Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 109 of 171
Found at i:35016058 original size:13 final size:13
Alignment explanation
Indices: 35016024--35016058 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
35016014 GTTTTATTTT
35016024 AAAACAAATAATA
1 AAAACAAATAATA
35016037 ACAAA-AAATAATA
1 A-AAACAAATAATA
35016050 AAAACAAAT
1 AAAACAAAT
35016059 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.15
13 14 0.70
14 3 0.15
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACAAATAATA
Found at i:35016575 original size:24 final size:24
Alignment explanation
Indices: 35016548--35016598 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
35016538 CACGCAATCC
*
35016548 TTTCG-CATTTTTTAAATTTTTTAA
1 TTTCGTCATTTTTCAAA-TTTTTAA
* *
35016572 TTTCGTCCTTTTTCACATTTTTAA
1 TTTCGTCATTTTTCAAATTTTTAA
35016596 TTT
1 TTT
35016599 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.20, C:0.14, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTCGTCATTTTTCAAATTTTTAA
Found at i:35016734 original size:30 final size:29
Alignment explanation
Indices: 35016678--35016845 Score: 144
Period size: 30 Copynumber: 5.7 Consensus size: 29
35016668 TGCCACTGGT
* ** *
35016678 CCCTGAACTTTTCAAAAAAAAT-ATTTTGA
1 CCCTAAACTTTTC-AAAAATTTCATTTTAA
*
35016707 CCCGTAAACTTTTCAAAAATTTGATTTTAA
1 CCC-TAAACTTTTCAAAAATTTCATTTTAA
* * **
35016737 CCCCCAAACTTTTCCAAAATCACATTTTAA
1 -CCCTAAACTTTTCAAAAATTTCATTTTAA
*
35016767 CCCTAATA-TTTTCCAAAATTTCATTTTAA
1 CCCTAA-ACTTTTCAAAAATTTCATTTTAA
*
35016796 CCCTTAAACTTTTGC-AAAATTTCATTTTGA
1 CCC-TAAACTTTT-CAAAAATTTCATTTTAA
* *
35016826 CCCTAAACTTTCCTAAAATT
1 CCCTAAACTTTTCAAAAATT
35016846 AAATTTTTAC
Statistics
Matches: 117, Mismatches: 14, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
28 1 0.01
29 51 0.44
30 61 0.52
31 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCAAAAATTTCATTTTAA
Found at i:35016791 original size:29 final size:29
Alignment explanation
Indices: 35016700--35016845 Score: 161
Period size: 30 Copynumber: 4.9 Consensus size: 29
35016690 CAAAAAAAAT
* * *
35016700 ATTTTGACCCGTAAACTTTTCAAAAATTTG
1 ATTTTAACCC-TAAACTTTTCCAAAATTTC
* **
35016730 ATTTTAACCCCCAAACTTTTCCAAAATCAC
1 ATTTTAA-CCCTAAACTTTTCCAAAATTTC
35016760 ATTTTAACCCTAATA-TTTTCCAAAATTTC
1 ATTTTAACCCTAA-ACTTTTCCAAAATTTC
*
35016789 ATTTTAACCCTTAAACTTTTGCAAAATTTC
1 ATTTTAACCC-TAAACTTTTCCAAAATTTC
*
35016819 ATTTTGACCCTAAAC-TTTCCTAAAATT
1 ATTTTAACCCTAAACTTTTCC-AAAATT
35016846 AAATTTTTAC
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
28 4 0.04
29 39 0.39
30 53 0.54
31 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTTTCCAAAATTTC
Found at i:35016794 original size:59 final size:58
Alignment explanation
Indices: 35016700--35016911 Score: 199
Period size: 59 Copynumber: 3.6 Consensus size: 58
35016690 CAAAAAAAAT
* * * *
35016700 ATTTTGACCCGTAAACTTTTCAAAAATTTGATTTTAACCCCCAAACTTTTCCAAAATCAC
1 ATTTTAACCC-TAAA-TTTTCCAAAATTTCATTTTAACCCCCAAACTTTTCCAAAATTAC
** * *
35016760 ATTTTAACCCTAATATTTTCCAAAATTTCATTTTAACCCTTAAACTTTTGCAAAATTTC
1 ATTTTAACCCTAA-ATTTTCCAAAATTTCATTTTAACCCCCAAACTTTTCCAAAATTAC
* * ** * ** *
35016819 ATTTTGACCCTAAACTTTCCTAAAATTAAATTTTTACCCCCAAACTTTTTTTAAAATTAA
1 ATTTTAACCCTAAATTTTCC-AAAATTTCATTTTAACCCCCAAAC-TTTTCCAAAATTAC
* * * *
35016879 ATTTTAACCCCAAATTCTCCGAAACTTCATTTT
1 ATTTTAACCCTAAATTTTCCAAAATTTCATTTT
35016912 TCAACCCCAT
Statistics
Matches: 122, Mismatches: 27, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
58 6 0.05
59 80 0.66
60 36 0.30
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (58 bp):
ATTTTAACCCTAAATTTTCCAAAATTTCATTTTAACCCCCAAACTTTTCCAAAATTAC
Found at i:35016851 original size:29 final size:29
Alignment explanation
Indices: 35016700--35016888 Score: 157
Period size: 30 Copynumber: 6.3 Consensus size: 29
35016690 CAAAAAAAAT
* * **
35016700 ATTTTGACCCGTAAACTTTTCAAAAATTTG
1 ATTTTAACCC-TAAACTTTTCCAAAATTAC
* *
35016730 ATTTTAACCCCCAAACTTTTCCAAAATCAC
1 ATTTTAA-CCCTAAACTTTTCCAAAATTAC
*
35016760 ATTTTAACCCTAATA-TTTTCCAAAATTTC
1 ATTTTAACCCTAA-ACTTTTCCAAAATTAC
* *
35016789 ATTTTAACCCTTAAACTTTTGCAAAATTTC
1 ATTTTAACCC-TAAACTTTTCCAAAATTAC
* *
35016819 ATTTTGACCCTAAAC-TTTCCTAAAATTAA
1 ATTTTAACCCTAAACTTTTCC-AAAATTAC
* * ** *
35016848 ATTTTTACCCCCAAACTTTTTTTAAAATTAA
1 A-TTTTAACCCTAAAC-TTTTCCAAAATTAC
35016879 ATTTTAACCC
1 ATTTTAACCC
35016889 CAAATTCTCC
Statistics
Matches: 131, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.03
29 40 0.31
30 72 0.55
31 12 0.09
32 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTTTCCAAAATTAC
Found at i:35025962 original size:48 final size:47
Alignment explanation
Indices: 35025888--35026011 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 47
35025878 ACTTCAAACC
* * **
35025888 TCATCTTCCTAATGAGATACATAGAAGTGGGTTAAAGCGAA-AAAGC-G
1 TCATCTTCCTGATGAGATA-AAAGAAGTGAATTAAAGC-AATAAAGCAG
* *
35025935 ATCATCTTCCTGATGAGATAAAGAGAAGTGAATTAAATCAATGAAGCAG
1 -TCATCTTCCTGATGAGATAAA-AGAAGTGAATTAAAGCAATAAAGCAG
35025984 TCATCTTCCTGATGAGATACAAAGAAGT
1 TCATCTTCCTGATGAGATA-AAAGAAGT
35026012 AGACCAAATC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
47 3 0.05
48 60 0.91
49 3 0.05
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (47 bp):
TCATCTTCCTGATGAGATAAAAGAAGTGAATTAAAGCAATAAAGCAG
Found at i:35026021 original size:48 final size:48
Alignment explanation
Indices: 35025936--35026029 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
35025926 GAAAAAGCGA
** *
35025936 TCATCTTCCTGATGAGATAAAGAGAAGTGAATTAAATCAATGAAGCAG
1 TCATCTTCCTGATGAGATAAAGAGAAGTGAACCAAATCAACGAAGCAG
35025984 TCATCTTCCTGATGAGATACAA-AGAAGT-AGACCAAATCAACGAAGC
1 TCATCTTCCTGATGAGATA-AAGAGAAGTGA-ACCAAATCAACGAAGC
35026030 GAAGCTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 1 0.02
48 38 0.93
49 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (48 bp):
TCATCTTCCTGATGAGATAAAGAGAAGTGAACCAAATCAACGAAGCAG
Found at i:35026373 original size:208 final size:208
Alignment explanation
Indices: 35025939--35026920 Score: 1342
Period size: 208 Copynumber: 4.7 Consensus size: 208
35025929 AAAGCGATCA
*
35025939 TCTTCCTGATGAGATA-AAGAGAAGTGAATTAAATCAATGAA-GCAGTCATCTTCCTGATGAGAT
1 TCTTCCTGATGAGATACAA-AGAAGTGGATTAAATCAAT-AAGGCAGTCATCTTCCTGATGAGAT
* * * ** * * **
35026002 ACAAAGAAGTAGACCAAATCAACGAAGCGAAGCTCAATACGAATGAGACTTCAAACTCAAATCTT
64 ACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAAC-CCCATCTT
* * * **
35026067 CCAGAAGAGATACAGAGAAGTGGGTCAAAGCAATGAATCTGTCATCTTCCTGATGAGATACAGAG
128 CCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTCCTGATGAGATACAGAG
* * *
35026132 AAGTAAACCGAATCCA
193 AAGTAGACCAAATCCG
* * * *
35026148 TCTTCCTGATAAGATACAAAGAAGTGGATTAAATCAATAAGGCAGTTATCTTCTTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATAAGGCAGTCATCTTCCTGATGAGATAC
* * *
35026213 AGAAAAGTAGACTAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTTCT
66 AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCT
* *
35026278 GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTTCTGATGAGATATAGAGAAG
131 GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTCCTGATGAGATACAGAGAAG
* *
35026343 TGGACCAAATTCG
196 TAGACCAAATCCG
* * * *
35026356 TCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATAAGGCAGTCATCTTCCTGATGAGATAC
* *
35026421 AGAGAAGTAGACCAAATGAATGAAGTAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCT
66 AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCT
* *
35026486 GATGAGATACAGAGAAGTGGGTCAGAGCAATAAAAAGGTCATCTTCCTGATGAGATACAGAGAAG
131 GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTCCTGATGAGATACAGAGAAG
*
35026551 TGGACCAAATCCG
196 TAGACCAAATCCG
* * * *
35026564 TCTTCATGATGAGATACATAGAAGTGGATTAAACCAATGAGGCAGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATAAGGCAGTCATCTTCCTGATGAGATAC
* * * *
35026629 AGAGAAGTAAACCTAATTAATGAAGCAAAGCTCAATGTGA-TGGAAACTTCAAACCCCACCTTCC
66 AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGT-GAAACTTCAAACCCCATCTTCC
* * * *
35026693 TGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGACGTAATCTTCCTGATGAGATACAGAGAA
130 TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTCCTGATGAGATACAGAGAA
*
35026758 GTAGACTAAATCCG
195 GTAGACCAAATCCG
* * * *
35026772 TCTTCCTGATGAGATATAGAGAAGTGGATTAAATCAATGAA-ACGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAAT-AAGGCAGTCATCTTCCTGATGAGATA
* * * * *
35026836 TAGAGAAGTAGACCAAATTAATGAAGCGAAGTTCAATGCGAGTGAAACTTCAAACCCCTATCTTC
65 CAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCC-ATCTTC
35026901 CTGATGAGATACAGAGAAGT
129 CTGATGAGATACAGAGAAGT
35026921 AGACCAAGAA
Statistics
Matches: 689, Mismatches: 78, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
207 1 0.00
208 561 0.81
209 125 0.18
210 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (208 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATAAGGCAGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCT
GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTCCTGATGAGATACAGAGAAG
TAGACCAAATCCG
Found at i:35026425 original size:85 final size:85
Alignment explanation
Indices: 35026277--35026437 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
35026267 CCCATCTTTC
* * * *
35026277 TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAAATGTCATCTTTCTGATGAGATATAGAGAA
1 TGATGAGATACAGAGAAGTGGATCAAAGCAATAAAAAGGTCATCTTCCTGATGAGATACAGAGAA
*
35026342 GTGGACCAAATTCGTCTTCT
66 GTAGACCAAATTCGTCTTCT
* * * ***
35026362 TGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAA
1 TGATGAGATACAGAGAAGTGGATCAAAGCAATAAAAAGGTCATCTTCCTGATGAGATACAGAGAA
35026427 GTAGACCAAAT
66 GTAGACCAAAT
35026438 GAATGAAGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (85 bp):
TGATGAGATACAGAGAAGTGGATCAAAGCAATAAAAAGGTCATCTTCCTGATGAGATACAGAGAA
GTAGACCAAATTCGTCTTCT
Found at i:35026785 original size:37 final size:37
Alignment explanation
Indices: 35026735--35026806 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
35026725 AAAGACGTAA
35026735 TCTTCCTGATGAGATACAGAGAAGTAGACTAAATCCG
1 TCTTCCTGATGAGATACAGAGAAGTAGACTAAATCCG
* * *
35026772 TCTTCCTGATGAGATATAGAGAAGTGGATTAAATC
1 TCTTCCTGATGAGATACAGAGAAGTAGACTAAATC
35026807 AATGAAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (37 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACTAAATCCG
Found at i:35026831 original size:85 final size:85
Alignment explanation
Indices: 35026688--35026853 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
35026678 CAAACCCCAC
*
35026688 CTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGACGTAATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGACGTAATCTTCCTGATGAGATACA
*
35026753 GAGAAGTAGACTAAATCCGT
66 GAGAAGTAGACCAAATCCGT
* * * * * * *
35026773 CTTCCTGATGAGATATAGAGAAGTGGATTAAATCAATGAA-ACGGTCATCTTCCTGATGAGATAT
1 CTTCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGAC-GTAATCTTCCTGATGAGATAC
35026837 AGAGAAGTAGACCAAAT
65 AGAGAAGTAGACCAAAT
35026854 TAATGAAGCG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 2 0.03
85 69 0.97
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (85 bp):
CTTCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGACGTAATCTTCCTGATGAGATACA
GAGAAGTAGACCAAATCCGT
Found at i:35028166 original size:28 final size:26
Alignment explanation
Indices: 35028134--35028202 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 26
35028124 TAAAACGAAT
35028134 AATAACAAAAAATAATAAAATAGATTT-A
1 AATAA-AAAAAA-AA-AAAATAGATTTGA
35028162 AATAAAAAATGAAAAAAAATAGATTTGA
1 AATAAAAAA--AAAAAAAATAGATTTGA
*
35028190 AA-AATAAAAAAAA
1 AATAAAAAAAAAAA
35028203 GGAACTCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 5 0.14
27 20 0.54
28 10 0.27
29 2 0.05
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (26 bp):
AATAAAAAAAAAAAAAATAGATTTGA
Found at i:35029003 original size:30 final size:30
Alignment explanation
Indices: 35028831--35029217 Score: 337
Period size: 30 Copynumber: 13.1 Consensus size: 30
35028821 CAAAAATAAT
* * *
35028831 ATTTTGACCCATAAAC-TTTCTAGAAATTAG
1 ATTTTGACCCCTAAACTTTTCCA-AAATTAC
* * * *
35028861 AATTTAACCCCCAAACTTTTCCAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
*
35028891 ATTTTGA--CCTAAACTTTTCCAAAATTGC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
35028919 ATTTTGACCCC-AAACATTTCCAAAATTTC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
35028948 ATTTTGATCCCTAAAC-TTCCCAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
*
35028977 ATTTTGACCCCTAAACTTTTCCAAAATTGC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
35029007 ATTTT-AACCCTAAACTTTTCCAAAATTGC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * ** *
35029036 ATTTTGA-TCATCGA-TTTTCATAAAATTAC
1 ATTTTGACCCCTAAACTTTTC-CAAAATTAC
* ** *
35029065 ATTTTAACCCCTAAA-TTTTCTTGAAATCAC
1 ATTTTGACCCCTAAACTTTTC-CAAAATTAC
* * * *
35029095 ATTTTAACCCTTAAACTTTTCTAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * *
35029125 TTTTTGA-CCCTAAAC-ATTCCTAAAATCAC
1 ATTTTGACCCCTAAACTTTTCC-AAAATTAC
* * *
35029154 ATTTTGACCCCCAACCTTTCCCAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
35029184 ATTTTTACCCTTAAACTTTTCCAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
35029214 ATTT
1 ATTT
35029218 GGCTCCAAAT
Statistics
Matches: 292, Mismatches: 53, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
28 33 0.11
29 117 0.40
30 129 0.44
31 13 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTTCCAAAATTAC
Found at i:35036015 original size:21 final size:22
Alignment explanation
Indices: 35035991--35036031 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35035981 ATTATGTATT
35035991 TAGTATAAGTTT-TTTTTTAAA
1 TAGTATAAGTTTATTTTTTAAA
*
35036012 TAGTATAGGTTTATTTTTTA
1 TAGTATAAGTTTATTTTTTA
35036032 TTGTGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (22 bp):
TAGTATAAGTTTATTTTTTAAA
Found at i:35046565 original size:50 final size:49
Alignment explanation
Indices: 35046506--35046643 Score: 174
Period size: 47 Copynumber: 2.8 Consensus size: 49
35046496 CCGAAACCCA
35046506 TTTGTGGACAAGCCACCACTGATTTGA-AGATAAACTGCCACTGATAACAC
1 TTTGTGGACAAGCCACCACTGATTT-ACAGATAAACTGCCACTG-TAACAC
* * * *
35046556 TTTGTGGACAAGCCACCAC--ATATACAGATATACTACTACTGTAACAC
1 TTTGTGGACAAGCCACCACTGATTTACAGATAAACTGCCACTGTAACAC
* * *
35046603 TTTGTGGACAAGTCATCATTGATTTACAGATAAACTGCCAC
1 TTTGTGGACAAGCCACCACTGATTTACAGATAAACTGCCAC
35046644 ATACTTCCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
47 23 0.31
48 16 0.22
49 16 0.22
50 19 0.26
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (49 bp):
TTTGTGGACAAGCCACCACTGATTTACAGATAAACTGCCACTGTAACAC
Found at i:35049052 original size:21 final size:21
Alignment explanation
Indices: 35049026--35049077 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
35049016 CCACTAAAAA
35049026 AGTATCGATAATATCACCTCG
1 AGTATCGATAATATCACCTCG
*
35049047 AGTATCGATAATTTCACCTCG
1 AGTATCGATAATATCACCTCG
35049068 AGTATCGATA
1 AGTATCGATA
35049078 TTTGTGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (21 bp):
AGTATCGATAATATCACCTCG
Found at i:35051184 original size:20 final size:20
Alignment explanation
Indices: 35051161--35051198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35051151 ACTTTAACCC
35051161 TTAAAATTATAAAATTTAAT
1 TTAAAATTATAAAATTTAAT
* *
35051181 TTAATATTTTAAAATTTA
1 TTAAAATTATAAAATTTA
35051199 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATTATAAAATTTAAT
Found at i:35054252 original size:30 final size:30
Alignment explanation
Indices: 35054216--35054276 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
35054206 TCGATATATG
*
35054216 ATGTGCTCAAATGCTCAAATGTTTGATGGC
1 ATGTGCTCAAATCCTCAAATGTTTGATGGC
*
35054246 ATGTGCTCAAATCCTTAAATGTTTGATGGC
1 ATGTGCTCAAATCCTCAAATGTTTGATGGC
35054276 A
1 A
35054277 CTTACAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (30 bp):
ATGTGCTCAAATCCTCAAATGTTTGATGGC
Found at i:35058316 original size:9 final size:8
Alignment explanation
Indices: 35058288--35058325 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
35058278 GCAATATATT
35058288 TTTTTCTAC
1 TTTTTCT-C
35058297 -TTTTCTC
1 TTTTTCTC
35058304 TTTTTCTC
1 TTTTTCTC
35058312 TTTTTCTTC
1 TTTTTC-TC
35058321 TTTTT
1 TTTTT
35058326 TTTATATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 19 0.70
9 7 0.26
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCTC
Found at i:35058949 original size:17 final size:17
Alignment explanation
Indices: 35058907--35058949 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
35058897 AAACGAACTA
35058907 ACAAATAAAATGCAACG
1 ACAAATAAAATGCAACG
* * *
35058924 ATAACTAAAATGCAATG
1 ACAAATAAAATGCAACG
*
35058941 ACAATTAAA
1 ACAAATAAA
35058950 TGAGATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.14, G:0.09, T:0.19
Consensus pattern (17 bp):
ACAAATAAAATGCAACG
Found at i:35059360 original size:9 final size:9
Alignment explanation
Indices: 35059346--35059378 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
35059336 TGAGGTAACA
35059346 TCTTCTTCC
1 TCTTCTTCC
35059355 TCTTCTTCC
1 TCTTCTTCC
35059364 TCTTCTTCC
1 TCTTCTTCC
35059373 TCTTCT
1 TCTTCT
35059379 GGTCCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCTTCC
Found at i:35059395 original size:9 final size:9
Alignment explanation
Indices: 35059344--35059400 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
35059334 GTTGAGGTAA
35059344 CATCTTCTT
1 CATCTTCTT
*
35059353 CCTCTTCTT
1 CATCTTCTT
*
35059362 CCTCTTCTT
1 CATCTTCTT
*
35059371 CCTCTTCTGGT
1 CATCTTCT--T
35059382 C--CTTCTT
1 CATCTTCTT
35059389 CATCTTCTT
1 CATCTTCTT
35059398 CAT
1 CAT
35059401 TCACCTTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
7 2 0.05
9 39 0.91
11 2 0.05
ACGTcount: A:0.05, C:0.39, G:0.04, T:0.53
Consensus pattern (9 bp):
CATCTTCTT
Found at i:35067128 original size:18 final size:18
Alignment explanation
Indices: 35067107--35067153 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
35067097 AAACTTGTGG
*
35067107 CTGCATCTGGTTGTATGA
1 CTGCATCTGGTTCTATGA
*
35067125 CTGCATCTAGTTCTATGA
1 CTGCATCTGGTTCTATGA
35067143 -TCGCATCTGGT
1 CT-GCATCTGGT
35067154 CCGGTTGCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (18 bp):
CTGCATCTGGTTCTATGA
Found at i:35078363 original size:20 final size:20
Alignment explanation
Indices: 35078320--35078364 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
35078310 TCATTAAGCT
* **
35078320 TTAATTAACCCTTTTTAGCC
1 TTAATTAAACCTTTTTAGAA
*
35078340 TTAATTAAACCTTTTTATAA
1 TTAATTAAACCTTTTTAGAA
35078360 TTAAT
1 TTAAT
35078365 ATAACTCATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAATTAAACCTTTTTAGAA
Found at i:35088639 original size:28 final size:28
Alignment explanation
Indices: 35088608--35088714 Score: 90
Period size: 28 Copynumber: 3.8 Consensus size: 28
35088598 AGAGCGATAC
35088608 TCTACTTACAACTCGGGTAGAGCTTTGA
1 TCTACTTACAACTCGGGTAGAGCTTTGA
* * *
35088636 TCTATTTATAGCTCGGGTAGAGCTTTGA
1 TCTACTTACAACTCGGGTAGAGCTTTGA
** * * * *
35088664 -CTTGTTTATAGCTCGGGTAAAGCTTTGG
1 TC-TACTTACAACTCGGGTAGAGCTTTGA
* * *
35088692 TTTGCTTACAACTCGGTTAGAGC
1 TCTACTTACAACTCGGGTAGAGC
35088715 GTAAATCTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.02
28 64 0.98
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (28 bp):
TCTACTTACAACTCGGGTAGAGCTTTGA
Found at i:35090271 original size:137 final size:137
Alignment explanation
Indices: 35089982--35090464 Score: 684
Period size: 137 Copynumber: 3.5 Consensus size: 137
35089972 AAAAATTTTA
*
35089982 ATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
1 ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
* * * * * *
35090047 TATATTCTTTTCAAAAGAATATTAATTTACATCTCTTTTATATTTTGACCGAAATAAATTACTAT
66 TATATTC-TTCCAAAAAAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATAT
* **
35090112 AACTCCTT
130 AATTGTTT
* * * **
35090120 ATATTAATAAATTCGGTAAAATATGTACAATTTATATTTTTTATGAATCCCATTCATATATTAAT
1 ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
* * *
35090185 TATATTCTTCCAAAAAAATATTAATTTTCATGTCTTTCATATTTTGACCAAAATTAATTAATATA
66 TATATTCTTCCAAAAAAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATA
35090250 ATTGTTT
131 ATTGTTT
* *
35090257 ATATTAATAAATTCGGT-AAATGTTATACAATTAATATTTAGTATGAATCAAATTCATATATTAA
1 ATATTAATAAATTCGGTAAAAT-ATATACAATTAATATTTTGTATGAATCAAATTCATATATTAA
* * * *
35090321 TTATATTCGTCCCAAAAAATATTAA-TTTCTATATATTTTATATTTTGACTGAAATTAATTAATA
65 TTATATTCTTCCAAAAAAATATTAATTTTC-ATATCTTTTATATTTTGACCGAAATTAATTAATA
35090385 TAATTGTTT
129 TAATTGTTT
*
35090394 ATATTAATAAATTCGGTAAAATATATACAATTAATA-TTTATATGAATCAAATTCATATATTAAT
1 ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
*
35090458 TTTATTC
66 TATATTC
35090465 ATGTTCTATA
Statistics
Matches: 307, Mismatches: 35, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
136 40 0.13
137 197 0.64
138 70 0.23
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (137 bp):
ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
TATATTCTTCCAAAAAAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATA
ATTGTTT
Found at i:35092184 original size:23 final size:22
Alignment explanation
Indices: 35092114--35092195 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
35092104 TTTAAGTGGA
35092114 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGAGGGTATA-TTGGT
* * *
35092137 TGTGTTCGAAGGGTAAATTGGT
1 TGTGTTTGGAGGGTATATTGGT
* *
35092159 TGTGTTTGGAGGCTATGATTGAT
1 TGTGTTTGGAGGGTAT-ATTGGT
*
35092182 TGTGTTTGGTGGGT
1 TGTGTTTGGAGGGT
35092196 TATAGCTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 17 0.35
23 31 0.65
ACGTcount: A:0.15, C:0.02, G:0.39, T:0.44
Consensus pattern (22 bp):
TGTGTTTGGAGGGTATATTGGT
Found at i:35106372 original size:17 final size:18
Alignment explanation
Indices: 35106336--35106375 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
35106326 TTTCTTCTCT
**
35106336 TTTTCAAATAGATCCTTA
1 TTTTCAAATAGAAACTTA
35106354 TTTTCAAATA-AAACTTA
1 TTTTCAAATAGAAACTTA
35106371 TTTTC
1 TTTTC
35106376 TAATTTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTCAAATAGAAACTTA
Found at i:35110309 original size:30 final size:29
Alignment explanation
Indices: 35110246--35110372 Score: 94
Period size: 30 Copynumber: 4.3 Consensus size: 29
35110236 TAAAATTGTT
* **
35110246 TTTGACCCCAAATTATCCAAAAA-TCATGT
1 TTTGACCCCAAACTATCCAAAAATTCA-AA
35110275 TTTGACCCACAAACTATCCAAAAATTCAAA
1 TTTGACCC-CAAACTATCCAAAAATTCAAA
* ** ***
35110305 TTTGACCCCTAAACTTTTTAAAAATTTTGA
1 TTTGACCCC-AAACTATCCAAAAATTCAAA
* * * *
35110335 TTTGACCCTTAAACTTTCTAAAAGTTCAAA
1 TTTGACCC-CAAACTATCCAAAAATTCAAA
35110365 TTTGACCC
1 TTTGACCC
35110373 AGTTTTAATG
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
29 9 0.11
30 67 0.85
31 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTGACCCCAAACTATCCAAAAATTCAAA
Found at i:35110474 original size:17 final size:17
Alignment explanation
Indices: 35110454--35110493 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
35110444 TCTTGTTTAT
35110454 CCTTTTTTTTATTAATC
1 CCTTTTTTTTATTAATC
35110471 CCTTTTTTTTATTAATC
1 CCTTTTTTTTATTAATC
35110488 CCTTTT
1 CCTTTT
35110494 ATATGCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (17 bp):
CCTTTTTTTTATTAATC
Found at i:35121036 original size:12 final size:12
Alignment explanation
Indices: 35121007--35121050 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
35120997 CGAAATTTGT
* *
35121007 TATTTTCACTGA
1 TATTTTGACTAA
*
35121019 TGTTTTGACTAA
1 TATTTTGACTAA
35121031 TATTTTGACTAA
1 TATTTTGACTAA
35121043 TATTTTGA
1 TATTTTGA
35121051 TATCTTCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (12 bp):
TATTTTGACTAA
Found at i:35121663 original size:50 final size:50
Alignment explanation
Indices: 35121605--35121712 Score: 135
Period size: 50 Copynumber: 2.2 Consensus size: 50
35121595 TCCTATACCT
* **
35121605 CTAAAGCTGTAGAGGAATGGATTAAAGTTGCAATGGCAAATATCATACAC
1 CTAAAGCTGTAGAGGAATAGATTAAAGCCGCAATGGCAAATATCATACAC
** * * * *
35121655 CTAAAGCTGTAGAGGGGTAGATTGAAGCCGCAATGGCGAATCTCATTCAC
1 CTAAAGCTGTAGAGGAATAGATTAAAGCCGCAATGGCAAATATCATACAC
35121705 CTAAAGCT
1 CTAAAGCT
35121713 ATGGAGGGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (50 bp):
CTAAAGCTGTAGAGGAATAGATTAAAGCCGCAATGGCAAATATCATACAC
Found at i:35121901 original size:39 final size:39
Alignment explanation
Indices: 35121834--35122046 Score: 205
Period size: 39 Copynumber: 5.4 Consensus size: 39
35121824 AAGTCACCAC
* **
35121834 ATCCTATCTTTTACCCCGACCATG-GGGCAGATTGAAGCA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCA
* * * * *
35121873 GTCTAATGTTTTACCCTAATCAGAGGGCAAATTGAAGCA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
* * ** * *
35121912 ATACAATCTTTTACTCTAATAAGAGGGTAGATTGAAGACC
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CA
* * *
35121952 ATCCAATCTTTTACCCTGACCATG-GGGCATATTGAATCA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCA
*
35121991 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACC
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CA
*
35122031 ATCCAATCTTTCACCC
1 ATCCAATCTTTTACCC
35122047 CTAAAGTTAT
Statistics
Matches: 138, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.01
39 91 0.66
40 44 0.32
41 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
Found at i:35121986 original size:79 final size:79
Alignment explanation
Indices: 35121897--35122046 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 79
35121887 CCTAATCAGA
* * *
35121897 GGGCAAATTGAAGCAATACAATCTTTTACTCTAATAAGAGGGTAGATTGAAGACCATCCAATCTT
1 GGGCAAATTGAAGCAATACAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACCATCCAATCTT
*
35121962 TTACCCTGACCATG
66 TCACCCTGACCATG
* * * *
35121976 GGGCATATTGAATCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTT
1 GGGCAAATTGAAGCAATACAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACCATCCAATCTT
35122041 TCACCC
66 TCACCC
35122047 CTAAAGTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (79 bp):
GGGCAAATTGAAGCAATACAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACCATCCAATCTT
TCACCCTGACCATG
Found at i:35122243 original size:51 final size:52
Alignment explanation
Indices: 35122172--35122334 Score: 128
Period size: 51 Copynumber: 3.2 Consensus size: 52
35122162 AGAAATGGAT
* * *
35122172 TGAAGCTAC--GAAGGCGAATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGA
1 TGAAGCTACAAGAAAGCAAATCCTTATCTCCCTGAAGTTGCAGT-GAGCAGGA
* *
35122223 TGAAGCTACAAG-AA-CAAATCC-TATAC-CCCTGAAGTTACAGTGGGTC-GGA
1 TGAAGCTACAAGAAAGCAAATCCTTAT-CTCCCTGAAGTTGCAGTGAG-CAGGA
* * * * *
35122272 TTAAAG-T-CATGAAAGCAAATCTTTATCTCCCTAAAGTTGCAGTGGAGCAAGA
1 -TGAAGCTACAAGAAAGCAAATCCTTATCTCCCTGAAGTTGCAGT-GAGCAGGA
35122324 TGAAGCTACAA
1 TGAAGCTACAA
35122335 CATCAAATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
48 3 0.04
49 8 0.09
50 28 0.33
51 37 0.44
52 6 0.07
53 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (52 bp):
TGAAGCTACAAGAAAGCAAATCCTTATCTCCCTGAAGTTGCAGTGAGCAGGA
Found at i:35123210 original size:16 final size:16
Alignment explanation
Indices: 35123189--35123231 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
35123179 TTCACATATA
35123189 TATATTATATTTACTT
1 TATATTATATTTACTT
* * *
35123205 TATATTTTACTTATTT
1 TATATTATATTTACTT
35123221 TATATTATATT
1 TATATTATATT
35123232 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATATTTACTT
Found at i:35123246 original size:27 final size:30
Alignment explanation
Indices: 35123189--35123246 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
35123179 TTCACATATA
35123189 TATATTATATTTACTTTATATTTTACTTATTT
1 TATATTATATTTAC-TTATATTTTAC-TATTT
*
35123221 TATATTATA-TTA-TTATTTTTTA-TATT
1 TATATTATATTTACTTATATTTTACTATT
35123247 GAAACTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.16
29 9 0.36
31 3 0.12
32 9 0.36
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (30 bp):
TATATTATATTTACTTATATTTTACTATTT
Found at i:35123999 original size:29 final size:29
Alignment explanation
Indices: 35123959--35124022 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
35123949 ACTTTATTTT
*
35123959 AAAATTGTTTTTGAC-CCCAAACTATCTA
1 AAAATTATTTTTGACTCCCAAACTATCTA
*
35123987 AAAATTATATTTTGACTCCTAAACTATCTA
1 AAAATTAT-TTTTGACTCCCAAACTATCTA
35124017 AAAATT
1 AAAATT
35124023 CAAATTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 7 0.22
29 7 0.22
30 18 0.56
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTATTTTTGACTCCCAAACTATCTA
Found at i:35124040 original size:30 final size:29
Alignment explanation
Indices: 35123972--35124153 Score: 163
Period size: 30 Copynumber: 6.1 Consensus size: 29
35123962 ATTGTTTTTG
* * * *
35123972 ACCCCAAACTATCTAAAAATT-ATATTTTG
1 ACCCTAAACTTTCTAAAAATTCA-AATTTA
*
35124001 ACTCCTAAACTATCTAAAAATTCAAATTTA
1 AC-CCTAAACTTTCTAAAAATTCAAATTTA
35124031 ACCCTTAAACTTT-TAAAAATTCAAATTTA
1 ACCC-TAAACTTTCTAAAAATTCAAATTTA
* *
35124060 ACCCCTGAACTTTCCAAAAATTCAAA-TTA
1 A-CCCTAAACTTTCTAAAAATTCAAATTTA
* * *** *
35124089 GACCCTCGAACTTTTTAAAAATTTTGATTTG
1 -ACCCT-AAACTTTCTAAAAATTCAAATTTA
35124120 ACTCCTAAACTTTCTAAAAATTCAAATTTA
1 AC-CCTAAACTTTCTAAAAATTCAAATTTA
35124150 ACCC
1 ACCC
35124154 GATTTTAATG
Statistics
Matches: 126, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
29 37 0.29
30 83 0.66
31 6 0.05
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
ACCCTAAACTTTCTAAAAATTCAAATTTA
Found at i:35124139 original size:60 final size:58
Alignment explanation
Indices: 35123972--35124153 Score: 188
Period size: 60 Copynumber: 3.1 Consensus size: 58
35123962 ATTGTTTTTG
* * *
35123972 ACCC-CAAACTATCTAAAAATT-ATATTTTGACTCCTAAACTATCTAAAAATTCAAATTTA
1 ACCCTCAAACT-TTTAAAAATTCA-AATTTGACTCCTAAACTTTCTAAAAATTCAAA-TTA
* * * * *
35124031 ACCCTTAAACTTTTAAAAATTCAAATTTAACCCCTGAACTTTCCAAAAATTCAAATTA
1 ACCCTCAAACTTTTAAAAATTCAAATTTGACTCCTAAACTTTCTAAAAATTCAAATTA
* ***
35124089 GACCCTCGAACTTTTTAAAAATTTTGATTTGACTCCTAAACTTTCTAAAAATTCAAATTTA
1 -ACCCTCAAAC-TTTTAAAAATTCAAATTTGACTCCTAAACTTTCTAAAAATTCAAA-TTA
35124150 ACCC
1 ACCC
35124154 GATTTTAATG
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
58 3 0.03
59 47 0.47
60 48 0.48
61 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (58 bp):
ACCCTCAAACTTTTAAAAATTCAAATTTGACTCCTAAACTTTCTAAAAATTCAAATTA
Found at i:35125411 original size:23 final size:23
Alignment explanation
Indices: 35125385--35125433 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
35125375 TGGGCAACTA
35125385 TAGTTATTGGTCAACTACAATTT
1 TAGTTATTGGTCAACTACAATTT
* *
35125408 TAGTTATTGGTCAATTTCAATTT
1 TAGTTATTGGTCAACTACAATTT
35125431 TAG
1 TAG
35125434 CAGTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (23 bp):
TAGTTATTGGTCAACTACAATTT
Found at i:35130159 original size:93 final size:93
Alignment explanation
Indices: 35130051--35130238 Score: 286
Period size: 93 Copynumber: 2.0 Consensus size: 93
35130041 ACAATTCTTC
* * * *
35130051 AACTTCTTTTAATTTGGCCACTCTCTTCATTTTTCGTTCGATTTTGACCCCATTTTGTTTGATTT
1 AACTTATTTTAATTTGGCCACTCTCTTCACTTTTCGTTCCATTTTGACCCCATTTTGTTTGAATT
**
35130116 TGAATTTCGGCACTCCAATTATATTCCT
66 TGAATTTCAACACTCCAATTATATTCCT
* * *
35130144 AACTTATTTTAATTTGGCCCCTCTCTTCACTTTTCGTTCCATTTTGGCCTCATTTTGTTTGAATT
1 AACTTATTTTAATTTGGCCACTCTCTTCACTTTTCGTTCCATTTTGACCCCATTTTGTTTGAATT
*
35130209 TGAATTTCAACACTCCAATTGTATTCCT
66 TGAATTTCAACACTCCAATTATATTCCT
35130237 AA
1 AA
35130239 TAAGAAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (93 bp):
AACTTATTTTAATTTGGCCACTCTCTTCACTTTTCGTTCCATTTTGACCCCATTTTGTTTGAATT
TGAATTTCAACACTCCAATTATATTCCT
Found at i:35131558 original size:15 final size:15
Alignment explanation
Indices: 35131534--35131579 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
35131524 CGAGCCTATG
35131534 TTTG-AAAGTATGAT
1 TTTGTAAAGTATGAT
* *
35131548 TTTTTAAAGTACGAT
1 TTTGTAAAGTATGAT
*
35131563 TTTGTAAACTATG-T
1 TTTGTAAAGTATGAT
35131577 TTT
1 TTT
35131580 ACAACCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (15 bp):
TTTGTAAAGTATGAT
Found at i:35150353 original size:18 final size:18
Alignment explanation
Indices: 35150330--35150371 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35150320 CGACCCATGG
35150330 CACCTCCGATAAGGCCTC
1 CACCTCCGATAAGGCCTC
** *
35150348 CACCTCCTTTAAGGCCTT
1 CACCTCCGATAAGGCCTC
35150366 CACCTC
1 CACCTC
35150372 TTCCTGTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.45, G:0.12, T:0.24
Consensus pattern (18 bp):
CACCTCCGATAAGGCCTC
Found at i:35158035 original size:29 final size:31
Alignment explanation
Indices: 35157983--35158044 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
35157973 ATTCTAGCAA
35157983 AAAAAGAGAGAAATAGTGAAAAAAA-ATAAAG
1 AAAAAGAGAGAAATAGTGAAAAAAACA-AAAG
35158014 AAAAAGA-A-AAATGAGT-AAAAAAACAAAAG
1 AAAAAGAGAGAAAT-AGTGAAAAAAACAAAAG
35158043 AA
1 AA
35158045 GAAAATCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 17 0.59
30 5 0.17
31 7 0.24
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (31 bp):
AAAAAGAGAGAAATAGTGAAAAAAACAAAAG
Found at i:35160993 original size:26 final size:28
Alignment explanation
Indices: 35160936--35160994 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
35160926 CGAAGGGGTT
* *
35160936 TAAAGGAACAATGAAAGGAAAAAATAAT
1 TAAAGGAACAAGGAAAGGAAAAAATAAA
*
35160964 TAAAGGAA-AAGGAGAGG-AAAAATAAA
1 TAAAGGAACAAGGAAAGGAAAAAATAAA
35160990 TAAAG
1 TAAAG
35160995 AGGACAGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 7 0.25
28 8 0.29
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.12
Consensus pattern (28 bp):
TAAAGGAACAAGGAAAGGAAAAAATAAA
Found at i:35169273 original size:21 final size:21
Alignment explanation
Indices: 35169225--35169279 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
35169215 TTGATAGCTG
* *
35169225 TAAAATTAATTATTCTAAAAA
1 TAAAATTAAATATTATAAAAA
*
35169246 T-AAATTAAATATTATAACAA
1 TAAAATTAAATATTATAAAAA
35169266 TAAAATTAAA-ATTA
1 TAAAATTAAATATTA
35169280 ATCATGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTAAATATTATAAAAA
Found at i:35169467 original size:22 final size:22
Alignment explanation
Indices: 35169395--35169467 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
35169385 ATAAATTATC
* * *
35169395 AAAAGTATATTTAAATTTAATAA
1 AAAATTATAATTAAATTT-GTAA
* *
35169418 TAAAATTATAATTATATTTGTAC
1 -AAAATTATAATTAAATTTGTAA
*
35169441 TAAATTATAATTAAATCTT-TAA
1 AAAATTATAATTAAAT-TTGTAA
35169463 AAAAT
1 AAAAT
35169468 ATGTATATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 20 0.51
23 4 0.10
24 15 0.38
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (22 bp):
AAAATTATAATTAAATTTGTAA
Found at i:35169841 original size:18 final size:18
Alignment explanation
Indices: 35169789--35169842 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
35169779 GTTATGATAA
*
35169789 ATTATTTAAATATCATTT
1 ATTATTTAAATATAATTT
*
35169807 ATTA-TTATAT-TAA---
1 ATTATTTAAATATAATTT
35169820 ATTATTTAAATATAATTT
1 ATTATTTAAATATAATTT
35169838 ATTAT
1 ATTAT
35169843 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
13 4 0.14
14 5 0.18
15 3 0.11
16 2 0.07
17 5 0.18
18 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTAAATATAATTT
Found at i:35169855 original size:28 final size:30
Alignment explanation
Indices: 35169786--35169876 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
35169776 ACAGTTATGA
*
35169786 TAAATTATTTAAATATCATTTATTATTATAT
1 TAAATTATTTAAATATAATTTATTA-TATAT
35169817 TAAATTATTTAAATATAATTTATTATAT-T
1 TAAATTATTTAAATATAATTTATTATATAT
* *
35169846 TAAGTT-TTTAAA-ATATTTTA-TATATCAT
1 TAAATTATTTAAATATAATTTATTATAT-AT
35169874 TAA
1 TAA
35169877 TTTTACAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
26 5 0.09
27 7 0.13
28 10 0.18
29 6 0.11
30 3 0.05
31 24 0.44
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (30 bp):
TAAATTATTTAAATATAATTTATTATATAT
Found at i:35169880 original size:27 final size:27
Alignment explanation
Indices: 35169788--35169895 Score: 87
Period size: 28 Copynumber: 3.8 Consensus size: 27
35169778 AGTTATGATA
* *
35169788 AATTATTTAAATATCATTTATTATTATATTA
1 AATT-TTTAAA-ATAATTTA-TA-TATATTT
35169819 AATTATTTAAATATAATTTAT-TATATTT
1 AATT-TTTAAA-ATAATTTATATATATTT
*
35169847 AAGTTTTTAAAATATTTTATATATCA-TT
1 AA-TTTTTAAAATAATTTATATAT-ATTT
35169875 AA-TTTTACAAATAATTTATAT
1 AATTTTTA-AAATAATTTATAT
35169896 TAATTACTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.07
27 20 0.29
28 21 0.30
29 3 0.04
30 1 0.01
31 19 0.28
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTTTTAAAATAATTTATATATATTT
Found at i:35169901 original size:26 final size:26
Alignment explanation
Indices: 35169824--35169901 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
35169814 TATTAAATTA
*
35169824 TTTAAATATAATTTAT-TATATTTAAGTT
1 TTTAAA-ATAATTTATATATAATTAA--T
* *
35169852 TTTAAAATATTTTATATATCATTAAT
1 TTTAAAATAATTTATATATAATTAAT
35169878 TTTACAAATAATTTATAT-TAATTA
1 TTTA-AAATAATTTATATATAATTA
35169902 CTTAAAAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.23
27 20 0.47
28 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (26 bp):
TTTAAAATAATTTATATATAATTAAT
Found at i:35172876 original size:23 final size:25
Alignment explanation
Indices: 35172836--35172882 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
35172826 TTTCTTAGAT
35172836 TTAGGTTTTTAGTCATTT-CTTTTC
1 TTAGGTTTTTAGTCATTTCCTTTTC
*
35172860 TTAGG-TTTTAGTTATTTCCTTTT
1 TTAGGTTTTTAGTCATTTCCTTTT
35172883 GTTCTTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.64
Consensus pattern (25 bp):
TTAGGTTTTTAGTCATTTCCTTTTC
Found at i:35174773 original size:21 final size:21
Alignment explanation
Indices: 35174723--35174794 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
35174713 AAAATTTAAA
*
35174723 ACAAACATAATGAGGAGAGTT
1 ACAAACATTATGAGGAGAGTT
35174744 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATTATGAGGAGAGTT
*
35174766 ACAAACATTATAAGGAGAGTT
1 ACAAACATTATGAGGAGAGTT
35174787 ACAAACAT
1 ACAAACAT
35174795 AATGTTTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 28 0.58
22 20 0.42
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (21 bp):
ACAAACATTATGAGGAGAGTT
Found at i:35179570 original size:21 final size:21
Alignment explanation
Indices: 35179546--35179600 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
35179536 GAAATTTAAA
35179546 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
*
35179567 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
35179589 ACAAACATAATG
1 ACAAACATAATG
35179601 TTTTGTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:35184437 original size:24 final size:24
Alignment explanation
Indices: 35184396--35184460 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
35184386 CTATACTAAT
*
35184396 TAGAGTTTAAATGTGAAACT-AAAAA
1 TAGAGTTT-AATGGGAAA-TGAAAAA
35184421 TAGAGTTTAATGGGAAATGAAAAA
1 TAGAGTTTAATGGGAAATGAAAAA
* *
35184445 CAGTGTTTAATTGGGA
1 TAGAGTTTAA-TGGGA
35184461 GAAAAAAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 21 0.60
25 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (24 bp):
TAGAGTTTAATGGGAAATGAAAAA
Found at i:35186391 original size:25 final size:25
Alignment explanation
Indices: 35186362--35186441 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
35186352 TAATCAGAGT
*
35186362 TTTAAGTGTGAAACTAAAAATAAAG
1 TTTAAGTGTGAAACTAAAAACAAAG
*
35186387 TTTAAGTATGAAACTAAAAACAAAG
1 TTTAAGTGTGAAACTAAAAACAAAG
* *
35186412 TTTAAGTGAGAAACTAAAAACAATG
1 TTTAAGTGTGAAACTAAAAACAAAG
35186437 TTTAA
1 TTTAA
35186442 CTAGGAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.28
Consensus pattern (25 bp):
TTTAAGTGTGAAACTAAAAACAAAG
Found at i:35188193 original size:46 final size:44
Alignment explanation
Indices: 35188140--35188233 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 44
35188130 GATTCGCTGT
35188140 AATGGAATAGAGCTGTAATCAGTATT-TTAGTTATTTGGTTGAACGG
1 AATGGAATAGAGCTGTAAT-AGTATTCTT-G-TATTTGGTTGAACGG
* *
35188186 AATGGAATAGAGCTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAGTATTCTTGTATTTGGTTGAACGG
35188230 AATG
1 AATG
35188234 ATGCTATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 17 0.38
45 7 0.16
46 21 0.47
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAGTATTCTTGTATTTGGTTGAACGG
Found at i:35188228 original size:39 final size:41
Alignment explanation
Indices: 35188140--35188245 Score: 103
Period size: 46 Copynumber: 2.5 Consensus size: 41
35188130 GATTCGCTGT
35188140 AATGGAATAGAGCTGTAATCAGTATTTTAGTTATTTGGTTGAACGG
1 AATGGAATAGAGCTGTAAT-AGTATTTTAGTTATTTGGTT--A--G
*
35188186 AATGGAATAGAGCTGTAATAGTATTCTT-G-TGTTTGGTT-G
1 AATGGAATAGAGCTGTAATAGTATT-TTAGTTATTTGGTTAG
*
35188225 AATGGAAT-GATGCTATAATAG
1 AATGGAATAGA-GCTGTAATAG
35188246 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
38 2 0.04
39 18 0.32
44 8 0.14
45 7 0.12
46 21 0.38
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (41 bp):
AATGGAATAGAGCTGTAATAGTATTTTAGTTATTTGGTTAG
Found at i:35188409 original size:56 final size:56
Alignment explanation
Indices: 35188323--35188476 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 56
35188313 TTGTTGTTAA
* * * * *
35188323 ATTTTAATAAGATTGTTATTAAATATAATTTAATAAAAAATAAATAATTTAATCAT
1 ATTTTAATATGATTATTATTAAATACAATTTAATAAAAAATAAATAATTTAATAAC
* * *
35188379 ATTTTAACATGATTATTATTAAATACAATTTAATAAAATAGTATATAATTTAATAAC
1 ATTTTAATATGATTATTATTAAATACAATTTAATAAAA-AATAAATAATTTAATAAC
* *
35188436 ATTCTTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 ATT-TTAATATGATTATTATT-AAATA-CAATTTAATAAAAA
35188477 TCATAATATA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 34 0.41
57 17 0.20
58 16 0.19
59 14 0.17
60 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (56 bp):
ATTTTAATATGATTATTATTAAATACAATTTAATAAAAAATAAATAATTTAATAAC
Found at i:35189769 original size:51 final size:51
Alignment explanation
Indices: 35189690--35189819 Score: 197
Period size: 51 Copynumber: 2.5 Consensus size: 51
35189680 ACTCACGATG
* * * * *
35189690 ACTCACGATGACACTGAGTCATCAGACCTTTAATCCATCATGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATCCATTT
*
35189741 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATCCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATCCATTT
*
35189792 ACTCACGATGACACTTAATCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
35189820 CTTTCGTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATCCATTT
Found at i:35196981 original size:51 final size:50
Alignment explanation
Indices: 35196863--35197049 Score: 232
Period size: 51 Copynumber: 3.6 Consensus size: 50
35196853 ATTCATTTAA
* ** *
35196863 TACTAACGATGACA-TCTAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAT-GG-ATTCATT
* *
35196916 TACTCACGATGACACTGAGTCATTGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCAT-ATGGATTCATT
* *
35196967 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCAT-ATGGATTCATT
*
35197018 TACTCATGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
35197050 TCGTTTATAG
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
51 83 0.69
52 9 0.08
53 27 0.22
54 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATATGGATTCATT
Found at i:35197039 original size:102 final size:104
Alignment explanation
Indices: 35196863--35197049 Score: 263
Period size: 102 Copynumber: 1.8 Consensus size: 104
35196853 ATTCATTTAA
** *
35196863 TACTAACGATGACATCTAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATGA
1 TACTAACGATGACATCTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATGA
*
35196928 CACTGAGTCATTGGACCTTTAATCCATCATGGATTCATT
66 CACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
* * * *
35196967 TACTCACGATGACA-CTTAGTCATCGGACCT-TTAATCCTTAAAGG-ATTCATTTACTCATGATG
1 TACTAACGATGACATC-TAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATG
*
35197029 ACACTTAGTCATCGGACCTTT
65 ACACTGAGTCATCGGACCTTT
35197050 TCGTTTATAG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
102 35 0.48
103 11 0.15
104 27 0.37
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (104 bp):
TACTAACGATGACATCTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATGA
CACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
Found at i:35201678 original size:33 final size:32
Alignment explanation
Indices: 35201636--35201704 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
35201626 CTTAATTTAA
35201636 AATTCAAATTAATCCTTTTAAAATCCTAACTAG
1 AATTCAAATTAATCCTTTTAAAATCCTAA-TAG
* * *
35201669 AATTCAAATTACTCCTTTTCAAATCGTAATAG
1 AATTCAAATTAATCCTTTTAAAATCCTAATAG
35201701 AATT
1 AATT
35201705 TATCTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (32 bp):
AATTCAAATTAATCCTTTTAAAATCCTAATAG
Found at i:35205124 original size:52 final size:52
Alignment explanation
Indices: 35205046--35205226 Score: 274
Period size: 52 Copynumber: 3.5 Consensus size: 52
35205036 ATTGCATTTA
* * *
35205046 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCTTAAAGGAATCAT
1 ATACTCACGATGACACATAGTAATCGGACCTCATAATCCTTAAAGGATTCAT
* *
35205098 ATACTCACGATGACACATAGTTATCGGACCTCAAAAT-CTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTAATCGGACCTCATAATCCT-TAAAGGATTCAT
* *
35205150 AAACTCACGATGACACATAGTAATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTAATCGGACCTCATAATCCTTAAAGGATTCAT
*
35205202 ATACTCATGATGACACATAGTAATC
1 ATACTCACGATGACACATAGTAATC
35205227 AAACCTTTTT
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.02
52 114 0.97
53 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTAATCGGACCTCATAATCCTTAAAGGATTCAT
Found at i:35212249 original size:52 final size:52
Alignment explanation
Indices: 35212168--35212354 Score: 279
Period size: 52 Copynumber: 3.6 Consensus size: 52
35212158 ATTTCATTTA
* * *
35212168 ATACTCACGATGACACATAGTTATTGGACCTCTTAATCCGTAAAGGAATT-AT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG-ATTCAT
*
35212220 ATACTCACGATGACACATAATCATCGGACC-CAATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTC-ATAATCCGTAAAGGATTCAT
* * *
35212272 ATACTCATGATGACACGTAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
35212324 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
35212355 TTTTCATTTA
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
51 4 0.03
52 117 0.96
53 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:35215720 original size:37 final size:37
Alignment explanation
Indices: 35215644--35215837 Score: 212
Period size: 37 Copynumber: 5.2 Consensus size: 37
35215634 TGAAATGGCC
* * **
35215644 TTATGCTCTAACCGAGACATAAACAAATCACATAT--CA
1 TTATGCTCTAACCGAGACGTAAGC-CTTC-CATATAACA
* * *
35215681 TTATGCTTTAACCCAAACGTAAGCCTTCCATATAACA
1 TTATGCTCTAACCGAGACGTAAGCCTTCCATATAACA
* * *
35215718 TTACGCTCTAACCGAGATGTAAGTCTTCCATATAACA
1 TTATGCTCTAACCGAGACGTAAGCCTTCCATATAACA
** * * *
35215755 TTACACTCGAATCGAGACGTCAGCCTTCCATATAACA
1 TTATGCTCTAACCGAGACGTAAGCCTTCCATATAACA
*
35215792 TTATGCTCTAACCGAGACGCAAGCCTTCCATATAACA
1 TTATGCTCTAACCGAGACGTAAGCCTTCCATATAACA
35215829 TTATGCTCT
1 TTATGCTCT
35215838 CCATCGGAGT
Statistics
Matches: 130, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
35 5 0.04
36 2 0.02
37 123 0.95
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (37 bp):
TTATGCTCTAACCGAGACGTAAGCCTTCCATATAACA
Found at i:35221334 original size:23 final size:22
Alignment explanation
Indices: 35221306--35221370 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
35221296 CTCTTCGTTA
*
35221306 TTTAGCACATTTAGTGCTTTCCG
1 TTTAGCACATTT-GTGCTCTCCG
* *
35221329 TTTAGCTCATTTGTGCTCTCTG
1 TTTAGCACATTTGTGCTCTCCG
* *
35221351 TATAGCACATTGGTGCTCTC
1 TTTAGCACATTTGTGCTCTC
35221371 AGTTCATTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.43
Consensus pattern (22 bp):
TTTAGCACATTTGTGCTCTCCG
Found at i:35222897 original size:37 final size:37
Alignment explanation
Indices: 35222856--35223051 Score: 302
Period size: 37 Copynumber: 5.3 Consensus size: 37
35222846 AATCACATAG
*
35222856 CATTACGCTCTAATCGAGATGTAAGCCTTCCATATAA
1 CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
* *
35222893 CATTACGCTTTAATCGAGACGTAAGTCTTCCATATAA
1 CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
*
35222930 CATTACACTCTAATCGAGACGTAAGCCTTCCATATAA
1 CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
* **
35222967 CATTACGCTCTAACCGAGGTGTAAGCCTTCCATATAA
1 CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
* *
35223004 CATTATGCTCTAACCGAGACGTAAGCCTTCCATATAA
1 CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
*
35223041 CATTACACTCT
1 CATTACGCTCT
35223052 TGATAGTACT
Statistics
Matches: 144, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 144 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (37 bp):
CATTACGCTCTAATCGAGACGTAAGCCTTCCATATAA
Found at i:35227715 original size:32 final size:33
Alignment explanation
Indices: 35227644--35227715 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
35227634 ATTAGTTTAA
* *
35227644 AATTCAAATTAATCCTTTTAAAATCCTAACTAG
1 AATTTAAATTAATCATTTTAAAATCCTAACTAG
*
35227677 AATTTAAATTACTCATTTTCAAAA-CCTAA-TAG
1 AATTTAAATTAATCATTTT-AAAATCCTAACTAG
35227709 AATTTAA
1 AATTTAA
35227716 CTTTCTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 10 0.29
33 21 0.60
34 4 0.11
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (33 bp):
AATTTAAATTAATCATTTTAAAATCCTAACTAG
Found at i:35228276 original size:37 final size:37
Alignment explanation
Indices: 35228177--35228276 Score: 146
Period size: 37 Copynumber: 2.7 Consensus size: 37
35228167 CAAGAAAATC
* *
35228177 ACAGTTTATACTACATATTTGGTATATGATCGATACG
1 ACAGTTTATACTACATATATGTTATATGATCGATACG
* * * *
35228214 ATAGTTTATACTACATATATTTTATATGATTGGTACG
1 ACAGTTTATACTACATATATGTTATATGATCGATACG
35228251 ACAGTTTATACTACATATATGTTATA
1 ACAGTTTATACTACATATATGTTATA
35228277 CGTTCGTTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (37 bp):
ACAGTTTATACTACATATATGTTATATGATCGATACG
Found at i:35231370 original size:14 final size:14
Alignment explanation
Indices: 35231299--35231376 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 14
35231289 TCAATGCAAC
* *
35231299 TCTCAACTTTTTGT
1 TCTCAATTTTTTAT
* * *
35231313 TCTCGATTTGTTGT
1 TCTCAATTTTTTAT
*
35231327 TCTCAATTTCTTAT
1 TCTCAATTTTTTAT
* **
35231341 TCTCAATTGTCAAT
1 TCTCAATTTTTTAT
*
35231355 TCTCGATTTTTTAT
1 TCTCAATTTTTTAT
*
35231369 TCTAAATT
1 TCTCAATT
35231377 CTCAATTCCA
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 48 1.00
ACGTcount: A:0.19, C:0.18, G:0.08, T:0.55
Consensus pattern (14 bp):
TCTCAATTTTTTAT
Found at i:35231391 original size:28 final size:28
Alignment explanation
Indices: 35231326--35231384 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
35231316 CGATTTGTTG
* *
35231326 TTCTCAATTTCTTATTCTCAATTGTCAA
1 TTCTCAATTTCTTATTCTAAATTCTCAA
* *
35231354 TTCTCGATTTTTTATTCTAAATTCTCAA
1 TTCTCAATTTCTTATTCTAAATTCTCAA
35231382 TTC
1 TTC
35231385 CAAATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCTCAATTTCTTATTCTAAATTCTCAA
Found at i:35231981 original size:252 final size:252
Alignment explanation
Indices: 35231526--35232031 Score: 890
Period size: 252 Copynumber: 2.0 Consensus size: 252
35231516 TTAAATTATT
35231526 TAATTTTAATACGTTAATTATTATGATGTTAAGAAAATATTATTAAATTATTTAATTTTAAATAG
1 TAATTTTAATACGTTAATTATTATGATGTTAAGAAAATATTATTAAATTATTTAATTTTAAATAG
* * * *
35231591 TTTGCTATTATGTTGTTCAGATTATTAATTTTTATGTTTATATACTTAGGCTGAAGATTGAATTT
66 TTTACTATTATGTTGTTCAAATTATTAATTTTTATGTTTATATACATAGACTGAAGATTGAATTT
* *
35231656 TGGAAAGGCACATAAACAACTTAAGCATAGGTGCACTAGAGGTCATTCATGGAAACTTGTGAGAT
131 TGGAAACGCACATAAACAACTTAAGCATAGGTGCACTAGAGGTCATTCATGGAAACTTGCGAGAT
*
35231721 GTAGGATTTTTATACGTGGCTCGCATGCTCAAGGGACTAAATTGGATCCCCAACTCA
196 GCAGGATTTTTATACGTGGCTCGCATGCTCAAGGGACTAAATTGGATCCCCAACTCA
* *
35231778 TAATTTTAATACGTTACTTATTATGATGTTAAGAAAATATTATTAAATTATTTAATTTTAAGTAG
1 TAATTTTAATACGTTAATTATTATGATGTTAAGAAAATATTATTAAATTATTTAATTTTAAATAG
35231843 -TTACTATTATGTTGTTCAAATTATTAATTTTTTATGTTTATATACATAGACTGAAGATTGAATT
66 TTTACTATTATGTTGTTCAAATTATTAA-TTTTTATGTTTATATACATAGACTGAAGATTGAATT
35231907 TTGGAAACGCACATAAACAACTTAAGCGA-AGGTGCACTAGAGGTCATTCATGGAAACTTGCGAG
130 TTGGAAACGCACATAAACAACTTAAGC-ATAGGTGCACTAGAGGTCATTCATGGAAACTTGCGAG
*
35231971 ATGCAGGATTTTTATACGTGGCTCGCATGCTCGAGGGACTAAATTGGATCCCCAACTCA
194 ATGCAGGATTTTTATACGTGGCTCGCATGCTCAAGGGACTAAATTGGATCCCCAACTCA
35232030 TA
1 TA
35232032 GGTGCTTTGG
Statistics
Matches: 242, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
251 25 0.10
252 216 0.89
253 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (252 bp):
TAATTTTAATACGTTAATTATTATGATGTTAAGAAAATATTATTAAATTATTTAATTTTAAATAG
TTTACTATTATGTTGTTCAAATTATTAATTTTTATGTTTATATACATAGACTGAAGATTGAATTT
TGGAAACGCACATAAACAACTTAAGCATAGGTGCACTAGAGGTCATTCATGGAAACTTGCGAGAT
GCAGGATTTTTATACGTGGCTCGCATGCTCAAGGGACTAAATTGGATCCCCAACTCA
Found at i:35233619 original size:63 final size:63
Alignment explanation
Indices: 35233440--35233622 Score: 172
Period size: 63 Copynumber: 2.9 Consensus size: 63
35233430 ATTTTACACG
** * * * * *
35233440 AGCACCACATCACGCGCAATTGTTCCCTGCACCAACACAATCATCACCACTTTATTTCACACA
1 AGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCACCAGTTTATTACAAACA
* * * * ** * * *
35233503 AGCACCACTTCATGCACAACCA-TCCTCTATATCGACACATTCATCA-TAGGTTTATTACAAACA
1 AGCACCACATCACGCGCAATCATTCCT-TGCACCGACACAATCATCACCA-GTTTATTACAAACA
* *
35233566 AGCATCACAACACGCGCAATCATTCCTTGCACCGACACAATCATCACCAGTTTATTA
1 AGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCACCAGTTTATTA
35233623 TTCACAAGAA
Statistics
Matches: 89, Mismatches: 27, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
62 4 0.04
63 80 0.90
64 5 0.06
ACGTcount: A:0.33, C:0.34, G:0.09, T:0.24
Consensus pattern (63 bp):
AGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCACCAGTTTATTACAAACA
Found at i:35233630 original size:63 final size:62
Alignment explanation
Indices: 35233424--35233653 Score: 169
Period size: 63 Copynumber: 3.6 Consensus size: 62
35233414 CATACAGCAG
* ** * *
35233424 CAGTTTATTTTACACGAGCACCACATCACGCGCAATTGTTCCCTGCACCAACACAATCATCAC
1 CAGTTTA-TTTACACAAGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCAC
* * * * * ** * *
35233487 CACTTTATTTCACACAAGCACCACTTCATGCACAACCA-TCCTCTATATCGACACATTCATCA-
1 CAGTTTATTT-ACACAAGCACCACATCACGCGCAATCATTCCT-TGCACCGACACAATCATCAC
* * *
35233549 TAGGTTTA-TTACAAACAAGCATCACAACACGCGCAATCATTCCTTGCACCGACACAATCATCAC
1 CA-GTTTATTTAC--ACAAGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCAC
* * * * * *
35233613 CAGTTTATTATTCACAAGAACCATAGCATGCACAATCATTC
1 CAGTTTATT-TACACAAGCACCACATCACGCGCAATCATTC
35233654 GATGCACTGA
Statistics
Matches: 124, Mismatches: 34, Indels: 18
0.70 0.19 0.10
Matches are distributed among these distances:
61 2 0.02
62 9 0.07
63 105 0.85
64 6 0.05
65 2 0.02
ACGTcount: A:0.33, C:0.32, G:0.09, T:0.25
Consensus pattern (62 bp):
CAGTTTATTTACACAAGCACCACATCACGCGCAATCATTCCTTGCACCGACACAATCATCAC
Found at i:35238691 original size:31 final size:30
Alignment explanation
Indices: 35238656--35238738 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
35238646 ATTTCCTTCC
*
35238656 TTCTTCCCTTTTTCCATTTTTTTCTTCCATT
1 TTCTTCCCTTTTTCCATTTTATT-TTCCATT
* * * * *
35238687 TTCTTCACTGTTGCAAGTGTTATTTTCCATT
1 TTCTTCCCTTTTTCCA-TTTTATTTTCCATT
*
35238718 TTCTTCCCTTCTTCCATTTTA
1 TTCTTCCCTTTTTCCATTTTA
35238739 GCCCCTGGAG
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
30 4 0.10
31 30 0.77
32 5 0.13
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.58
Consensus pattern (30 bp):
TTCTTCCCTTTTTCCATTTTATTTTCCATT
Found at i:35240506 original size:37 final size:38
Alignment explanation
Indices: 35240411--35240506 Score: 88
Period size: 37 Copynumber: 2.6 Consensus size: 38
35240401 AAATATTCCT
* * * * * *
35240411 GCGACAACAGTTTTGGTGAAATCTAGAAGTGCTCATGCG
1 GCGACAA-TGTTTAGGTGCAATCTAAAAGTACTCATGCA
* *
35240450 GGGACAAT-TTTAGGCGCAATCTAAAAGTACTCATGCA
1 GCGACAATGTTTAGGTGCAATCTAAAAGTACTCATGCA
*
35240487 GCGAC-ATGTTTGGGTGCAAT
1 GCGACAATGTTTAGGTGCAAT
35240507 TCTAGATTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
36 2 0.04
37 37 0.82
39 6 0.13
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (38 bp):
GCGACAATGTTTAGGTGCAATCTAAAAGTACTCATGCA
Found at i:35244742 original size:18 final size:18
Alignment explanation
Indices: 35244719--35244768 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
35244709 AAAATGCAGG
*
35244719 AAATGATGTTAACATTTT
1 AAATGATGTTAACATTTC
35244737 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACATTTC
35244755 AAATGATGTTAACA
1 AAATGATGTTAACA
35244769 ATGATGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:35245292 original size:72 final size:72
Alignment explanation
Indices: 35245201--35245373 Score: 292
Period size: 72 Copynumber: 2.4 Consensus size: 72
35245191 CAATGCTAAA
35245201 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATCCATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATCCATGTTCTACTTATTTAT
35245266 GTGTAAT
66 GTGTAAT
* * **
35245273 CTAGTTTTATAAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATCCATGTTCTACTTATTTAT
35245338 GTGTAAT
66 GTGTAAT
* *
35245345 TTAGTTTTATCAATAGTTGTTTATATTTG
1 CTAGTTTTATCAATAGTTGTTTATGTTTG
35245374 ATTTAGTATG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATCCATGTTCTACTTATTTAT
GTGTAAT
Found at i:35247070 original size:14 final size:15
Alignment explanation
Indices: 35247052--35247092 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
35247042 ACAATTGTGC
35247052 TAATATTTAAATATA
1 TAATATTTAAATATA
35247067 -AATATTT-AATA-A
1 TAATATTTAAATATA
*
35247079 TTATATTTAAATAT
1 TAATATTTAAATAT
35247093 TTAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 1 0.05
13 10 0.45
14 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTTAAATATA
Found at i:35247076 original size:21 final size:21
Alignment explanation
Indices: 35247052--35247096 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35247042 ACAATTGTGC
*
35247052 TAATATTTAAATATAAATATT
1 TAATAATTAAATATAAATATT
* *
35247073 TAATAATTATATTTAAATATT
1 TAATAATTAAATATAAATATT
35247094 TAA
1 TAA
35247097 AATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATAATTAAATATAAATATT
Found at i:35247342 original size:13 final size:13
Alignment explanation
Indices: 35247303--35247353 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
35247293 TAAACCAAAT
*
35247303 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
**
35247316 TTTTCCACCA-CAC
1 TTTT-CAAAAGCAC
*
35247329 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
35247342 TTTTCAAAAGCA
1 TTTTCAAAAGCA
35247354 ATGCTAAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
12 2 0.07
13 24 0.83
14 3 0.10
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:35248641 original size:39 final size:37
Alignment explanation
Indices: 35248545--35248643 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 37
35248535 TTAGGTGCAT
** ** *
35248545 TTTACTTCGGACGTTTCGATGAGTGTTGGACACAACC
1 TTTACTTCGGATTTTTCGATGAGCATTGGACACAAAC
** *
35248582 TTTACTTC-GATTATACCGATGAGCATTGGGCACAAAC
1 TTTACTTCGGATT-TTTCGATGAGCATTGGACACAAAC
35248619 TAATTACTTCGGATTTTTCGATGAG
1 T--TTACTTCGGATTTTTCGATGAG
35248644 GCACTGGGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
36 2 0.04
37 27 0.56
39 15 0.31
40 4 0.08
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (37 bp):
TTTACTTCGGATTTTTCGATGAGCATTGGACACAAAC
Found at i:35248803 original size:118 final size:118
Alignment explanation
Indices: 35248555--35248839 Score: 288
Period size: 118 Copynumber: 2.4 Consensus size: 118
35248545 TTTACTTCGG
* * * * * *
35248555 ACGTTTCGATGAGTGTT-GGACACAACCTTTACTTCGATTATACCGATGAGCATTGGGCACAAAC
1 ACGTTTCCATGAGTGTTGGGA-ACAACTTTTACTTTGATTATACCCATGAACATTGGACACAAAC
* ** * * **
35248619 TAATTACTTCGGATTTTTCGATGAGGCACTGGGTGCAAAATGGTTACTTTGACA
65 TAATTACTTCGAAAATCTCGATGAGGCACTGGGTGCAAAATGGTAACTACGACA
* * * * * **
35248673 ATGTATCCATGAGTGCTGGGTACAACTTTTACTTTGATTATGCCCATGAACATTGGATGCAAACT
1 ACGTTTCCATGAGTGTTGGGAACAACTTTTACTTTGATTATACCCATGAACATTGGACACAAACT
*
35248738 AATTACTTCGAACAATCT-GATGAGGCACTGGGTGTC-AAATGGTAACTACGACT
66 AATTACTTCGAA-AATCTCGATGAGGCACTGGGTG-CAAAATGGTAACTACGACA
* * * * *
35248791 ACGTTTCTATGAGTTTTGGGAACAATTTTTACTTTGATCATACCGATGA
1 ACGTTTCCATGAGTGTTGGGAACAACTTTTACTTTGATTATACCCATGA
35248840 GCGTTGAGCG
Statistics
Matches: 133, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
118 128 0.96
119 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (118 bp):
ACGTTTCCATGAGTGTTGGGAACAACTTTTACTTTGATTATACCCATGAACATTGGACACAAACT
AATTACTTCGAAAATCTCGATGAGGCACTGGGTGCAAAATGGTAACTACGACA
Found at i:35250232 original size:13 final size:13
Alignment explanation
Indices: 35250215--35250244 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
35250205 TATGATTACG
35250215 CTTTTTAATT-AT
1 CTTTTTAATTAAT
35250227 CTTTTTAATTAAT
1 CTTTTTAATTAAT
35250240 CTTTT
1 CTTTT
35250245 AAAACAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTTTTAATTAAT
Found at i:35250617 original size:21 final size:20
Alignment explanation
Indices: 35250593--35250642 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
35250583 AAAAGATAAT
*
35250593 AATAGTTTGAAATTTCAATTA
1 AATAATTTGAAATTT-AATTA
* *
35250614 AATAATTTTAAATTTAATTT
1 AATAATTTGAAATTTAATTA
35250634 AA-AATTTGA
1 AATAATTTGA
35250643 GAAAAGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (20 bp):
AATAATTTGAAATTTAATTA
Found at i:35251392 original size:18 final size:18
Alignment explanation
Indices: 35251369--35251406 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35251359 GGAAAGTTGG
35251369 CCAAAATTTTAATTTACC
1 CCAAAATTTTAATTTACC
35251387 CCAAAATTTTAATTTACC
1 CCAAAATTTTAATTTACC
35251405 CC
1 CC
35251407 CTTTCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (18 bp):
CCAAAATTTTAATTTACC
Found at i:35256690 original size:58 final size:58
Alignment explanation
Indices: 35256602--35256747 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 58
35256592 ATATATTATA
* * * *
35256602 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAACTATTATTAAATTACA-TATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAA-TATAATTAAA-TAAATTAAT
* *
35256662 A-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
35256719 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
35256748 CATTAAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
56 3 0.04
57 13 0.17
58 47 0.62
59 8 0.11
60 5 0.07
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:35256898 original size:44 final size:46
Alignment explanation
Indices: 35256843--35256930 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 46
35256833 TTACAGCATC
* *
35256843 ATTCCATTTAACCAAACACA-AGAAT-A-TTATTACAGCTCTATTTT
1 ATTCCAATTAACCAAACA-ATAGAATCACTGATTACAGCTCTATTTT
*
35256887 ATTCCAATTAACCAAACAATTGAATCACTGATTACAGCTCTATT
1 ATTCCAATTAACCAAACAATAGAATCACTGATTACAGCTCTATT
35256931 CCATTACAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 21 0.55
45 1 0.03
46 15 0.39
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.34
Consensus pattern (46 bp):
ATTCCAATTAACCAAACAATAGAATCACTGATTACAGCTCTATTTT
Found at i:35256938 original size:16 final size:16
Alignment explanation
Indices: 35256917--35256970 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
35256907 TGAATCACTG
*
35256917 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCC
* *
35256933 ATTACAGTTTTATTTC
1 ATTACAGTTCTATTCC
* *
35256949 ATTACATTTCTATTCT
1 ATTACAGTTCTATTCC
35256965 ATTACA
1 ATTACA
35256971 ACGAATCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:35264099 original size:18 final size:18
Alignment explanation
Indices: 35264038--35264095 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
35264028 GACCCGATAG
35264038 CATCCCATGTGGCGCATA
1 CATCCCATGTGGCGCATA
* *
35264056 TATCCCATGTGGCACATA
1 CATCCCATGTGGCGCATA
*
35264074 CATCTCATGTGGCGCATA
1 CATCCCATGTGGCGCATA
35264092 CATC
1 CATC
35264096 TCATATGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (18 bp):
CATCCCATGTGGCGCATA
Found at i:35264114 original size:18 final size:18
Alignment explanation
Indices: 35264047--35264103 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
35264037 GCATCCCATG
* * *
35264047 TGGCGCATATATCCCATG
1 TGGCGCATACATCTCATA
* *
35264065 TGGCACATACATCTCATG
1 TGGCGCATACATCTCATA
35264083 TGGCGCATACATCTCATA
1 TGGCGCATACATCTCATA
35264101 TGG
1 TGG
35264104 TGAGTACATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (18 bp):
TGGCGCATACATCTCATA
Found at i:35276082 original size:2 final size:2
Alignment explanation
Indices: 35276075--35276105 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35276065 GATATCATTT
35276075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35276106 TTGTATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35276339 original size:40 final size:40
Alignment explanation
Indices: 35276199--35276330 Score: 228
Period size: 40 Copynumber: 3.3 Consensus size: 40
35276189 GGTATTTTCG
35276199 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
* *
35276239 AATAAATGAAAAGGTTGAAAATGATATTATCTGGAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
* *
35276279 AATAAACGAAAAGGTTGAAAAGGATATTATCCGAAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
35276319 AATAAATGAAAA
1 AATAAATGAAAA
35276331 ATTCGAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.23
Consensus pattern (40 bp):
AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
Found at i:35277169 original size:12 final size:13
Alignment explanation
Indices: 35277152--35277181 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35277142 AATAATTACA
35277152 TGAAATGG-TATG
1 TGAAATGGTTATG
35277164 TGAAATGGTTATG
1 TGAAATGGTTATG
35277177 TGAAA
1 TGAAA
35277182 ACATATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
TGAAATGGTTATG
Found at i:35279937 original size:14 final size:14
Alignment explanation
Indices: 35279898--35279940 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
35279888 CAAATAATTT
35279898 TAAAATTATTAAAA
1 TAAAATTATTAAAA
* ** *
35279912 TTATTTTTTTAAAA
1 TAAAATTATTAAAA
35279926 TAAAATTATTAAAA
1 TAAAATTATTAAAA
35279940 T
1 T
35279941 TATTAAATAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTATTAAAA
Found at i:35280014 original size:29 final size:30
Alignment explanation
Indices: 35279962--35280019 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
35279952 TTTAATTTTT
35279962 AATTTCATCTTCTTCCTCATTATTTCTTCCTC
1 AATTTCATCTTCTTCCTCA-TATTT-TTCCTC
35279994 AATTTCATCTTCTTCC-C-TATTTTTCC
1 AATTTCATCTTCTTCCTCATATTTTTCC
35280020 ATTTAGCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
31 1 0.04
32 16 0.62
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTTCATCTTCTTCCTCATATTTTTCCTC
Found at i:35280674 original size:9 final size:9
Alignment explanation
Indices: 35280650--35280709 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
35280640 GATGATGATT
35280650 ATAATTTTAAA
1 ATAATTTT--A
35280661 ATAATTTTA
1 ATAATTTTA
35280670 ATAATTTT-
1 ATAATTTTA
35280678 AT-ATTTTA
1 ATAATTTTA
*
35280686 A-AA---AA
1 ATAATTTTA
35280691 ATAATTTTA
1 ATAATTTTA
35280700 ATAATTTTA
1 ATAATTTTA
35280709 A
1 A
35280710 AATCATTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 5 0.12
8 4 0.10
9 20 0.49
11 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATAATTTTA
Found at i:35280687 original size:27 final size:29
Alignment explanation
Indices: 35280648--35280708 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
35280638 ATGATGATGA
35280648 TTATAATTTT-AAAATAATTTTAATAATT
1 TTATAATTTTAAAAATAATTTTAATAATT
35280676 TTAT-ATTTTAAAAAAATAATTTTAATAATT
1 TTATAATTTT--AAAAATAATTTTAATAATT
35280706 TTA
1 TTA
35280709 AAATCATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 5 0.17
28 4 0.13
30 21 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATAATTTTAAAAATAATTTTAATAATT
Found at i:35280695 original size:21 final size:23
Alignment explanation
Indices: 35280669--35280711 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
35280659 AAATAATTTT
35280669 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
35280690 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
35280712 TCATTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:35285601 original size:17 final size:17
Alignment explanation
Indices: 35285579--35285613 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35285569 TTTTGAGAGC
35285579 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAAG-TAAA
35285596 ATAAAATAGAAAGTAAA
1 ATAAAATAGAAAGTAAA
35285613 A
1 A
35285614 GCAAAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAGTAAA
Found at i:35295365 original size:3 final size:3
Alignment explanation
Indices: 35295357--35295382 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35295347 CCAATATCCA
35295357 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
35295383 CATATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:35301221 original size:23 final size:23
Alignment explanation
Indices: 35301187--35301538 Score: 479
Period size: 23 Copynumber: 15.3 Consensus size: 23
35301177 GTTATGAAAC
* *
35301187 TTAAGCATAAATAATATTAATAT
1 TTAAGCACAAATCATATTAATAT
* *
35301210 TTGAGCACAAATCATATTATTAT
1 TTAAGCACAAATCATATTAATAT
*
35301233 TTGAGCACAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
* *
35301256 TTAAGCATAAATCACATTAATAT
1 TTAAGCACAAATCATATTAATAT
**
35301279 TTGCGCACAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
*
35301302 TTATGCACAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
*
35301325 TTGAGCACAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
* * *
35301348 TTAAGCATAAATCACATTAATAC
1 TTAAGCACAAATCATATTAATAT
* *
35301371 TTAAGTACAAATAATATTAATAT
1 TTAAGCACAAATCATATTAATAT
* *
35301394 TTAACCATAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
*
35301417 TTAAGCACAAATCACATTAATAT
1 TTAAGCACAAATCATATTAATAT
* *
35301440 TTAATCATAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
*
35301463 TTAAGCACAAATCACATTAATAT
1 TTAAGCACAAATCATATTAATAT
*
35301486 TTAAGCATAAATCATATTAATAT
1 TTAAGCACAAATCATATTAATAT
* *
35301509 TTGAGCACAAATTATATTAATAT
1 TTAAGCACAAATCATATTAATAT
35301532 TTAAGCA
1 TTAAGCA
35301539 TGGATATAAG
Statistics
Matches: 285, Mismatches: 44, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 285 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (23 bp):
TTAAGCACAAATCATATTAATAT
Found at i:35301316 original size:92 final size:92
Alignment explanation
Indices: 35301187--35301539 Score: 535
Period size: 92 Copynumber: 3.8 Consensus size: 92
35301177 GTTATGAAAC
* * *
35301187 TTAAGCATAAATAATATTAATATTTGAGCACAAATCATATTATTATTTGAGCACAAATCATATTA
1 TTAAGCACAAATAATATTAATATTTAAGCACAAATCATATTAATATTTGAGCACAAATCATATTA
35301252 ATATTTAAGCATAAATCACATTAATAT
66 ATATTTAAGCATAAATCACATTAATAT
** * *
35301279 TTGCGCACAAATCATATTAATATTTATGCACAAATCATATTAATATTTGAGCACAAATCATATTA
1 TTAAGCACAAATAATATTAATATTTAAGCACAAATCATATTAATATTTGAGCACAAATCATATTA
*
35301344 ATATTTAAGCATAAATCACATTAATAC
66 ATATTTAAGCATAAATCACATTAATAT
* * * * *
35301371 TTAAGTACAAATAATATTAATATTTAACCATAAATCATATTAATATTTAAGCACAAATCACATTA
1 TTAAGCACAAATAATATTAATATTTAAGCACAAATCATATTAATATTTGAGCACAAATCATATTA
* *
35301436 ATATTTAATCATAAATCATATTAATAT
66 ATATTTAAGCATAAATCACATTAATAT
* * * *
35301463 TTAAGCACAAATCACATTAATATTTAAGCATAAATCATATTAATATTTGAGCACAAATTATATTA
1 TTAAGCACAAATAATATTAATATTTAAGCACAAATCATATTAATATTTGAGCACAAATCATATTA
35301528 ATATTTAAGCAT
66 ATATTTAAGCAT
35301540 GGATATAAGA
Statistics
Matches: 233, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 233 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (92 bp):
TTAAGCACAAATAATATTAATATTTAAGCACAAATCATATTAATATTTGAGCACAAATCATATTA
ATATTTAAGCATAAATCACATTAATAT
Found at i:35310509 original size:23 final size:23
Alignment explanation
Indices: 35310479--35310914 Score: 615
Period size: 23 Copynumber: 19.0 Consensus size: 23
35310469 ACTTGAACGT
35310479 AAATCATATTAATATTTAAGCAC
1 AAATCATATTAATATTTAAGCAC
*
35310502 AAATCATATTAATATTTGAGCAC
1 AAATCATATTAATATTTAAGCAC
*
35310525 AAATCATATTAATATTTAAGCAT
1 AAATCATATTAATATTTAAGCAC
* *
35310548 AAATCACATTAATATTTGCA-CAC
1 AAATCATATTAATATTT-AAGCAC
*
35310571 AAATCATATTAATATTTATGCAC
1 AAATCATATTAATATTTAAGCAC
*
35310594 AAATCATATTAATATTTGAGCAC
1 AAATCATATTAATATTTAAGCAC
*
35310617 AAATCATATTAATATTTAAGCAT
1 AAATCATATTAATATTTAAGCAC
* *
35310640 AAATCACATTAATACTTAAGCAC
1 AAATCATATTAATATTTAAGCAC
*
35310663 AAATCATATTAATATTTAAGCAT
1 AAATCATATTAATATTTAAGCAC
* *
35310686 AAATCACATTAATATTTGCA-CAC
1 AAATCATATTAATATTT-AAGCAC
*
35310709 AAATCATATTAATATTTATGCAC
1 AAATCATATTAATATTTAAGCAC
35310732 AAATCATATTAATATTTAAGCAC
1 AAATCATATTAATATTTAAGCAC
* *
35310755 AAATCATATTAATATTTAATCAT
1 AAATCATATTAATATTTAAGCAC
* *
35310778 AAATCATATTAATATTTAAGGAT
1 AAATCATATTAATATTTAAGCAC
* * *
35310801 AAATCACATTAATATTTAATCAT
1 AAATCATATTAATATTTAAGCAC
35310824 AAATCATATTAATATTTAAGCAC
1 AAATCATATTAATATTTAAGCAC
* *
35310847 AAATCACATTAATATTTAAGCAT
1 AAATCATATTAATATTTAAGCAC
* * *
35310870 AAATCACAATAATATTTGAGCAC
1 AAATCATATTAATATTTAAGCAC
35310893 AAATCATATTAATATTTAAGCA
1 AAATCATATTAATATTTAAGCA
35310915 TGCATATAAG
Statistics
Matches: 365, Mismatches: 44, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
23 363 0.99
24 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.36
Consensus pattern (23 bp):
AAATCATATTAATATTTAAGCAC
Found at i:35318395 original size:18 final size:19
Alignment explanation
Indices: 35318372--35318417 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
35318362 TTTTCCTGCC
*
35318372 CTCTTTCTTTAC-TCTTTG
1 CTCTTTCTCTACTTCTTTG
35318390 CTCTTTCTCTACTTCTTT-
1 CTCTTTCTCTACTTCTTTG
*
35318408 TTCTTTCTCT
1 CTCTTTCTCT
35318418 CAATAGAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.63
Consensus pattern (19 bp):
CTCTTTCTCTACTTCTTTG
Found at i:35321787 original size:159 final size:159
Alignment explanation
Indices: 35321498--35321819 Score: 495
Period size: 159 Copynumber: 2.0 Consensus size: 159
35321488 CAAACCAGTT
35321498 ACTTGTTCTTGGATACACATCGTTACTCGCACTGAGAGGTGGAGTGATTGTATTTGAGTCAGGAT
1 ACTTGTTCTTGGATACACATCGTTACTCGCACTGAGAGGTGGAGTGATTGTATTTGAGTCAGGAT
* * * *
35321563 TAAGTAAGGAGTTGTTGTTGGAAAGAACTCAAAGGGACTTCATTGCAACGACAATTCATCTATAT
66 TAAGTAAGGAGCTGTTATTGGAAAGAACTCAAAAGGACTTCATTGCAACGAAAATTCATCTATAT
*
35321628 CTTACCTTATCGACGCATCTAGCGTTGCA
131 CTTACCTTATCGACGCATCTAGCGCTGCA
*
35321657 ACTTGTTCTTGGATACACATCGTTACTTGCAAC-GAGAGGTGGAGTGATTGTATTTGAGTC-GAG
1 ACTTGTTCTTGGATACACATCGTTACTCGC-ACTGAGAGGTGGAGTGATTGTATTTGAGTCAG-G
* * *
35321720 ATTAAGTAGGGAGCTGTTATTGGTAAGAACTCAAAAGGACTTCATTGCAGCGAAAATTCATCTAT
64 ATTAAGTAAGGAGCTGTTATTGGAAAGAACTCAAAAGGACTTCATTGCAACGAAAATTCATCTAT
* * * *
35321785 ATCTTGCCTTGTCTATGCATCTAGCGCTGCA
129 ATCTTACCTTATCGACGCATCTAGCGCTGCA
35321816 ACTT
1 ACTT
35321820 AGCAATATTC
Statistics
Matches: 148, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
158 1 0.01
159 145 0.98
160 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (159 bp):
ACTTGTTCTTGGATACACATCGTTACTCGCACTGAGAGGTGGAGTGATTGTATTTGAGTCAGGAT
TAAGTAAGGAGCTGTTATTGGAAAGAACTCAAAAGGACTTCATTGCAACGAAAATTCATCTATAT
CTTACCTTATCGACGCATCTAGCGCTGCA
Found at i:35322748 original size:15 final size:15
Alignment explanation
Indices: 35322728--35322758 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35322718 AAGGGAAAAG
35322728 AAAATTTTAAAACAA
1 AAAATTTTAAAACAA
*
35322743 AAAATTTTAACACAA
1 AAAATTTTAAAACAA
35322758 A
1 A
35322759 CACAAGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTTAAAACAA
Found at i:35323543 original size:43 final size:43
Alignment explanation
Indices: 35323495--35323586 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
35323485 CCTTTAGCGA
* *
35323495 CGTTTTTCCTATAAACGCCGCTAATGCTCT-TAACCTTTTGTGG
1 CGTTTTTCCCATAAACACCGCTAATGCTCTAT-ACCTTTTGTGG
* * *
35323538 TG-TTTTCCCATAAACACCGCTATTGGTCTATACCTTTTGTGG
1 CGTTTTTCCCATAAACACCGCTAATGCTCTATACCTTTTGTGG
35323580 CGTTTTT
1 CGTTTTT
35323587 TTACATAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 35 0.85
43 6 0.15
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.42
Consensus pattern (43 bp):
CGTTTTTCCCATAAACACCGCTAATGCTCTATACCTTTTGTGG
Found at i:35329991 original size:11 final size:11
Alignment explanation
Indices: 35329975--35329999 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35329965 TCTTCTAAAG
35329975 AATACATATCA
1 AATACATATCA
35329986 AATACATATCA
1 AATACATATCA
35329997 AAT
1 AAT
35330000 TTGATATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
AATACATATCA
Found at i:35330895 original size:41 final size:42
Alignment explanation
Indices: 35330776--35330895 Score: 156
Period size: 41 Copynumber: 2.9 Consensus size: 42
35330766 GGGAAAACGT
* *
35330776 CGCTAATGCTCTTATCTTTTGCGGCATTTTCTCAA-AAATGC
1 CGCTAATGCTCATACCTTTTGCGGCATTTTCTCAATAAATGC
* * *
35330817 CGCTAATTCTAATACCTTTTGTGGCATTTTCTC-ATAAATGC
1 CGCTAATGCTCATACCTTTTGCGGCATTTTCTCAATAAATGC
* *
35330858 CGCTAATGCTCATACCTTTTGCGACGTTTT-TCAATAAA
1 CGCTAATGCTCATACCTTTTGCGGCATTTTCTCAATAAA
35330896 CATCACTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 3 0.04
41 64 0.96
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (42 bp):
CGCTAATGCTCATACCTTTTGCGGCATTTTCTCAATAAATGC
Found at i:35330918 original size:82 final size:78
Alignment explanation
Indices: 35330832--35331011 Score: 171
Period size: 82 Copynumber: 2.2 Consensus size: 78
35330822 ATTCTAATAC
* * * *
35330832 CTTTTGTGGCATTTTCTCATAAATGCCGCTAATGCTCATACCTTTTGCGACGTTTTTCAATAAAC
1 CTTTT-TGGCATTTTCTCATAAACGCCACTAATGCT-ATACCTTTTGCGACGTTTATCAAAAAAC
35330897 ATCACTAATGCTCTTA
64 ATCACTAATGCT-TTA
* * * ** * *
35330913 TCTTTTTCGGCGTTTTTCCCATAAGCGCCACTTTTGCTTTACCTTTTGCGACGTTTATGAAAAAA
1 -CTTTTT-GGC-ATTTTCTCATAAACGCCACTAATGCTATACCTTTTGCGACGTTTATCAAAAAA
* *
35330978 CATTACTATTGCTTTA
63 CATCACTAATGCTTTA
35330994 CTTTTTATGGCATTTTCT
1 C-TTTT-TGGCATTTTCT
35331012 GTACAAACGC
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
80 6 0.08
81 11 0.14
82 43 0.54
83 19 0.24
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (78 bp):
CTTTTTGGCATTTTCTCATAAACGCCACTAATGCTATACCTTTTGCGACGTTTATCAAAAAACAT
CACTAATGCTTTA
Found at i:35332581 original size:7 final size:7
Alignment explanation
Indices: 35332569--35332594 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35332559 ATATGATTAA
35332569 ATTATTT
1 ATTATTT
35332576 ATTATTT
1 ATTATTT
35332583 ATTATTT
1 ATTATTT
35332590 ATTAT
1 ATTAT
35332595 ATTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTATTT
Found at i:35332616 original size:58 final size:57
Alignment explanation
Indices: 35332456--35332618 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 57
35332446 ATATTATATA
* * *
35332456 TTATAATTTTTATTAATTCATATTTTAATAATTAATTATAATAAGAATATTATTAAATTAT
1 TTATTATTTTTATTAATT-ATA-TTTAATAA-TAATTATATTAA-AATATGATTAAATTAT
* *
35332517 ATATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTAT
1 TTATTATTTTTATT-AATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
*
35332574 TTATTATTTATTATTTATTATATTTAATAATAATCT-TATTAAAAT
1 TTATTATTT-TTATTAATTATATTTAATAATAAT-TATATTAAAAT
35332619 TTAATAAACA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
57 20 0.22
58 38 0.42
59 14 0.16
60 10 0.11
61 8 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (57 bp):
TTATTATTTTTATTAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
Found at i:35333451 original size:32 final size:30
Alignment explanation
Indices: 35333409--35333473 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
35333399 TTTTTAGTTT
35333409 TTTACCAAAATAAAATATAAAAAAAATATTTA
1 TTTACCAAAAT--AATATAAAAAAAATATTTA
* * *
35333441 TTTACTAAAATAATATACAAAAATTATTTA
1 TTTACCAAAATAATATAAAAAAAATATTTA
35333471 TTT
1 TTT
35333474 TATTTGACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 20 0.67
32 10 0.33
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (30 bp):
TTTACCAAAATAATATAAAAAAAATATTTA
Found at i:35333491 original size:36 final size:35
Alignment explanation
Indices: 35333437--35333509 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
35333427 AAAAAAAATA
*
35333437 TTTATTTACTAAAATAATA-TACAAAAATTATTTAT
1 TTTATTTACTAAAATAATATTA-AAAAATTATTAAT
*
35333472 TTTATTTGACTAAAGTAATATTAAAAAATTATTAAT
1 TTTATTT-ACTAAAATAATATTAAAAAATTATTAAT
35333508 TT
1 TT
35333510 AATAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 25 0.74
37 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTATTTACTAAAATAATATTAAAAAATTATTAAT
Found at i:35333794 original size:21 final size:19
Alignment explanation
Indices: 35333768--35333807 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 19
35333758 AAAGAGAAAC
35333768 AAGAAGAAGAACAGAGGAGAA
1 AAGAAGAA-AA-AGAGGAGAA
35333789 AAGAAGAAAAAGAGGAGAA
1 AAGAAGAAAAAGAGGAGAA
35333808 TTAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.65, C:0.03, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAAAGAGGAGAA
Found at i:35336846 original size:21 final size:20
Alignment explanation
Indices: 35336809--35336867 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
35336799 ATTGTTTCTA
* *
35336809 ATTTAGGGTTGAGGTTTAGG
1 ATTTAGAGTTTAGGTTTAGG
*
35336829 GTTTA-AGATTTAGAGTTTAGG
1 ATTTAGAG-TTTAG-GTTTAGG
35336850 ATTTAGAGTTTAGGTTTA
1 ATTTAGAGTTTAGGTTTA
35336868 TAGGTATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 16 0.50
22 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (20 bp):
ATTTAGAGTTTAGGTTTAGG
Done.