ACACGGCCTAGAACACGGGCATGTGGGGCAACTCAGAGAGTT
Found at i:28094802 original size:14 final size:12
Alignment explanation
Indices: 28094783--28094849 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
28094773 TGAACCCCTT
28094783 ATTAAACATAAAAA
1 ATTAAA-AT-AAAA
*
28094797 ATTAAAATTAAA
1 ATTAAAATAAAA
**
28094809 ATTAAAGGAAAA
1 ATTAAAATAAAA
*
28094821 GATAAAAATGAAAA
1 -ATTAAAAT-AAAA
*
28094835 ATAAAAATAAAA
1 ATTAAAATAAAA
28094847 ATT
1 ATT
28094850 TTAAATTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 18 0.42
13 15 0.35
14 10 0.23
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (12 bp):
ATTAAAATAAAA
Found at i:28094840 original size:13 final size:13
Alignment explanation
Indices: 28094816--28094848 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28094806 AAAATTAAAG
28094816 GAAAAGATAAAAAT
1 GAAAA-ATAAAAAT
28094830 GAAAAATAAAAAT
1 GAAAAATAAAAAT
28094843 -AAAAAT
1 GAAAAAT
28094849 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 8 0.42
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (13 bp):
GAAAAATAAAAAT
Found at i:28097216 original size:24 final size:24
Alignment explanation
Indices: 28097114--28097283 Score: 128
Period size: 24 Copynumber: 6.9 Consensus size: 24
28097104 ACACACTGCA
* *
28097114 GCTCTTATGAGCGTCCCATTATATG
1 GCTCTTATGAGCTTCCCGTTA-ATG
* *
28097139 GCTCTTCATGAGCTTTCCGCTTAAAG
1 GCTCTT-ATGAGCTTCCCG-TTAATG
* **
28097165 GCTCTTTGTGAGCTTCCTAATTAATG
1 GCTC-TTATGAGCTTCC-CGTTAATG
28097191 GCTCTCTA-GAGCTTCCCGTTAATG
1 GCTCT-TATGAGCTTCCCGTTAATG
** * * *
28097215 GCTCTTCGGAGCTACCTGTTATTG
1 GCTCTTATGAGCTTCCCGTTAATG
* **
28097239 GCTCGTATGAGCTTCCTAATT-ATG
1 GCTCTTATGAGCTTCC-CGTTAATG
28097263 GCTCTTATGAGCTTCCCGTTA
1 GCTCTTATGAGCTTCCCGTTA
28097284 TACAGCCGAA
Statistics
Matches: 111, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
23 3 0.03
24 53 0.48
25 17 0.15
26 33 0.30
27 5 0.05
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGTTAATG
Found at i:28097251 original size:48 final size:49
Alignment explanation
Indices: 28097132--28097340 Score: 167
Period size: 48 Copynumber: 4.2 Consensus size: 49
28097122 GAGCGTCCCA
* * * * *
28097132 TTATATGGCTCTTCATGAGCTTTCCGCTTAAAGGCTCTTTGTGAGCTTCCTAA
1 TTATATGGCTCGT-ATGAGCTTCCCG-TTAATGGCTCTTCG-GAGCTTCCT-G
* *
28097185 TTA-ATGGCTC-TCTAGAGCTTCCCGTTAATGGCTCTTCGGAGCTACCTG
1 TTATATGGCTCGTAT-GAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
** ** *
28097233 TTAT-TGGCTCGTATGAGCTTCCTAATT-ATGGCTCTTATGAGCTTCCCG
1 TTATATGGCTCGTATGAGCTTCC-CGTTAATGGCTCTTCGGAGCTTCCTG
** * * * *
28097281 TTATACAGC-CGAATAAGCTTCTCGTTAATGGCTCTCCGGAGCTTCCTG
1 TTATATGGCTCGTATGAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
28097329 TTATATGGCTCG
1 TTATATGGCTCG
28097341 AGAGAGGGCT
Statistics
Matches: 123, Mismatches: 26, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
47 2 0.02
48 72 0.59
49 16 0.13
50 13 0.11
51 10 0.08
52 7 0.06
53 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (49 bp):
TTATATGGCTCGTATGAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
Found at i:28100842 original size:36 final size:36
Alignment explanation
Indices: 28100791--28100863 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
28100781 AGTAAACTCT
*
28100791 ATTCAACTCAATAGCCTTTTAGATCTATTCTAACTA
1 ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
* * *
28100827 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTA
1 ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
28100863 A
1 A
28100864 AGCGCTCCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (36 bp):
ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
Found at i:28105568 original size:21 final size:21
Alignment explanation
Indices: 28105542--28105581 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28105532 TGTTGCAACC
28105542 CACACCCTGTGTTGAGCCACA
1 CACACCCTGTGTTGAGCCACA
28105563 CACACCCTGTGTTGAGCCA
1 CACACCCTGTGTTGAGCCA
28105582 TAGCCTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
CACACCCTGTGTTGAGCCACA
Found at i:28105914 original size:13 final size:13
Alignment explanation
Indices: 28105893--28105938 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
28105883 GAGCATTCTC
* *
28105893 TTTACTCTTTTAT
1 TTTATTCTTCTAT
28105906 TTTATTCTTCTAT
1 TTTATTCTTCTAT
28105919 TTTATTCTTCTAT
1 TTTATTCTTCTAT
28105932 TTATATT
1 TT-TATT
28105939 TCGTTAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTCTTCTAT
Found at i:28117393 original size:58 final size:59
Alignment explanation
Indices: 28117302--28117425 Score: 214
Period size: 58 Copynumber: 2.1 Consensus size: 59
28117292 CATTGTAAAC
*
28117302 AAATTATATTTTTTTGTACCAATCAAAATATTTTGTAAAAACGCAATAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
* *
28117361 AAATTATA-TTTTTTGTACCAATGAAAACATTTTGTAAAAACGCTATAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
28117419 AAATTAT
1 AAATTAT
28117426 TAATTGTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 54 0.87
59 8 0.13
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (59 bp):
AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
Found at i:28117525 original size:21 final size:21
Alignment explanation
Indices: 28117489--28117625 Score: 195
Period size: 21 Copynumber: 6.4 Consensus size: 21
28117479 GGTTAGGTTT
28117489 AGGGTTAGGG-TTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
28117509 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
28117530 AGGGTTTAGGGTTTTTAAGTTG
1 AGGG-TTAGGGTTTTTAAGTTA
***
28117552 TTTGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
28117573 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
28117594 AGGGTTTAGGGTTTTTAAGTTAA
1 AGGG-TTAGGGTTTTTAAGTT-A
*
28117617 AGTGTTAGG
1 AGGGTTAGG
28117626 CTTAGGCTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.10
21 52 0.50
22 38 0.37
23 4 0.04
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:28117559 original size:43 final size:43
Alignment explanation
Indices: 28117489--28117625 Score: 183
Period size: 43 Copynumber: 3.2 Consensus size: 43
28117479 GGTTAGGTTT
*
28117489 AGGGTTAGGG-TTTTAAGTTAAGG-GTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
**
28117530 AGGGTTTAGGGTTTTTAAGTT-GTTTGTTAGGGTTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
28117573 AGGGTTAGGGTTTTTAAGTTAAGGGT-TTAGGGTTTTTAAGTTAA
1 AGGGTTAGGGTTTTTAAGTT-AGGGTGTTAGGGTTTTTAAGTT-A
*
28117617 AGTGTTAGG
1 AGGGTTAGG
28117626 CTTAGGCTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
41 4 0.05
42 22 0.26
43 47 0.56
44 11 0.13
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (43 bp):
AGGGTTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
Found at i:28117573 original size:64 final size:63
Alignment explanation
Indices: 28117492--28117614 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 63
28117482 TAGGTTTAGG
28117492 GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
1 GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
28117555 GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
1 GTTAGGG-TTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
28117615 AAAGTGTTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 7 0.12
64 52 0.88
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (63 bp):
GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
Found at i:28117785 original size:12 final size:12
Alignment explanation
Indices: 28117765--28117807 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
28117755 AGGGTTTGTC
28117765 AATTAAATTATA
1 AATTAAATTATA
*
28117777 AATTTAATTATAA
1 AATTAAATTAT-A
28117790 AATATAAATTTATA
1 AAT-TAAA-TTATA
28117804 AATT
1 AATT
28117808 TTTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.38
13 5 0.19
14 7 0.27
15 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:28118322 original size:17 final size:19
Alignment explanation
Indices: 28118290--28118333 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
28118280 GACTCGAAAA
*
28118290 AGGAAACATATAA-GGGTT
1 AGGATACATATAAGGGGTT
*
28118308 ATGATACAT-TAAGGGGTT
1 AGGATACATATAAGGGGTT
28118326 AGGATACA
1 AGGATACA
28118334 CACCTGGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (19 bp):
AGGATACATATAAGGGGTT
Found at i:28120170 original size:51 final size:50
Alignment explanation
Indices: 28120114--28120218 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 50
28120104 TAATTTTTTT
28120114 AAAAT-AATTAAAATTAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGC
1 AAAATAAATT-AAA-TAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGC
* * *
28120165 AAAATAAAATTAAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGC
1 AAAAT-AAATTAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGC
28120216 AAA
1 AAA
28120219 TTGAGAGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 40 0.83
52 4 0.08
53 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (50 bp):
AAAATAAATTAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGC
Found at i:28120221 original size:11 final size:11
Alignment explanation
Indices: 28120205--28120246 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
28120195 ATTTGGAAGG
28120205 AAATTGAGAGC
1 AAATTGAGAGC
28120216 AAATTGAGAGC
1 AAATTGAGAGC
* *
28120227 AATTTGAGAGA
1 AAATTGAGAGC
28120238 AAATTGAGA
1 AAATTGAGA
28120247 AAATAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:28120223 original size:33 final size:34
Alignment explanation
Indices: 28120186--28120260 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
28120176 AAATATGGAT
* **
28120186 TTGAGAGAAATTTG-GAAGGAAATTGAGAGCA-AA
1 TTGAGAGAAATTTGAG-AGAAAATTGAGAAAATAA
*
28120219 TTGAGAGCAATTTGAGAGAAAATTGAGAAAATAA
1 TTGAGAGAAATTTGAGAGAAAATTGAGAAAATAA
28120253 TTGAGAGA
1 TTGAGAGA
28120261 GGATTAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 25 0.71
34 10 0.29
ACGTcount: A:0.47, C:0.03, G:0.28, T:0.23
Consensus pattern (34 bp):
TTGAGAGAAATTTGAGAGAAAATTGAGAAAATAA
Found at i:28124652 original size:20 final size:20
Alignment explanation
Indices: 28124612--28124666 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
28124602 AAGATTTTTT
28124612 TTTTTTA-AAAAT-TA-AAA
1 TTTTTTATAAAATATATAAA
*
28124629 TTTTTTATAAAATATATAAG
1 TTTTTTATAAAATATATAAA
*
28124649 TTTTGTGATAAAA-ATATA
1 TTTT-TTATAAAATATATA
28124667 TGGGCTCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 2 0.06
20 11 0.34
21 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTTATAAAATATATAAA
Found at i:28130354 original size:805 final size:805
Alignment explanation
Indices: 28128803--28130414 Score: 3197
Period size: 805 Copynumber: 2.0 Consensus size: 805
28128793 AGAAGAAGCA
28128803 TGGAGCGGAAGAAGACCCGATGTCAGTCATTTCAGAATCTTTGGGTGTATTGCTTATGCACATGT
1 TGGAGCGGAAGAAGACCCGATGTCAGTCATTTCAGAATCTTTGGGTGTATTGCTTATGCACATGT
28128868 CCCTGATAAAAAAAGAACGAAGTTAGAAGACAAAGGAGAAAAATGCATATTTCTTGGTGTTAGTA
66 CCCTGATAAAAAAAGAACGAAGTTAGAAGACAAAGGAGAAAAATGCATATTTCTTGGTGTTAGTA
28128933 AGTGTTCTAAAGCATTCAAGTTGTATAATCCTAGCACTAAGAAAATTGTCATCGGTCGGGATGTG
131 AGTGTTCTAAAGCATTCAAGTTGTATAATCCTAGCACTAAGAAAATTGTCATCGGTCGGGATGTG
28128998 ATTTTTGATGAAGAAAAGTTCTGGTGTTGGGATACACCAACAGTTTAAAGGAATGTTTCAGTAGA
196 ATTTTTGATGAAGAAAAGTTCTGGTGTTGGGATACACCAACAGTTTAAAGGAATGTTTCAGTAGA
28129063 CTTTGATGAAGAGCTACATGTTGAGGATAATTTGGAGCCGTTACATGAGCAAGAAACAATTCAAA
261 CTTTGATGAAGAGCTACATGTTGAGGATAATTTGGAGCCGTTACATGAGCAAGAAACAATTCAAA
28129128 AACCTGAAACTGCAACAGATCCAATGTCATCACGTACAAGAAGAAGGCCTGCTTGGATGAGGGAT
326 AACCTGAAACTGCAACAGATCCAATGTCATCACGTACAAGAAGAAGGCCTGCTTGGATGAGGGAT
28129193 TATGAAGTCCTAGGAATTAATCAATTTGAGGATCCACTCACCTATTATGTTTTGTTTTCAGATTG
391 TATGAAGTCCTAGGAATTAATCAATTTGAGGATCCACTCACCTATTATGTTTTGTTTTCAGATTG
28129258 TGATCTCGTGTTTTTTGAAGAGGCAATTAAACAATCAAAATGGAAGAGAGCAATGGATGATGAAA
456 TGATCTCGTGTTTTTTGAAGAGGCAATTAAACAATCAAAATGGAAGAGAGCAATGGATGATGAAA
28129323 TTGCAGCTATTGAAAAAAAAAACAAAACTTGAGAGTTAATTAAGCTTCCAAAATGACATAAAACC
521 TTGCAGCTATTGAAAAAAAAAACAAAACTTGAGAGTTAATTAAGCTTCCAAAATGACATAAAACC
28129388 ATTGATGTGAAGTGGGTTTATAAGATGAAACTGAAGGAAACCGGTGAACTTGACAAATGCAAAGC
586 ATTGATGTGAAGTGGGTTTATAAGATGAAACTGAAGGAAACCGGTGAACTTGACAAATGCAAAGC
28129453 AAGCTTGGTAGCAAAAGGTTATAGTCAGGAGTTCGGCATCGATTACAAGGAGGTATTCGCTCCAG
651 AAGCTTGGTAGCAAAAGGTTATAGTCAGGAGTTCGGCATCGATTACAAGGAGGTATTCGCTCCAG
28129518 TTGCTAGGCATGACACAATCAGATTGGTGATTGCATTGGCAGCTCAAAATTCTTGGCCGATTTTC
716 TTGCTAGGCATGACACAATCAGATTGGTGATTGCATTGGCAGCTCAAAATTCTTGGCCGATTTTC
* *
28129583 CAACTAGATGTCAAGTCGGCATTCT
781 CAACAAGATGTCAAGTCGACATTCT
28129608 TGGAGCGGAAGAAGACCCGATGTCAGTCATTTCAGAATCTTTGGGTGTATTGCTTATGCACATGT
1 TGGAGCGGAAGAAGACCCGATGTCAGTCATTTCAGAATCTTTGGGTGTATTGCTTATGCACATGT
*
28129673 CCTTGATAAAAAAAGAACGAAGTTAGAAGACAAAGGAGAAAAATGCATATTTCTTGGTGTTAGTA
66 CCCTGATAAAAAAAGAACGAAGTTAGAAGACAAAGGAGAAAAATGCATATTTCTTGGTGTTAGTA
28129738 AGTGTTCTAAAGCATTCAAGTTGTATAATCCTAGCACTAAGAAAATTGTCATCGGTCGGGATGTG
131 AGTGTTCTAAAGCATTCAAGTTGTATAATCCTAGCACTAAGAAAATTGTCATCGGTCGGGATGTG
28129803 ATTTTTGATGAAGAAAAGTTCTGGTGTTGGGATACACCAACAGTTTAAAGGAATGTTTCAGTAGA
196 ATTTTTGATGAAGAAAAGTTCTGGTGTTGGGATACACCAACAGTTTAAAGGAATGTTTCAGTAGA
28129868 CTTTGATGAAGAGCTACATGTTGAGGATAATTTGGAGCCGTTACATGAGCAAGAAACAATTCAAA
261 CTTTGATGAAGAGCTACATGTTGAGGATAATTTGGAGCCGTTACATGAGCAAGAAACAATTCAAA
28129933 AACCTGAAACTGCAACAGATCCAATGTCATCACGTACAAGAAGAAGGCCTGCTTGGATGAGGGAT
326 AACCTGAAACTGCAACAGATCCAATGTCATCACGTACAAGAAGAAGGCCTGCTTGGATGAGGGAT
28129998 TATGAAGTCCTAGGAATTAATCAATTTGAGGATCCACTCACCTATTATGTTTTGTTTTCAGATTG
391 TATGAAGTCCTAGGAATTAATCAATTTGAGGATCCACTCACCTATTATGTTTTGTTTTCAGATTG
28130063 TGATCTCGTGTTTTTTGAAGAGGCAATTAAACAATCAAAATGGAAGAGAGCAATGGATGATGAAA
456 TGATCTCGTGTTTTTTGAAGAGGCAATTAAACAATCAAAATGGAAGAGAGCAATGGATGATGAAA
28130128 TTGCAGCTATTGAAAAAAAAAACAAAACTTGAGAGTTAATTAAGCTTCCAAAATGACATAAAACC
521 TTGCAGCTATTGAAAAAAAAAACAAAACTTGAGAGTTAATTAAGCTTCCAAAATGACATAAAACC
28130193 ATTGATGTGAAGTGGGTTTATAAGATGAAACTGAAGGAAACCGGTGAACTTGACAAATGCAAAGC
586 ATTGATGTGAAGTGGGTTTATAAGATGAAACTGAAGGAAACCGGTGAACTTGACAAATGCAAAGC
28130258 AAGCTTGGTAGCAAAAGGTTATAGTCAGGAGTTCGGCATCGATTACAAGGAGGTATTCGCTCCAG
651 AAGCTTGGTAGCAAAAGGTTATAGTCAGGAGTTCGGCATCGATTACAAGGAGGTATTCGCTCCAG
28130323 TTGCTAGGCATGACACAATCAGATTGGTGATTGCATTGGCAGCTCAAAATTCTTGGCCGATTTTC
716 TTGCTAGGCATGACACAATCAGATTGGTGATTGCATTGGCAGCTCAAAATTCTTGGCCGATTTTC
28130388 CAACAAGATGTCAAGTCGACATTCT
781 CAACAAGATGTCAAGTCGACATTCT
28130413 TG
1 TG
28130415 CATGGAGACT
Statistics
Matches: 804, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
805 804 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (805 bp):
TGGAGCGGAAGAAGACCCGATGTCAGTCATTTCAGAATCTTTGGGTGTATTGCTTATGCACATGT
CCCTGATAAAAAAAGAACGAAGTTAGAAGACAAAGGAGAAAAATGCATATTTCTTGGTGTTAGTA
AGTGTTCTAAAGCATTCAAGTTGTATAATCCTAGCACTAAGAAAATTGTCATCGGTCGGGATGTG
ATTTTTGATGAAGAAAAGTTCTGGTGTTGGGATACACCAACAGTTTAAAGGAATGTTTCAGTAGA
CTTTGATGAAGAGCTACATGTTGAGGATAATTTGGAGCCGTTACATGAGCAAGAAACAATTCAAA
AACCTGAAACTGCAACAGATCCAATGTCATCACGTACAAGAAGAAGGCCTGCTTGGATGAGGGAT
TATGAAGTCCTAGGAATTAATCAATTTGAGGATCCACTCACCTATTATGTTTTGTTTTCAGATTG
TGATCTCGTGTTTTTTGAAGAGGCAATTAAACAATCAAAATGGAAGAGAGCAATGGATGATGAAA
TTGCAGCTATTGAAAAAAAAAACAAAACTTGAGAGTTAATTAAGCTTCCAAAATGACATAAAACC
ATTGATGTGAAGTGGGTTTATAAGATGAAACTGAAGGAAACCGGTGAACTTGACAAATGCAAAGC
AAGCTTGGTAGCAAAAGGTTATAGTCAGGAGTTCGGCATCGATTACAAGGAGGTATTCGCTCCAG
TTGCTAGGCATGACACAATCAGATTGGTGATTGCATTGGCAGCTCAAAATTCTTGGCCGATTTTC
CAACAAGATGTCAAGTCGACATTCT
Found at i:28132570 original size:104 final size:109
Alignment explanation
Indices: 28132437--28132639 Score: 308
Period size: 110 Copynumber: 1.9 Consensus size: 109
28132427 TTTTTATTGT
*
28132437 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA-CT-ATTA-TAAATTATT
1 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATATGATTAGTAAATTATT
*
28132499 TGTTTATTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
66 TGTTTAGTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
* *
28132543 AATTTTTATGTT-TTTTT-ATTTATTTTAAATTTATTTTGTTAGTAATTTATGATTAGGTTAATT
1 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA--TATGATTA-GTAAATT
28132606 ATTTGTTTAGTTTAATATTTATTGTGATTTGTTA
63 ATTTGTTTAGTTTAATATTTATTGTGATTTGTTA
28132640 TGAATGCAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
104 27 0.31
105 5 0.06
106 12 0.14
107 1 0.01
108 4 0.05
110 38 0.44
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (109 bp):
AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATATGATTAGTAAATTATT
TGTTTAGTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
Found at i:28135081 original size:33 final size:35
Alignment explanation
Indices: 28135015--28135096 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 35
28135005 TGGAACAAGC
* *
28135015 TTGGAACAAACTTTGTATTTATTTAATTGAGATTCA
1 TTGGAACAAACTTTGTA-TTATTTAAATAAGATTCA
*
28135051 TTGGAACAAATTTTGTA-T-TTTAAATAAGATTCA
1 TTGGAACAAACTTTGTATTATTTAAATAAGATTCA
*
28135084 TTGGTACAAACTT
1 TTGGAACAAACTT
28135097 GGAACAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 24 0.59
34 1 0.02
36 16 0.39
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (35 bp):
TTGGAACAAACTTTGTATTATTTAAATAAGATTCA
Found at i:28138806 original size:16 final size:16
Alignment explanation
Indices: 28138754--28138806 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
28138744 GTGGCCCCTC
28138754 AGTAAAATTTTAATTT
1 AGTAAAATTTTAATTT
**
28138770 AG-ACCATTTATAATTT
1 AGTAAAATTT-TAATTT
*
28138786 A-TAAAATTTTAAATT
1 AGTAAAATTTTAATTT
28138801 AGTAAA
1 AGTAAA
28138807 GATAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (16 bp):
AGTAAAATTTTAATTT
Found at i:28145524 original size:3 final size:3
Alignment explanation
Indices: 28145516--28145544 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28145506 ATTGTTAATG
28145516 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28145545 GTCCAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28150362 original size:2 final size:2
Alignment explanation
Indices: 28150355--28150393 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28150345 CCTCCCGACA
28150355 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28150394 GTGTCTTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28153981 original size:41 final size:41
Alignment explanation
Indices: 28153930--28154026 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
28153920 AAATATATCT
* *
28153930 TTTTCAACCTTTTCATGTGTTATCCTTTTCGGGTAATTTCC
1 TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
*
28153971 TTTTCAACCTTTCCATGTGTTATCCCTTTCGGGTAACTTCC
1 TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
28154012 TTTTCAACCTTTTCA
1 TTTTCAACCTTTTCA
28154027 AGAATTCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.48
Consensus pattern (41 bp):
TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
Found at i:28155185 original size:41 final size:41
Alignment explanation
Indices: 28155053--28155188 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 41
28155043 ACCAGTTTGG
* *
28155053 CACCCGGTGCCTCATC-AAATAAT-TCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAAATAATCT-GAAGTAGTAAATTGA
* * ** * * * *
28155093 CACTCAGTGTCTCATCG-GCTAAAC-CAA--AGTGAATTGG
1 CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
* *
28155130 CACCGAGTGCCTCATCGAATTAATCTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
*
28155171 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
28155189 CTCGAAGTCG
Statistics
Matches: 69, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
37 21 0.30
38 4 0.06
39 4 0.06
40 16 0.23
41 24 0.35
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
Found at i:28155389 original size:24 final size:24
Alignment explanation
Indices: 28155344--28155400 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
28155334 TATATATACC
28155344 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
28155368 AATTC-ATCACATACTAAA-TCAATA
1 AATTCAATCA-ATA-TAAATTCAATA
*
28155392 CATTTCAAT
1 -AATTCAAT
28155401 TGTAAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 14 0.50
25 8 0.29
26 2 0.07
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:28156157 original size:7 final size:7
Alignment explanation
Indices: 28156145--28156174 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28156135 CTTTATTATA
28156145 ATATAAT
1 ATATAAT
28156152 ATATAAT
1 ATATAAT
28156159 ATATAAT
1 ATATAAT
28156166 ATAT-AT
1 ATATAAT
28156172 ATA
1 ATA
28156175 CTTAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:28156164 original size:14 final size:13
Alignment explanation
Indices: 28156141--28156174 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
28156131 CTTTCTTTAT
28156141 TATA-ATATAATA
1 TATATATATAATA
28156153 TATAATATATAATA
1 TAT-ATATATAATA
28156167 TATATATA
1 TATATATA
28156175 CTTAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 6 0.30
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATATAATA
Found at i:28156235 original size:28 final size:30
Alignment explanation
Indices: 28156186--28156244 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
28156176 TTAACATTTA
* *
28156186 ATTTTTACTATTACAATATTATAAT-ATAT
1 ATTTTAACTATTAAAATATTATAATAATAT
*
28156215 ATTTTAACT-TTAAAATTTTATAATAATAT
1 ATTTTAACTATTAAAATATTATAATAATAT
28156244 A
1 A
28156245 CTTATGCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTAACTATTAAAATATTATAATAATAT
Found at i:28158481 original size:31 final size:32
Alignment explanation
Indices: 28158446--28158505 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
28158436 AAAAATAACA
*
28158446 AAATTGGGTTTTAGGTT-CTTAAAAGTTGAAG
1 AAATTGGGTTTTAAGTTCCTTAAAAGTTGAAG
***
28158477 AAATTTTTTTTTAAGTTCCTTAAAAGTTG
1 AAATTGGGTTTTAAGTTCCTTAAAAGTTG
28158506 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.54
32 11 0.46
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (32 bp):
AAATTGGGTTTTAAGTTCCTTAAAAGTTGAAG
Found at i:28168720 original size:16 final size:17
Alignment explanation
Indices: 28168693--28168727 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28168683 AGAGAGTTGA
28168693 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
28168710 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
28168726 GA
1 GA
28168728 TNNNNNNNNN
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:28174887 original size:20 final size:20
Alignment explanation
Indices: 28174862--28174899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28174852 ACCCCCTTTA
28174862 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
28174882 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
28174900 CGAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:28176932 original size:43 final size:43
Alignment explanation
Indices: 28176871--28176954 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
28176861 GGCTGTAATT
*
28176871 AACCGATTCTTTAGATCTTCAAAAGCTTCCAAACAAATTGAAC
1 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGAAC
28176914 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGA
1 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGA
28176955 GCATTGTATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (43 bp):
AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGAAC
Found at i:28180162 original size:39 final size:34
Alignment explanation
Indices: 28180097--28180175 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 34
28180087 AAGTAAGTGT
*
28180097 AGAAAAATAAACTCTAAAACTAAGAAAGAA-TAAG
1 AGAAAAAAAAACTCTAAAACTAAGAAA-AACTAAG
28180131 AGAAAATAAAAACTCTAAAAAACTTATAGAAAAACTAAG
1 AGAAAA-AAAAACTCT--AAAAC-TA-AGAAAAACTAAG
28180170 AGAAAA
1 AGAAAA
28180176 CCTAGAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 6 0.16
35 8 0.21
37 5 0.13
38 4 0.11
39 15 0.39
ACGTcount: A:0.66, C:0.09, G:0.10, T:0.15
Consensus pattern (34 bp):
AGAAAAAAAAACTCTAAAACTAAGAAAAACTAAG
Found at i:28184244 original size:6 final size:6
Alignment explanation
Indices: 28184225--28184254 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28184215 TATTCAGATA
28184225 AATATT AA-ATT AATATT AATATT AATATT A
1 AATATT AATATT AATATT AATATT AATATT A
28184255 TATCTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:28184244 original size:68 final size:72
Alignment explanation
Indices: 28184119--28184249 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 72
28184109 ACTTAATGAG
* * * *
28184119 TTTAATATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAGTTAAATTTAATATTAAGA
1 TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAATTTAATATTAAGA
28184184 TATTCAC
66 TATTCAC
*
28184191 TTTAAAATTAAATTAATAAAATA-ATAT-T-C-AGATAAATATTAAATT-AATATTAATATTAA
1 TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAAT-TTAATATTAA
28184250 TATTATATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
67 3 0.06
68 24 0.45
69 1 0.02
70 1 0.02
71 3 0.06
72 21 0.40
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (72 bp):
TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAATTTAATATTAAGA
TATTCAC
Found at i:28184248 original size:12 final size:11
Alignment explanation
Indices: 28184192--28184254 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
28184182 GATATTCACT
*
28184192 TTAAAATTAAA
1 TTAATATTAAA
28184203 TTAATA--AAA
1 TTAATATTAAA
*
28184212 -TAATATTCAGA
1 TTAATATT-AAA
*
28184223 TAAATATTAAA
1 TTAATATTAAA
28184234 TTAATATTAATA
1 TTAATATTAA-A
28184246 TTAATATTA
1 TTAATATTA
28184255 TATCTATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.12
9 3 0.07
11 18 0.43
12 16 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:28184687 original size:24 final size:25
Alignment explanation
Indices: 28184658--28184708 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
28184648 AAATATCATA
*
28184658 TTAATTTTAATTAATT-TGATTAAT
1 TTAATTTTAATTAATTAAGATTAAT
* *
28184682 TTAATTTTACTTGATTAAGATTAAT
1 TTAATTTTAATTAATTAAGATTAAT
28184707 TT
1 TT
28184709 TCTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (25 bp):
TTAATTTTAATTAATTAAGATTAAT
Found at i:28196346 original size:16 final size:17
Alignment explanation
Indices: 28196317--28196349 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28196307 ATTAGAATAA
*
28196317 AATAAAGTTCTAATATT
1 AATAAACTTCTAATATT
28196334 AATAAACTT-TAATATT
1 AATAAACTTCTAATATT
28196350 TTGATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAACTTCTAATATT
Found at i:28208584 original size:20 final size:20
Alignment explanation
Indices: 28208559--28208596 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28208549 CTATTTCAAC
*
28208559 TTGAAACATCGAGTAGTTAT
1 TTGAAACATCGAGCAGTTAT
28208579 TTGAAACATCGAGCAGTT
1 TTGAAACATCGAGCAGTT
28208597 TGATCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TTGAAACATCGAGCAGTTAT
Found at i:28213925 original size:42 final size:42
Alignment explanation
Indices: 28213867--28213978 Score: 161
Period size: 42 Copynumber: 2.7 Consensus size: 42
28213857 GATGCAAGGG
28213867 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
1 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
* *
28213909 ACACATGGCCAAAACACACGCCCATGTGCTAGGTCATGTGTC
1 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
* ** * *
28213951 ACATACGGCTGAGACACACGCCCGTGTG
1 ACACACGGCCAAAACACACGCCCATGTG
28213979 GACAAAATAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (42 bp):
ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
Found at i:28216303 original size:50 final size:50
Alignment explanation
Indices: 28216231--28216375 Score: 200
Period size: 50 Copynumber: 2.9 Consensus size: 50
28216221 CATTGAGATT
* *
28216231 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * *
28216281 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATTGGCACCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * *
28216331 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28216376 GTACAAGAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:28219555 original size:80 final size:83
Alignment explanation
Indices: 28219446--28219619 Score: 327
Period size: 80 Copynumber: 2.1 Consensus size: 83
28219436 TACAATAGTA
28219446 AAAATATAATTTTATTATTTTAATAGTTTATATCCTTATAATATTTAAAAGATTAAATCAAATTT
1 AAAATATAATTTTATTATTTTAATAGTTTATATCCTTATAATATTTAAAAGATTAAATCAAATTT
28219511 TTATAATTTTTAGAT-G-
66 TTATAATTTTTAGATGGC
28219527 AAAATATAATTTTA-TATTTTAATAGTTTATATCCTTATAATATTTAAAAGATTAAATCAAATTT
1 AAAATATAATTTTATTATTTTAATAGTTTATATCCTTATAATATTTAAAAGATTAAATCAAATTT
28219591 TTATAATTTTTAGATGGC
66 TTATAATTTTTAGATGGC
28219609 AAAATATAATT
1 AAAATATAATT
28219620 ATACCTTTAT
Statistics
Matches: 91, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
80 65 0.71
81 15 0.16
82 11 0.12
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (83 bp):
AAAATATAATTTTATTATTTTAATAGTTTATATCCTTATAATATTTAAAAGATTAAATCAAATTT
TTATAATTTTTAGATGGC
Found at i:28219655 original size:16 final size:17
Alignment explanation
Indices: 28219630--28219662 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28219620 ATACCTTTAT
*
28219630 TTTTACTAA-TTTAAAA
1 TTTTAATAATTTTAAAA
28219646 TTTTAATAATTTTAAAA
1 TTTTAATAATTTTAAAA
28219663 AATTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATAATTTTAAAA
Found at i:28225555 original size:3 final size:3
Alignment explanation
Indices: 28225547--28225578 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28225537 CAAAATCATT
*
28225547 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28225579 GCCATGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.