Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 157 of 210
Found at i:47571469 original size:2 final size:2
Alignment explanation
Indices: 47571458--47571498 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
47571448 CATTATTCTC
47571458 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47571498 T
1 T
47571499 GTTAAGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47572927 original size:15 final size:15
Alignment explanation
Indices: 47572909--47572948 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
47572899 CCCTAGCCCT
*
47572909 TAAATCCTAAACCCC
1 TAAACCCTAAACCCC
*
47572924 TAAACCCTTAACCCC
1 TAAACCCTAAACCCC
*
47572939 TAACCCCTAA
1 TAAACCCTAA
47572949 CCCTTATATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCTAAACCCC
Found at i:47572943 original size:44 final size:42
Alignment explanation
Indices: 47572872--47572984 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 42
47572862 CTTGAATTCT
* * *
47572872 TAAACCCTAAATCATTAACCCTTTAACCCCTAGCCCTTAAATCC
1 TAAACCCTAAATCCTTAACCC-CTAACCCCTAACCCTTAAAT-C
* *
47572916 TAAACCCCTAAACCCTTAACCCCTAACCCCTAACCCTTATATC
1 TAAA-CCCTAAATCCTTAACCCCTAACCCCTAACCCTTAAATC
* *
47572959 TCAAACCCTAAATCCATACCCCCTAA
1 T-AAACCCTAAATCCTTAACCCCTAA
47572985 TCCTTAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
43 20 0.34
44 24 0.41
45 15 0.25
ACGTcount: A:0.35, C:0.41, G:0.01, T:0.24
Consensus pattern (42 bp):
TAAACCCTAAATCCTTAACCCCTAACCCCTAACCCTTAAATC
Found at i:47572965 original size:22 final size:20
Alignment explanation
Indices: 47572896--47572966 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 20
47572886 TTAACCCTTT
*
47572896 AACCCCTAGCCCTTAAATCCTA
1 AACCCCTAACCCTT-AATCC-A
* *
47572918 AACCCCTAAACCCTTAACCCCT
1 AACCCCT-AACCCTTAA-TCCA
47572940 AACCCCTAACCCTTATATCTCA
1 AACCCCTAACCCTTA-ATC-CA
47572962 AACCC
1 AACCC
47572967 TAAATCCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 9 0.22
22 23 0.57
23 8 0.20
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.21
Consensus pattern (20 bp):
AACCCCTAACCCTTAATCCA
Found at i:47573182 original size:35 final size:35
Alignment explanation
Indices: 47573111--47573185 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
47573101 CAATATTATC
* **
47573111 TTTATAATATTTATTTTTTTGTATAAAGTTTGAAA
1 TTTATAATATTTATTTTATTGTATAAAGAATGAAA
47573146 TTTATAATATTTTATTTTATTG-ATAAATGAAT-AAA
1 TTTATAATA-TTTATTTTATTGTATAAA-GAATGAAA
47573181 TTTAT
1 TTTAT
47573186 CTAATTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (35 bp):
TTTATAATATTTATTTTATTGTATAAAGAATGAAA
Found at i:47579863 original size:28 final size:29
Alignment explanation
Indices: 47579827--47579891 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
47579817 CAGAAGCTAG
* *
47579827 AAACTGAAAA-TTAATAAAAGGGAAGAAT
1 AAACCGAAAATTTAAGAAAAGGGAAGAAT
47579855 AAACCGAAAATTTAAGAAAAGGGAAGAAT
1 AAACCGAAAATTTAAGAAAAGGGAAGAAT
47579884 AAAGCCGA
1 AAA-CCGA
47579892 GGAAGATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 9 0.27
29 20 0.61
30 4 0.12
ACGTcount: A:0.58, C:0.08, G:0.20, T:0.14
Consensus pattern (29 bp):
AAACCGAAAATTTAAGAAAAGGGAAGAAT
Found at i:47582658 original size:31 final size:30
Alignment explanation
Indices: 47582600--47582658 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
47582590 TTTTCGAGCC
* *
47582600 TAGGGGCAAAATTGTAATTTTGTAAAATTT
1 TAGGGGCAAAAATGTAATTTTGCAAAATTT
* *
47582630 TAGGGGGAAAAATGTACTTTTGGCAAAAT
1 TAGGGGCAAAAATGTAATTTT-GCAAAAT
47582659 GTGATTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTTTGCAAAATTT
Found at i:47583009 original size:101 final size:102
Alignment explanation
Indices: 47582893--47583077 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
47582883 AAAGTGATGG
* *
47582893 TCACGTGTGTCGTACTATGTGCAAGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
47582956 ACTATGTGCAGGCTACTATGCGTACCGGATAGCGTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCGTCGA
* * *
47582994 TCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
*
47583059 CTATGTGTAGGCTACTATG
66 CTATGTGCAGGCTACTATG
47583078 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCGTCGA
Found at i:47583015 original size:51 final size:49
Alignment explanation
Indices: 47582892--47583085 Score: 187
Period size: 51 Copynumber: 3.9 Consensus size: 49
47582882 TAAAGTGATG
* *
47582892 GTCACGTGTGTCGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-G---GATAGGTC
* *
47582945 G-CA--TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCGTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-GTC
* * * *
47582992 GATCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATAGTGATG
1 G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-G-TC
* * * *
47583044 GTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCGG
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
47583086 TATCATTAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
46 5 0.04
47 4 0.03
49 3 0.03
50 30 0.26
51 70 0.60
52 4 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGGTC
Found at i:47583085 original size:102 final size:101
Alignment explanation
Indices: 47582893--47583085 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
47582883 AAAGTGATGG
* *
47582893 TCACGTGTGTCGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTAC
*
47582958 TATGTGCAGGCTACTATGCGTACCGGATAGCGTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCGTCGA
* * *
47582994 TCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGA-A-TGATAGGTCACATGTGTAGT
* *
47583058 ACTATGTGTAGGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
47583086 TATCATTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 38 0.46
102 40 0.49
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCGTCGA
Found at i:47583172 original size:46 final size:43
Alignment explanation
Indices: 47583081--47583184 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 43
47583071 TACTATGTGA
* *
47583081 ACCGGTATCATTAATTATAAGGTGGTTGATATGTGTTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGATATGTGCTGATCCC
* *
47583124 ACCGGATATCATTGATTACAAAGGGTGGTTGCTATGTGCTGAGT-CC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGATATGTGCTGA-TCCC
47583170 ACCGTGTATCTATTA
1 ACCG-GTATC-ATTA
47583185 TTATTCCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
43 5 0.10
44 11 0.22
45 2 0.04
46 27 0.54
47 5 0.10
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGATATGTGCTGATCCC
Found at i:47583324 original size:16 final size:16
Alignment explanation
Indices: 47583303--47583334 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47583293 TGATTGAAAG
*
47583303 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
47583319 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
47583335 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:47589301 original size:44 final size:44
Alignment explanation
Indices: 47589193--47589301 Score: 164
Period size: 44 Copynumber: 2.5 Consensus size: 44
47589183 AACTCATCGG
* * *
47589193 AATAATAATAGATACACGATGGCCTGCACAGAGTCCGTACCACC
1 AATAATAACAGATACACGGTGGCCTGCACAGAGTCCGTACCACA
* * *
47589237 AATAATAACAGATACGCGGTGGCCTGCACATAGTCCGTCCCACA
1 AATAATAACAGATACACGGTGGCCTGCACAGAGTCCGTACCACA
47589281 AATAATAACAGATACACGGTG
1 AATAATAACAGATACACGGTG
47589302 CATCAGCACA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (44 bp):
AATAATAACAGATACACGGTGGCCTGCACAGAGTCCGTACCACA
Found at i:47589350 original size:43 final size:43
Alignment explanation
Indices: 47589291--47589420 Score: 206
Period size: 43 Copynumber: 3.0 Consensus size: 43
47589281 AATAATAACA
*
47589291 GATACACGGTGCATCAGCACATAGCACCACCCTTATAGTCAAT
1 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
* * * *
47589334 GATACACAGTGGATCAGCACATAACACCACCCGTATAATCAAT
1 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
*
47589377 GATACCCGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
1 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
47589420 G
1 G
47589421 TAATCCGGTA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (43 bp):
GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
Found at i:47590846 original size:44 final size:45
Alignment explanation
Indices: 47590776--47591756 Score: 210
Period size: 44 Copynumber: 20.8 Consensus size: 45
47590766 TATGGTGAAT
* * * * *
47590776 CTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAAGCCA-CCAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * *
47590820 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* ** * * * *** *
47590865 CTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAATTTAGAAATTATGGTGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GA---AG--A-CA--GCAAAC
** * * *
47590919 CTTATCTTACTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* ** * *
47590963 CTTATCTCCCTGAAGTTGTAGCAGAGCAGACTGAAGACAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * * *
47591008 CTTATTTCCC-GAGCGTTGCAGTGGAACAGATTAAAGTTACA-AATTATGGTGGAT
1 CTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAG--ACAGCA--A------AC
** * * * *
47591062 CTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGCAGCCA-CCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * ** *
47591106 CTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAAGACAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * * * * *
47591151 CTTATTTCTCT-AGCGTTGCAGTGGAACATATTAAAGCTACAAATTATGGCAGAT
1 CTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAG--AC-----A--GCAAAC
* ** * * * *
47591205 CTTATCTTCCTGAAGTTGCAGTATAACAGATTGAAGCCA-CCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * * ** *
47591249 CTTATCTCCCTAAAGCTCCAG-CGAGCAGACTGAAGATTGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* *
47591293 CTTATTTCCCTGAAGATGCAGTGGAGCAGATTGAAG-CTA-CAAATTATGGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAC-AGC-AA--A---C
* * * * * * * *
47591343 TGTTCTTATCTTCCTGAATTTGCAGTGAAGCAAATTGAGGCCA-CCAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * *
47591391 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAATACAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * * * * * * *
47591436 CTTTTTTTCCTGACGTTACAGTAGAACAGATTAAAG-CTAGAAATTATGGTGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAC-AG-CA--A------AC
* * * *
47591490 CTTATCTTCCTGAAGTTGCAGTGGAGAAGATTGAAGCCA-CCAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * *
47591534 CTTATCTCTCTGAAGTTACAGCGGAGCAGACTGAAGACAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* ** * * * * *
47591579 CTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGATACA-AATTATGGTGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ACAGCA--A------AC
* * * *
47591633 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * * * *
47591677 CTTATCTCACTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
* * *
47591722 CTTATTTCCCTGAAGTTACAGTGGAGTAGATTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
47591757 ATTACCATAC
Statistics
Matches: 650, Mismatches: 214, Indels: 145
0.64 0.21 0.14
Matches are distributed among these distances:
43 10 0.02
44 235 0.36
45 185 0.28
46 4 0.01
47 11 0.02
48 4 0.01
49 2 0.00
50 5 0.01
51 1 0.00
52 7 0.01
53 2 0.00
54 179 0.28
55 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAAC
Found at i:47591753 original size:143 final size:143
Alignment explanation
Indices: 47590501--47591746 Score: 1717
Period size: 143 Copynumber: 8.7 Consensus size: 143
47590491 TTACACCCTA
* * * * * *
47590501 GAAGTTGTAGTAGAGCAGATTGAAGCCACCAACCTTATCTCCCTAAAGTTGCAGCGGAGTAGACA
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* * * *
47590566 GAAGACAGCGAATCTTATTTCCCTGAAGATGCAGTGGAACAGATTAAAGCTACAACTTATGGTGG
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
* *
47590631 TTCTTATCTTTCT
131 ATCTTATCTTCCT
* * *
47590644 AAAATTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* * * * * * * * *
47590709 AAAGACAGTAAATCTTATTTCCTTGGCATTGCAGTGGAATAGATTAAAGATAGAAATTATGGTGA
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
*
47590774 ATCTTATCTTCTT
131 ATCTTATCTTCCT
* *
47590787 GAAGTTGTAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* ** *
47590852 GAAGACAGCAAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAATTTAGAAATTATGGTGG
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
*
47590917 ATCTTATCTTACT
131 ATCTTATCTTCCT
* *
47590930 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGTAGCAGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
*
47590995 GAAGACAGCAAATCTTATTTCCC-GAGCGTTGCAGTGGAACAGATTAAAGTTACAAATTATGGTG
66 GAAGACAGCAAATCTTATTTCCCTGA-CGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTG
*
47591059 GATCTTATCTTTCT
130 GATCTTATCTTCCT
* *
47591073 GAAGTTGCAGTGGAGCAGATTGCAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
** * * **
47591138 GAAGACAGTGAATCTTATTTCTCT-AGCGTTGCAGTGGAACATATTAAAGCTACAAATTATGGCA
66 GAAGACAGCAAATCTTATTTCCCTGA-CGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTG
47591202 GATCTTATCTTCCT
130 GATCTTATCTTCCT
** * * * *
47591216 GAAGTTGCAGTATAACAGATTGAAGCCACCAGCCTTATCTCCCTAAAGCTCCAGC-GAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
** * * * *
47591280 GAAGATTGCAAATCTTATTTCCCTGAAGATGCAGTGGAGCAGATTGAAGCTACAAATTATGGCT-
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGG-TG
*
47591344 GTTCTTATCTTCCT
130 GATCTTATCTTCCT
* * * *
47591358 GAATTTGCAGTGAAGCAAATTGAGGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* * * * * *
47591423 GAATACAGCAAATCTTTTTTTCCTGACGTTACAGTAGAACAGATTAAAGCTAGAAATTATGGTGG
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
47591488 ATCTTATCTTCCT
131 ATCTTATCTTCCT
* * * *
47591501 GAAGTTGCAGTGGAGAAGATTGAAGCCACCAACCTTATCTCTCTGAAGTTACAGCGGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* * *
47591566 GAAGACAGCAAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGATACAAATTATGGTGG
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
47591631 ATCTTATCTTCCT
131 ATCTTATCTTCCT
* * *
47591644 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCACTGAAGTTGTAGTGGAGCAGACT
1 GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
* * *
47591709 GAAGATAGCAAATCTTATTTCCCTGAAGTTACAGTGGA
66 GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGA
47591747 GTAGATTGAA
Statistics
Matches: 967, Mismatches: 130, Indels: 12
0.87 0.12 0.01
Matches are distributed among these distances:
142 119 0.12
143 848 0.88
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (143 bp):
GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT
GAAGACAGCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGG
ATCTTATCTTCCT
Found at i:47595231 original size:38 final size:38
Alignment explanation
Indices: 47595150--47595232 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
47595140 GAAACAACAT
* * *
47595150 ACATGCTTAACATGTATTCAGTTTAACATTAGCAGTAG
1 ACATGCTTAACATGTATTCAGTTCAACAATAACAGTAG
*
47595188 ACATGCTTAACATGTATTC-GATTCAACAATAATAGTA-
1 ACATGCTTAACATGTATTCAG-TTCAACAATAACAGTAG
47595225 AGCATGCT
1 A-CATGCT
47595233 GAATATGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 2 0.05
38 37 0.95
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (38 bp):
ACATGCTTAACATGTATTCAGTTCAACAATAACAGTAG
Found at i:47598393 original size:25 final size:25
Alignment explanation
Indices: 47598361--47598413 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
47598351 GTTACAAATT
**
47598361 TTTGTTTTTAAGTTGTGTCTTTTAA
1 TTTGTTTTTAAGTCATGTCTTTTAA
*
47598386 TTTGTTTTTAGGTCATGTCTTTTAA
1 TTTGTTTTTAAGTCATGTCTTTTAA
47598411 TTT
1 TTT
47598414 TCTCTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (25 bp):
TTTGTTTTTAAGTCATGTCTTTTAA
Found at i:47600036 original size:17 final size:17
Alignment explanation
Indices: 47600014--47600051 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
47600004 TAATTGAAAA
47600014 TTAATATTTTCA-ATGAT
1 TTAATATTTTCACAT-AT
47600031 TTAATATTTTCACATAT
1 TTAATATTTTCACATAT
47600048 TTAA
1 TTAA
47600052 CAATTCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAATATTTTCACATAT
Found at i:47600646 original size:82 final size:81
Alignment explanation
Indices: 47600488--47600650 Score: 299
Period size: 82 Copynumber: 2.0 Consensus size: 81
47600478 AAGTTCTTTA
47600488 CCACTACACCTATAATCATTATTGAATAAATTTTAAAAAATATTTCTTCACATAAAATGTTTTCT
1 CCACTACACCTATAATCATTATTGAATAAATTTTAAAAAATATTTCTTCACATAAAATGTTTTCT
47600553 CCCACCCACATTGTGT
66 CCCACCCACATTGTGT
47600569 CCACTACACCTATAATCATTATTGAATAAATTTTAAAAAAATATTTCTTCACATAAAATGTTTTC
1 CCACTACACCTATAATCATTATTGAATAAATTTT-AAAAAATATTTCTTCACATAAAATGTTTTC
* *
47600634 TCCCGCTCACATTGTGT
65 TCCCACCCACATTGTGT
47600651 ATCTATACGA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
81 34 0.43
82 45 0.57
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (81 bp):
CCACTACACCTATAATCATTATTGAATAAATTTTAAAAAATATTTCTTCACATAAAATGTTTTCT
CCCACCCACATTGTGT
Found at i:47601242 original size:50 final size:51
Alignment explanation
Indices: 47601188--47601292 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 51
47601178 GGGATTAGTC
* * *
47601188 CATATTATTTAAGGGGTAGGACGAATCATATATTTGTGTTTATATTTTTT-
1 CATATTATTTAAGGGGTAGAACCAATCATATATTTGGGTTTATATTTTTTA
*
47601238 CATATTATTTAAGGTGTAGAACCAATCATATATTTGGGTTTATATTTTTTA
1 CATATTATTTAAGGGGTAGAACCAATCATATATTTGGGTTTATATTTTTTA
47601289 CATA
1 CATA
47601293 GATAAATTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 46 0.92
51 4 0.08
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (51 bp):
CATATTATTTAAGGGGTAGAACCAATCATATATTTGGGTTTATATTTTTTA
Found at i:47609504 original size:18 final size:18
Alignment explanation
Indices: 47609483--47609529 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
47609473 ATAATAATTT
*
47609483 AAAATTAAAAATTTAATA
1 AAAATTAAAAATGTAATA
*
47609501 AAAACTAAAAATGTAATA
1 AAAATTAAAAATGTAATA
*
47609519 ATAATTAAAAA
1 AAAATTAAAAA
47609530 ACATTAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATTAAAAATGTAATA
Found at i:47615715 original size:30 final size:30
Alignment explanation
Indices: 47615681--47615787 Score: 142
Period size: 30 Copynumber: 3.6 Consensus size: 30
47615671 TCTGGGCTAG
* * * *
47615681 AGCCCTATACAGTAACAGTGTGTAGGCCAT
1 AGCCCAATACAGTAACAGAGTGTGGGCCTT
* *
47615711 AGCCCAATATAGTAACAGAGAGTGGGCCTT
1 AGCCCAATACAGTAACAGAGTGTGGGCCTT
* *
47615741 AGCCCAATACAATAACAAAGTGTGGGCCTT
1 AGCCCAATACAGTAACAGAGTGTGGGCCTT
47615771 AGCCCAATACAGTAACA
1 AGCCCAATACAGTAACA
47615788 AGGCAAATGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (30 bp):
AGCCCAATACAGTAACAGAGTGTGGGCCTT
Found at i:47615925 original size:26 final size:26
Alignment explanation
Indices: 47615896--47615998 Score: 161
Period size: 26 Copynumber: 4.0 Consensus size: 26
47615886 ACACCAATAT
*
47615896 CGCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
47615922 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* * *
47615948 TGCAGCAGAGCTGCCAGTATCAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
*
47615974 CGCAACAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
47615999 TTTGTGGCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:47616301 original size:81 final size:81
Alignment explanation
Indices: 47616175--47616475 Score: 349
Period size: 81 Copynumber: 3.7 Consensus size: 81
47616165 CATAATAGTC
* * * * *
47616175 ATTTTACCCTATGGA-GGTGTTTCAGTCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCTT
1 ATTTTACCCT-TCGAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCTT
* *
47616239 TCAAGGATATTTCGATC
65 TCAAGGGTATTTCGATA
* * * * *
47616256 ATTTTACCCTTCGAGGGTATTTTAGTAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCGTT
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCTTT
47616321 CAAGGGTATTTC-AGTA
66 CAAGGGTATTTCGA-TA
* * * *
47616337 ATTTTACCCTTCGGGGGTATTTCAATAATTTTACCCTTCGAGGGTATTTCAGTAATTTTA-CTCA
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCT-T
*
47616401 TCAAGGGTATTTTGATA
65 TCAAGGGTATTTCGATA
* * * *
47616418 ATTTTACTCATCGAGGGTATTTC-GATAATTTTACCCATCAAGGGTATTTCGGTAATTT
1 ATTTTACCCTTCGAGGGTATTTCAG-TAATTTTACCCTTCGAGGGTATTTCGGTAATTT
47616476 GCCCACAAAT
Statistics
Matches: 186, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
80 5 0.03
81 180 0.97
82 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (81 bp):
ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCTTT
CAAGGGTATTTCGATA
Found at i:47616407 original size:27 final size:27
Alignment explanation
Indices: 47616175--47616475 Score: 288
Period size: 27 Copynumber: 11.1 Consensus size: 27
47616165 CATAATAGTC
* * *
47616175 ATTTTACCCTATGGA-GGTGTTTCAGTC
1 ATTTTACCCT-TCGAGGGTATTTCAGTA
* * *
47616202 ATTTTACCCTTTGAGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* * * *
47616229 ATTTTACCTTTCAAGGATATTTC-GATC
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
*
47616256 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* *
47616283 ATTTTACCCTTCGGGGGTATTT-TGATA
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
* *
47616310 ATTTTACCGTTCAAGGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* *
47616337 ATTTTACCCTTCGGGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
47616364 ATTTTACCCTTCGAGGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* * * *
47616391 ATTTTACTCATCAAGGGTATTT-TGATA
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
* *
47616418 ATTTTACTCATCGAGGGTATTTC-GATA
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
* * *
47616445 ATTTTACCCATCAAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
47616472 ATTT
1 ATTT
47616476 GCCCACAAAT
Statistics
Matches: 235, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.03
27 226 0.96
28 3 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCAGTA
Found at i:47616457 original size:54 final size:54
Alignment explanation
Indices: 47616202--47616475 Score: 334
Period size: 54 Copynumber: 5.1 Consensus size: 54
47616192 TGTTTCAGTC
* * * * * *
47616202 ATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCTTTCAAGGATATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTCGATA
* ** *
47616256 ATTTTACCCTTCGAGGGTATTTTAGTAATTTTACCCTTCGGGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTCGATA
* * ** *
47616310 ATTTTACCGTTCAAGGGTATTTCAGTAATTTTACCCTTCGGGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTCGATA
* * *
47616364 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACTCATCAAGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTCGATA
* * * *
47616418 ATTTTACTCATCGAGGGTATTTC-GATAATTTTACCCATCAAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCAG-TAATTTTACCCTTCAAGGGTATTTCGATA
47616472 ATTT
1 ATTT
47616476 GCCCACAAAT
Statistics
Matches: 191, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 1 0.01
54 190 0.99
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (54 bp):
ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTCGATA
Found at i:47624403 original size:28 final size:28
Alignment explanation
Indices: 47624333--47624389 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
47624323 AGGGAAAATG
* *
47624333 ACTAGTTAAAAAGAATATCAGGGGTTTC
1 ACTAATTAAAAATAATATCAGGGGTTTC
47624361 ACTAATTAAAAATAATATCAGGGGTTTC
1 ACTAATTAAAAATAATATCAGGGGTTTC
47624389 A
1 A
47624390 TAAATTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (28 bp):
ACTAATTAAAAATAATATCAGGGGTTTC
Found at i:47629854 original size:35 final size:35
Alignment explanation
Indices: 47629810--47629912 Score: 145
Period size: 35 Copynumber: 2.9 Consensus size: 35
47629800 ACACCAAATT
* *
47629810 CTCACAAGAGCTAGTCCAACTGAAAAACGCCAATG
1 CTCATAAGAGCTAGTCCAACTGAAAAACGCCAATA
* *
47629845 CTCATAAGAGCTAGTCCAACCGAAAAATGCCAATA
1 CTCATAAGAGCTAGTCCAACTGAAAAACGCCAATA
*
47629880 CTGATAAGAGCTAGTCCAACT-AAAACACGCCAA
1 CTCATAAGAGCTAGTCCAACTGAAAA-ACGCCAA
47629913 ATAGAGAGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 4 0.07
35 56 0.93
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.16
Consensus pattern (35 bp):
CTCATAAGAGCTAGTCCAACTGAAAAACGCCAATA
Found at i:47637314 original size:24 final size:24
Alignment explanation
Indices: 47637248--47637315 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 24
47637238 GACTATAGTA
*
47637248 GAAAGATGTTATGGCATCA-GGAT
1 GAAAGATGTTATGACATCATGGAT
* * *
47637271 GAAA-ATGAGTAAGAC--CATGGCT
1 GAAAGATG-TTATGACATCATGGAT
47637293 GAAAGATGTTATGACATCATGGA
1 GAAAGATGTTATGACATCATGGA
47637316 AAATAGGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
21 2 0.06
22 15 0.45
23 11 0.33
24 5 0.15
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.24
Consensus pattern (24 bp):
GAAAGATGTTATGACATCATGGAT
Found at i:47642240 original size:63 final size:63
Alignment explanation
Indices: 47642141--47642264 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
47642131 TTAGTTTCAA
*
47642141 TAAGTGTTTCTCTTCGTTTCTGTCATGAATCTCTTAGCGACTAAAGTGGTAATGTTTTTTCGG
1 TAAGTGTTTCCCTTCGTTTCTGTCATGAATCTCTTAGCGACTAAAGTGGTAATGTTTTTTCGG
*
47642204 TAAGTGTTTCCCTTCGTTTCTGTCATGAATCTCTTAGTGACTAAAGTGGTAATGTTTTTTC
1 TAAGTGTTTCCCTTCGTTTCTGTCATGAATCTCTTAGCGACTAAAGTGGTAATGTTTTTTC
47642265 TCTGTGATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (63 bp):
TAAGTGTTTCCCTTCGTTTCTGTCATGAATCTCTTAGCGACTAAAGTGGTAATGTTTTTTCGG
Found at i:47664180 original size:7 final size:7
Alignment explanation
Indices: 47664164--47664346 Score: 96
Period size: 7 Copynumber: 25.6 Consensus size: 7
47664154 TTTATTTTAT
*
47664164 TTTAGTG
1 TTTAGGG
47664171 TTTAGGG
1 TTTAGGG
*
47664178 TTTAGGA
1 TTTAGGG
*
47664185 TTTAAGG
1 TTTAGGG
**
47664192 TTTACAG
1 TTTAGGG
*
47664199 TCTAGGG
1 TTTAGGG
47664206 TTTAGGG
1 TTTAGGG
47664213 TTTTAGGG
1 -TTTAGGG
* *
47664221 TATATGG
1 TTTAGGG
*
47664228 TTTAGTG
1 TTTAGGG
*
47664235 TTTTGGG
1 TTTAGGG
47664242 TTTAGGG
1 TTTAGGG
* *
47664249 TTTAATGT
1 TTT-AGGG
*
47664257 TTTTGGG
1 TTTAGGG
47664264 TTTAGGG
1 TTTAGGG
* *
47664271 TTTAATGT
1 TTT-AGGG
*
47664279 TTTTGGG
1 TTTAGGG
* *
47664286 TTTAAGA
1 TTTAGGG
*
47664293 TTTGGGG
1 TTTAGGG
*
47664300 TTTAGTGT
1 TTTAG-GG
**
47664308 TTTATAG
1 TTTAGGG
*
47664315 TTTAGTG
1 TTTAGGG
*
47664322 TTTAAGG
1 TTTAGGG
*
47664329 TTTAGGA
1 TTTAGGG
*
47664336 TTTAGTG
1 TTTAGGG
47664343 TTTA
1 TTTA
47664347 AGATTTAATA
Statistics
Matches: 124, Mismatches: 48, Indels: 8
0.69 0.27 0.04
Matches are distributed among these distances:
7 102 0.82
8 22 0.18
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:47664187 original size:22 final size:22
Alignment explanation
Indices: 47664164--47664346 Score: 105
Period size: 22 Copynumber: 8.5 Consensus size: 22
47664154 TTTATTTTAT
47664164 TTTAGTGTTTAGGGTTTAGGA-
1 TTTAGTGTTTAGGGTTTAGGAG
** *
47664185 TTTAAG-GTTTACAGTCTAGG-G
1 TTT-AGTGTTTAGGGTTTAGGAG
* * *
47664206 TTTAGGGTTTTAGGGTATATG-G
1 TTTAGTG-TTTAGGGTTTAGGAG
*
47664228 TTTAGTGTTTTGGGTTTAGG-G
1 TTTAGTGTTTAGGGTTTAGGAG
* *
47664249 TTTAATGTTTTTGGGTTTAGG-G
1 TTTAGTG-TTTAGGGTTTAGGAG
* * *
47664271 TTTAATGTTTTTGGGTTTAAGA-
1 TTTAGTG-TTTAGGGTTTAGGAG
* * * *
47664293 TTTGGGGTTTAGTGTTTTA-TAG
1 TTTAGTGTTTAG-GGTTTAGGAG
*
47664315 TTTAGTGTTTAAGGTTTAGGA-
1 TTTAGTGTTTAGGGTTTAGGAG
47664336 TTTAGTGTTTA
1 TTTAGTGTTTA
47664347 AGATTTAATA
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.02
21 56 0.43
22 71 0.55
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.50
Consensus pattern (22 bp):
TTTAGTGTTTAGGGTTTAGGAG
Found at i:47664188 original size:21 final size:21
Alignment explanation
Indices: 47664164--47664380 Score: 111
Period size: 21 Copynumber: 10.1 Consensus size: 21
47664154 TTTATTTTAT
47664164 TTTAGTGTTTAGGGTTTAGGA
1 TTTAGTGTTTAGGGTTTAGGA
** * *
47664185 TTTAAG-GTTTACAGTCTAGGG
1 TTT-AGTGTTTAGGGTTTAGGA
* *
47664206 TTTAGGGTTTTAGGGTATATGG-
1 TTTAGTG-TTTAGGGTTTA-GGA
* *
47664228 TTTAGTGTTTTGGGTTTAGGG
1 TTTAGTGTTTAGGGTTTAGGA
* * *
47664249 TTTAATGTTTTTGGGTTTAGGG
1 TTTAGTG-TTTAGGGTTTAGGA
* * *
47664271 TTTAATGTTTTTGGGTTTAAGA
1 TTTAGTG-TTTAGGGTTTAGGA
* * * *
47664293 TTTGGGGTTTAGTGTTTTA-TA
1 TTTAGTGTTTAG-GGTTTAGGA
*
47664314 GTTTAGTGTTTAAGGTTTAGGA
1 -TTTAGTGTTTAGGGTTTAGGA
* * **
47664336 TTTAGTGTTTAAGATTTAATA
1 TTTAGTGTTTAGGGTTTAGGA
47664357 TTTA-TGTTTTAGGG-TTAGGGA
1 TTTAGTG-TTTAGGGTTTA-GGA
47664378 TTT
1 TTT
47664381 CGATAAAAAT
Statistics
Matches: 154, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
20 9 0.06
21 74 0.48
22 69 0.45
23 2 0.01
ACGTcount: A:0.19, C:0.01, G:0.29, T:0.50
Consensus pattern (21 bp):
TTTAGTGTTTAGGGTTTAGGA
Found at i:47664266 original size:36 final size:34
Alignment explanation
Indices: 47664170--47664345 Score: 100
Period size: 36 Copynumber: 4.9 Consensus size: 34
47664160 TTATTTTAGT
* * ** **
47664170 GTTTAGGGTTTAGGATTTAAGGTTTACAGTCTAGG
1 GTTTAGGGTTTAAGATTTAGGGTTTAGTGT-TTTG
* * * *
47664205 GTTTAGGGTTTTAGGGTATATGGTTTAGTGTTTTGG
1 GTTTAGGG-TTTAAGATTTAGGGTTTAGTGTTTT-G
* * *
47664241 GTTTAGGGTTTAATGTTTTTGGGTTTAGGGTTTAATG
1 GTTTAGGGTTTAA-GATTTAGGGTTTAGTGTTT--TG
* * * *
47664278 TTTTTGGGTTTAAGATTTGGGGTTTAGTGTTTTATA
1 GTTTAGGGTTTAAGATTTAGGGTTTAGTG-TTT-TG
* * *
47664314 GTTTAGTGTTTAAGGTTTAGGATTTAGTGTTT
1 GTTTAGGGTTTAAGATTTAGGGTTTAGTGTTT
47664346 AAGATTTAAT
Statistics
Matches: 110, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
35 16 0.15
36 78 0.71
37 15 0.14
38 1 0.01
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.50
Consensus pattern (34 bp):
GTTTAGGGTTTAAGATTTAGGGTTTAGTGTTTTG
Found at i:47664286 original size:15 final size:15
Alignment explanation
Indices: 47664268--47664310 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47664258 TTTGGGTTTA
*
47664268 GGGTTTAATGTTTTT
1 GGGTTTAATGTTTTG
*
47664283 GGGTTTAA-GATTTG
1 GGGTTTAATGTTTTG
*
47664297 GGGTTTAGTGTTTT
1 GGGTTTAATGTTTT
47664311 ATAGTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
GGGTTTAATGTTTTG
Found at i:47665122 original size:125 final size:124
Alignment explanation
Indices: 47664982--47665584 Score: 634
Period size: 125 Copynumber: 5.0 Consensus size: 124
47664972 GTTTATGATT
* *
47664982 AAAACGCCGCAAAAAAACATTTTACTTTAAACAAAACGACGTG-GTTTTGAGTGGCATCTTTAGT
1 AAAACGCCGCAAAAAAACATTTTACTTTAAACAAAACG--GTGCATTTTAAGTGGCATCTTTAGT
* * *
47665046 GGTATTAGCGGCACCAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
64 GGCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
* * *
47665107 AAAACGTCGC-AAAAAA-A--TTACTTTAAACCAAACGGTGCCATTTTAAGTGGCGTCTTTAGTG
1 AAAACGCCGCAAAAAAACATTTTACTTTAAACAAAACGGTG-CATTTTAAGTGGCATCTTTAGTG
* *
47665168 GCATTAGCGGTGCTAGGTGAAAAACGCCGCAATAAATCGAGCATTAGCGGCGCTAGGTAA
65 GCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
* * * **
47665228 AAAACGCCACAAAAAAACATTTTACTTTAAACAAAACGGCGCCATTTTCAGTGGTGTCTTTAGTG
1 AAAACGCCGCAAAAAAACATTTTACTTTAAACAAAACGGTG-CATTTTAAGTGGCATCTTTAGTG
*
47665293 GCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGTGGCGCTAGGTAA
65 GCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
* * * *
47665353 AAAACGCCACAAAAAAAAACATTTTACTTTAAACAAAACGGTGCCGTTTTTATTGGCATC---AG
1 AAAACGCCGC--AAAAAAACATTTTACTTTAAACAAAACGGTG-CATTTTAAGTGGCATCTTTAG
* * *
47665415 TGG---T------GCTAGGTGAAAAACACTGCAATAGAGCGAGCATTAGCGGGCGCTAGGTAA
63 TGGCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGC-GGCGCTAGGTAA
* * *
47665469 AAAACGCCAG-AAAAAAACATTTTACTTTAAACAAAATGGTG------ACGT----T-TTTAATG
1 AAAACGCC-GCAAAAAAACATTTTACTTTAAACAAAACGGTGCATTTTAAGTGGCATCTTTAGTG
* ** * * *
47665522 GCGTTAGCAACACTAGGTGAAAAACACCACAATAGATCGAGCATTAGCGGCGCTAGGTAA
65 GCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
47665582 AAA
1 AAA
47665585 TCATCACAAA
Statistics
Matches: 417, Mismatches: 39, Indels: 56
0.81 0.08 0.11
Matches are distributed among these distances:
103 1 0.00
105 4 0.01
107 1 0.00
108 1 0.00
113 15 0.04
114 63 0.15
115 33 0.08
116 20 0.05
119 3 0.01
121 99 0.24
122 6 0.01
123 2 0.00
124 11 0.03
125 116 0.28
127 42 0.10
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (124 bp):
AAAACGCCGCAAAAAAACATTTTACTTTAAACAAAACGGTGCATTTTAAGTGGCATCTTTAGTGG
CATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGCGGCGCTAGGTAA
Found at i:47665440 original size:115 final size:113
Alignment explanation
Indices: 47665286--47665584 Score: 418
Period size: 114 Copynumber: 2.6 Consensus size: 113
47665276 CAGTGGTGTC
* * *
47665286 TTTAGTGGCATTAGCGGCGCTAGGTGAAAAACGCCGCAATAGATCGAGCATTAGTGGCGCTAGGT
1 TTTAATGGCATTAGCGGCGCTAGGTGAAAAACACCGCAATAGATCGAGCATTAGCGGCGCTAGGT
*
47665351 AAAAAACGCCACAAAAAAAAACATTTTACTTTAAACAAAACGGTGCCGTT
66 AAAAAACG-C-CAAAAAAAAACATTTTACTTTAAACAAAACGGTGACGTT
* * * * * *
47665401 TTTATTGGCATCAGTGGTGCTAGGTGAAAAACACTGCAATAGAGCGAGCATTAGCGGGCGCTAGG
1 TTTAATGGCATTAGCGGCGCTAGGTGAAAAACACCGCAATAGATCGAGCATTAGC-GGCGCTAGG
* *
47665466 TAAAAAACGCCAGAAAAAAACATTTTACTTTAAACAAAATGGTGACGTT
65 TAAAAAACGCCAAAAAAAAACATTTTACTTTAAACAAAACGGTGACGTT
* ** * *
47665515 TTTAATGGCGTTAGCAACACTAGGTGAAAAACACCACAATAGATCGAGCATTAGCGGCGCTAGGT
1 TTTAATGGCATTAGCGGCGCTAGGTGAAAAACACCGCAATAGATCGAGCATTAGCGGCGCTAGGT
47665580 AAAAA
66 AAAAA
47665585 TCATCACAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
113 15 0.09
114 80 0.50
115 48 0.30
116 18 0.11
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (113 bp):
TTTAATGGCATTAGCGGCGCTAGGTGAAAAACACCGCAATAGATCGAGCATTAGCGGCGCTAGGT
AAAAAACGCCAAAAAAAAACATTTTACTTTAAACAAAACGGTGACGTT
Found at i:47671969 original size:9 final size:9
Alignment explanation
Indices: 47671955--47671984 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
47671945 AAATGATAAT
47671955 CATAACTTA
1 CATAACTTA
47671964 CATAACTTA
1 CATAACTTA
*
47671973 CATAATTTA
1 CATAACTTA
47671982 CAT
1 CAT
47671985 TGACAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:47674689 original size:17 final size:18
Alignment explanation
Indices: 47674667--47674701 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47674657 ATTTGGGTCA
47674667 TGTGGG-CCACACAGGCG
1 TGTGGGCCCACACAGGCG
*
47674684 TGTGGGCCCACACGGGCG
1 TGTGGGCCCACACAGGCG
47674702 AACATCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.11
Consensus pattern (18 bp):
TGTGGGCCCACACAGGCG
Found at i:47675661 original size:18 final size:18
Alignment explanation
Indices: 47675638--47675685 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
47675628 TCCGCAATAA
47675638 AATAACGTTTTG-AAATTG
1 AATAACGTTTTGTAAA-TG
*
47675656 AATAACGATTTGTAAATG
1 AATAACGTTTTGTAAATG
*
47675674 AATAATGTTTTG
1 AATAACGTTTTG
47675686 GAAACGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (18 bp):
AATAACGTTTTGTAAATG
Found at i:47679911 original size:42 final size:42
Alignment explanation
Indices: 47679849--47679965 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
47679839 TTAGTAAAAT
* * * * * *
47679849 CGCCGCTAAAGGTCAAGTTCTTTAGTGGTGTTTTTGGGGAAG
1 CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
*
47679891 CGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
1 CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
* *
47679933 CACCGCTAAAGGTCATGTTCTATAACGGCGTTT
1 CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTT
47679966 TTCTGCATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (42 bp):
CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
Found at i:47681483 original size:27 final size:27
Alignment explanation
Indices: 47681436--47681499 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
47681426 AAATATTCTC
*
47681436 TAAAATAAT-AAATGTTAATTTATCGA
1 TAAAATAATAAAATATTAATTTATCGA
* * *
47681462 TAAATTAATAAAATATTTATTTATTGA
1 TAAAATAATAAAATATTAATTTATCGA
*
47681489 TAAACTAATAA
1 TAAAATAATAA
47681500 CCTCAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (27 bp):
TAAAATAATAAAATATTAATTTATCGA
Found at i:47685708 original size:30 final size:30
Alignment explanation
Indices: 47685685--47685743 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
47685675 CAGTAGTAGT
*
47685685 GTGTGGGCCATAACCCAATACAGTAACAGA
1 GTGTGGCCCATAACCCAATACAGTAACAGA
* *
47685715 GTGTGGCCCTTAGCCCAATACAGTAACAG
1 GTGTGGCCCATAACCCAATACAGTAACAG
47685744 TGCAAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
GTGTGGCCCATAACCCAATACAGTAACAGA
Found at i:47686127 original size:27 final size:27
Alignment explanation
Indices: 47686097--47686289 Score: 162
Period size: 27 Copynumber: 7.1 Consensus size: 27
47686087 TATAACGATC
*
47686097 ATTTTATCCTATAG-GGGTATTTCAGTT
1 ATTTTA-CCTATCGAGGGTATTTCAGTT
* *
47686124 ATTTTACCTATCGAGGGTATTTTAGTA
1 ATTTTACCTATCGAGGGTATTTCAGTT
47686151 ATTTTACCCT-TCGAGGGTATTTC-GATT
1 ATTTTA-CCTATCGAGGGTATTTCAG-TT
* * *
47686178 ATTTTACCTATCGAGGGTATTTTAATA
1 ATTTTACCTATCGAGGGTATTTCAGTT
* *
47686205 ATTTTACCCATCGAGGGTATTTC-GATA
1 ATTTTACCTATCGAGGGTATTTCAG-TT
* * *
47686232 ATTTTACCCATCGAGGGCATTTC-GATA
1 ATTTTACCTATCGAGGGTATTTCAG-TT
* ** * *
47686259 ATTTTACCCATTAAGGGTATTTTAGTC
1 ATTTTACCTATCGAGGGTATTTCAGTT
47686286 ATTT
1 ATTT
47686290 GCCCACGAAT
Statistics
Matches: 142, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.07
27 128 0.90
28 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (27 bp):
ATTTTACCTATCGAGGGTATTTCAGTT
Found at i:47686169 original size:54 final size:54
Alignment explanation
Indices: 47686111--47686280 Score: 229
Period size: 54 Copynumber: 3.1 Consensus size: 54
47686101 TATCCTATAG
47686111 GGGTATTTC-AGTTATTTTACCTATCGAGGGTATTTTAGTAATTTTACCCTTCGA
1 GGGTATTTCGA-TTATTTTACCTATCGAGGGTATTTTAGTAATTTTACCCTTCGA
* *
47686165 GGGTATTTCGATTATTTTACCTATCGAGGGTATTTTAATAATTTTACCCATCGA
1 GGGTATTTCGATTATTTTACCTATCGAGGGTATTTTAGTAATTTTACCCTTCGA
* * * * *
47686219 GGGTATTTCGATAATTTTACCCATCGAGGGCA-TTTCGATAATTTTACCCATT-AA
1 GGGTATTTCGATTATTTTACCTATCGAGGGTATTTTAG-TAATTTTACCC-TTCGA
47686273 GGGTATTT
1 GGGTATTT
47686281 TAGTCATTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
53 3 0.03
54 99 0.95
55 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (54 bp):
GGGTATTTCGATTATTTTACCTATCGAGGGTATTTTAGTAATTTTACCCTTCGA
Found at i:47686218 original size:81 final size:81
Alignment explanation
Indices: 47686083--47686282 Score: 235
Period size: 81 Copynumber: 2.5 Consensus size: 81
47686073 TCATCTCTTA
** * * * * *
47686083 AGGGTATAACGATCATTTTATCCTATAG-GGGTATTTCAGTTATTTTACCTATCGAGGGTATTTT
1 AGGGTATTTCGATAATTTTA-CCTATAGAGGGTATTTTAATAATTTTACCCATCGAGGGTA-TTT
*
47686147 AG-TAATTTTACCCTTCG
64 AGATAATTTTACCCATCG
* * *
47686164 AGGGTATTTCGATTATTTTACCTATCGAGGGTATTTTAATAATTTTACCCATCGAGGGTATTTCG
1 AGGGTATTTCGATAATTTTACCTATAGAGGGTATTTTAATAATTTTACCCATCGAGGGTATTTAG
47686229 ATAATTTTACCCATCG
66 ATAATTTTACCCATCG
* *
47686245 AGGGCATTTCGATAATTTTACCCATTA-AGGGTATTTTA
1 AGGGTATTTCGATAATTTTACCTA-TAGAGGGTATTTTA
47686283 GTCATTTGCC
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
80 10 0.10
81 91 0.89
82 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (81 bp):
AGGGTATTTCGATAATTTTACCTATAGAGGGTATTTTAATAATTTTACCCATCGAGGGTATTTAG
ATAATTTTACCCATCG
Found at i:47688855 original size:5 final size:5
Alignment explanation
Indices: 47688845--47688876 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
47688835 TTCAAAAAAT
47688845 AATTA AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AA
47688877 GTTAGAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:47693169 original size:16 final size:17
Alignment explanation
Indices: 47693132--47693171 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
47693122 TATGGTATGA
47693132 ATTTTTATAATATCGGG
1 ATTTTTATAATATCGGG
47693149 A-TTTTATAAT-T-GGG
1 ATTTTTATAATATCGGG
47693163 AGTTTTTAT
1 A-TTTTTAT
47693172 GTAACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 1 0.05
16 15 0.71
17 1 0.05
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (17 bp):
ATTTTTATAATATCGGG
Found at i:47694736 original size:17 final size:17
Alignment explanation
Indices: 47694714--47694747 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47694704 TCAAAAGTCA
47694714 GTTA-TTTATTTTTAATT
1 GTTATTTTA-TTTTAATT
47694731 GTTATTTTATTTTAATT
1 GTTATTTTATTTTAATT
47694748 TTAGAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
GTTATTTTATTTTAATT
Found at i:47706942 original size:17 final size:17
Alignment explanation
Indices: 47706920--47706961 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
47706910 TTCGGGGTGT
47706920 TATAAAAATATTTAAAA
1 TATAAAAATATTTAAAA
47706937 TATAAAAATATTTAAAA
1 TATAAAAATATTTAAAA
*
47706954 AATAAAAA
1 TATAAAAA
47706962 CTCTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAAAAATATTTAAAA
Found at i:47709519 original size:41 final size:41
Alignment explanation
Indices: 47709462--47709659 Score: 209
Period size: 41 Copynumber: 4.8 Consensus size: 41
47709452 TTTTTTAAAC
*
47709462 CTTTAGCGGCGTTTTTATCTAAGCACCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGT
* *
47709503 CTTTAGCGGCGTTTTTATCTGAA-CGCCGCTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTATCT-AAGCGCCGCTAATGCTCGGGT
* * * *
47709544 CTTTGGCAGCGTTTTTATATAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGT
* * * * **
47709585 CTTTAGCGGCGTTTTTAACTGAGCGCCACTAATTCTCTTGT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGT
* * ** * *
47709626 CTTCAGCGGCATTTGAAGCTAAGCGCCACTAATG
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATG
47709660 TATTTACCTT
Statistics
Matches: 129, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.02
41 125 0.97
42 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGT
Found at i:47709598 original size:82 final size:82
Alignment explanation
Indices: 47709461--47709622 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
47709451 ATTTTTTAAA
* * * *
47709461 CCTTTAGCGGCGTTTTTATCTAAGCACCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTATCTGAA
1 CCTTTAGCAGCGTTTTTATATAAGCACCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAA
*
47709526 CGCCGCTAATGCTCTGG
66 CGCCACTAATGCTCTGG
* * *
47709543 CCTTTGGCAGCGTTTTTATATAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAG
1 CCTTTAGCAGCGTTTTTATATAAGCACCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAA
*
47709608 CGCCACTAATTCTCT
66 CGCCACTAATGCTCT
47709623 TGTCTTCAGC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (82 bp):
CCTTTAGCAGCGTTTTTATATAAGCACCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAA
CGCCACTAATGCTCTGG
Found at i:47711019 original size:7 final size:7
Alignment explanation
Indices: 47711009--47711087 Score: 59
Period size: 7 Copynumber: 10.4 Consensus size: 7
47710999 AATTTAATGT
47711009 TTAGGGG
1 TTAGGGG
47711016 TTAGGGGG
1 TTA-GGGG
47711024 ATTTAGGGG
1 --TTAGGGG
*
47711033 TTAAGGG
1 TTAGGGG
* **
47711040 TTATGCT
1 TTAGGGG
47711047 TTAGGGG
1 TTAGGGG
47711054 TTAGGGG
1 TTAGGGG
47711061 ATTTAGGGG
1 --TTAGGGG
*
47711070 TAAGGGG
1 TTAGGGG
47711077 TTAGAGGG
1 TTAG-GGG
47711085 TTA
1 TTA
47711088 TGGATTTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
7 33 0.58
8 10 0.18
9 11 0.19
10 3 0.05
ACGTcount: A:0.20, C:0.01, G:0.47, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:47714521 original size:34 final size:31
Alignment explanation
Indices: 47714443--47714567 Score: 120
Period size: 31 Copynumber: 4.2 Consensus size: 31
47714433 CATATCATTT
* *
47714443 AATTAATTAATATACATAGATTACATAACTTA
1 AATTAA-TATTATACATAAATTACATAACTTA
* *
47714475 CATTAATTTTATACATAAATTACATAACTT-
1 AATTAATATTATACATAAATTACATAACTTA
* * *
47714505 AA-TGA-ATTA-ATAT-TA-TACATAACTTA
1 AATTAATATTATACATAAATTACATAACTTA
*
47714531 CATTAATATTATACATAAATTACATAACTT-
1 AATTAATATTATACATAAATTACATAACTTA
47714561 AATTAAT
1 AATTAAT
47714568 TAATTAGGAC
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
25 10 0.14
26 2 0.03
27 5 0.07
28 7 0.10
29 5 0.07
30 8 0.11
31 31 0.42
32 5 0.07
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (31 bp):
AATTAATATTATACATAAATTACATAACTTA
Found at i:47714524 original size:25 final size:22
Alignment explanation
Indices: 47714495--47714548 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
47714485 ATACATAAAT
47714495 TACATAACTTAATGAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
47714520 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
47714542 TACATAA
1 TACATAA
47714549 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:47714525 original size:56 final size:56
Alignment explanation
Indices: 47714464--47714571 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 56
47714454 ATACATAGAT
*
47714464 TACATAACTTACATTAATTTTATACATAAATTACATAACTTAATGAATTAATATTA
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATGAATTAATATTA
*
47714520 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAAT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATGAATTAAT
47714572 TAGGACAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (56 bp):
TACATAACTTACATTAATATTATACATAAATTACATAACTTAATGAATTAATATTA
Found at i:47714538 original size:22 final size:22
Alignment explanation
Indices: 47714510--47714555 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
47714500 AACTTAATGA
*
47714510 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
47714532 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
47714554 AT
1 AT
47714556 AACTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:47714723 original size:9 final size:9
Alignment explanation
Indices: 47714709--47715066 Score: 140
Period size: 9 Copynumber: 39.7 Consensus size: 9
47714699 TTAATTAATA
47714709 TACATAAAT
1 TACATAAAT
*
47714718 TACATAACT
1 TACATAAAT
47714727 TACATTAATATT
1 TACA-TAA-A-T
47714739 ATACATAAAT
1 -TACATAAAT
*
47714749 TACATAACT
1 TACATAAAT
*
47714758 TA-ATTAAT
1 TACATAAAT
47714766 TA-AT--A-
1 TACATAAAT
47714771 TACATAAAT
1 TACATAAAT
*
47714780 TACATAACT
1 TACATAAAT
47714789 TACATTAAGATT
1 TACA-TAA-A-T
47714801 ATACATAAAT
1 -TACATAAAT
*
47714811 TACATAACT
1 TACATAAAT
*
47714820 TA-ATTAAT
1 TACATAAAT
*
47714828 TA-ATAACT
1 TACATAAAT
*
47714836 TACATAACT
1 TACATAAAT
*
47714845 TACATAACT
1 TACATAAAT
*
47714854 TAC--AACT
1 TACATAAAT
*
47714861 TACATAACT
1 TACATAAAT
***
47714870 TACATTTTTT
1 TACA-TAAAT
*
47714880 TA-AT-TAT
1 TACATAAAT
47714887 T-CATAAAT
1 TACATAAAT
*
47714895 TACATAACT
1 TACATAAAT
47714904 TACATTAATATT
1 TACA-TAA-A-T
47714916 ATACATAAAT
1 -TACATAAAT
*
47714926 TACATAACT
1 TACATAAAT
*
47714935 TA-ATTAAT
1 TACATAAAT
*
47714943 ATACTTAAAT
1 -TACATAAAT
*
47714953 TACATAACT
1 TACATAAAT
47714962 TACATTAATATT
1 TACA-TAA-A-T
47714974 ATACATAAAT
1 -TACATAAAT
*
47714984 TACATAACT
1 TACATAAAT
* *
47714993 TA-GTTAAT
1 TACATAAAT
*
47715001 TA-AT-ATT
1 TACATAAAT
*
47715008 ATACATAACT
1 -TACATAAAT
*
47715018 TACATAACT
1 TACATAAAT
47715027 TACAT-AA-
1 TACATAAAT
*
47715034 TACATAACT
1 TACATAAAT
* * *
47715043 TATATGACT
1 TACATAAAT
*
47715052 TACATAACT
1 TACATAAAT
47715061 TACATA
1 TACATA
47715067 GCATAATTTT
Statistics
Matches: 275, Mismatches: 40, Indels: 68
0.72 0.10 0.18
Matches are distributed among these distances:
5 2 0.01
6 3 0.01
7 19 0.07
8 39 0.14
9 150 0.55
10 26 0.09
11 4 0.01
12 16 0.06
13 16 0.06
ACGTcount: A:0.47, C:0.14, G:0.01, T:0.39
Consensus pattern (9 bp):
TACATAAAT
Found at i:47714743 original size:22 final size:22
Alignment explanation
Indices: 47714718--47714815 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
47714708 ATACATAAAT
*
47714718 TACATAACTTACATTAATATTA
1 TACATAAATTACATTAATATTA
*
47714740 TACATAAATTACA-TAACT-TAA
1 TACATAAATTACATTAA-TATTA
*
47714761 TTA-ATTAATATACA-TAA-A-T-
1 -TACATAAAT-TACATTAATATTA
* *
47714780 TACATAACTTACATTAAGATTA
1 TACATAAATTACATTAATATTA
47714802 TACATAAATTACAT
1 TACATAAATTACAT
47714816 AACTTAATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
18 6 0.10
19 7 0.12
20 1 0.02
21 11 0.18
22 35 0.58
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (22 bp):
TACATAAATTACATTAATATTA
Found at i:47714838 original size:25 final size:29
Alignment explanation
Indices: 47714702--47715066 Score: 281
Period size: 31 Copynumber: 12.8 Consensus size: 29
47714692 NNNTTAATTA
47714702 ATTAA-TATACATAAATTACATAACTTAC
1 ATTAACTATACATAAATTACATAACTTAC
*
47714730 ATTAATATTATACATAAATTACATAACTTA-
1 ATT-A-ACTATACATAAATTACATAACTTAC
*
47714760 ATTAATTAATATACATAAATTACATAACTTAC
1 ATT-A--ACTATACATAAATTACATAACTTAC
*
47714792 ATTAAGATTATACATAAATTACATAACTTA-
1 ATT-A-ACTATACATAAATTACATAACTTAC
*
47714822 ATTAA-T-TA-ATAACTTACATAACTTAC
1 ATTAACTATACATAAATTACATAACTTAC
*
47714848 A-TAACT-TAC--AACTTACATAACTTAC
1 ATTAACTATACATAAATTACATAACTTAC
* *
47714873 ATTTTTTTAATTATTCATAAATTACATAACTTAC
1 A-----TTAACTATACATAAATTACATAACTTAC
*
47714907 ATTAATATTATACATAAATTACATAACTTA-
1 ATT-A-ACTATACATAAATTACATAACTTAC
*
47714937 ATTAA-TATACTTAAATTACATAACTTAC
1 ATTAACTATACATAAATTACATAACTTAC
*
47714965 ATTAATATTATACATAAATTACATAACTTA-
1 ATT-A-ACTATACATAAATTACATAACTTAC
* *
47714995 GTTAA-T-TA-AT-ATTATACATAACTTAC
1 ATTAACTATACATAAAT-TACATAACTTAC
*
47715021 A-TAACT-TACAT-AA-TACATAACTTAT
1 ATTAACTATACATAAATTACATAACTTAC
* *
47715046 A-TGACT-TACATAACTTACATA
1 ATTAACTATACATAAATTACATA
47715067 GCATAATTTT
Statistics
Matches: 291, Mismatches: 17, Indels: 59
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.01
25 73 0.25
26 12 0.04
27 32 0.11
28 9 0.03
29 7 0.02
30 16 0.05
31 117 0.40
32 7 0.02
34 16 0.05
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (29 bp):
ATTAACTATACATAAATTACATAACTTAC
Found at i:47714862 original size:16 final size:16
Alignment explanation
Indices: 47714830--47714873 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 16
47714820 TAATTAATTA
47714830 ATAACTTACATAACTTAC
1 ATAACTTAC--AACTTAC
47714848 ATAACTTACAACTTAC
1 ATAACTTACAACTTAC
47714864 ATAACTTACA
1 ATAACTTACA
47714874 TTTTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 17 0.65
18 9 0.35
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAACTTACAACTTAC
Found at i:47714909 original size:115 final size:114
Alignment explanation
Indices: 47714699--47715031 Score: 382
Period size: 115 Copynumber: 2.8 Consensus size: 114
47714689 NNNNNNTTAA
* *
47714699 TTAATTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTA
1 TTAATTAATATACATAAATTACATAACTTACA-T-A-ACT-TAC--AACTTACATAACTTAATTA
47714764 ATTAATATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAAC
60 ATTAATATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAAC
* **
47714819 TTAATTAAT-TA-ATAACTTACATAACTTACATAACTTACAACTTACATAACTTACATTTTTTTA
1 TTAATTAATATACATAAATTACATAACTTACATAACTTACAACTTACATAACTTA-A-TTAATTA
* *
47714882 ATTATTCATAAATTACATAACTTACATTAATATTATACATAAATTACATAAC
64 A-TATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAAC
* * * *
47714934 TTAATTAATATACTTAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTA
1 TTAATTAATATACATAAATTACATAACTTACA-T-A-ACT-TAC--AACTTACATAACTTAATTA
*
47714999 ATTAATATTATACATAACTTACATAACTTACAT
60 ATT-A-A-TATACATAAATTACATAACTTACAT
47715032 AATACATAAC
Statistics
Matches: 184, Mismatches: 16, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
112 14 0.08
113 1 0.01
114 9 0.05
115 59 0.32
116 3 0.02
117 18 0.10
118 19 0.10
119 3 0.02
120 11 0.06
121 7 0.04
122 1 0.01
123 39 0.21
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.40
Consensus pattern (114 bp):
TTAATTAATATACATAAATTACATAACTTACATAACTTACAACTTACATAACTTAATTAATTAAT
ATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAAC
Found at i:47715004 original size:173 final size:173
Alignment explanation
Indices: 47714703--47715044 Score: 555
Period size: 173 Copynumber: 2.0 Consensus size: 173
47714693 NNTTAATTAA
47714703 TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTA
1 TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAAC---ATTAATTA
47714768 ATATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAACTTAATTAATTAATA
63 ATATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAACTTAATTAATTAAT-
*
47714833 ACT-TACATAACTTACATAACTTACA-ACTTACATAACTTACATTTTT
127 ACTATACATAACTTACATAACTTACATA-ATACATAACTTACATTTTT
*
47714879 TTAATTATTCATAAATTACATAACTTACATTAATATTATACATAAATTACATAAC-TTAATTAAT
1 TTAA-TATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACATTAATTAAT
* * * *
47714943 ATACTTAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
65 ATACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAACTTAATTAATTAATACT
47715008 ATACATAACTTACATAACTTACATAATACATAACTTA
130 ATACATAACTTACATAACTTACATAATACATAACTTA
47715045 TATGACTTAC
Statistics
Matches: 157, Mismatches: 6, Indels: 9
0.91 0.03 0.05
Matches are distributed among these distances:
172 2 0.01
173 101 0.64
174 1 0.01
176 4 0.03
177 49 0.31
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (173 bp):
TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACATTAATTAATA
TACATAAATTACATAACTTACATTAAGATTATACATAAATTACATAACTTAATTAATTAATACTA
TACATAACTTACATAACTTACATAATACATAACTTACATTTTT
Found at i:47715063 original size:34 final size:34
Alignment explanation
Indices: 47715015--47715139 Score: 155
Period size: 34 Copynumber: 3.5 Consensus size: 34
47715005 ATTATACATA
47715015 ACTTACATAACTTACATAATACATAACTTATATG
1 ACTTACATAACTTACATAATACATAACTTATATG
* *
47715049 ACTTACATAACTTACATAGCATAATTTTCATAA--TAAATA
1 ACTTACATAACTTACATA--AT-A----CATAACTTATATG
47715088 ACTTACATAACTTACATAATACATAACTTATATG
1 ACTTACATAACTTACATAATACATAACTTATATG
47715122 ACTTACATAACTTACATA
1 ACTTACATAACTTACATA
47715140 GCATAATTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
32 5 0.06
34 40 0.51
36 3 0.04
37 3 0.04
39 22 0.28
41 5 0.06
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (34 bp):
ACTTACATAACTTACATAATACATAACTTATATG
Found at i:47715093 original size:73 final size:73
Alignment explanation
Indices: 47715012--47715218 Score: 337
Period size: 73 Copynumber: 2.9 Consensus size: 73
47715002 AATATTATAC
47715012 ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATTTT
1 ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATTTT
47715077 CATAATAA
66 CATAATAA
47715085 ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATTTT
1 ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATTTT
*
47715150 CATAATAC
66 CATAATAA
* * * * * *
47715158 ATAACTTACATAATTTTCATAATAAATAACTTACAT-A-ATACATAACTTACATAGCTTAATT
1 ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATT
47715219 ATACTTATTC
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
71 22 0.17
72 1 0.01
73 104 0.82
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.36
Consensus pattern (73 bp):
ATAACTTACATAACTTACATAATACATAACTTATATGACTTACATAACTTACATAGCATAATTTT
CATAATAA
Found at i:47715097 original size:9 final size:9
Alignment explanation
Indices: 47715085--47715215 Score: 97
Period size: 9 Copynumber: 15.9 Consensus size: 9
47715075 TTCATAATAA
47715085 ATAACTTAC
1 ATAACTTAC
47715094 ATAACTTAC
1 ATAACTTAC
47715103 ATAA--TAC
1 ATAACTTAC
*
47715110 ATAACTTAT
1 ATAACTTAC
*
47715119 ATGACTTAC
1 ATAACTTAC
47715128 ATAACTTAC
1 ATAACTTAC
*
47715137 AT-A---GC
1 ATAACTTAC
* *
47715142 ATAATTTTC
1 ATAACTTAC
47715151 ATAA--TAC
1 ATAACTTAC
47715158 ATAACTTAC
1 ATAACTTAC
* *
47715167 ATAATTTTC
1 ATAACTTAC
*
47715176 ATAA--TAA
1 ATAACTTAC
47715183 ATAACTTAC
1 ATAACTTAC
47715192 ATAA--TAC
1 ATAACTTAC
47715199 ATAACTTAC
1 ATAACTTAC
*
47715208 ATAGCTTA
1 ATAACTTA
47715216 ATTATACTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 25 0.26
8 1 0.01
9 67 0.69
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:47715097 original size:25 final size:25
Alignment explanation
Indices: 47715068--47715196 Score: 131
Period size: 25 Copynumber: 5.2 Consensus size: 25
47715058 ACTTACATAG
47715068 CATAATTTTCATAATAAATAACTTA
1 CATAATTTTCATAATAAATAACTTA
* * *
47715093 CATAACTTACATAATACATAACTTA
1 CATAATTTTCATAATAAATAACTTA
* * * * *
47715118 TATGACTTACATAACT---T-ACATA
1 CATAATTTTCATAA-TAAATAACTTA
*
47715140 GCATAATTTTCATAATACATAACTTA
1 -CATAATTTTCATAATAAATAACTTA
47715166 CATAATTTTCATAATAAATAACTTA
1 CATAATTTTCATAATAAATAACTTA
47715191 CATAAT
1 CATAAT
47715197 ACATAACTTA
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.06
23 11 0.13
25 65 0.76
26 5 0.06
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (25 bp):
CATAATTTTCATAATAAATAACTTA
Found at i:47721909 original size:22 final size:22
Alignment explanation
Indices: 47721883--47721924 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47721873 TGTTTGTGGG
* *
47721883 AAAAGTGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
47721905 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
47721925 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:47723962 original size:28 final size:29
Alignment explanation
Indices: 47723931--47723993 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
47723921 AGAAGGAGAG
47723931 GGAAAGAG-GAAGAAAGAAAGAAAGAA-AA
1 GGAAAGAGAGAAGAAAGAAAGAAA-AAGAA
*
47723959 GGAAAG-GAGAGGAAAGAAAGAAAAAGAA
1 GGAAAGAGAGAAGAAAGAAAGAAAAAGAA
47723987 GGAAAGA
1 GGAAAGA
47723994 AAAGGAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (29 bp):
GGAAAGAGAGAAGAAAGAAAGAAAAAGAA
Found at i:47723963 original size:10 final size:10
Alignment explanation
Indices: 47723942--47724002 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
47723932 GAAAGAGGAA
47723942 GAAAG-AAA-
1 GAAAGAAAAG
47723950 GAAAGAAAAG
1 GAAAGAAAAG
* *
47723960 GAAAGGAGAG
1 GAAAGAAAAG
47723970 GAAAG-AAA-
1 GAAAGAAAAG
47723978 GAAA-AAGAAG
1 GAAAGAA-AAG
47723988 GAAAGAAAAG
1 GAAAGAAAAG
47723998 GAAAG
1 GAAAG
47724003 GAGAAGAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 10 0.23
9 7 0.16
10 25 0.57
11 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:47723964 original size:5 final size:5
Alignment explanation
Indices: 47723942--47724004 Score: 53
Period size: 5 Copynumber: 13.4 Consensus size: 5
47723932 GAAAGAGGAA
* * * *
47723942 GAAA- GAAA- GAAAG AAAAG GAAAG GAGAG GAAA- GAAAG AAAAA G-AAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
*
47723988 GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GA
47724005 GAAGAGAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
4 15 0.33
5 31 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:47723985 original size:38 final size:38
Alignment explanation
Indices: 47723923--47724023 Score: 125
Period size: 38 Copynumber: 2.6 Consensus size: 38
47723913 GGGGGAAGAG
*
47723923 AAGGAGAGGGAAAG-AGGAAGAAAGAAAGAAAGAAAAGGA
1 AAGGAGA-GGAAAGAAAGAA-AAAGAAAGAAAGAAAAGGA
*
47723962 AAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAGGAGAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGA
*
47724000 AAGGAGAAGAGAAA-AAAAAAAAAG
1 AAGGAG-AG-GAAAGAAAGAAAAAG
47724024 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
38 30 0.54
39 22 0.39
40 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (38 bp):
AAGGAGAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGA
Found at i:47723999 original size:28 final size:28
Alignment explanation
Indices: 47723942--47724002 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
47723932 GAAAGAGGAA
* *
47723942 GAAAGAAAGAAAGAAAAGGAAAGGAGAG
1 GAAAGAAAGAAAGAAAAGGAAAGAAAAG
47723970 GAAAGAAAGAAA-AAGAAGGAAAGAAAAG
1 GAAAGAAAGAAAGAA-AAGGAAAGAAAAG
47723998 GAAAG
1 GAAAG
47724003 GAGAAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
GAAAGAAAGAAAGAAAAGGAAAGAAAAG
Found at i:47724858 original size:160 final size:152
Alignment explanation
Indices: 47724463--47724942 Score: 477
Period size: 160 Copynumber: 3.1 Consensus size: 152
47724453 AAAAATGGTA
* * *
47724463 TATTTAAAAAACACACTAAATTAATAAATTTCAACCATAATGTACTAAAATAATGTAAAAAAATA
1 TATTTAAAAAACACACTAAATTAATAAAATTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * * **
47724528 AAATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATAAGAACAAATTGCC
66 AAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGG-GAAAAAAATACGAAAAAAGGGCC
47724593 GAAATAAGAGTGTTTTACTAAAT
130 GAAATAAGAGTGTTTTACTAAAT
* * * * * * * *
47724616 TTTTTAAAAATTCAGA-AATAATTAATACAAATATTTCAAGCAAAATGTACTTAAATAATATAAA
1 TATTTAAAAA-ACACACTA-AATTAAT--AAA-A-TTCAAACATAATGTACTAAAATAATGTAAA
* *
47724680 ATAATAAAA-TACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATTCGGGAAAATAATACGA
60 ATAATAAAATTA-GAAAAT-ATGATA-TTTT-TT-AAAGTAATAAAATGCGGGAAAAAAATACGA
** * * *
47724743 GTAAAGGGCATG-AATAAAGGGTTTTTTTACACTAAAT
120 AAAAAGGGC-CGAAAT-AAGAG-TGTTTT--ACTAAAT
* * *
47724780 TAATTTAAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTAT
1 T-ATTTAAAAAACACACTAAATTAATAAAATTCAAACATAATGTACTAAAATAATGTAAAATAAT
47724845 AAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGC-GGATAAAAAATACGAAAAAAGGGC
65 AAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGGA-AAAAAATACGAAAAAAGGGC
*
47724909 C-AAAGTAAGAGTCTTTTACTAAAT
129 CGAAA-TAAGAGTGTTTTACTAAAT
*
47724933 TTTTTAAAAA
1 TATTTAAAAA
47724943 TTCAGGAAAA
Statistics
Matches: 264, Mismatches: 40, Indels: 47
0.75 0.11 0.13
Matches are distributed among these distances:
152 8 0.03
153 18 0.07
154 10 0.04
155 5 0.02
156 12 0.05
157 34 0.13
158 44 0.17
159 12 0.05
160 63 0.24
161 23 0.09
162 8 0.03
164 18 0.07
165 9 0.03
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (152 bp):
TATTTAAAAAACACACTAAATTAATAAAATTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGGAAAAAAATACGAAAAAAGGGCCG
AAATAAGAGTGTTTTACTAAAT
Found at i:47724943 original size:61 final size:61
Alignment explanation
Indices: 47724878--47724998 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
47724868 TTAAAGTAAT
47724878 AAAATGC-GGATAAAAAATACGAAAAAAGGGCC-AAAGTAAGAGTCTTTTACTAAATTTTTTA
1 AAAATGCAGGA-AAAAAATACGAAAAAAGGGCCGAAA-TAAGAGTCTTTTACTAAATTTTTTA
* * * * * * * *
47724939 AAAATTCAGGAAAATAGTACGAATAAATGGCCGAAATGAGAGTTTTTTACTAACTTTTTT
1 AAAATGCAGGAAAAAAATACGAAAAAAGGGCCGAAATAAGAGTCTTTTACTAAATTTTTT
47724999 TTGAATTTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 44 0.88
62 6 0.12
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (61 bp):
AAAATGCAGGAAAAAAATACGAAAAAAGGGCCGAAATAAGAGTCTTTTACTAAATTTTTTA
Found at i:47730249 original size:16 final size:16
Alignment explanation
Indices: 47730228--47730260 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47730218 TTATACTGAA
47730228 AATAATACTAACTAAC
1 AATAATACTAACTAAC
*
47730244 AATAATACTAAGTAAC
1 AATAATACTAACTAAC
47730260 A
1 A
47730261 TCTAAACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (16 bp):
AATAATACTAACTAAC
Found at i:47730446 original size:10 final size:10
Alignment explanation
Indices: 47730418--47730454 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
47730408 AAAATACCTT
47730418 TTTTTCTCTTC
1 TTTTTCTC-TC
*
47730429 TCTTTCTCTC
1 TTTTTCTCTC
47730439 TTTTTCTCTC
1 TTTTTCTCTC
47730449 TTTTTC
1 TTTTTC
47730455 AGGCAACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:47737208 original size:24 final size:25
Alignment explanation
Indices: 47737181--47737238 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
47737171 AAAATTTTAG
* * *
47737181 TAAATATTAGGTA-AAAATTTAAAA
1 TAAATAATAGATATAAAACTTAAAA
*
47737205 TAAATAATATATATAAAACTTAAAA
1 TAAATAATAGATATAAAACTTAAAA
*
47737230 TAAACAATA
1 TAAATAATA
47737239 ATAATAGAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (25 bp):
TAAATAATAGATATAAAACTTAAAA
Found at i:47739339 original size:111 final size:115
Alignment explanation
Indices: 47739134--47739351 Score: 354
Period size: 111 Copynumber: 1.9 Consensus size: 115
47739124 TCATTCATCC
*
47739134 CTACACACCATGTTGTGGATGAACCATTAGTAATTACAGATGAACTGAACTACCAGTAATAAAAG
1 CTACACACCATGTTGTGGATGAACCATTAGTAATTACA-ATGAACTGAACTACCAGTAATAAAAA
* *
47739199 TTGTGGATGAACAATAAAAATTTTTAGATAAAAAGTTTGCAGTTTAATAAT
65 TTGTGGATGAACAACAAAAATTTTCAGATAAAAAGTTTGCAGTTTAATAAT
*
47739250 CTACACACCATGTTGTGGATGAATCATTAGTAATTAC-A-G-A-TGAACTACCAGTAATAAAAAT
1 CTACACACCATGTTGTGGATGAACCATTAGTAATTACAATGAACTGAACTACCAGTAATAAAAAT
*
47739311 TGTGGATGAACCACAAAAATTTTCAGATAAAAAGTTTGCAG
66 TGTGGATGAACAACAAAAATTTTCAGATAAAAAGTTTGCAG
47739352 ACAAGCTGCC
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
111 58 0.60
112 1 0.01
113 1 0.01
114 1 0.01
116 36 0.37
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (115 bp):
CTACACACCATGTTGTGGATGAACCATTAGTAATTACAATGAACTGAACTACCAGTAATAAAAAT
TGTGGATGAACAACAAAAATTTTCAGATAAAAAGTTTGCAGTTTAATAAT
Found at i:47742764 original size:20 final size:19
Alignment explanation
Indices: 47742713--47742765 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
47742703 GACACCAAAA
*
47742713 AAATCTTTTTCATAATTTTTG
1 AAAT-TTTTT-ATAATGTTTG
47742734 AAACTTTTTTATAATGTTTG
1 AAA-TTTTTTATAATGTTTG
47742754 TAAATTTTTTAT
1 -AAATTTTTTAT
47742766 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.59
21 11 0.38
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
AAATTTTTTATAATGTTTG
Found at i:47745165 original size:18 final size:18
Alignment explanation
Indices: 47745121--47745168 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
47745111 ATTTTTTTCC
* *
47745121 AAATTTTATAATTTTTTA
1 AAATTTTATAAATTTTGA
**
47745139 AAA-AATATAAATTTTGA
1 AAATTTTATAAATTTTGA
47745156 AAATTTTATAAAT
1 AAATTTTATAAAT
47745169 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTTTATAAATTTTGA
Found at i:47745477 original size:16 final size:17
Alignment explanation
Indices: 47745458--47745493 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
47745448 TTAAATTTTA
47745458 AAAATA-AAAAATACAT
1 AAAATATAAAAATACAT
47745474 AAAATATAAAAATACAT
1 AAAATATAAAAATACAT
47745491 AAA
1 AAA
47745494 GATTACAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATATAAAAATACAT
Found at i:47746445 original size:91 final size:91
Alignment explanation
Indices: 47746287--47746455 Score: 203
Period size: 91 Copynumber: 1.9 Consensus size: 91
47746277 AAAAACGCCG
* * * * * *
47746287 AAAAATTTTAACCGAAACGCAGCGTTTCGTCTTGAGCTATAGCGCCGTCAGCGGCGCTTACCCGA
1 AAAAATTTTAACCAAAACGCAGCGTTCCGGCTTGACCTATAGAGCCGTCAGCGACGCTTACCCGA
* *
47746352 AAACGCTGCTATAAATCAAGCGCTGC
66 AAACACCGCTATAAATCAAGCGCTGC
** * * * **
47746378 AAAAATTTTGGCCAAAACGCATCGTTCCGGCTTGACCTATAGAGGCGTTAGCGACGCTTACTTGA
1 AAAAATTTTAACCAAAACGCAGCGTTCCGGCTTGACCTATAGAGCCGTCAGCGACGCTTACCCGA
47746443 AAACACCGCTATA
66 AAACACCGCTATA
47746456 CCTCAATTAG
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
91 63 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (91 bp):
AAAAATTTTAACCAAAACGCAGCGTTCCGGCTTGACCTATAGAGCCGTCAGCGACGCTTACCCGA
AAACACCGCTATAAATCAAGCGCTGC
Found at i:47746553 original size:204 final size:203
Alignment explanation
Indices: 47746258--47746662 Score: 578
Period size: 207 Copynumber: 2.0 Consensus size: 203
47746248 TATATCCCGT
* *
47746258 AATTAGCGGCACTTAACTAAAAAACGCCGAAAAATTTTAACCGAAACGCAGCGTTTCGTCTTGAG
1 AATTAGCGGCACTTAACTAAAAAACGCCAAAAAATTTTAACCGAAACGCAACGTTTCGTCTTGAG
* * *
47746323 CTATAGCGCCGTCAGCGGCGCTTACCCGAAAACGCTGCTATAAATCA-AGCGCTGCAAAAATTTT
66 CTATAGCGCCGTCAGCAGCACTTACCCGAAAACGCTGCTATAAATCACAGCGCCGCAAAAATTTT
* * *
47746387 GGCCAAAACGCATCGTTCCGGCTTGACCTATAGAGGCGTTAGCGACGCTTACTTGAAAACACCGC
131 GACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCATTAGCGACGCTTACTTGAAAACACCGC
47746452 TATACCTC
196 TATACCTC
**
47746460 AATTAGCGGTGCTTAACTAAAAAACCGCCAAAAAATTTTAAACCGAAACGCAACGTTTCGTCTTG
1 AATTAGCGGCACTTAACTAAAAAA-CGCCAAAAAATTTT-AACCGAAACGCAACGTTTCGTCTTG
* * * * *
47746525 AGCTATAGTGCCGTTAGCAGCACTTACCCGAAAAGGCTGCTATATATCAGCTTGCGCCGCAAAAA
64 AGCTATAGCGCCGTCAGCAGCACTTACCCGAAAACGCTGCTATAAATCA-C-AGCGCCGCAAAAA
* * ** * *
47746590 TTTTGACTAAAACGCATCGTTCCAGCTTGACCTATAGAGGCATTAGTGGTGCTTATTTGAAAACG
127 TTTTGACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCATTAGCGACGCTTACTTGAAAACA
47746655 CCGCTATA
192 CCGCTATA
47746663 GAGCAACTTT
Statistics
Matches: 177, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
202 22 0.12
203 13 0.07
204 67 0.38
207 75 0.42
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (203 bp):
AATTAGCGGCACTTAACTAAAAAACGCCAAAAAATTTTAACCGAAACGCAACGTTTCGTCTTGAG
CTATAGCGCCGTCAGCAGCACTTACCCGAAAACGCTGCTATAAATCACAGCGCCGCAAAAATTTT
GACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCATTAGCGACGCTTACTTGAAAACACCGC
TATACCTC
Found at i:47747251 original size:46 final size:46
Alignment explanation
Indices: 47747199--47747293 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
47747189 ACAAAGATAG
* *
47747199 AAACCAAAATATTATCTCCCAAACTTTAGCATTTAATTTCCTAATT
1 AAACCAAAATATTATCTCCCAAACTTTAGCATCTAATCTCCTAATT
* *
47747245 AAACCAAAATATTTTCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCCAAACTTTAGCATCTAATCTCCTAATT
47747291 AAA
1 AAA
47747294 AGAAAATAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCCAAACTTTAGCATCTAATCTCCTAATT
Found at i:47751807 original size:22 final size:22
Alignment explanation
Indices: 47751782--47751858 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
47751772 CCAAAATATT
47751782 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
47751804 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
47751828 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
47751850 ATCTCCTAA
1 ATCTCCTAA
47751859 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:47751821 original size:46 final size:46
Alignment explanation
Indices: 47751769--47751863 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
47751759 ACAAAGATAG
47751769 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
47751815 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
47751861 AAA
1 AAA
47751864 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:47751976 original size:22 final size:21
Alignment explanation
Indices: 47751951--47751993 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
47751941 TGGTGGTTAT
*
47751951 TGTTTGTGGTTTACGGGTTTAA
1 TGTTTATGGTTTA-GGGTTTAA
47751973 TGTTTATGGTTTAGGGTTTAA
1 TGTTTATGGTTTAGGGTTTAA
47751994 GATTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.51
Consensus pattern (21 bp):
TGTTTATGGTTTAGGGTTTAA
Found at i:47752089 original size:21 final size:21
Alignment explanation
Indices: 47752065--47752110 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
47752055 CTAATTGATG
* *
47752065 GGTTTAGGGTTTAAGGTTTAT
1 GGTTTAGGGTTTAAGATTTAC
*
47752086 GGTTTGGGGTTTAAGATTTAC
1 GGTTTAGGGTTTAAGATTTAC
47752107 GGTT
1 GGTT
47752111 AAGGCTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATTTAC
Found at i:47752143 original size:106 final size:107
Alignment explanation
Indices: 47751958--47752149 Score: 262
Period size: 106 Copynumber: 1.8 Consensus size: 107
47751948 TATTGTTTGT
* * * * *
47751958 GGTTTACGGGTTTAATGTTTATGGTTTAGGGTTTAAGATTTTCAATTAATGTTTATGATATAGTG
1 GGTTTACGGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTACAATTAAGGCTTAAGATATAGTG
* *
47752023 TGGATTGGATTTTGGGGTTTGGAGTTTTATGGCTAATTGATG
66 GGGATTGAATTTTGGGGTTTGGAGTTTTATGGCTAATTGATG
* **
47752065 GGTTTA-GGGTTTAAGGTTTATGGTTTGGGGTTTAAGATTTACGGTTAAGGCTTACAG-TATAGT
1 GGTTTACGGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTACAATTAAGGCTTA-AGATATAGT
*
47752128 GGGGATTTAATTTTGGGGTTTG
65 GGGGATTGAATTTTGGGGTTTG
47752150 ATGGTTTGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
106 66 0.90
107 7 0.10
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (107 bp):
GGTTTACGGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTACAATTAAGGCTTAAGATATAGTG
GGGATTGAATTTTGGGGTTTGGAGTTTTATGGCTAATTGATG
Found at i:47752254 original size:15 final size:15
Alignment explanation
Indices: 47752234--47752263 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47752224 GATATTTTAG
*
47752234 AATATAAATGTAAAT
1 AATATAAATATAAAT
47752249 AATATAAATATAAAT
1 AATATAAATATAAAT
47752264 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:47752510 original size:21 final size:20
Alignment explanation
Indices: 47752470--47752507 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
47752460 AATATATTGA
*
47752470 TGTATTTATTTTTTAAAATG
1 TGTAATTATTTTTTAAAATG
47752490 TGTAATTATTTTTTAAAA
1 TGTAATTATTTTTTAAAA
47752508 ATGCATTACT
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:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TGTAATTATTTTTTAAAATG
Found at i:47753049 original size:19 final size:19
Alignment explanation
Indices: 47753027--47753071 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
47753017 CTGTCATCTA
*
47753027 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
47753046 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
47753065 CCCCAAA
1 CCCCAAA
47753072 CCCGACGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.22
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:47753436 original size:14 final size:14
Alignment explanation
Indices: 47753417--47753443 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47753407 CGTTGAAATT
47753417 TATATATATGTATA
1 TATATATATGTATA
47753431 TATATATATGTAT
1 TATATATATGTAT
47753444 TAAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:47754631 original size:21 final size:21
Alignment explanation
Indices: 47754602--47754647 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
47754592 CAGCAACTTA
*
47754602 AAGCTGAGGCGGAAGCGAGGG
1 AAGCGGAGGCGGAAGCGAGGG
* *
47754623 AAGCGGAGGCTGCAGCGAGGG
1 AAGCGGAGGCGGAAGCGAGGG
47754644 AAGC
1 AAGC
47754648 AGAGCAGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.50, T:0.04
Consensus pattern (21 bp):
AAGCGGAGGCGGAAGCGAGGG
Found at i:47755138 original size:43 final size:43
Alignment explanation
Indices: 47755091--47755369 Score: 396
Period size: 43 Copynumber: 6.5 Consensus size: 43
47755081 TTAGGATCTA
** *
47755091 TAGCGGCAATTGTGGGATAAGCACCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * * *
47755134 TAGCGGCGTTTTTGAGATAAGCGCCGCTAAAAAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
47755177 TAGCGGTGTTTGTGGGATAAGCGCCGCTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * * * *
47755220 TAACGGCGTTTGTGGAATAAACGCCACTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
47755263 TAGCGGCGTTTGTGGGATAAGCGCTGCTAAAGAGCATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
47755306 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
47755349 TAGCAGCGTTTGTGGAATAAG
1 TAGCGGCGTTTGTGGGATAAG
47755370 TGCCTCAAAA
Statistics
Matches: 209, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 209 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
Found at i:47757294 original size:50 final size:50
Alignment explanation
Indices: 47757235--47757420 Score: 210
Period size: 51 Copynumber: 3.7 Consensus size: 50
47757225 TCATGCAATA
* *
47757235 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGATTTTCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGATTTTCGGTT
* ** *
47757285 CACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGGCCTTCCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAA-GATTTTCGGTT
* * * *** ** *
47757336 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCGTTATTTATCTATA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGATTT-TCGGTT
*
47757387 CACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 CACGTAGTAGCCTGCACATAGTACTACACACGTG
47757421 TTCGCAGACA
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 39 0.34
51 75 0.66
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (50 bp):
CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGATTTTCGGTT
Found at i:47764994 original size:50 final size:49
Alignment explanation
Indices: 47764935--47765120 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 49
47764925 TCATGCAATA
*
47764935 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGCTTTTCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGA-CAAGCTTTTCGGTT
* * *
47764985 CACGTAGTAGCCTACACATAGTACTACACACGTGACAAAGGCCTTCCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGAC-AA-GCTTTTCGGTT
* * * * * * * *
47765036 CACATAGTAGCCTGCACTTAGTACAACACATGTGAC-CGTTATTTATCGATA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACAAG--CTTT-TCGGTT
* *
47765087 CACGTAATAGCCTGCACTTAGTACTACACACGTG
1 CACGTAGTAGCCTGCACATAGTACTACACACGTG
47765121 TTCGCAGACA
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 38 0.34
51 73 0.65
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
CACGTAGTAGCCTGCACATAGTACTACACACGTGACAAGCTTTTCGGTT
Found at i:47766537 original size:21 final size:21
Alignment explanation
Indices: 47766513--47766576 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
47766503 AAGGAGATTG
47766513 GATCTTGCTACATTGAAGGGT
1 GATCTTGCTACATTGAAGGGT
* ***
47766534 GATC-TG---CATTTATTTG-
1 GATCTTGCTACATTGAAGGGT
47766550 GATCTTGCTACATTGAAGGGT
1 GATCTTGCTACATTGAAGGGT
47766571 GATCTT
1 GATCTT
47766577 TGACATTATT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
20 8 0.27
21 10 0.33
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (21 bp):
GATCTTGCTACATTGAAGGGT
Found at i:47770025 original size:43 final size:43
Alignment explanation
Indices: 47769978--47770061 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
47769968 TATCAGCATG
*** *
47769978 ATCTTGCTCAAAGTGATAGTTCCTTTTATTGACTATCAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATTGACGATCAAATTT
*
47770021 ATCTTGCTCAAAGTGATAAAACTTTTTATTGACGATCAAAT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATTGACGATCAAAT
47770062 AAATTCTCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (43 bp):
ATCTTGCTCAAAGTGATAAAACCTTTTATTGACGATCAAATTT
Found at i:47775584 original size:34 final size:34
Alignment explanation
Indices: 47775482--47775595 Score: 88
Period size: 36 Copynumber: 3.2 Consensus size: 34
47775472 ATGCATTTAT
* * *
47775482 ATATATAATTATTCAAAT-ACATATGCCAAAAGCAT
1 ATATATACTTA-TC-AATCACATATGCCAAATGCAC
* * * *
47775517 ATATTTATACTTATCAATTACATGTGTCGAATGCAC
1 ATA--TATACTTATCAATCACATATGCCAAATGCAC
47775553 ATATATACTTAT-AATCCACATATGCCAAATGCATAC
1 ATATATACTTATCAAT-CACATATGCCAAATGC--AC
47775589 ATATATA
1 ATATATA
47775596 TCCAACAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
33 3 0.05
34 21 0.33
35 6 0.10
36 26 0.41
37 7 0.11
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (34 bp):
ATATATACTTATCAATCACATATGCCAAATGCAC
Found at i:47776354 original size:78 final size:77
Alignment explanation
Indices: 47776201--47776356 Score: 172
Period size: 76 Copynumber: 2.0 Consensus size: 77
47776191 ATGTACATAT
** * * *
47776201 ATACATATTCGAATCTAACATATATACATATATAATTTTGTACTTAGATTCGAAACAAGTACTTA
1 ATACATATTCGAATCTAACA-ATATACATATATAATTTCATACTTAGACTCGAAACAAGCAATTA
*
47776266 TACTTGTATACAC
65 TACTTATATACAC
* * * *
47776279 ATACATTTTCGAATTTAAC-ATATACATATATAATTTCATACTTATACTC-AATATAAGCAATTA
1 ATACATATTCGAATCTAACAATATACATATATAATTTCATACTTAGACTCGAA-ACAAGCAATTA
* *
47776342 TACATATATATAC
65 TACTTATATACAC
47776355 AT
1 AT
47776357 GCTTATTGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
75 2 0.03
76 46 0.71
78 17 0.26
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (77 bp):
ATACATATTCGAATCTAACAATATACATATATAATTTCATACTTAGACTCGAAACAAGCAATTAT
ACTTATATACAC
Found at i:47776568 original size:78 final size:78
Alignment explanation
Indices: 47776466--47776899 Score: 771
Period size: 78 Copynumber: 5.6 Consensus size: 78
47776456 CTATTCAACA
* *
47776466 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
47776530 AACATACATACTT
66 AACATACATACTT
47776543 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
47776608 AACATACATACTT
66 AACATACATACTT
* * *
47776621 TTAGCTAAATTCAAGAATTTGTTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
47776686 AACATACATACTT
66 AACATACATACTT
* *
47776699 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAATTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
47776764 AACATACATACTT
66 AACATACATACTT
47776777 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
47776842 AACATACATACTT
66 AACATACATACTT
* *
47776855 TTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATA-TATCC
47776900 ACTATTAGTT
Statistics
Matches: 343, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
77 14 0.04
78 324 0.94
79 5 0.01
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (78 bp):
TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:47776971 original size:156 final size:154
Alignment explanation
Indices: 47776470--47776961 Score: 588
Period size: 156 Copynumber: 3.1 Consensus size: 154
47776460 TCAACATTAA
* *
47776470 CTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATATAACA
1 CTAAATTCAAGAA-TT-TGCATGTATATACATATATATCCGAACTTTATATATATAAATATAACA
47776534 TACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACT-TTA-TA
64 TACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCC--ACTATTATTA
* *
47776597 TATATAAATATAAC--ATACATACTTTTAG
127 TATAT-TAT-TAACTTAAACATACTTTTAG
*
47776625 CTAAATTCAAGAATTTGTTCATGTATATACATATATATTCGAACTTTATATATATAAATATAACA
1 CTAAATTCAAGAATTTG--CATGTATATACATATATATCCGAACTTTATATATATAAATATAACA
* * *
47776690 TACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAATTTTA-TAT
64 TACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATA-TCCACTATTATTAT
* * *
47776754 ATATAAATATAAC--ATACATACTTTTAA
128 ATAT-TAT-TAACTTAAACATACTTTTAG
*
47776781 CTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATATAACA
1 CTAAATTCAAGAA-TT-TGCATGTATATACATATATATCCGAACTTTATATATATAAATATAACA
* * *
47776846 TACATACTTTTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCCACTATTAGTTC
64 TACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATA-TATCCACTATTA-TTA
*
47776911 TATATTATTGAACTTTAAACAAAC-TTTAG
127 TATATTATT-AAC-TTAAACATACTTTTAG
* *
47776940 CTAACATACATGTAATTTGCAT
1 CTAA-ATTCAAG-AATTTGCAT
47776962 CATTAATATA
Statistics
Matches: 300, Mismatches: 21, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
154 1 0.00
155 14 0.05
156 240 0.80
157 11 0.04
158 7 0.02
159 12 0.04
160 13 0.04
161 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (154 bp):
CTAAATTCAAGAATTTGCATGTATATACATATATATCCGAACTTTATATATATAAATATAACATA
CATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCACTATTATTATATA
TTATTAACTTAAACATACTTTTAG
Found at i:47779386 original size:26 final size:24
Alignment explanation
Indices: 47779356--47779404 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
47779346 ATACTAAATA
*
47779356 ATTTAAGAATAAAATAATAAAATATC
1 ATTTAAAAATAAAAT--TAAAATATC
*
47779382 ATTTAAAAATCAAATTAAAATAT
1 ATTTAAAAATAAAATTAAAATAT
47779405 TAATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTAAAAATAAAATTAAAATATC
Found at i:47784129 original size:19 final size:19
Alignment explanation
Indices: 47784105--47784141 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
47784095 TCTAAAACCA
47784105 AAAAAATTGTTGAAGAAGG
1 AAAAAATTGTTGAAGAAGG
47784124 AAAAAATTGTTGAAGAAG
1 AAAAAATTGTTGAAGAAG
47784142 ACTTTAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
AAAAAATTGTTGAAGAAGG
Found at i:47786078 original size:40 final size:39
Alignment explanation
Indices: 47786019--47786097 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
47786009 GTAGTTAAAT
**
47786019 TTCTTTTTGGATGTGCAATTTAAGCTTGTACTTAAGAGC
1 TTCTTTTTGGATGAACAATTTAAGCTTGTACTTAAGAGC
* *
47786058 TTCTATTTTGGATGAACAATTTAAGCTTGTGCTTAGGAGC
1 TTCT-TTTTGGATGAACAATTTAAGCTTGTACTTAAGAGC
47786098 AATGTGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.42
Consensus pattern (39 bp):
TTCTTTTTGGATGAACAATTTAAGCTTGTACTTAAGAGC
Found at i:47788620 original size:27 final size:27
Alignment explanation
Indices: 47788567--47788622 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
47788557 ACTATTGCTT
* *
47788567 TTGTGATTTAATTACTTTTGTGTATAA
1 TTGTGATTAAATTACTTTTGTGAATAA
*
47788594 TTGTGATTAAATTTCTTTT-TGCAATAA
1 TTGTGATTAAATTACTTTTGTG-AATAA
47788621 TT
1 TT
47788623 TTGACTATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.55
Consensus pattern (27 bp):
TTGTGATTAAATTACTTTTGTGAATAA
Found at i:47788733 original size:20 final size:20
Alignment explanation
Indices: 47788685--47788733 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
47788675 TTGAAAACGG
47788685 AAATGAATATAGTTGAGTTC
1 AAATGAATATAGTTGAGTTC
*
47788705 AAGCT-AATAT-GTTGATGTTC
1 AA-ATGAATATAGTTGA-GTTC
47788725 AAATGAATA
1 AAATGAATA
47788734 GAAGTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 6 0.25
20 17 0.71
21 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (20 bp):
AAATGAATATAGTTGAGTTC
Found at i:47792021 original size:43 final size:43
Alignment explanation
Indices: 47791969--47792251 Score: 263
Period size: 43 Copynumber: 6.6 Consensus size: 43
47791959 TTATGTGAAA
47791969 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
* * *
47792012 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
* * ** *
47792055 AAACGCAGCTAAAGATCTTGACCTTTAGCGGCATTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
* * *
47792098 AAACGCCGCTAAAGATCGTGATCTTTAGCGGCGC-TTTAGATAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATA-AC
* * * * * * **
47792141 AAATGTCGCTAAAGATCGTGAGCTTTAGCGACGC-TCTAGCCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTA-TAAC
* * * *
47792184 AAACGCCGCTAAAGA--ATAAACCTTTAGCGACGCTTCTAGCAA-
1 AAACGCCGCTAAAGATCAT-GACCTTTAGCGGCGCTTTTA-TAAC
* *
47792226 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGATCATGACCTTTA
47792252 AAAAAATATA
Statistics
Matches: 205, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.01
42 38 0.19
43 165 0.80
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
Found at i:47792230 original size:42 final size:42
Alignment explanation
Indices: 47792163--47792251 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
47792153 AGATCGTGAG
* *
47792163 CTTTAGCGACGCTCTAGCCACAAACGCCGCTAAAGA-ATAAAC
1 CTTTAGCGACGCTCTAGCCAAAAACGCCGCTAAAAACAT-AAC
47792205 CTTTAGCGACGCTTCTAG-CAAAAACGCCGCTAAAAACATAAC
1 CTTTAGCGACGC-TCTAGCCAAAAACGCCGCTAAAAACATAAC
47792247 CTTTA
1 CTTTA
47792252 AAAAAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 36 0.84
43 7 0.16
ACGTcount: A:0.36, C:0.29, G:0.15, T:0.20
Consensus pattern (42 bp):
CTTTAGCGACGCTCTAGCCAAAAACGCCGCTAAAAACATAAC
Found at i:47794073 original size:18 final size:18
Alignment explanation
Indices: 47794052--47794091 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47794042 AAAATAAAAT
47794052 AAAAGAATAAAAGCAATA
1 AAAAGAATAAAAGCAATA
** *
47794070 AAAAGCGTGAAAGCAATA
1 AAAAGAATAAAAGCAATA
47794088 AAAA
1 AAAA
47794092 AGACAGACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAATAAAAGCAATA
Found at i:47798016 original size:34 final size:34
Alignment explanation
Indices: 47797969--47798036 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
47797959 ATTTCTAAAC
* * * **
47797969 CCTAAATCACTAACTCTTAACTTTTAACCCCTAA
1 CCTAAACCACTAACCCCTAACTACTAACCCCTAA
*
47798003 CCTAAACCCCTAACCCCTAACTACTAACCCCTAA
1 CCTAAACCACTAACCCCTAACTACTAACCCCTAA
47798037 ACCTTATCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (34 bp):
CCTAAACCACTAACCCCTAACTACTAACCCCTAA
Found at i:47798018 original size:20 final size:20
Alignment explanation
Indices: 47797993--47798036 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
47797983 TCTTAACTTT
47797993 TAACCCCTAACCTA-AACCCC
1 TAACCCCTAA-CTACAACCCC
47798013 TAACCCCTAACTACTAACCCC
1 TAACCCCTAACTAC-AACCCC
47798034 TAA
1 TAA
47798037 ACCTTATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 10 0.45
21 9 0.41
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (20 bp):
TAACCCCTAACTACAACCCC
Found at i:47798100 original size:70 final size:69
Alignment explanation
Indices: 47798017--47798149 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 69
47798007 AACCCCTAAC
* * *
47798017 CCCTAACTACTAACCCCTAAACCTTATCTAATATATAAATTCAAAA-ACATTAATTAATCTAAAC
1 CCCTAACCACTAACCCCTAAACCTTATCTAATA-AAAAATT-AAAACACACTAATTAATCTAAAC
47798081 TCGAAT
64 TCGAAT
* * *
47798087 CCCTAACCCCTAACCCCTAAACCTTATTTCATAAAAAATTAAAACACACTAATTAATCTAAAC
1 CCCTAACCACTAACCCCTAAACCTTATCTAATAAAAAATTAAAACACACTAATTAATCTAAAC
47798150 CCTAAAGCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
68 4 0.07
69 23 0.41
70 29 0.52
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (69 bp):
CCCTAACCACTAACCCCTAAACCTTATCTAATAAAAAATTAAAACACACTAATTAATCTAAACTC
GAAT
Found at i:47798162 original size:69 final size:70
Alignment explanation
Indices: 47798017--47798163 Score: 181
Period size: 69 Copynumber: 2.1 Consensus size: 70
47798007 AACCCCTAAC
** * * *
47798017 CCCTAACTACTAACCCCTAAACCTTATCTAATATATAAATTCAAAAACATTAATTAATCTAAACT
1 CCCTAACCCCTAACCCCTAAACCTTATCTAATATAAAAATTCAAAAACACTAATTAATCTAAACC
*
47798082 CGAAT
66 CGAAA
* *
47798087 CCCTAACCCCTAACCCCTAAACCTTATTTCATA-AAAAATT-AAAACACACTAATTAATCTAAAC
1 CCCTAACCCCTAACCCCTAAACCTTATCTAATATAAAAATTCAAAA-ACACTAATTAATCTAAAC
*
47798150 CCTAAA
65 CCGAAA
*
47798156 GCCTAACC
1 CCCTAACC
47798164 TGACATCGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
68 4 0.06
69 33 0.50
70 29 0.44
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.27
Consensus pattern (70 bp):
CCCTAACCCCTAACCCCTAAACCTTATCTAATATAAAAATTCAAAAACACTAATTAATCTAAACC
CGAAA
Found at i:47798647 original size:19 final size:19
Alignment explanation
Indices: 47798607--47798649 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47798597 AATTTTAATT
*
47798607 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
47798626 AATAGTAAAT-AACAGATAA
1 AATA-TAAATAAACAAATAA
47798645 AATAT
1 AATAT
47798650 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:47798711 original size:41 final size:41
Alignment explanation
Indices: 47798654--47798811 Score: 280
Period size: 41 Copynumber: 3.9 Consensus size: 41
47798644 AAATATTTTT
*
47798654 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
47798695 GCGGCGCTTTTTCAAAAACACTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
47798736 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
47798777 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGA
47798812 TAGGTCATAA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:47798896 original size:41 final size:39
Alignment explanation
Indices: 47798850--47798941 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
47798840 AGGTTTTTTT
*
47798850 GCGGCGTTTTTCCAAAAAACGCCGTTAATGCTTGATCTTTA
1 GCGGCGTTTTT--AAAAAACGCCGCTAATGCTTGATCTTTA
** * *
47798891 GCGGCGTTTTGTGTAAAGCGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTT-TAAAAAACGCCGCTAATGCTTGATCTTTA
*
47798931 GCGGCATTTTT
1 GCGGCGTTTTT
47798942 TGTCCAAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 32 0.73
41 10 0.23
42 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAACGCCGCTAATGCTTGATCTTTA
Done.