Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 144 of 279
Found at i:46742420 original size:16 final size:17
Alignment explanation
Indices: 46742401--46742433 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46742391 AATTTTATAG
46742401 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
46742417 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
46742434 TACGTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:46749240 original size:18 final size:18
Alignment explanation
Indices: 46749219--46749267 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
46749209 TCTGCTTTTG
46749219 CTTTTAAATTT-AAAAGTA
1 CTTTT-AATTTCAAAAGTA
46749237 CTTTTAATTTCAAAAGTTA
1 CTTTTAATTTCAAAAG-TA
46749256 TCTGTTTAATTT
1 -CT-TTTAATTT
46749268 TACTTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 2 0.07
20 2 0.07
21 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (18 bp):
CTTTTAATTTCAAAAGTA
Found at i:46754529 original size:197 final size:197
Alignment explanation
Indices: 46754194--46754582 Score: 778
Period size: 197 Copynumber: 2.0 Consensus size: 197
46754184 GGGATAATAC
46754194 CAAGCAACAAAATCCACGCTACTTTTCATTAATCAAAGTTGCGGCTCACACCAGGTATTGGTAAT
1 CAAGCAACAAAATCCACGCTACTTTTCATTAATCAAAGTTGCGGCTCACACCAGGTATTGGTAAT
46754259 TGCAACCTAAGATTTACCTAGGAATTATGAACATCAGTGTCTTATATAATCTTATATATATAGTG
66 TGCAACCTAAGATTTACCTAGGAATTATGAACATCAGTGTCTTATATAATCTTATATATATAGTG
46754324 TATATATATCATGATTCACGTGAATCCAAACTTTTCAAAAAAAGATAAAGAGTACTCAATTATAT
131 TATATATATCATGATTCACGTGAATCCAAACTTTTCAAAAAAAGATAAAGAGTACTCAATTATAT
46754389 AT
196 AT
46754391 CAAGCAACAAAATCCACGCTACTTTTCATTAATCAAAGTTGCGGCTCACACCAGGTATTGGTAAT
1 CAAGCAACAAAATCCACGCTACTTTTCATTAATCAAAGTTGCGGCTCACACCAGGTATTGGTAAT
46754456 TGCAACCTAAGATTTACCTAGGAATTATGAACATCAGTGTCTTATATAATCTTATATATATAGTG
66 TGCAACCTAAGATTTACCTAGGAATTATGAACATCAGTGTCTTATATAATCTTATATATATAGTG
46754521 TATATATATCATGATTCACGTGAATCCAAACTTTTCAAAAAAAGATAAAGAGTACTCAATTA
131 TATATATATCATGATTCACGTGAATCCAAACTTTTCAAAAAAAGATAAAGAGTACTCAATTA
46754583 ATTCCAACTT
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 192 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (197 bp):
CAAGCAACAAAATCCACGCTACTTTTCATTAATCAAAGTTGCGGCTCACACCAGGTATTGGTAAT
TGCAACCTAAGATTTACCTAGGAATTATGAACATCAGTGTCTTATATAATCTTATATATATAGTG
TATATATATCATGATTCACGTGAATCCAAACTTTTCAAAAAAAGATAAAGAGTACTCAATTATAT
AT
Found at i:46755762 original size:33 final size:33
Alignment explanation
Indices: 46755725--46755797 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
46755715 TATTAAGTGC
*
46755725 AGTGACAAAAACATATTATATTTTTAAGAAAAT
1 AGTGACAAAAACATATTATATTTTTAAAAAAAT
*
46755758 AGTGACAAAAATATATTATATTTTTAAAAAAAT
1 AGTGACAAAAACATATTATATTTTTAAAAAAAT
*
46755791 AATGACA
1 AGTGACA
46755798 TTTGAACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.33
Consensus pattern (33 bp):
AGTGACAAAAACATATTATATTTTTAAAAAAAT
Found at i:46756984 original size:16 final size:16
Alignment explanation
Indices: 46756959--46756991 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46756949 TTATTTATAT
*
46756959 TTATTCATATAATAAA
1 TTATTAATATAATAAA
46756975 TTATTAATATAATAAA
1 TTATTAATATAATAAA
46756991 T
1 T
46756992 ATAATTTATT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAATATAATAAA
Found at i:46757641 original size:287 final size:287
Alignment explanation
Indices: 46757125--46757698 Score: 1148
Period size: 287 Copynumber: 2.0 Consensus size: 287
46757115 CACTTCACAG
46757125 GTTTATAATTTAGTCTTTGTAATTTTATTTTCAAGAATTTAGTCCCTTTACTTTTCAAATTTGAA
1 GTTTATAATTTAGTCTTTGTAATTTTATTTTCAAGAATTTAGTCCCTTTACTTTTCAAATTTGAA
46757190 AATCAAGTCCAATTGTTGACATCATTAATTTTTTTTGTCAATTTTGTTGATGTCATATTTTTAAA
66 AATCAAGTCCAATTGTTGACATCATTAATTTTTTTTGTCAATTTTGTTGATGTCATATTTTTAAA
46757255 TAAAAGATACCCACTTAGTAGTCATCTAATTAAAAAATGATGTTGTAATGAATCTGAATTTAACA
131 TAAAAGATACCCACTTAGTAGTCATCTAATTAAAAAATGATGTTGTAATGAATCTGAATTTAACA
46757320 TAATATTTTTAATATATGTAAAAAAATGTAAAATATAAAATTATAGATAAAAAATAAATTCAATT
196 TAATATTTTTAATATATGTAAAAAAATGTAAAATATAAAATTATAGATAAAAAATAAATTCAATT
46757385 AAACAATGAAAAAATAAGAAAATCTCA
261 AAACAATGAAAAAATAAGAAAATCTCA
46757412 GTTTATAATTTAGTCTTTGTAATTTTATTTTCAAGAATTTAGTCCCTTTACTTTTCAAATTTGAA
1 GTTTATAATTTAGTCTTTGTAATTTTATTTTCAAGAATTTAGTCCCTTTACTTTTCAAATTTGAA
46757477 AATCAAGTCCAATTGTTGACATCATTAATTTTTTTTGTCAATTTTGTTGATGTCATATTTTTAAA
66 AATCAAGTCCAATTGTTGACATCATTAATTTTTTTTGTCAATTTTGTTGATGTCATATTTTTAAA
46757542 TAAAAGATACCCACTTAGTAGTCATCTAATTAAAAAATGATGTTGTAATGAATCTGAATTTAACA
131 TAAAAGATACCCACTTAGTAGTCATCTAATTAAAAAATGATGTTGTAATGAATCTGAATTTAACA
46757607 TAATATTTTTAATATATGTAAAAAAATGTAAAATATAAAATTATAGATAAAAAATAAATTCAATT
196 TAATATTTTTAATATATGTAAAAAAATGTAAAATATAAAATTATAGATAAAAAATAAATTCAATT
46757672 AAACAATGAAAAAATAAGAAAATCTCA
261 AAACAATGAAAAAATAAGAAAATCTCA
46757699 AATGTATGTT
Statistics
Matches: 287, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 287 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (287 bp):
GTTTATAATTTAGTCTTTGTAATTTTATTTTCAAGAATTTAGTCCCTTTACTTTTCAAATTTGAA
AATCAAGTCCAATTGTTGACATCATTAATTTTTTTTGTCAATTTTGTTGATGTCATATTTTTAAA
TAAAAGATACCCACTTAGTAGTCATCTAATTAAAAAATGATGTTGTAATGAATCTGAATTTAACA
TAATATTTTTAATATATGTAAAAAAATGTAAAATATAAAATTATAGATAAAAAATAAATTCAATT
AAACAATGAAAAAATAAGAAAATCTCA
Found at i:46758472 original size:42 final size:42
Alignment explanation
Indices: 46758421--46758665 Score: 341
Period size: 42 Copynumber: 5.8 Consensus size: 42
46758411 GTTTACAAAC
* *
46758421 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
46758463 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
46758505 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AA
* * * * *
46758547 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTTGGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
46758589 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-ATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-A
* * *
46758631 GAAAACGCCGCTAAAGATCATGTTCTGTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
46758666 TTTTTTTTCT
Statistics
Matches: 183, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 3 0.02
42 176 0.96
43 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:46758573 original size:126 final size:126
Alignment explanation
Indices: 46758432--46758668 Score: 395
Period size: 126 Copynumber: 1.9 Consensus size: 126
46758422 AAAACGCCGT
*
46758432 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
*
46758497 GCTTAGA-AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCAC
66 GCTTA-ATAAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAATGCCAC
* *
46758558 TAAAGACCATGTTCTTTAGCGGCGCTTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
** *
46758623 GCTTAATGGAAAACGCCGCTAAAGATCATGTTCTGTAGCGGCGTTT
66 GCTTAATAAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTT
46758669 TTTTTCTAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 1 0.01
126 102 0.99
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (126 bp):
TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
GCTTAATAAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAATGCCAC
Found at i:46758721 original size:84 final size:82
Alignment explanation
Indices: 46758421--46758767 Score: 327
Period size: 84 Copynumber: 4.1 Consensus size: 82
46758411 GTTTACAAAC
* * * **
46758421 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC-ATT-TTAAAAAACGCCGCTAAAGATCATGT
*
46758486 TCTTTAGCGGCGCTTAGAA
64 TCTTTAGCGGCGCTTTGAA
* * * *
46758505 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGACCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTT-T-AAAAAACGCCGCTAAAGATCATGT
*
46758570 TCTTTAGCGGCGCTTTGGA
64 TCTTTAGCGGCGCTTTGAA
**
46758589 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC-GCTTAATGGAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTAA---AAAACGCCGCTAAAGATCATG
* * ***
46758653 TTCTGTAGCGGCGTTTTTTTT
63 TTCTTTAGCGGCG-CTTTGAA
** * * * * * * *
46758674 CTAATCGCCGCTAAAGAATATGTTCTTTAGTGGCATTTTTTACAAACGCCGCAAAAGAACATGTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCA-TTTTAAAAAACGCCGCTAAAGATCATGTT
* *
46758739 CTTTAGTGGCGCTTTTATA
65 CTTTAGCGGCGCTTTGA-A
46758758 CAAAAACGCC
1 -AAAAACGCC
46758768 ACTATTTTTG
Statistics
Matches: 214, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
81 2 0.01
82 1 0.00
83 7 0.03
84 163 0.76
85 38 0.18
87 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTAAAAAACGCCGCTAAAGATCATGTTC
TTTAGCGGCGCTTTGAA
Found at i:46758721 original size:126 final size:126
Alignment explanation
Indices: 46758432--46758752 Score: 376
Period size: 126 Copynumber: 2.5 Consensus size: 126
46758422 AAAACGCCGT
* * * * *
46758432 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
*
46758497 GCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCAC
66 GCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAATGCCAC
* *
46758558 TAAAGACCATGTTCTTTAGCGGCGCTTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
** * * ***** *
46758623 GCTTA-ATGGAAAACGCCGCTAAAGATCATGTTCTGTAGCGGCGTTTTTTTTCTAATCGCCGC
66 GCTTAGA-AAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAAT-GCCAC
* * *** * * *
46758685 TAAAGAATATGTTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAAAGAACATGTTCTTTAGTGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
46758749 GCTT
66 GCTT
46758753 TTATACAAAA
Statistics
Matches: 169, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
125 1 0.01
126 144 0.85
127 24 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (126 bp):
TAAAGAACATGTTCTTTAGCGGCGATTTGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
GCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAATGCCAC
Found at i:46758844 original size:14 final size:14
Alignment explanation
Indices: 46758821--46758854 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
46758811 GCCCTCCTGT
*
46758821 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
46758835 AGCAACATTTCAAA
1 AGCAACATTTCAAA
46758849 AGCAAC
1 AGCAAC
46758855 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:46759146 original size:21 final size:21
Alignment explanation
Indices: 46759078--46759148 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
46759068 TTTTGCTCTG
* *
46759078 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
46759099 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
46759120 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
46759141 CTCTGCTT
1 CTCTGCTT
46759149 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:46764622 original size:18 final size:18
Alignment explanation
Indices: 46764599--46764763 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
46764589 AATTGCAATG
46764599 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
46764617 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
46764635 GTAAGTTAAATGTAAG-T-T
1 GTAAGTT--ATGTAAGTTAT
*
46764653 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
46764672 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
*
46764690 GT-A-TTGTGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
46764704 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
46764722 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
*
46764738 -TATGTATTATGTAAG-T-T
1 GTAAG--TTATGTAAGTTAT
46764755 GTAAGTTAT
1 GTAAGTTAT
46764764 TATGTATTGT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 14 0.12
17 8 0.07
18 61 0.53
19 15 0.13
20 4 0.03
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:46764647 original size:11 final size:9
Alignment explanation
Indices: 46764599--46764763 Score: 69
Period size: 7 Copynumber: 19.0 Consensus size: 9
46764589 AATTGCAATG
46764599 GTAAGTTAT
1 GTAAGTTAT
46764608 GTAAGTTAT
1 GTAAGTTAT
46764617 GTAAGTTAAAT
1 GTAAGTT--AT
46764628 GT-A-TTAT
1 GTAAGTTAT
46764635 GTAAGTTAAAT
1 GTAAGTT--AT
46764646 GTAAG-T-T
1 GTAAGTTAT
46764653 GTAAGTTAT
1 GTAAGTTAT
*
46764662 -TATGTATTAT
1 GTAAG--TTAT
46764672 GTAAG-T-T
1 GTAAGTTAT
46764679 GTAAGTTAAAT
1 GTAAGTT--AT
*
46764690 GT-A-TTGT
1 GTAAGTTAT
46764697 GTAAG-T-T
1 GTAAGTTAT
46764704 GTAAGTTAAAT
1 GTAAGTT--AT
46764715 GT-A-TTAT
1 GTAAGTTAT
46764722 GTAAG-T-T
1 GTAAGTTAT
46764729 GTAAGTTAT
1 GTAAGTTAT
*
46764738 -TATGTATTAT
1 GTAAG--TTAT
46764748 GTAAG-T-T
1 GTAAGTTAT
46764755 GTAAGTTAT
1 GTAAGTTAT
46764764 TATGTATTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 60
0.65 0.03 0.32
Matches are distributed among these distances:
7 41 0.34
8 18 0.15
9 27 0.22
10 12 0.10
11 23 0.19
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:46764674 original size:19 final size:19
Alignment explanation
Indices: 46764613--46764909 Score: 78
Period size: 19 Copynumber: 15.6 Consensus size: 19
46764603 GTTATGTAAG
*
46764613 TTATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
*
46764631 TTATGTAAGTTA-AATGTAA
1 TTATGTAAGTTATTATGT-A
*
46764650 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
46764668 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
*
46764693 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
46764718 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
46764734 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
46764752 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
46764770 TTGTGTAAGTTGCAAGTTAAATGTA
1 TTATGTAAGTT---A-TT--ATGTA
* *
46764795 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
46764811 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
46764829 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* * *
46764847 TTGTGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
46764863 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
46764881 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
46764899 TTGTGTAAGTT
1 TTATGTAAGTT
46764910 GTAAGTTAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 71
0.68 0.10 0.23
Matches are distributed among these distances:
14 3 0.01
15 18 0.08
16 11 0.05
17 3 0.01
18 53 0.25
19 60 0.28
20 3 0.01
21 1 0.00
22 2 0.01
23 5 0.02
24 1 0.00
25 52 0.25
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (19 bp):
TTATGTAAGTTATTATGTA
Found at i:46764678 original size:26 final size:26
Alignment explanation
Indices: 46764644--46765025 Score: 531
Period size: 26 Copynumber: 15.2 Consensus size: 26
46764634 TGTAAGTTAA
46764644 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
46764670 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
46764695 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764720 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764746 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
46764772 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764797 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764823 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
46764849 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764875 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
46764901 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
46764926 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
46764944 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
46764969 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
46764995 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
46765022 ATGT
1 ATGT
46765026 CGACAAGATT
Statistics
Matches: 323, Mismatches: 21, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 104 0.32
26 179 0.55
27 11 0.03
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:46764949 original size:43 final size:46
Alignment explanation
Indices: 46764644--46765026 Score: 277
Period size: 51 Copynumber: 7.7 Consensus size: 46
46764634 TGTAAGTTAA
* * *
46764644 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TATATGTATT
* *
46764695 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCA--TGTAA--TA-TATGTATT
* * * * *
46764746 ATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGCAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TATATGTATT
* *
46764797 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TA-TATGTATT
* * *
46764849 GTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TA-TATGTATT
* *
46764901 GTGTAAGTTGTAAGTTAAATGTATTATGTCA-GTCA-A-ATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCATGTAATATATGTATT
*
46764944 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCA--TGTAA--TA-TATGTATT
46764995 ATGTAAGTAATGTAAGTTAAATGTATTATGTC
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTC
46765027 GACAAGATTT
Statistics
Matches: 300, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
43 36 0.12
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
50 24 0.08
51 114 0.38
52 97 0.32
53 21 0.07
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (46 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTCATGTAATATATGTATT
Found at i:46764977 original size:18 final size:18
Alignment explanation
Indices: 46764909--46764952 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
46764899 TTGTGTAAGT
46764909 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
* *
46764927 TGTCAGTCAAATGTATTA
1 TGTAAGTTAAATGTATTA
46764945 TGTAAGTT
1 TGTAAGTT
46764953 GTAAGTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:46767658 original size:7 final size:7
Alignment explanation
Indices: 46767605--46767680 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
46767595 ACCTTAATCA
*
46767605 CTAAACT
1 CTAAACC
46767612 CTCAAACC
1 CT-AAACC
46767620 CTAAACC
1 CTAAACC
** *
46767627 AAAAACA
1 CTAAACC
46767634 CTAAA-C
1 CTAAACC
* *
46767640 CTACATC
1 CTAAACC
*
46767647 GTAAACC
1 CTAAACC
46767654 CTAAACC
1 CTAAACC
*
46767661 CTAAACT
1 CTAAACC
46767668 CTAAACC
1 CTAAACC
46767675 CTAAAC
1 CTAAAC
46767681 TAGAATTCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:46767743 original size:17 final size:17
Alignment explanation
Indices: 46767721--46767770 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
46767711 TATCCTATTT
46767721 CCTACATTATATAATAA
1 CCTACATTATATAATAA
46767738 CCTACATTATATAATAA
1 CCTACATTATATAATAA
*
46767755 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
46767771 TCTAGCGGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:46767973 original size:113 final size:111
Alignment explanation
Indices: 46767792--46768142 Score: 411
Period size: 113 Copynumber: 3.1 Consensus size: 111
46767782 TTCCCACAAC
* * * *
46767792 GCGCCGCTAATAATATGTTTTACCGGCGTTTTACCATAAGCGCCAC-AACTGGTAGTATACATCA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-T-GTAGTATACATCA
46767856 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
63 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
* * *
46767905 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAAT-GTAGTATACATCAA
* * * * *
46767970 GACCAAA-CTCTGCGTTTTGGTTAA-GAAATATTGCGGCGCTTTTCACTAC
64 GACCAAAGCGCTGCGTTTTGGTTAATG---TTTTGCGGCGCTTTACAATAA
* * * *
46768019 TCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCCACTACTGCTAGTATACATCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATG-TAGTATACATCAA
* * *
46768084 GACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTCCAATAA
64 GACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
*
46768132 GCGCCACTAAT
1 GCGCCGCTAAT
46768143 CCTAATATAC
Statistics
Matches: 200, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.00
112 16 0.08
113 87 0.44
114 80 0.40
115 16 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGTAGTATACATCAAGA
CCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
Found at i:46768244 original size:188 final size:188
Alignment explanation
Indices: 46767927--46768324 Score: 688
Period size: 188 Copynumber: 2.1 Consensus size: 188
46767917 CTATGCTTTA
* * * *
46767927 GCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
46767992 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
46768057 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
46768115 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
* * *
46768180 AAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTAGTAGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
* *
46768245 AGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
* * *
46768303 GCGACGCTTTACAATAAGCGCC
1 GCGGCGTTTTCCAATAAGCGCC
46768325 GCTACTACTA
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
188 198 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (188 bp):
GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
Found at i:46768365 original size:113 final size:114
Alignment explanation
Indices: 46768115--46768540 Score: 464
Period size: 114 Copynumber: 3.7 Consensus size: 114
46768105 TTAATATTTT
* ** *
46768115 GCGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCGTTTT-AATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
* * * *
46768179 TAAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
** * * ** *
46768229 GTAGCGTTTTAATATAAGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGT
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
* * * * ** * * *
46768294 T-A-ATATTTTGCGACGCTTTACAATAAGCGCCGCTACTACTATGCGTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* * *
46768342 GCGGCGTTTTTAA-ATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCG-TTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
*
46768406 TAAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* ** * *
46768456 GCGGCGTTTGAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGA
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
** *
46768521 TAAGAGCTTTTGCGGCGCTT
65 TAAGAAATATTGCGGCGCTT
46768541 GGTAGTAAAC
Statistics
Matches: 252, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
112 14 0.06
113 76 0.30
114 119 0.47
115 43 0.17
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (114 bp):
GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
Found at i:46769135 original size:38 final size:39
Alignment explanation
Indices: 46769068--46769147 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
46769058 TATTTGTGAG
46769068 TGAGTTAATTATTCAATTAAGTGAATGTAATAATT-TTT
1 TGAGTTAATTATTCAATTAAGTGAATGTAATAATTCTTT
* * * *
46769106 TGAGTTAATTCTTCTATTCAA-TGATTGTAATATTTCTTT
1 TGAGTTAATTATTCAATT-AAGTGAATGTAATAATTCTTT
46769145 TGA
1 TGA
46769148 TATCATTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 28 0.78
39 8 0.22
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (39 bp):
TGAGTTAATTATTCAATTAAGTGAATGTAATAATTCTTT
Found at i:46771986 original size:16 final size:15
Alignment explanation
Indices: 46771956--46772002 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
46771946 TATAATAAAT
*
46771956 AAAGTATCAA-ATAA
1 AAAGAATCAATATAA
* *
46771970 AATAGGATCAATCTAA
1 AA-AGAATCAATATAA
46771986 AAAGAATCAATATAA
1 AAAGAATCAATATAA
46772001 AA
1 AA
46772003 CCTACATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 2 0.07
15 20 0.74
16 5 0.19
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAGAATCAATATAA
Found at i:46772806 original size:13 final size:14
Alignment explanation
Indices: 46772790--46772825 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
46772780 CAATCTCATA
46772790 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
46772803 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
46772816 TCTC-ATTTCA
1 TCTCAATTTCA
46772826 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:46772815 original size:18 final size:19
Alignment explanation
Indices: 46772777--46772817 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
46772767 TGGTTCATGT
46772777 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
46772796 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
46772814 TTTC
1 TTTC
46772818 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:46773007 original size:39 final size:38
Alignment explanation
Indices: 46772940--46773074 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
46772930 ACCAATATGG
* * *
46772940 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
46772979 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
46773017 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
46773058 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
46773075 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:46773340 original size:18 final size:19
Alignment explanation
Indices: 46773314--46773352 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
46773304 TTTCAATTCA
46773314 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
46773333 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
46773351 AT
1 AT
46773353 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:46774678 original size:5 final size:5
Alignment explanation
Indices: 46774668--46774724 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
46774658 TTACTTATTT
* *
46774668 ATATA ATATA ATATAA TATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA AT-ATA ATATA
46774716 ATAT- ATATA
1 ATATA ATATA
46774725 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:46774689 original size:17 final size:17
Alignment explanation
Indices: 46774667--46774722 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
46774657 TTTACTTATT
46774667 TATATAATATAATATAA
1 TATATAATATAATATAA
*
46774684 TATATAATATACTAT-A
1 TATATAATATAATATAA
*
46774700 -ATATAATAATAATTTAA
1 TATATAAT-ATAATATAA
46774717 TATATA
1 TATATA
46774723 TATTTTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 15 0.45
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAATATAATATAA
Found at i:46774693 original size:22 final size:21
Alignment explanation
Indices: 46774668--46774725 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
46774658 TTACTTATTT
46774668 ATATAATATAATATAATATATA
1 ATATAATATAATATAATA-ATA
*
46774690 ATATACTATAATATAATAATA
1 ATATAATATAATATAATAATA
*
46774711 ATTTAATATATATAT
1 ATATAATATA-ATAT
46774726 TTTAACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAATATAATATAATAATA
Found at i:46777335 original size:27 final size:26
Alignment explanation
Indices: 46777289--46777342 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
46777279 TTGTTAAAGG
* *
46777289 TGATTTTTTTAGTTTCTTTCTTTTTC
1 TGATTTTGTTAGTTTCTTTCATTTTC
*
46777315 TGATTTTGTTATTATTCTTTCATTTTC
1 TGATTTTGTTAGT-TTCTTTCATTTTC
46777342 T
1 T
46777343 TCTTGCGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.70
Consensus pattern (26 bp):
TGATTTTGTTAGTTTCTTTCATTTTC
Found at i:46778226 original size:25 final size:22
Alignment explanation
Indices: 46778172--46778226 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
46778162 TATTATTTTA
* *
46778172 TGTAAATATTTTCTAAATTTAT
1 TGTATATATTTTCTAAAATTAT
*
46778194 TGTGTATATTTTCTTTAAAATTAT
1 TGTATATATTTTC--TAAAATTAT
46778218 TCGTATATA
1 T-GTATATA
46778227 GCTTGGCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.42
24 9 0.35
25 6 0.23
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (22 bp):
TGTATATATTTTCTAAAATTAT
Found at i:46780017 original size:12 final size:12
Alignment explanation
Indices: 46779996--46780025 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46779986 TGCCACCATG
*
46779996 GTCACAAAGGGA
1 GTCACTAAGGGA
46780008 GTCACTAAGGGA
1 GTCACTAAGGGA
46780020 GTCACT
1 GTCACT
46780026 GATGAGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (12 bp):
GTCACTAAGGGA
Found at i:46787630 original size:9 final size:9
Alignment explanation
Indices: 46787616--46787653 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
46787606 TTATAGCAAC
46787616 AAAAAAAA-
1 AAAAAAAAG
46787624 AAAAAAAAG
1 AAAAAAAAG
46787633 AAAAAAAAG
1 AAAAAAAAG
46787642 AAAAAAGAAG
1 AAAAAA-AAG
46787652 AA
1 AA
46787654 GAAGTGCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.29
9 15 0.54
10 5 0.18
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:46787638 original size:16 final size:16
Alignment explanation
Indices: 46787617--46787650 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46787607 TATAGCAACA
46787617 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
*
46787633 AAAAAAAAGAAAAAAG
1 AAAAAAAAAAAAAAAG
46787649 AA
1 AA
46787651 GAAGAAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:46787640 original size:19 final size:19
Alignment explanation
Indices: 46787616--46787653 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
46787606 TTATAGCAAC
46787616 AAAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAGAA
* *
46787635 AAAAAAGAAAAAAGAAGAA
1 AAAAAAAAAAAAAAAAGAA
46787654 GAAGTGCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAGAA
Found at i:46791602 original size:24 final size:24
Alignment explanation
Indices: 46791554--46791604 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
46791544 TTGTGCTTAA
* *
46791554 AAACTGATGGTAAACGAATTGAAG
1 AAACTGACGGTAAACGAATTAAAG
46791578 AAACTGACGGTAAAC-AAGTTAAAG
1 AAACTGACGGTAAACGAA-TTAAAG
46791602 AAA
1 AAA
46791605 TTTGGACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.18
Consensus pattern (24 bp):
AAACTGACGGTAAACGAATTAAAG
Found at i:46799540 original size:2 final size:2
Alignment explanation
Indices: 46799535--46799565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46799525 TATATATATG
46799535 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
46799566 CGCAATGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46801145 original size:149 final size:149
Alignment explanation
Indices: 46800875--46801164 Score: 492
Period size: 149 Copynumber: 1.9 Consensus size: 149
46800865 ATAGTTGTCA
* * * *
46800875 ATGTTTTGTCAGCAAAAGCACAACTTCATTGACAAAACGTCGTAAAACTGAATTAACAAATGCAC
1 ATGTTTTATCAACAAAACCACAACTTCATTGACAAAACATCGTAAAACTGAATTAACAAATGCAC
46800940 CAGCCGGGAATCGAACCCGGGTCTGTACCGTGGCAGGGTACTATTCTACCACTAGACCACTGGTG
66 CAGCCGGGAATCGAACCCGGGTCTGTACCGTGGCAGGGTACTATTCTACCACTAGACCACTGGTG
46801005 C-TAGTTGTTCCGAAAAACT
131 CTTA-TTGTTCCGAAAAACT
* * * *
46801024 ATGTTTTATCAACAAAACCACAACTTCATTGTCGAAATATCGTAAAATTGAATTAACAAATGCAC
1 ATGTTTTATCAACAAAACCACAACTTCATTGACAAAACATCGTAAAACTGAATTAACAAATGCAC
46801089 CAGCCGGGAATCGAACCCGGGTCTGTACCGTGGCAGGGTACTATTCTACCACTAGACCACTGGTG
66 CAGCCGGGAATCGAACCCGGGTCTGTACCGTGGCAGGGTACTATTCTACCACTAGACCACTGGTG
46801154 CTTATTGTTCC
131 CTTATTGTTCC
46801165 CAGGAACTAA
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
149 130 0.98
150 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (149 bp):
ATGTTTTATCAACAAAACCACAACTTCATTGACAAAACATCGTAAAACTGAATTAACAAATGCAC
CAGCCGGGAATCGAACCCGGGTCTGTACCGTGGCAGGGTACTATTCTACCACTAGACCACTGGTG
CTTATTGTTCCGAAAAACT
Found at i:46802545 original size:4 final size:4
Alignment explanation
Indices: 46802536--46802561 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
46802526 AAATTTTGTC
46802536 TTTG TTTG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTTG TT
46802562 GATGTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:46812777 original size:39 final size:39
Alignment explanation
Indices: 46812732--46812811 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
46812722 AATTGCCTAA
46812732 AAAAATACTCACCTCATTAATTCAACCAATTGTAAGTCT
1 AAAAATACTCACCTCATTAATTCAACCAATTGTAAGTCT
46812771 AAAAATACTCACCTCATTAATTCAACCAATTGTAAGTCT
1 AAAAATACTCACCTCATTAATTCAACCAATTGTAAGTCT
46812810 AA
1 AA
46812812 CATGTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (39 bp):
AAAAATACTCACCTCATTAATTCAACCAATTGTAAGTCT
Found at i:46815054 original size:47 final size:45
Alignment explanation
Indices: 46814984--46815092 Score: 130
Period size: 47 Copynumber: 2.4 Consensus size: 45
46814974 AGCTTAAGAT
46814984 CGAATGGCCAATGTGATGAATGTGAAAGTGCATACATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTG-A-ACATGTGATAAGGC
** * *
46815031 CGAATGGTTAATGTGAT-ATATGTGTAAGTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGTGAACATGTGATAAGGC
*
46815076 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
46815093 AAAGTGTGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 21 0.40
46 7 0.13
47 25 0.47
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (45 bp):
CGAATGGCCAATGTGATGAATGTGAAAGTGAACATGTGATAAGGC
Found at i:46815217 original size:39 final size:40
Alignment explanation
Indices: 46815163--46815247 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
46815153 AAATGAATTG
* * * *
46815163 TGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
46815202 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
46815242 TGCTGG
1 TGCTGG
46815248 TGAATTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:46818433 original size:26 final size:26
Alignment explanation
Indices: 46818395--46818478 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
46818385 CATGAAATTC
* *
46818395 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
46818421 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
46818447 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
46818473 TTATCA
1 TTATCA
46818479 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:46825790 original size:40 final size:38
Alignment explanation
Indices: 46825741--46825829 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 38
46825731 AACACACAAG
* * **
46825741 TTTGGCACCCAACGTCTTATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAACGTCTCATCGGATAAACCGAAGT-A-AA
** *
46825781 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGTAAA
1 TTTGACACCCAACGTCTCATCGGATAAACCGAAGTAAA
46825819 -TTGACACCCAA
1 TTTGACACCCAA
46825830 TACCTCATCG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
37 10 0.24
38 2 0.05
39 1 0.02
40 28 0.68
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (38 bp):
TTTGACACCCAACGTCTCATCGGATAAACCGAAGTAAA
Found at i:46825878 original size:41 final size:41
Alignment explanation
Indices: 46825765--46825881 Score: 116
Period size: 41 Copynumber: 3.0 Consensus size: 41
46825755 TCTTATCGGA
* * * *
46825765 TAATTCGAAGTAATAATTTGACACCCAGTGTCTCATCG-GC
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
* * ** *
46825805 TAAACCG-A--AGTAAATTGACACCCAATACCTCATCGAAT
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
*
46825843 TAATCCGAAGTAGTAAATTGACACTCAGTGTCTCATCGA
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
46825882 CTCGAAGTCG
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
37 22 0.37
38 6 0.10
39 2 0.03
40 5 0.08
41 24 0.41
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (41 bp):
TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
Found at i:46829248 original size:34 final size:33
Alignment explanation
Indices: 46829183--46829250 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
46829173 AAAAGTATTG
* * *
46829183 ACTATAAATATGAAATATTTGTAATATTATTAT
1 ACTATAAATATAAAATATTTGTAACAATATTAT
46829216 ACTATTAAATATAAAATA-TTGTAAACAATATTAT
1 ACTA-TAAATATAAAATATTTGT-AACAATATTAT
46829250 A
1 A
46829251 TCAAGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (33 bp):
ACTATAAATATAAAATATTTGTAACAATATTAT
Found at i:46848045 original size:107 final size:106
Alignment explanation
Indices: 46847853--46848077 Score: 387
Period size: 107 Copynumber: 2.1 Consensus size: 106
46847843 TATTTATCTT
* * *
46847853 ATTTTTTATTTAATGTTATAATATTACTATAGTATTTAATATTTTATTGTTATTGTTTTTTATGC
1 ATTTATTATTTAATGTTATAATATTACTATAGTATTTAATATTTTATTGTTATTATTTTTTATGA
* *
46847918 TAAATATAGATAAATATATCATCTATTTAAATTCAACTTTTA
66 TAAATATAAATAAATATATCATCTATTTAAATTC-ACCTTTA
46847960 ATTTATTATTTAATGTTATAATATTACTATAGTATTTAATATTTTATTGTTATTATTTTTTATGA
1 ATTTATTATTTAATGTTATAATATTACTATAGTATTTAATATTTTATTGTTATTATTTTTTATGA
*
46848025 TAAATATAAATAAATGTATCATCTATTTAAATTCACCTTTA
66 TAAATATAAATAAATATATCATCTATTTAAATTCACCTTTA
46848066 ATTTATTATTTA
1 ATTTATTATTTA
46848078 TTTAAAAATT
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 18 0.16
107 94 0.84
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (106 bp):
ATTTATTATTTAATGTTATAATATTACTATAGTATTTAATATTTTATTGTTATTATTTTTTATGA
TAAATATAAATAAATATATCATCTATTTAAATTCACCTTTA
Found at i:46856106 original size:16 final size:16
Alignment explanation
Indices: 46856068--46856106 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
46856058 TTAATTCAAT
46856068 AATATTATAAAATTTA
1 AATATTATAAAATTTA
*
46856084 AAAATTAT-AAATTTA
1 AATATTATAAAATTTA
46856099 GAATATTA
1 -AATATTA
46856107 AATTTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATTATAAAATTTA
Found at i:46871522 original size:21 final size:20
Alignment explanation
Indices: 46871492--46871531 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
46871482 TTAGGCTTCA
46871492 GGTTTAGGTTT-GTGATTTAG
1 GGTTTAGGTTTAGT-ATTTAG
46871512 GGTTTGAGGTTTAGTATTTA
1 GGTTT-AGGTTTAGTATTTA
46871532 AGTTTAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 11 0.61
22 2 0.11
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (20 bp):
GGTTTAGGTTTAGTATTTAG
Found at i:46875768 original size:243 final size:245
Alignment explanation
Indices: 46875269--46875850 Score: 763
Period size: 246 Copynumber: 2.4 Consensus size: 245
46875259 TGTTGTAGAA
*
46875269 ATATATTATTTTTAGTGATAGATAATAATAATGATTTTAATGATCATTGTTAAAATGTCATTATG
1 ATATATTATTTTTAGTGATAGATAATAATAATGATTTTAATGATC---GTTAAAATATCATTATG
* * * *
46875334 C----A-TTT--ATCTTATTTGTTTTAACGGTTAATTAAAATATAATTATGAATTTATTTAAACA
63 CATTTATTTTAAATCTAATTTATTTTAACGGTCAATTAAAATATAATTATGAATTTATTCAAACA
46875392 ATTTATCAATCAAAATATGTGTTTATTTTAGTGAGTGAAAGTAATAACGGTTTTAACGGCTAACT
128 ATTTATCAATCAAAATATGTGTTTATTTTAGTGAGTGAAAGTAATAACGGTTTTAACGGC--ACT
**
46875457 AAAATATCCTTATATATATATTTTTTGTTATAGATAATTTTAATTATTGTGGCCAAAT
191 AAAATA--CTTATATATATA-TTTTTGTTATAGATAATTTTAATTACCGTGGCCAAAT
46875515 ATATATTATTTTTAGTGATAGATAATAATAATGATTTTAATGATCGTTAAAATATCATTATGCAT
1 ATATATTATTTTTAGTGATAGATAATAATAATGATTTTAATGATCGTTAAAATATCATTATGCAT
46875580 TTATGTTGTAAATCTAATTTATTTTAACGGTCAATTAAAATATAATTATGAATTTATTCAAACAA
66 TTAT-TT-TAAATCTAATTTATTTTAACGGTCAATTAAAATATAATTATGAATTTATTCAAACAA
* * * * *
46875645 TTTATCGATCAAAATATGTGTTTTTTTTAGTGAGTGAGAGTGATAACGGTTTTAACTGC-CTAAA
129 TTTATCAATCAAAATATGTGTTTATTTTAGTGAGTGAAAGTAATAACGGTTTTAACGGCACTAAA
* *
46875709 ATA-TTCT-TATATA-TTTTGTTGTAGATAATTTTAATTACCGTGGCCAAAT
194 ATACTTATATATATATTTTTGTTATAGATAATTTTAATTACCGTGGCCAAAT
* * * * *
46875758 GTATATTATTTTTAGTGATCGAAAATAATAATAATGATTTTAATAATCTTTAAAATACCATTATG
1 ATATATTATTTTTAGTGAT---AGATAATAATAATGATTTTAATGATCGTTAAAATATCATTATG
*
46875823 CATTTATATCATAAATCTAATTTTATTT
63 CATTTAT-T-TTAAATCTAA-TTTATTT
46875851 AGGCATTTCT
Statistics
Matches: 301, Mismatches: 21, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
243 68 0.23
245 6 0.02
246 104 0.35
247 8 0.03
249 10 0.03
250 1 0.00
252 104 0.35
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (245 bp):
ATATATTATTTTTAGTGATAGATAATAATAATGATTTTAATGATCGTTAAAATATCATTATGCAT
TTATTTTAAATCTAATTTATTTTAACGGTCAATTAAAATATAATTATGAATTTATTCAAACAATT
TATCAATCAAAATATGTGTTTATTTTAGTGAGTGAAAGTAATAACGGTTTTAACGGCACTAAAAT
ACTTATATATATATTTTTGTTATAGATAATTTTAATTACCGTGGCCAAAT
Found at i:46881666 original size:18 final size:18
Alignment explanation
Indices: 46881643--46881699 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
46881633 CCCAACTACT
*
46881643 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
46881661 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
46881679 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
46881697 GTA
1 GTA
46881700 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:46890423 original size:47 final size:46
Alignment explanation
Indices: 46890322--46890462 Score: 174
Period size: 47 Copynumber: 3.0 Consensus size: 46
46890312 CATTTCACAT
* * ** * *
46890322 ACCGAGGCCATAGCCCAGCCATGGTCTTATACGGATCACATATCAC
1 ACCGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCAC
* * *
46890368 ACTGATGCCATATCCTAGATATGGTCTTATACAGTAGCACATATCAC
1 ACCGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCAC
*
46890415 ACCGATGCCATATCCCGGATATGGTCTTATACGGAAGCACATATCAC
1 ACCGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCAC
46890462 A
1 A
46890463 TTTCTCCAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
46 26 0.32
47 55 0.68
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCAC
Found at i:46892798 original size:52 final size:52
Alignment explanation
Indices: 46892629--46892926 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
46892619 ATATCACATA
* * * * *
46892629 CCGAGGCCATAGCCCAGCCATGGTCTTACACGG-ATCACATACCACA---CT
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
* * * * * * *
46892677 --GATGCCATATCTCAGATATGGTCTTATGCAGTAGCACATATCACA-----
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
* * * *
46892722 CCGATGCCATATCCCGGATATGGTCTTATACGGAAGCACATATCACATTTCT
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
* *
46892774 TCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACAAATCACATTTCT
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
*
46892826 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACAAATCACATTTCT
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
* *
46892878 CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAATCACATTTCACAT
1 CCGAAGCCATAGCCCAGCTATGGTCTTATACGG-AAGCACATATCACAT
46892927 GCTGCCATGG
Statistics
Matches: 216, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
46 23 0.11
47 51 0.24
52 130 0.60
53 12 0.06
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (52 bp):
CCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTTCT
Found at i:46895717 original size:12 final size:12
Alignment explanation
Indices: 46895700--46895733 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
46895690 TTGTAAACAG
*
46895700 GGGCATGGGCAT
1 GGGCATGGGAAT
46895712 GGGCATGGGAAT
1 GGGCATGGGAAT
*
46895724 TGGCATGGGA
1 GGGCATGGGA
46895734 GAGGCGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.50, T:0.18
Consensus pattern (12 bp):
GGGCATGGGAAT
Found at i:46896301 original size:12 final size:13
Alignment explanation
Indices: 46896278--46896308 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
46896268 CGCATAGTTT
46896278 AAAAATGTTTTTC
1 AAAAATGTTTTTC
*
46896291 AAAAATGTTTTTG
1 AAAAATGTTTTTC
46896304 AAAAA
1 AAAAA
46896309 GACAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (13 bp):
AAAAATGTTTTTC
Found at i:46904029 original size:60 final size:60
Alignment explanation
Indices: 46903936--46904057 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
46903926 GATGATATGT
* * *
46903936 TATGTAGAGGATGTCATTGAGAGTTTTTAGGACAATGTGGCGAGCCCTGAAGTTGTAATC
1 TATGTAGAGGATGTCATTGAGAGTTCTTAGGACAATATGGCGAGCCCTGAAGTCGTAATC
* * * *
46903996 TATGTAGAGGTTGTCATTGAGAGTTCTTAGGACAATATGGCGAGGCTTGAAGTCGTCATC
1 TATGTAGAGGATGTCATTGAGAGTTCTTAGGACAATATGGCGAGCCCTGAAGTCGTAATC
46904056 TA
1 TA
46904058 CCCAACATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (60 bp):
TATGTAGAGGATGTCATTGAGAGTTCTTAGGACAATATGGCGAGCCCTGAAGTCGTAATC
Found at i:46919399 original size:24 final size:24
Alignment explanation
Indices: 46919354--46919400 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
46919344 TTATTTTTTG
*
46919354 TATGTTATTTTTTAAATAATATTA
1 TATGTTATTTTTTAAACAATATTA
46919378 TATGTTA-TTTTTAAACACATATT
1 TATGTTATTTTTTAAACA-ATATT
46919401 TAATTTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
TATGTTATTTTTTAAACAATATTA
Found at i:46920977 original size:22 final size:22
Alignment explanation
Indices: 46920938--46920982 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
46920928 ATATATTAGG
46920938 AAAATTCCATGATAAAGAAATAA
1 AAAATTCCATGATAAAG-AATAA
* *
46920961 AAAATTTCATG-TCAAGAATAA
1 AAAATTCCATGATAAAGAATAA
46920982 A
1 A
46920983 TCAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAATTCCATGATAAAGAATAA
Found at i:46922454 original size:47 final size:47
Alignment explanation
Indices: 46922385--46922530 Score: 168
Period size: 47 Copynumber: 3.1 Consensus size: 47
46922375 TTTTATTAAG
* *
46922385 TGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATA
1 TGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATA
* *
46922432 TGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATA
1 TGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATA
* * * ** * *
46922479 CGTGAT-CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATA
1 TGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATA
46922527 TGTG
1 TGTG
46922531 ACTATGTGCA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
46 26 0.31
47 47 0.57
48 10 0.12
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (47 bp):
TGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATA
Found at i:46929617 original size:2 final size:2
Alignment explanation
Indices: 46929612--46929637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46929602 TATATATATC
46929612 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
46929638 CGAAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46939642 original size:16 final size:17
Alignment explanation
Indices: 46939606--46939639 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
46939596 AAAATATTGT
46939606 TATATATATTTTTTAAAA
1 TATATATATTTTTT-AAA
46939624 TATATATATTTTTTAA
1 TATATATATTTTTTAA
46939640 TATTTCACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATATTTTTTAAA
Found at i:46945155 original size:21 final size:20
Alignment explanation
Indices: 46945111--46945147 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
46945101 AATTATGATT
46945111 GAAGAAAAATTCATAAAGCA
1 GAAGAAAAATTCATAAAGCA
46945131 -AAGAGAAAATT-ATAAAG
1 GAAGA-AAAATTCATAAAG
46945148 GGAGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.62, C:0.05, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAGAAAAATTCATAAAGCA
Found at i:46951755 original size:21 final size:21
Alignment explanation
Indices: 46951729--46951769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46951719 ATCTGCTCAA
* *
46951729 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
46951750 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
46951770 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:46958129 original size:15 final size:15
Alignment explanation
Indices: 46958109--46958139 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46958099 AATTCCCTCG
46958109 CCTGTAAATATATGT
1 CCTGTAAATATATGT
46958124 CCTGTAAATATATGT
1 CCTGTAAATATATGT
46958139 C
1 C
46958140 AAAGCATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (15 bp):
CCTGTAAATATATGT
Found at i:46961928 original size:38 final size:38
Alignment explanation
Indices: 46961885--46961958 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
46961875 CTAATTGGCA
* * *
46961885 ATTGGAGAATGTTATAAGATGCTTTTCAGAGCAAGTCG
1 ATTGGAGAATGTTAAAAGATGCTTTTAAAAGCAAGTCG
*
46961923 ATTGGAGAATGTTAAAAGATTCTTTTAAAAGCAAGT
1 ATTGGAGAATGTTAAAAGATGCTTTTAAAAGCAAGT
46961959 GTGGGGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (38 bp):
ATTGGAGAATGTTAAAAGATGCTTTTAAAAGCAAGTCG
Found at i:46988985 original size:13 final size:13
Alignment explanation
Indices: 46988967--46988992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46988957 GCAGGGGAGA
46988967 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
46988980 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
46988993 GGAGAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:46988990 original size:17 final size:17
Alignment explanation
Indices: 46988968--46989002 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46988958 CAGGGGAGAA
46988968 AAAGAAAGAAAGAAAAG
1 AAAGAAAGAAAGAAAAG
**
46988985 AAAGAAAGGGAGAAAAG
1 AAAGAAAGAAAGAAAAG
46989002 A
1 A
46989003 GAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAAG
Found at i:46991329 original size:79 final size:79
Alignment explanation
Indices: 46991245--46991402 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
46991235 TTCAGATAAC
46991245 TATTAAGTAAGAATTTCATTCATATCGAAATAAATTATACAGACTTTGTCTTATCTTCGACGATA
1 TATTAAGTAAGAATTTCATTCATATCGAAATAAATTATACAGACTTTGTCTTATCTTCGACGATA
46991310 TCATCTTTCTTTTT
66 TCATCTTTCTTTTT
46991324 TATTAAGTAAGAATTTCATTCATATCGAAATAAATTATACAGACTTTGTCTTATCTTCGACGATA
1 TATTAAGTAAGAATTTCATTCATATCGAAATAAATTATACAGACTTTGTCTTATCTTCGACGATA
46991389 TCATCTTTCTTTTT
66 TCATCTTTCTTTTT
46991403 CACGGACAGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (79 bp):
TATTAAGTAAGAATTTCATTCATATCGAAATAAATTATACAGACTTTGTCTTATCTTCGACGATA
TCATCTTTCTTTTT
Found at i:46992452 original size:22 final size:22
Alignment explanation
Indices: 46992402--46992501 Score: 87
Period size: 22 Copynumber: 4.4 Consensus size: 22
46992392 CACTAATGAA
*
46992402 CAGAGAGCACTGAA-GTGCT-AT
1 CAGAGAGCAC-AAATGTGCTAAT
*
46992423 ACAAAGAGCACAAATGTGCTAAT
1 -CAGAGAGCACAAATGTGCTAAT
****
46992446 CAGAGAGCACTGGCGTGCTAAATAT
1 CAGAGAGCACAAATGTGCT--A-AT
46992471 CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACAAATGTGCTAAT
46992493 CAGAGAGCA
1 CAGAGAGCA
46992502 TTGACGTGCT
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
21 2 0.03
22 39 0.63
23 3 0.05
24 1 0.02
25 17 0.27
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (22 bp):
CAGAGAGCACAAATGTGCTAAT
Found at i:46992477 original size:25 final size:24
Alignment explanation
Indices: 46992444--46992601 Score: 176
Period size: 25 Copynumber: 6.5 Consensus size: 24
46992434 AAATGTGCTA
46992444 ATCAGAGAGCACTGGCGTGCTAAAT
1 ATCAGAGAGCACTGGCGTGCT-AAT
****
46992469 ATCAGAGAGCACAAATGTGCT-A-
1 ATCAGAGAGCACTGGCGTGCTAAT
* *
46992491 ATCAGAGAGCATTGACGTGCTATAT
1 ATCAGAGAGCACTGGCGTGCTA-AT
46992516 ATCAGAGAGCACTGGCGTGCTAAT
1 ATCAGAGAGCACTGGCGTGCTAAT
**
46992540 ATTCAGAGAGCACTGGCGTATTAAT
1 A-TCAGAGAGCACTGGCGTGCTAAT
*
46992565 AATCAGAAAGCACTGGCGTGCTAAT
1 -ATCAGAGAGCACTGGCGTGCTAAT
46992590 AATCAGAGAGCA
1 -ATCAGAGAGCA
46992602 TGCTGAAGTC
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
22 17 0.15
23 1 0.01
24 4 0.04
25 89 0.79
26 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (24 bp):
ATCAGAGAGCACTGGCGTGCTAAT
Found at i:46992481 original size:47 final size:46
Alignment explanation
Indices: 46992402--46992527 Score: 184
Period size: 47 Copynumber: 2.7 Consensus size: 46
46992392 CACTAATGAA
* *
46992402 CAGAGAGCACTGAAGTGCT-ATA-CAAAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAATGTGCTAAT
*
46992446 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCT-AATATCAGAGAGCACAAATGTGCTAAT
*
46992493 CAGAGAGCATTGACGTGCTATATATCAGAGAGCAC
1 CAGAGAGCACTGACGTGCTA-ATATCAGAGAGCAC
46992528 TGGCGTGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 17 0.23
46 4 0.05
47 52 0.71
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (46 bp):
CAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAATGTGCTAAT
Found at i:46992536 original size:47 final size:46
Alignment explanation
Indices: 46992438--46992589 Score: 169
Period size: 47 Copynumber: 3.2 Consensus size: 46
46992428 GAGCACAAAT
****
46992438 GTGCTAATCAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAAT
1 GTGCTAATCAGAGAGCACTGGCGTGCT-AATATCAGAGAGCACTGGC
* *
46992485 GTGCTAATCAGAGAGCATTGACGTGCTATATATCAGAGAGCACTGGC
1 GTGCTAATCAGAGAGCACTGGCGTGCTA-ATATCAGAGAGCACTGGC
** *
46992532 GTGCTAATATTCAGAGAGCACTGGCGTATTAATAATCAGAAAGCACTGGC
1 GTGCT-A-A-TCAGAGAGCACTGGCGTGCTAAT-ATCAGAGAGCACTGGC
46992582 GTGCTAAT
1 GTGCTAAT
46992590 AATCAGAGAG
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
46 1 0.01
47 45 0.51
48 2 0.02
49 4 0.04
50 37 0.42
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (46 bp):
GTGCTAATCAGAGAGCACTGGCGTGCTAATATCAGAGAGCACTGGC
Found at i:47000446 original size:15 final size:16
Alignment explanation
Indices: 47000426--47000457 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
47000416 CTTCAAGTTG
47000426 ATATTTTTTAT-TTTT
1 ATATTTTTTATATTTT
47000441 ATATTTTTTATATTTT
1 ATATTTTTTATATTTT
47000457 A
1 A
47000458 AAATTTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATATTTTTTATATTTT
Found at i:47000822 original size:19 final size:19
Alignment explanation
Indices: 47000794--47000870 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
47000784 AAAAATATAT
47000794 AAAATAATTTTAAAAAATTC
1 AAAAT-ATTTTAAAAAATTC
* ** *
47000814 AAATTATTTTTTAAAATTA
1 AAAATATTTTAAAAAATTC
*
47000833 AAAATATTTATAAAAATTTC
1 AAAATATTT-TAAAAAATTC
*
47000853 AAAAATATTCTAAAAAAT
1 -AAAATATTTTAAAAAAT
47000871 ATATAAAGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 19 0.43
20 17 0.39
21 8 0.18
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATTTTAAAAAATTC
Found at i:47001993 original size:4 final size:4
Alignment explanation
Indices: 47001984--47002027 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
47001974 CATCTATGCA
47001984 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47002028 CATCAGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:47003568 original size:21 final size:21
Alignment explanation
Indices: 47003542--47003582 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47003532 TGGATATGGA
*
47003542 TACATGCCAGGTTACCCTGGC
1 TACATGCCAAGTTACCCTGGC
*
47003563 TACATGCCAAGTTATCCTGG
1 TACATGCCAAGTTACCCTGG
47003583 TTATGGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (21 bp):
TACATGCCAAGTTACCCTGGC
Found at i:47014105 original size:16 final size:17
Alignment explanation
Indices: 47014084--47014116 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47014074 AATTGAACTG
47014084 ATATTTT-TATTCAAAT
1 ATATTTTATATTCAAAT
47014100 ATATTTTGATATTCAAA
1 ATATTTT-ATATTCAAA
47014117 CTACTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
ATATTTTATATTCAAAT
Found at i:47017631 original size:53 final size:53
Alignment explanation
Indices: 47017550--47017700 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
47017540 CTTACACGGT
* *
47017550 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
47017605 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
47017658 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
47017701 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:47025149 original size:53 final size:53
Alignment explanation
Indices: 47025068--47025218 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
47025058 CTTACACGGT
* *
47025068 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
47025123 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
47025176 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
47025219 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:47039744 original size:20 final size:20
Alignment explanation
Indices: 47039721--47039896 Score: 104
Period size: 20 Copynumber: 8.9 Consensus size: 20
47039711 AAGAATATTT
*
47039721 AAAATATATAAAAAATTGTA
1 AAAATATATTAAAAATTGTA
* * *
47039741 AAAAAATATTAGAACTT-TA
1 AAAATATATTAAAAATTGTA
*
47039760 AAAA-A-A-TAAATATTGTTA
1 AAAATATATTAAAAATTG-TA
*
47039778 AAAATAT-TTTAAAATTGTA
1 AAAATATATTAAAAATTGTA
*
47039797 AAAA-AGTTATTAAAAATTATA
1 AAAATA--TATTAAAAATTGTA
*
47039818 AAACACTAT-TTAAAATTTGTA
1 AAA-A-TATATTAAAAATTGTA
* *
47039839 AAGATCATA--AAAAATTGTG
1 AAAAT-ATATTAAAAATTGTA
*
47039858 AAAAT-TATTAAAAAATTGCA
1 AAAATATATT-AAAAATTGTA
47039878 AATAAT-TATTAAAAATTGT
1 AA-AATATATTAAAAATTGT
47039897 GAATAAGTGG
Statistics
Matches: 119, Mismatches: 20, Indels: 34
0.69 0.12 0.20
Matches are distributed among these distances:
16 5 0.04
17 3 0.03
18 8 0.07
19 26 0.22
20 42 0.35
21 32 0.27
22 2 0.02
24 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (20 bp):
AAAATATATTAAAAATTGTA
Found at i:47039901 original size:20 final size:21
Alignment explanation
Indices: 47039846--47039902 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
47039836 GTAAAGATCA
47039846 TAAAAAATTGTGAA-AATTAT
1 TAAAAAATTGTGAATAATTAT
**
47039866 TAAAAAATTGCAAATAATTAT
1 TAAAAAATTGTGAATAATTAT
47039887 T-AAAAATTGTGAATAA
1 TAAAAAATTGTGAATAA
47039903 GTGGCATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (21 bp):
TAAAAAATTGTGAATAATTAT
Found at i:47040115 original size:10 final size:10
Alignment explanation
Indices: 47040101--47040149 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
47040091 AAGTTGAAGT
*
47040101 TAATTTTTTT
1 TAATTTTTTA
**
47040111 TAATTTTAAA
1 TAATTTTTTA
*
47040121 TAATATTTTA
1 TAATTTTTTA
*
47040131 TAATTTTTAA
1 TAATTTTTTA
47040141 TAATTTTTT
1 TAATTTTTT
47040150 TTTACAATTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:47040129 original size:20 final size:19
Alignment explanation
Indices: 47040105--47040150 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
47040095 TGAAGTTAAT
47040105 TTTTTTTAATTTTAAATAA
1 TTTTTTTAATTTTAAATAA
* *
47040124 TATTTTATAATTTTTAATAA
1 T-TTTTTTAATTTTAAATAA
47040144 TTTTTTT
1 TTTTTTT
47040151 TTACAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTTAATTTTAAATAA
Found at i:47040188 original size:34 final size:31
Alignment explanation
Indices: 47040125--47040194 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 31
47040115 TTTAAATAAT
* *
47040125 ATTTTATAATTTTTAATAATTTTTTTTTACA
1 ATTTTAAAATTTTTAACAATTTTTTTTTACA
47040156 ATTTTAAAATGTTTCTAACAATATTTTTTTTACA
1 ATTTTAAAAT-TTT-TAACAAT-TTTTTTTTACA
47040190 ATTTT
1 ATTTT
47040195 TTTTAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 9 0.26
32 3 0.09
33 6 0.18
34 16 0.47
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTTAAAATTTTTAACAATTTTTTTTTACA
Found at i:47040238 original size:30 final size:29
Alignment explanation
Indices: 47040182--47040276 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
47040172 AACAATATTT
** *
47040182 TTTTTACAATTTTTTTTAGTAATTTAAATA
1 TTTTTACAATTTTTAATA-TATTTTAAATA
*
47040212 TTCTTTACAATTTTT-GTATATTTTTAAATAA
1 TT-TTTACAATTTTTAATATA-TTTTAAAT-A
*
47040243 TTTTTACTATTTTTAATATATTTTACAATA
1 TTTTTACAATTTTTAATATATTTTA-AATA
47040273 TTTT
1 TTTT
47040277 AATATGGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
29 2 0.04
30 32 0.57
31 22 0.39
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTACAATTTTTAATATATTTTAAATA
Found at i:47040264 original size:11 final size:10
Alignment explanation
Indices: 47040204--47040276 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
47040194 TTTTTAGTAA
47040204 TTTAAATATT
1 TTTAAATATT
*
47040214 CTTTACA-ATT
1 -TTTAAATATT
**
47040224 TTTGTATATT
1 TTTAAATATT
47040234 TTTAAATAATT
1 TTTAAAT-ATT
*
47040245 TTT-ACTATT
1 TTTAAATATT
47040254 TTT-AATATAT
1 TTTAAATAT-T
47040264 TTTACAATATT
1 TTTA-AATATT
47040275 TT
1 TT
47040277 AATATGGTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 14 0.28
10 17 0.34
11 14 0.28
12 5 0.10
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTAAATATT
Found at i:47040267 original size:19 final size:21
Alignment explanation
Indices: 47040230--47040281 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
47040220 AATTTTTGTA
47040230 TATTTTTAA-ATAATTTTTAC
1 TATTTTTAATATAATTTTTAC
47040250 TATTTTTAATAT-A-TTTTAC
1 TATTTTTAATATAATTTTTAC
*
47040269 AATATTTTAATAT
1 TAT-TTTTAATAT
47040282 GGTCAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.28
20 19 0.66
21 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTTAATATAATTTTTAC
Found at i:47040439 original size:17 final size:19
Alignment explanation
Indices: 47040400--47040443 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
47040390 GCAGGGGTCA
47040400 AAAAAATATAATGAAATAAT
1 AAAAAA-ATAATGAAATAAT
*
47040420 AAAAAAAT-ATG-AATATT
1 AAAAAAATAATGAAATAAT
47040437 AAAAAAA
1 AAAAAAA
47040444 AAGAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 2 0.09
20 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAAATAATGAAATAAT
Found at i:47045931 original size:3 final size:3
Alignment explanation
Indices: 47045923--47045968 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
47045913 AAAAGGAAAA
* *
47045923 AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG GAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
47045969 GAGCATCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47048274 original size:124 final size:124
Alignment explanation
Indices: 47048054--47048302 Score: 471
Period size: 124 Copynumber: 2.0 Consensus size: 124
47048044 CCTGCATGTG
*
47048054 TTGCGGATACACCACAACTCTCTTGAGCTTCCTGATATTAGGCTTGCAAGAACTTCCCGATATAG
1 TTGCGGATACACCACAACTCTCTTGAGCTTCCTGATATTAGGCTTGCAAGAACTTCCCGATATAC
47048119 AGCTCGTATGAGTTTCCTGTTACTTAGTTGATGGTCCTAAAACTAACTAAAAATTCAAC
66 AGCTCGTATGAGTTTCCTGTTACTTAGTTGATGGTCCTAAAACTAACTAAAAATTCAAC
*
47048178 TTGCGGATACACCACAACTCTCTTGAGCTTCCTGATATTGGGCTTGCAAGAACTTCCCGATATAC
1 TTGCGGATACACCACAACTCTCTTGAGCTTCCTGATATTAGGCTTGCAAGAACTTCCCGATATAC
*
47048243 AGCTCGTATGAGTTTCCTGTTACTTAGTTGATGGTCCTGAAACTAACTAAAAATTCAAC
66 AGCTCGTATGAGTTTCCTGTTACTTAGTTGATGGTCCTAAAACTAACTAAAAATTCAAC
47048302 T
1 T
47048303 AAGGCAAGCG
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (124 bp):
TTGCGGATACACCACAACTCTCTTGAGCTTCCTGATATTAGGCTTGCAAGAACTTCCCGATATAC
AGCTCGTATGAGTTTCCTGTTACTTAGTTGATGGTCCTAAAACTAACTAAAAATTCAAC
Found at i:47048396 original size:34 final size:34
Alignment explanation
Indices: 47048353--47048423 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
47048343 AGACCAGAAA
47048353 TACCGTATCCACGAGGACTAAAAGTACTAGTAAT
1 TACCGTATCCACGAGGACTAAAAGTACTAGTAAT
47048387 TACCGTATCCACGAGGACTAAAAGTACTAGTAAT
1 TACCGTATCCACGAGGACTAAAAGTACTAGTAAT
47048421 TAC
1 TAC
47048424 TATCTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (34 bp):
TACCGTATCCACGAGGACTAAAAGTACTAGTAAT
Found at i:47050544 original size:479 final size:479
Alignment explanation
Indices: 47049648--47051033 Score: 2657
Period size: 479 Copynumber: 2.9 Consensus size: 479
47049638 AGTTCACATG
* * *
47049648 TGTAATATCCTGATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCACAAAATCCGAGATATAA
1 TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
* *
47049713 ATAATTATTTTATGATTATTTTAAGGTCTATGATATGATTGCATGATTGCGTGAAAATTTCGTGA
66 ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
*
47049778 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGAAAAACTT
131 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
*
47049843 GCATTCTAG-AAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
196 GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
*
47049907 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAGCCAGCTTGT
261 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
47049972 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
326 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
47050037 GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACATTTAGCTGGTAAGATTTTCGGGGACG
391 GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACATTTAGCTGGTAAGATTTTCGGGGACG
47050102 AAAATCCCTAAAGGAGGGGAGAGT
456 AAAATCCCTAAAGGAGGGGAGAGT
47050126 TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
1 TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
47050191 ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
66 ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
47050256 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
131 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
47050321 GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
196 GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
47050386 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
261 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
47050451 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
326 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
47050516 GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACATTTAGCTGGTAAGATTTTCGGGGACG
391 GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACATTTAGCTGGTAAGATTTTCGGGGACG
47050581 AAAATCCCTAAAGGAGGGGAGAGT
456 AAAATCCCTAAAGGAGGGGAGAGT
47050605 TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
1 TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
47050670 ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
66 ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
47050735 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
131 AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
47050800 GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
196 GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
47050865 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
261 GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
47050930 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
326 CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
* ** *
47050995 GTTCGACTCCGGCAACGGTCTCGGGTACGGGGCGTTACA
391 GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACA
47051034 ACATGAGCTT
Statistics
Matches: 895, Mismatches: 12, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
478 197 0.22
479 698 0.78
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (479 bp):
TGTAATATTCTGATTTTGGGCCTAGTCGGAATAGTGATTTCGTGACCACAAAATCCGAGATAGAA
ATAATTATTTTATGATTATTTTATGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
AGGAATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTT
GCATTATAGAAAAAAATTACTAGATAGATATATGAGTCTAGTTTCAGGAAAAATTTACGGAATTG
GATTTCAAGTTTAGGAACTCGAGATATGATTTTTAAAGCGACTGTGATGCAGTTAACCAGCTTGT
CTGGAAATTTTAAAATGAATTGTATGAGCTGTTTAAGTAATGAATTAAGTCCGTTAACACCTCGT
GTTCAACTCCGAAAACAGTCTCGGGTACGGGGCGTTACATTTAGCTGGTAAGATTTTCGGGGACG
AAAATCCCTAAAGGAGGGGAGAGT
Found at i:47054093 original size:38 final size:38
Alignment explanation
Indices: 47054042--47054114 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
47054032 TAGCAAATTG
47054042 CACTTACCACACTCTTTCAAAGTTAGTTAACGTATTTA
1 CACTTACCACACTCTTTCAAAGTTAGTTAACGTATTTA
* *
47054080 CACTTACCACACTCTTTTAAGGTTAGTTAACGTAT
1 CACTTACCACACTCTTTCAAAGTTAGTTAACGTAT
47054115 CGTTATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (38 bp):
CACTTACCACACTCTTTCAAAGTTAGTTAACGTATTTA
Found at i:47056710 original size:32 final size:32
Alignment explanation
Indices: 47056642--47056718 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
47056632 AAATTCTAGT
* *
47056642 TTGTTGGATTTTGAAATTATTATGTCTTGAAT
1 TTGTTGGATATTGAAATTATTATGTCTTGAAC
* * *
47056674 TTGTTGGATATTGAATTTGTTATGT-TTTAAGC
1 TTGTTGGATATTGAAATTATTATGTCTTGAA-C
47056706 TTGTTGGATATTG
1 TTGTTGGATATTG
47056719 CAATGATTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATGTCTTGAAC
Found at i:47058993 original size:24 final size:24
Alignment explanation
Indices: 47058954--47059012 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
47058944 GGGTCAACAT
* *
47058954 TGGCACTAAGTGTGC-GAATTTGAA
1 TGGCACTATGTATGCGGAA-TTGAA
47058978 TGGCACTATGTATGCGGAATTGAA
1 TGGCACTATGTATGCGGAATTGAA
47059002 TGGCACTATGT
1 TGGCACTATGT
47059013 GTGCTGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (24 bp):
TGGCACTATGTATGCGGAATTGAA
Found at i:47061819 original size:24 final size:24
Alignment explanation
Indices: 47061780--47061849 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
47061770 GGGTTTACGT
*
47061780 TGGCACTAAGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* *
47061804 TGGCACTATGTATGCGGAATTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
47061828 TGGCACTATGTGTGCTGATTTG
1 TGGCACTATGTGTGCGGATTTG
47061850 GATGTCAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:47063920 original size:19 final size:20
Alignment explanation
Indices: 47063896--47063939 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
47063886 TCCAAAAACT
47063896 AGAAAAATAAATCA-TTTCC
1 AGAAAAATAAATCATTTTCC
*
47063915 AGAAAAGTAAATCATTTTCC
1 AGAAAAATAAATCATTTTCC
47063935 AGAAA
1 AGAAA
47063940 TCATTTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (20 bp):
AGAAAAATAAATCATTTTCC
Found at i:47063959 original size:14 final size:14
Alignment explanation
Indices: 47063923--47063960 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
47063913 CCAGAAAAGT
*
47063923 AAATCATTTTCCAG
1 AAATCATTTTCCAA
47063937 AAATCATTTTCCGAA
1 AAATCATTTTCC-AA
47063952 AAAT-ATTTT
1 AAATCATTTT
47063961 ACTGGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:47066713 original size:31 final size:31
Alignment explanation
Indices: 47066678--47066749 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
47066668 TTTTATAGTT
47066678 TTTTAATTAGATAATTATTATT-TATTTAATA
1 TTTTAATTAGATAATTATTATTAT-TTTAATA
* * *
47066709 TTTTAATAAGATATTTATTATTATTTTATTA
1 TTTTAATTAGATAATTATTATTATTTTAATA
*
47066740 TTTTATTTAG
1 TTTTAATTAG
47066750 TATATATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (31 bp):
TTTTAATTAGATAATTATTATTATTTTAATA
Found at i:47066715 original size:23 final size:22
Alignment explanation
Indices: 47066689--47066748 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
47066679 TTTAATTAGA
47066689 TAATTATTATTTATTTAATATTT
1 TAATTA-TATTTATTTAATATTT
* *
47066712 TAATAAGATATTTA-TTATTATTT
1 TAAT--TATATTTATTTAATATTT
47066735 T-ATTAT-TTTATTTA
1 TAATTATATTTATTTA
47066749 GTATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 4 0.13
20 5 0.16
22 2 0.06
23 13 0.42
24 6 0.19
25 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TAATTATATTTATTTAATATTT
Found at i:47066763 original size:2 final size:2
Alignment explanation
Indices: 47066758--47066782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47066748 AGTATATATA
47066758 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
47066783 ATGAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:47069051 original size:18 final size:19
Alignment explanation
Indices: 47069012--47069054 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
47069002 TTAAAAAGTT
*
47069012 TTTTATATTTAATTTTTAA
1 TTTTATATTTAATTTTAAA
47069031 TTTT-TATTT-ATTTTAAGA
1 TTTTATATTTAATTTTAA-A
47069049 TTTTAT
1 TTTTAT
47069055 TATGAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTATATTTAATTTTAAA
Found at i:47069536 original size:18 final size:18
Alignment explanation
Indices: 47069510--47069548 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
47069500 TGAATTTTAC
*
47069510 AATTTAAATAACTTGAAT
1 AATTCAAATAACTTGAAT
47069528 AATTCAAATAACTTGAAT
1 AATTCAAATAACTTGAAT
47069546 AAT
1 AAT
47069549 AGTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (18 bp):
AATTCAAATAACTTGAAT
Found at i:47069639 original size:20 final size:21
Alignment explanation
Indices: 47069600--47069655 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
47069590 ATATTTACAA
47069600 AAAAAATTTCAAAATAATTT-T
1 AAAAAA-TTCAAAATAATTTAT
47069621 CAAAAAATTCAAAAT-ATTTAT
1 -AAAAAATTCAAAATAATTTAT
*
47069642 AAAAATTTCAAAAT
1 AAAAAATTCAAAAT
47069656 TTATATCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.53
21 9 0.28
22 6 0.19
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTAT
Found at i:47074715 original size:21 final size:21
Alignment explanation
Indices: 47074690--47074733 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
47074680 ATTGGGCTGT
* *
47074690 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
47074711 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
47074732 TA
1 TA
47074734 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:47078256 original size:38 final size:38
Alignment explanation
Indices: 47078205--47078280 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
47078195 AAAACTCACT
47078205 TATGTATGATTTCTCTATGACTCCATCTTTTCCATGGC
1 TATGTATGATTTCTCTATGACTCCATCTTTTCCATGGC
*
47078243 TATGTATGATTTCTCTATGATTCCATCTTTTCCATGGC
1 TATGTATGATTTCTCTATGACTCCATCTTTTCCATGGC
47078281 AAATCAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.46
Consensus pattern (38 bp):
TATGTATGATTTCTCTATGACTCCATCTTTTCCATGGC
Found at i:47092181 original size:30 final size:29
Alignment explanation
Indices: 47092147--47092217 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
47092137 TTTAATAAAA
* *
47092147 ATAAATTATACCTTAACCTCTTTTAAAATT
1 ATAAATTATAACTTAACC-CTTTAAAAATT
* *
47092177 ATAAAAATT-TAATTTAATCCTTTAAAAATT
1 AT--AAATTATAACTTAACCCTTTAAAAATT
47092207 ATAAATTATAA
1 ATAAATTATAA
47092218 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
28 5 0.15
29 3 0.09
30 14 0.41
31 7 0.21
32 5 0.15
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAAATTATAACTTAACCCTTTAAAAATT
Found at i:47092603 original size:7 final size:7
Alignment explanation
Indices: 47092591--47092615 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47092581 ATATAGATAT
47092591 TATATTA
1 TATATTA
47092598 TATATTA
1 TATATTA
47092605 TATATTA
1 TATATTA
47092612 TATA
1 TATA
47092616 AAGTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:47093795 original size:13 final size:13
Alignment explanation
Indices: 47093786--47093828 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
47093776 ATGCTTTTGC
47093786 AAAGTGCTTTTAA
1 AAAGTGCTTTTAA
* *
47093799 AAAGTGCTGTGAA
1 AAAGTGCTTTTAA
47093812 AAAGTGCTTTTGAA
1 AAAGTGCTTTT-AA
47093826 AAA
1 AAA
47093829 TTTGGTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (13 bp):
AAAGTGCTTTTAA
Found at i:47097842 original size:18 final size:18
Alignment explanation
Indices: 47097819--47097853 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
47097809 TTTTTATAAT
47097819 TTTGTATA-ATCTTTTAAG
1 TTTGTATATAT-TTTTAAG
47097837 TTTGTATATATTTTTAA
1 TTTGTATATATTTTTAA
47097854 AAATTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTGTATATATTTTTAAG
Found at i:47097860 original size:20 final size:19
Alignment explanation
Indices: 47097837--47097875 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47097827 ATCTTTTAAG
*
47097837 TTTGTATATATTTTTAAAAA
1 TTTGAATATA-TTTTAAAAA
*
47097857 TTTGAATTTATTTTAAAAA
1 TTTGAATATATTTTAAAAA
47097876 AATATACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTGAATATATTTTAAAAA
Found at i:47109389 original size:15 final size:17
Alignment explanation
Indices: 47109369--47109406 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
47109359 TTGACAAATT
47109369 ATTTTAA-TAAT-TTAA
1 ATTTTAAGTAATGTTAA
*
47109384 ATTTTAAGTAATGTTAT
1 ATTTTAAGTAATGTTAA
47109401 ATTTTA
1 ATTTTA
47109407 GTTTTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 4 0.20
17 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
ATTTTAAGTAATGTTAA
Found at i:47115852 original size:9 final size:10
Alignment explanation
Indices: 47115828--47115868 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
47115818 GTTATAAAAC
47115828 ATAATTATAT
1 ATAATTATAT
47115838 -TAATTATAT
1 ATAATTATAT
*
47115847 AT-ATTAAAT
1 ATAATTATAT
47115856 AATAATTATAT
1 -ATAATTATAT
47115867 AT
1 AT
47115869 TTATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 15 0.58
10 5 0.19
11 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATAATTATAT
Found at i:47115852 original size:18 final size:18
Alignment explanation
Indices: 47115831--47115874 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
47115821 ATAAAACATA
47115831 ATTATATTAATTATATAT
1 ATTATATTAATTATATAT
*
47115849 ATTAAATAATAATTATATAT
1 ATT--ATATTAATTATATAT
47115869 -TTATAT
1 ATTATAT
47115875 CAAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 3 0.14
18 3 0.14
19 2 0.09
20 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATTAATTATATAT
Found at i:47118652 original size:18 final size:18
Alignment explanation
Indices: 47118629--47118669 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
47118619 ACATTGCTTC
*
47118629 TAAAAAATATTTTTGAGA
1 TAAAAAATATTTTTAAGA
47118647 TAAAAAATATTTTTAAGA
1 TAAAAAATATTTTTAAGA
47118665 TAAAA
1 TAAAA
47118670 GTATTATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAAAAATATTTTTAAGA
Found at i:47124530 original size:5 final size:5
Alignment explanation
Indices: 47124520--47124559 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
47124510 AATAATTAAG
47124520 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
47124560 AAAAGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:47125656 original size:27 final size:28
Alignment explanation
Indices: 47125592--47125660 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
47125582 GAATATCAAA
*
47125592 CCCAAACACACCCGGAATATTATAAATCCT
1 CCCAAACACA-CCGG-ATATAATAAATCCT
*
47125622 -CCATAACACACCGG-TATAATATATCCT
1 CCCA-AACACACCGGATATAATAAATCCT
47125649 CCCAAACACACC
1 CCCAAACACACC
47125661 AATAAGGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 19 0.54
28 3 0.09
29 7 0.20
30 6 0.17
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.19
Consensus pattern (28 bp):
CCCAAACACACCGGATATAATAAATCCT
Done.