Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_pilon, whole genome shotgun sequence
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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1997640 original size:44 final size:44
Alignment explanation
Indices: 1997580--1997674 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
1997570 CAATAAATTC
* *
1997580 ATAAAAGATAGAAAAA-GAAGAAGAGAAAAAGAAAATAAGATAGA
1 ATAAAAGATAGAAAAAGGAA-AAGAGAAAAAGAAAAGAAGAAAGA
* *
1997624 ATAAAATATAGGAAAAGGAAAAGAGAAAAAGAAAAGAAGAAAGA
1 ATAAAAGATAGAAAAAGGAAAAGAGAAAAAGAAAAGAAGAAAGA
1997668 A-AAAAGA
1 ATAAAAGA
1997675 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 5 0.11
44 37 0.82
45 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (44 bp):
ATAAAAGATAGAAAAAGGAAAAGAGAAAAAGAAAAGAAGAAAGA
Found at i:1997668 original size:70 final size:72
Alignment explanation
Indices: 1997582--1997744 Score: 183
Period size: 73 Copynumber: 2.2 Consensus size: 72
1997572 ATAAATTCAT
* *
1997582 AAAAGATAGAAA-AAGAAGAAGAGAAAAAGAAAATAAGATAGAATAA-AATATAG-GAA-AAGGA
1 AAAAGA-AGAAAGAA-AA-AAGA-AAAAAGAAAA-AAGATAGAAAAAGAATA-AGAGAACAAGAA
1997643 AAAGA-GAAAAAG
60 AAAGAGGAAAAAG
1997655 AAAAGAAGAAAGAAAAAAGAAAAAAGAAAAAAGATAGAAAAAGAATAAGAGAACAAGAAAAAGAT
1 AAAAGAAGAAAGAAAAAAGAAAAAAGAAAAAAGATAGAAAAAGAATAAGAGAACAAGAAAAAGA-
*
1997720 GGAAGAAG
65 GGAAAAAG
*
1997728 AAAATAAAGAAAGAAAA
1 AAAA-GAAGAAAGAAAA
1997745 TAAAAAGAGA
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
69 13 0.16
70 17 0.22
71 13 0.16
72 7 0.09
73 18 0.23
74 11 0.14
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (72 bp):
AAAAGAAGAAAGAAAAAAGAAAAAAGAAAAAAGATAGAAAAAGAATAAGAGAACAAGAAAAAGAG
GAAAAAG
Found at i:1997670 original size:18 final size:18
Alignment explanation
Indices: 1997647--1997715 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
1997637 AAAGGAAAAG
1997647 AGAAAAAGAAAAGAAGAA
1 AGAAAAAGAAAAGAAGAA
1997665 AGAAAAAAGAAAA-AAGAA
1 AG-AAAAAGAAAAGAAGAA
*
1997683 A-AAAGATAGAAAAAGAATAA
1 AGAAA-A-AG-AAAAGAAGAA
*
1997703 GAGAACAAGAAAA
1 -AGAAAAAGAAAA
1997716 AGATGGAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
16 3 0.07
17 1 0.02
18 10 0.24
19 18 0.43
20 6 0.14
21 2 0.05
22 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (18 bp):
AGAAAAAGAAAAGAAGAA
Found at i:1997675 original size:25 final size:25
Alignment explanation
Indices: 1997641--1997718 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 25
1997631 ATAGGAAAAG
*
1997641 GAAAAGAGAAAAAGAAAAGAAGAAA
1 GAAAAAAGAAAAAGAAAAGAAGAAA
*
1997666 GAAAAAAGAAAAAAGAAAA-AAGATA
1 GAAAAAAG-AAAAAGAAAAGAAGAAA
1997691 G-AAAAAGAATAAGAGAACAAGAA-AAA
1 GAAAAAAGAA-AA-AGAA-AAGAAGAAA
1997717 GA
1 GA
1997719 TGGAAGAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 2 0.05
24 8 0.18
25 17 0.39
26 15 0.34
27 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.03
Consensus pattern (25 bp):
GAAAAAAGAAAAAGAAAAGAAGAAA
Found at i:1997677 original size:6 final size:6
Alignment explanation
Indices: 1997635--1997718 Score: 64
Period size: 6 Copynumber: 13.3 Consensus size: 6
1997625 TAAAATATAG
*
1997635 GAAAAG GAAAAGA GAAAAA G-AAAA GAAGAAA GAAAAAA GAAAAAA GAAAAA
1 GAAAAA GAAAA-A GAAAAA GAAAAA GAA-AAA G-AAAAA G-AAAAA GAAAAA
* * *
1997686 -AGATA GAAAAA GAATAAGA GAACAA GAAAAA GA
1 GAAAAA GAAAAA GAA-AA-A GAAAAA GAAAAA GA
1997719 TGGAAGAAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
5 8 0.12
6 27 0.42
7 23 0.36
8 6 0.09
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:1997718 original size:14 final size:14
Alignment explanation
Indices: 1997589--1997718 Score: 88
Period size: 14 Copynumber: 9.1 Consensus size: 14
1997579 CATAAAAGAT
*
1997589 AGAAAAAGAAGAAG
1 AGAAAAAGAAAAAG
1997603 AGAAAAAGAAAATA-
1 AGAAAAAGAAAA-AG
* * *
1997617 AGATAGAATAAAATAT
1 AGA-AAAAGAAAA-AG
* *
1997633 AGGAAAAGGAAAAG
1 AGAAAAAGAAAAAG
1997647 AGAAAAAG-AAAAG
1 AGAAAAAGAAAAAG
*
1997660 A-AGAAAGAAAAA-
1 AGAAAAAGAAAAAG
1997672 AGAAAAAAGAAAAAAG
1 AG-AAAAAG-AAAAAG
*
1997688 ATAGAAAAAGAATAAG
1 --AGAAAAAGAAAAAG
*
1997704 AGAACAAGAAAAAG
1 AGAAAAAGAAAAAG
1997718 A
1 A
1997719 TGGAAGAAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.07
13 10 0.11
14 40 0.43
15 21 0.23
16 7 0.08
17 6 0.07
18 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (14 bp):
AGAAAAAGAAAAAG
Found at i:1997741 original size:13 final size:13
Alignment explanation
Indices: 1997725--1997780 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
1997715 AAGATGGAAG
1997725 AAGAAAATAAAGA
1 AAGAAAATAAAGA
1997738 AAGAAAATAAA-A
1 AAGAAAATAAAGA
*
1997750 AGAGATGAAAAAAAGA
1 A-AGA--AAATAAAGA
*
1997766 GAGAAAATAAAGA
1 AAGAAAATAAAGA
1997779 AA
1 AA
1997781 ATAAATCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.06
13 23 0.66
15 9 0.26
16 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (13 bp):
AAGAAAATAAAGA
Found at i:1999642 original size:41 final size:42
Alignment explanation
Indices: 1999548--1999651 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
1999538 CCCAAATTGG
* * * *
1999548 TAAGTCCTTCAGGCCATCAGTTAGTCTTTCAAGCATGATGAT
1 TAAGTCCTTCGGGCCATCTGTCAGTCTTTCAAGCAAGATGAT
* * * *
1999590 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGTTGA-
1 TAAGTCCTTCGGGCCATCTGTCAGTCTTTCAAGCAAGATGAT
1999631 TAAGTCCTTCGGGCCATCTGT
1 TAAGTCCTTCGGGCCATCTGT
1999652 AAAACCTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
41 19 0.37
42 33 0.63
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTGTCAGTCTTTCAAGCAAGATGAT
Found at i:1999858 original size:42 final size:42
Alignment explanation
Indices: 1999811--1999910 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 42
1999801 TGGTAAGTCA
1999811 TTCGGGTCATC-AGTAAGTCTCTT-GAGC-ATGATGATTAAATCC
1 TTCGGGTCATCTAGTAAGTCT-TTCGAGCAAT-ATGA-TAAATCC
* *
1999853 TTCGGGTCA-CTTGTAAGTCTTTCGAGCAATATGATAAGTCC
1 TTCGGGTCATCTAGTAAGTCTTTCGAGCAATATGATAAATCC
*
1999894 TTCGGGCCATCTA-TAAG
1 TTCGGGTCATCTAGTAAG
1999911 ACCTTTGAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
41 21 0.42
42 27 0.54
43 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (42 bp):
TTCGGGTCATCTAGTAAGTCTTTCGAGCAATATGATAAATCC
Found at i:1999905 original size:256 final size:256
Alignment explanation
Indices: 1999290--2000064 Score: 1083
Period size: 257 Copynumber: 3.0 Consensus size: 256
1999280 TTCTTACTTA
* * * *
1999290 GTAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCAAGATCAATAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * * *
1999355 AGTCTTTCGACCAAGAGGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCA
66 AGTCTTTCGAGCAATATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGTAGGATGTTTTCA
* * * * *
1999420 CATGAATTTGAAAAATGAAAAAGTGATTTCCAAAGTTTATCATTTAATGTTTTCAAAAAATAAAA
131 CATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAA
1999485 TTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTG
196 TTTTT-AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTG
* * *
1999547 GTAAGTCCTTCAGGCCATCAGTTAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
*
1999612 AGTCTTTCGAGCAAGT-TGATAAGTCCTTCGGGCCATCTGTAAAACCTTCGGGTAGGATGTTCTT
66 AGTCTTTCGAGCAA-TATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGTAGGATGTT-TT
* *
1999676 -ACATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATCTAATGTTTTCATAAAATGA
129 CACATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGA
*
1999740 AATTTTTAAATAGAAAGAAAGTGATTTCCAAAGTTTCTTA-CCAGTAAATTATTTCCCAAATTG
194 AATTTTTAAA-AGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTG
* *
1999803 GTAAGTCATTCGGGTCATCAGTAAGTCTCTT-GAGCATGATGATTAAATCCTTCGGGTCA-CTTG
1 GTAAGTCCTTCGGGCCATCAGTAAGTCT-TTCGAGCATGATGATTAAATCCTTCGGGTCATC-TG
* * * * *
1999866 TAAGTCTTTCGAGCAATATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGAGCAGGATGTTTT
64 TCAGTCTTTCGAGCAATATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGTAGGATGTTTT
** * *** * *
1999931 CACATGATTTTTTAAAAAAATGAGAAAGCGATTTTTGAATTTTCTCATTTAATGTTTTCAGAAAA
129 CACAT-A-AATTT-GAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAA
* *
1999996 TGAAATTTTTAAAAACTAATAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAAT
191 TGAAATTTTT-AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAAT
2000061 TG
255 TG
2000063 GT
1 GT
2000065 CTATCAGATG
Statistics
Matches: 462, Mismatches: 44, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
255 4 0.01
256 138 0.30
257 207 0.45
258 5 0.01
259 80 0.17
260 28 0.06
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (256 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
AGTCTTTCGAGCAATATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGTAGGATGTTTTCA
CATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAA
TTTTTAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTG
Found at i:2000538 original size:38 final size:38
Alignment explanation
Indices: 2000496--2000672 Score: 300
Period size: 38 Copynumber: 4.7 Consensus size: 38
2000486 GAAGCTTCAA
* * *
2000496 CTTGACTTTCTCGTGAAAAGAAGTCAATCTTTGTTACT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
2000534 CTTGACTTCCTCGTGAAGAGAAGTTAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
2000572 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
2000610 CTTGACTTACTCGTGAAGAGAAGTCAATCTTTTTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
2000648 CTTGACTTCCTCGTGAAGAGAAGTC
1 CTTGACTTCCTCGTGAAGAGAAGTC
2000673 TGTAATACCC
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 131 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (38 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:2002581 original size:59 final size:59
Alignment explanation
Indices: 2002482--2002610 Score: 152
Period size: 59 Copynumber: 2.2 Consensus size: 59
2002472 CAGCAGGCTG
** *
2002482 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTAGG-CACAACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGT-GGACACAACCTTATGTGT
* ** * **
2002541 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGGCCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
*
2002600 CATACTCGGGA
1 CATATTCGGGA
2002611 TTGCATTACG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.03
59 57 0.97
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:2002707 original size:20 final size:20
Alignment explanation
Indices: 2002667--2002708 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2002657 TTGTATATTG
* *
2002667 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
2002687 GGCTATTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
2002707 GG
1 GG
2002709 TTATGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:2002777 original size:44 final size:44
Alignment explanation
Indices: 2002709--2002900 Score: 302
Period size: 44 Copynumber: 4.4 Consensus size: 44
2002699 TGGTATATGG
* *
2002709 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
2002753 TTATGGATAAATGGTAAGTATATT-GT-AAATAAGCTTAC-AGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
2002794 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
2002838 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGTTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
2002882 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
2002901 ATATTGCACA
Statistics
Matches: 139, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
41 27 0.19
42 14 0.10
43 14 0.10
44 72 0.52
45 2 0.01
46 10 0.07
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:2002852 original size:85 final size:88
Alignment explanation
Indices: 2002709--2002900 Score: 302
Period size: 85 Copynumber: 2.2 Consensus size: 88
2002699 TGGTATATGG
* *
2002709 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTA
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTA
2002773 TATT-GT-AAATAAGCTTAC-AGC
65 TATTGGTAAAATAAGCTTACGAGC
2002794 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTAT
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTAT
*
2002859 ATTGGTAAAATAAGTTTACGAGC
66 ATTGGTAAAATAAGCTTACGAGC
2002882 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
2002901 ATATTGCACA
Statistics
Matches: 98, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
85 64 0.65
86 3 0.03
87 11 0.11
88 9 0.09
89 1 0.01
90 10 0.10
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (88 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTAT
ATTGGTAAAATAAGCTTACGAGC
Found at i:2003921 original size:38 final size:38
Alignment explanation
Indices: 2003773--2003921 Score: 194
Period size: 38 Copynumber: 3.9 Consensus size: 38
2003763 GGGTGTTACA
* **
2003773 AAGTCAATCTTTGTTATTCTTGACTTCCTTGTAAAGAG
1 AAGTCAATCTTTGTTATTCTTGACTTCCTCGCGAAGAG
* * *
2003811 AAGTAAATCTTTGTT-TCTCTTGACTTCCTCGTGAAGAT
1 AAGTCAATCTTTGTTAT-TCTTGACTTCCTCGCGAAGAG
* *
2003849 AAGTCAATCTTTGTTATTCCTGACTCTCGT-GCGAAGAG
1 AAGTCAATCTTTGTTATTCTTGACT-TCCTCGCGAAGAG
2003887 AAGTCAATCTTTGTTATTCTTGACTTCCTCGCGAA
1 AAGTCAATCTTTGTTATTCTTGACTTCCTCGCGAA
2003922 AAAAAAGGCA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
37 4 0.04
38 88 0.92
39 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (38 bp):
AAGTCAATCTTTGTTATTCTTGACTTCCTCGCGAAGAG
Found at i:2003992 original size:45 final size:45
Alignment explanation
Indices: 2003940--2004072 Score: 151
Period size: 45 Copynumber: 3.0 Consensus size: 45
2003930 CAATCTTTCG
* *
2003940 GTGTTGT-CTTCCTTGACTTTCTCGTGAAGAGGAGTCAATATTTTA
1 GTGTTGTCCTT-CTTGACTTTCTCATGAAGAGAAGTCAATATTTTA
* * * * **
2003985 GTGTTGTCCTTCTTGACTTTTTCACGAAGAAAAATCAATCCTTTA
1 GTGTTGTCCTTCTTGACTTTCTCATGAAGAGAAGTCAATATTTTA
* * *
2004030 ATGTTGTCCTTTTTGACTTTCTCATGTAGAGAAGTCAATATTT
1 GTGTTGTCCTTCTTGACTTTCTCATGAAGAGAAGTCAATATTT
2004073 CTGTAATGTT
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
45 67 0.96
46 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (45 bp):
GTGTTGTCCTTCTTGACTTTCTCATGAAGAGAAGTCAATATTTTA
Found at i:2004839 original size:134 final size:134
Alignment explanation
Indices: 2004675--2005751 Score: 1535
Period size: 134 Copynumber: 8.1 Consensus size: 134
2004665 TCTTTGAAAG
* * * * *
2004675 GTCTGAACTCCCCTAAAGAGTAGTGGAGCAGATTTTTCTTCTTTCAGATTTGGTATTCCTCAAAA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
** *
2004740 ATAGTGAAGCAAATAGATTTTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTC
66 GCAGTGAAGCAAATAGATTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTC
2004805 TCGA
131 TCGA
* *
2004809 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTT-TTTCAAATTTGGTCTTCTTGAAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * * * * *
2004873 GCAGTAAAGTAAATCGA-TTCTGATTAAATATTCCCTGAAGAGCAGCGAAGTGGATCAAAGTTTT
66 GCAGTGAAGCAAATAGATTTC-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
*
2004937 CTCAA
130 CTCGA
* * *
2004942 GTCTGATCTCCCCTAAAGAGTAATGGAGCATATTTTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * *
2005007 GCGGTGAAGCAAATTGA-TTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCGAAGTTTTC
66 GCAGTGAAGCAAATAGATTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTC
2005071 TCGA
131 TCGA
* * * *
2005075 GTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTATTCTTCTTTCAGATTTGGTCTTCTTGAAAA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * * *
2005140 GCAGTGAAGCAAATCA-AATTCGATTCAATCTTCACTGAAGAGAAGTGAAGTGGATCAATGTTTT
66 GCAGTGAAGCAAAT-AGATTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
2005204 CTCGA
130 CTCGA
2005209 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * * *
2005274 GCAGTGAAGCAAATCGA-TTCTAATTTAATCTTCCCTGAAGAGCAGTGAAGTGGATCGAAGTTTT
66 GCAGTGAAGCAAATAGATTTC-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
2005338 CTCGA
130 CTCGA
* *
2005343 GTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGGCTTCCTGAAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * * * *
2005408 GCAGTGAAGCAAATCA-AATTCGATTCAATCTTCACTGAATAGAAGTGAAGTGGATCAATGTTTT
66 GCAGTGAAGCAAAT-AGATTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
*
2005472 ATCGA
130 CTCGA
2005477 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* *
2005542 GCAGTGAAGCAAATTGA-TTCTGATTCAATCTTCCCTGAAGAGCAGTGAAGTTGATCAAAGTTTT
66 GCAGTGAAGCAAATAGATTTC-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTT
2005606 CTCGA
130 CTCGA
* * * *
2005611 GTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCATCTTCTTTCAGATTTGGTATTCCTGGAGA
1 GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
* * * * *
2005676 GCAGTGAAGCAAATCGATTTCGATTCAATTTTCCCTGAAGAACAGTGGAA-TGAATCAATG-TTT
66 GCAGTGAAGCAAATAGATTTCGATTCAATCTTCCCTGAAGAGCAGT-GAAGTGGATCAAAGTTTT
2005739 CTCGA
130 CTCGA
*
2005744 -TCTAATCT
1 GTCTGATCT
2005752 ACCATGCAGA
Statistics
Matches: 848, Mismatches: 83, Indels: 26
0.89 0.09 0.03
Matches are distributed among these distances:
132 9 0.01
133 244 0.29
134 586 0.69
135 9 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (134 bp):
GTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGA
GCAGTGAAGCAAATAGATTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTC
TCGA
Found at i:2005937 original size:3 final size:3
Alignment explanation
Indices: 2005913--2006055 Score: 211
Period size: 3 Copynumber: 48.0 Consensus size: 3
2005903 GGACCCATTT
* *
2005913 TTA TTT TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2005959 TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2006002 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2006050 TTA TTA
1 TTA TTA
2006056 AGATTTATTT
Statistics
Matches: 129, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
2 6 0.05
3 117 0.91
4 6 0.05
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2011883 original size:20 final size:20
Alignment explanation
Indices: 2011811--2011884 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
2011801 CAAAAATAAC
* *
2011811 TTTTTGATATCTCCCTTGTG
1 TTTTTGAAATTTCCCTTGTG
* * *
2011831 TTTTTAAAATTTCCCACTATAG
1 TTTTTGAAATTTCCC-TTGT-G
* *
2011853 -TATTGATATTTCCCTTGTG
1 TTTTTGAAATTTCCCTTGTG
2011872 TTTTTGAAATTTC
1 TTTTTGAAATTTC
2011885 ACAAAATAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 1 0.03
20 24 0.62
21 13 0.33
22 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTTGAAATTTCCCTTGTG
Found at i:2013171 original size:23 final size:21
Alignment explanation
Indices: 2013145--2013218 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 21
2013135 AAGGGCAACA
*
2013145 TAGAGATGTCTCGAAGGACCATG
1 TAGA-ATGTC-CGAAGGACCACG
*
2013168 TAGAAATGTCCTGAATGACCACG
1 TAG-AATGTCC-GAAGGACCACG
* *
2013191 TAGAATTGTCCCGAAGGATCGCG
1 TAGAA-TGT-CCGAAGGACCACG
2013214 TAGAA
1 TAGAA
2013219 GCCTCAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 3 0.07
23 36 0.86
24 3 0.07
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (21 bp):
TAGAATGTCCGAAGGACCACG
Found at i:2016151 original size:22 final size:22
Alignment explanation
Indices: 2016101--2016151 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
2016091 TATTAATAAA
*
2016101 ATTAATATTATTTATTAATTTC
1 ATTAAAATTATTTATTAATTTC
*
2016123 ATAAAAATTATTTTATTGAA-TT-
1 ATTAAAATTA-TTTATT-AATTTC
2016145 ATTAAAA
1 ATTAAAA
2016152 ATTTAAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 14 0.58
23 8 0.33
24 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTAAAATTATTTATTAATTTC
Found at i:2019733 original size:32 final size:32
Alignment explanation
Indices: 2019660--2019733 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
2019650 GTTCAATTAC
* *
2019660 TGATGTGACATATGTCATGTTATTATTTTAGG
1 TGATGTGACATATATCACGTTATTATTTTAGG
** * *
2019692 TGACATGACATATATTACGTTATTATTTTGGG
1 TGATGTGACATATATCACGTTATTATTTTAGG
2019724 TGATGTGACA
1 TGATGTGACA
2019734 CATGTAAATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (32 bp):
TGATGTGACATATATCACGTTATTATTTTAGG
Found at i:2021726 original size:17 final size:18
Alignment explanation
Indices: 2021701--2021738 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2021691 ACTTAGTATT
2021701 TTTAGTAAAATAAAAT-A
1 TTTAGTAAAATAAAATGA
* *
2021718 TTTATTAAAATTAAATGA
1 TTTAGTAAAATAAAATGA
2021736 TTT
1 TTT
2021739 TAGATGTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TTTAGTAAAATAAAATGA
Found at i:2022694 original size:23 final size:23
Alignment explanation
Indices: 2022650--2022701 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2022640 TCAATATATT
* **
2022650 CTTTTTTAATTGGTTTTGGATTA
1 CTTTTTTAATTGATTTCAGATTA
* *
2022673 CTTTTTTTATTGATTTCAGATTG
1 CTTTTTTAATTGATTTCAGATTA
2022696 CTTTTT
1 CTTTTT
2022702 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.63
Consensus pattern (23 bp):
CTTTTTTAATTGATTTCAGATTA
Found at i:2023584 original size:23 final size:23
Alignment explanation
Indices: 2023553--2023621 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2023543 AAACTAAACT
*
2023553 GAACCAGATACATTTACCAACCC
1 GAACTAGATACATTTACCAACCC
** * *
2023576 GAACTAGATTTATTAACCAACTC
1 GAACTAGATACATTTACCAACCC
* *
2023599 GAACTGGATCCATTTACCAACCC
1 GAACTAGATACATTTACCAACCC
2023622 AAATTGGATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.23
Consensus pattern (23 bp):
GAACTAGATACATTTACCAACCC
Found at i:2023694 original size:18 final size:18
Alignment explanation
Indices: 2023671--2023714 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2023661 GTTTGACCTA
*
2023671 GTTTGATTGACTTGATAT
1 GTTTGATCGACTTGATAT
2023689 GTTTGATCGACTTGATAT
1 GTTTGATCGACTTGATAT
2023707 GTTTGATC
1 GTTTGATC
2023715 TAGTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.48
Consensus pattern (18 bp):
GTTTGATCGACTTGATAT
Found at i:2026369 original size:21 final size:21
Alignment explanation
Indices: 2026343--2026383 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2026333 TTTCATTGAA
*
2026343 AAGAAAA-AAATAAATGAAAAG
1 AAGAAAAGAAA-AAAGGAAAAG
2026364 AAGAAAAGAAAAAAGGAAAA
1 AAGAAAAGAAAAAAGGAAAA
2026384 AGGTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
AAGAAAAGAAAAAAGGAAAAG
Found at i:2027806 original size:21 final size:21
Alignment explanation
Indices: 2027782--2027843 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
2027772 CAGAGACACT
*
2027782 TACCAAAGTACTTCATCTACA
1 TACCAAGGTACTTCATCTACA
*
2027803 TACCAAGGTACTTCACCTACA
1 TACCAAGGTACTTCATCTACA
*
2027824 TTCCAAGGTACTTCATCTAC
1 TACCAAGGTACTTCATCTAC
2027844 TTCCACTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (21 bp):
TACCAAGGTACTTCATCTACA
Found at i:2029559 original size:13 final size:13
Alignment explanation
Indices: 2029541--2029566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2029531 TTCGGGTAAG
2029541 TGTTTTTCAAGCA
1 TGTTTTTCAAGCA
2029554 TGTTTTTCAAGCA
1 TGTTTTTCAAGCA
2029567 CTAGGATCCA
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:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TGTTTTTCAAGCA
Found at i:2032070 original size:54 final size:54
Alignment explanation
Indices: 2031956--2032402 Score: 605
Period size: 54 Copynumber: 8.3 Consensus size: 54
2031946 TTACCAAATA
2031956 GGCACTAAGTGTGCAAAGTACGAAATTCATCA-ATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
2032009 GGCACTAAGTGTGCAAAGTACAAAATTCATTATATGTTGATAAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
2032063 GGTACTAAATGTGCAAA-TAACGAAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
2032117 GACACTAAGTGTGCAAAGTACGTAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* **
2032171 GGCACTAAGTGTGCAAAGTACGTAATTCATCATATGTTGATGAATAAATGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * * *
2032225 AGCACTAAGTGTG-AAAATCACGGAATTCATCATATGTTGATGAATAACTGTTTT
1 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATATGTTGATGAATAACCGTTTC
** * *
2032279 AACACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATAAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
2032333 AGCATTAAGTGTGC-AATTAACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
2032387 GACACTATGTGTGCAA
1 GGCACTAAGTGTGCAA
2032403 CCCACAAAAT
Statistics
Matches: 349, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
53 37 0.11
54 307 0.88
55 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:2032380 original size:27 final size:27
Alignment explanation
Indices: 2032298--2032380 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
2032288 TGTGCAAAGC
*
2032298 ACGAAATTCATCATATGTTGATAAATA
1 ACGAAATTCATCATATGTTGATGAATA
* * *
2032325 ACCG--TTTCAGCATTAAG-TG-TGCAATTA
1 A-CGAAATTCATCA-TATGTTGATG-AA-TA
2032352 ACGAAATTCATCATATGTTGATGAATA
1 ACGAAATTCATCATATGTTGATGAATA
2032379 AC
1 AC
2032381 CGTTTCGACA
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
25 1 0.02
26 12 0.29
27 14 0.34
28 12 0.29
29 2 0.05
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (27 bp):
ACGAAATTCATCATATGTTGATGAATA
Found at i:2037353 original size:29 final size:29
Alignment explanation
Indices: 2037308--2037368 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
2037298 AGGAAAGCTG
2037308 ATAAGATCGAAAGACATTACTAAGAACTC
1 ATAAGATCGAAAGACATTACTAAGAACTC
*
2037337 ATAAGATTGAGAA-ACATTACTAAGAACTC
1 ATAAGATCGA-AAGACATTACTAAGAACTC
2037366 ATA
1 ATA
2037369 GTAACCTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (29 bp):
ATAAGATCGAAAGACATTACTAAGAACTC
Found at i:2043467 original size:18 final size:19
Alignment explanation
Indices: 2043442--2043525 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
2043432 AAATTTAGTT
2043442 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* **
2043460 TGTATATTATAAATT-TGGTT-
1 T-T-TA-TATTAATTATAATTC
*
2043480 TTTATATTAGTTATAATTC
1 TTTATATTAATTATAATTC
*
2043499 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
2043518 -TTATATTA
1 TTTATATTA
2043526 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.11
18 14 0.26
19 20 0.38
20 6 0.11
21 7 0.13
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:2043475 original size:38 final size:39
Alignment explanation
Indices: 2043432--2043508 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
2043422 TTACCTTTTG
2043432 AAATTTAGTTTTTATATTAATTATAATT-TGTATATTAT
1 AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
* * *
2043470 AAATTTGGTTTTTATATTAGTTATAATTCTTTATATTAT
1 AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
2043509 TTATAATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 26 0.74
39 9 0.26
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (39 bp):
AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
Found at i:2043504 original size:19 final size:19
Alignment explanation
Indices: 2043480--2043525 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
2043470 AAATTTGGTT
2043480 TTTATATTAGTTATAATTC
1 TTTATATTAGTTATAATTC
*
2043499 TTTATATTATTTATAATTC
1 TTTATATTAGTTATAATTC
2043518 -TTATATTA
1 TTTATATTA
2043526 TAAATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATATTAGTTATAATTC
Found at i:2043539 original size:13 final size:14
Alignment explanation
Indices: 2043505--2043541 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2043495 ATTCTTTATA
2043505 TTATTTAT-AATTC
1 TTATTTATAAATTC
2043518 TTATATTATAAATT-
1 TTAT-TTATAAATTC
2043532 TTATTTATAA
1 TTATTTATAA
2043542 TCATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:2046207 original size:82 final size:82
Alignment explanation
Indices: 2046051--2046268 Score: 212
Period size: 82 Copynumber: 2.7 Consensus size: 82
2046041 CACTTTAGCG
* * * ** * * * *
2046051 GTTTTT-TATACAATCGCCGTAATA-GGTTCATCCATAATGGCGCTTCTTAACAAATGCCATGAC
1 GTTTTTATATA-AAT-GCCATAATAGGGTTCATCTATAGTGGCATTTTTTAATAAATACCAT-AA
2046114 AA-AGTAGTACTTTAAC-GAT
63 AAGAGTAGTACTTTAACAG-T
**** **
2046133 GTTTTTATATAAATTTTGT-ATAGGGTTCATCTATAGTGGTGTTTTTTCAATAAATACCATAAAA
1 GTTTTTATATAAATGCCATAATAGGGTTCATCTATAGTGGCATTTTTT-AATAAATACCATAAAA
*
2046197 GAGTAGTACTTTAGCAGT
65 GAGTAGTACTTTAACAGT
2046215 GTTTTTATATAAATGCCATAATAGGGTTCATCTATAGTGGCATTTTTTAATAAA
1 GTTTTTATATAAATGCCATAATAGGGTTCATCTATAGTGGCATTTTTTAATAAA
2046269 CGCGCTAAAC
Statistics
Matches: 112, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
80 3 0.03
81 24 0.21
82 54 0.48
83 31 0.28
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (82 bp):
GTTTTTATATAAATGCCATAATAGGGTTCATCTATAGTGGCATTTTTTAATAAATACCATAAAAG
AGTAGTACTTTAACAGT
Found at i:2059031 original size:18 final size:18
Alignment explanation
Indices: 2059010--2059053 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2059000 AAGATTAAGA
2059010 TTTGGGTTTGGATTCAGG
1 TTTGGGTTTGGATTCAGG
**
2059028 TTTGGGTTTGGATTTGGG
1 TTTGGGTTTGGATTCAGG
2059046 TTTGGGTT
1 TTTGGGTT
2059054 CATGTTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.02, G:0.41, T:0.50
Consensus pattern (18 bp):
TTTGGGTTTGGATTCAGG
Found at i:2059071 original size:6 final size:6
Alignment explanation
Indices: 2059010--2059053 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
2059000 AAGATTAAGA
* ** *
2059010 TTTGGG TTTGGA TTCAGG TTTGGG TTTGGA TTTGGG TTTGGG TT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TT
2059054 CATGTTTGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.07, C:0.02, G:0.41, T:0.50
Consensus pattern (6 bp):
TTTGGG
Found at i:2059523 original size:103 final size:99
Alignment explanation
Indices: 2059292--2059613 Score: 355
Period size: 103 Copynumber: 3.2 Consensus size: 99
2059282 GGAAGAATCC
* * * *
2059292 GGATGAACACAGATGAACAAGGGTTTAATTTTTGGGTGTTTGATAAAAAAATAGGAATGAGTTTA
1 GGATGAACACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGATAAAAAAAT-GAAATG-GTTTG
* * *
2059357 GGTTTTGGTGTTTGTCAAGATCAAATAATGG--TTTG
64 GGTTTTGGTGTTTGTGAAGATCAAA-GAGGGTTTTTG
* ** * **
2059392 GGAAAGAACTGGGAT-AAAAAGGGTTGAA-TTTTGTATGTTTGATCGAGAAAAAATGAAATGGTT
1 GG-ATGAACACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGAT--A-AAAAAATGAAATGGTT
* *
2059455 TGGGTTTTGGTGTTTGTGAATATTAAAGGAGGGTTTTTTG
62 TGGGTTTTGGTGTTTGTGAAGATCAAA-GAGGG-TTTTTG
*
2059495 GGATGAACATGGATGAACAAGGGTTGAATTTTTGGGTGTTTGATAAAAAAACATGAAATGGTTTG
1 GGATGAACACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGAT-AAAAAA-ATGAAATGGTTTG
*
2059560 TGTTTTGGTGTTTGTGAAGATCAGAAGAGGGTTTTTG
64 GGTTTTGGTGTTTGTGAAGATCA-AAGAGGGTTTTTG
2059597 GGATGAACACGGATGAA
1 GGATGAACACGGATGAA
2059614 AAAAGATGAA
Statistics
Matches: 184, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
99 13 0.07
100 42 0.23
101 14 0.08
102 43 0.23
103 57 0.31
104 15 0.08
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (99 bp):
GGATGAACACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGATAAAAAAATGAAATGGTTTGGG
TTTTGGTGTTTGTGAAGATCAAAGAGGGTTTTTG
Found at i:2063380 original size:25 final size:25
Alignment explanation
Indices: 2063333--2063396 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
2063323 CAATTCTTTC
* *
2063333 AATTAATATATATGTTTATATTAATA
1 AATTAATATATA-GTTTAAATTAACA
2063359 AATTAATATATAGTTTAAATTAACA
1 AATTAATATATAGTTTAAATTAACA
2063384 AATTAATATATAG
1 AATTAATATATAG
2063397 GTTATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (25 bp):
AATTAATATATAGTTTAAATTAACA
Found at i:2063438 original size:35 final size:33
Alignment explanation
Indices: 2063387--2063473 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
2063377 ATTAACAAAT
*
2063387 TAATATATAGGTTATATATACGAATGAACTATA
1 TAATATATAGTTTATATATACGAATGAACTATA
* *
2063420 TAATATATAGTTTATATATACTAATGAATTATA
1 TAATATATAGTTTATATATACGAATGAACTATA
*
2063453 TACTATATAGTTTATATATAC
1 TAATATATAGTTTATATATAC
2063474 CATATAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (33 bp):
TAATATATAGTTTATATATACGAATGAACTATA
Found at i:2063439 original size:18 final size:18
Alignment explanation
Indices: 2063416--2063490 Score: 84
Period size: 18 Copynumber: 4.3 Consensus size: 18
2063406 ACGAATGAAC
*
2063416 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
**
2063434 TATATACTA-AT-GAAT-
1 TATATACTATATAGTTTA
2063449 TATATACTATATAGTTTA
1 TATATACTATATAGTTTA
* *
2063467 TATATACCATATAATTTA
1 TATATACTATATAGTTTA
2063485 TATATA
1 TATATA
2063491 GTTTTTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 9 0.19
16 4 0.09
17 4 0.09
18 30 0.64
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:2063499 original size:13 final size:13
Alignment explanation
Indices: 2063481--2063506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2063471 TACCATATAA
2063481 TTTATATATAGTT
1 TTTATATATAGTT
2063494 TTTATATATAGTT
1 TTTATATATAGTT
2063507 CATATGTAAA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTATATATAGTT
Found at i:2063687 original size:20 final size:20
Alignment explanation
Indices: 2063664--2063889 Score: 56
Period size: 20 Copynumber: 10.8 Consensus size: 20
2063654 TCAACTATAG
2063664 TATATAGTTTATATATAAAT
1 TATATAGTTTATATATAAAT
* * **
2063684 TATAT--TTAATGTAGTTTAT
1 TATATAGTTTATATA-TAAAT
* * *
2063703 ATATATAGTTCATATGTAAAC
1 -TATATAGTTTATATATAAAT
* *
2063724 TATACTA-TATATATATATAT
1 TATA-TAGTTTATATATAAAT
* *
2063744 TATAGTA-TATAAATATCAACTAT
1 TATA-TAGTTTATATAT-AA--AT
*
2063767 AGTATATAGTTTATATACAAA-
1 --TATATAGTTTATATATAAAT
2063788 T-TATAGTTTATATATATATAT
1 TATATAGTTTATATATA-A-AT
*
2063809 ATATATA-TATATATATATATCAT
1 -TATATAGT-T-TATATATA-AAT
* *
2063832 TACATA-TATACTATATAAATAGTT
1 TATATAGTTTA-TATAT-AA-A--T
* *
2063856 TATATAG-TTATACATAAAC
1 TATATAGTTTATATATAAAT
2063875 TATATAGTTTATATA
1 TATATAGTTTATATA
2063890 GTTTATATGT
Statistics
Matches: 150, Mismatches: 31, Indels: 50
0.65 0.13 0.22
Matches are distributed among these distances:
18 20 0.13
19 12 0.08
20 45 0.30
21 11 0.07
22 18 0.12
23 13 0.09
24 21 0.14
25 10 0.07
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATAGTTTATATATAAAT
Found at i:2063773 original size:65 final size:64
Alignment explanation
Indices: 2063700--2063824 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
2063690 TAATGTAGTT
**
2063700 TATATATATAGTTCATATGTAAACTATACTATATATATATATAT-TATAGTATATAAATATCAAC
1 TATATATATAGTTCATATACAAACTATACTATATATATATATATATATA-TATATAAATATCAAC
* * * * *
2063764 TATAGTATATAGTTTATATACAAATTATAGTTTATATATATATATATATATATATATATAT
1 TATA-TATATAGTTCATATACAAACTATACTATATATATATATATATATATATATAAATAT
2063825 ATATCATTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 4 0.08
65 44 0.85
66 4 0.08
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (64 bp):
TATATATATAGTTCATATACAAACTATACTATATATATATATATATATATATATAAATATCAAC
Found at i:2063839 original size:105 final size:106
Alignment explanation
Indices: 2063639--2063848 Score: 288
Period size: 105 Copynumber: 2.0 Consensus size: 106
2063629 AATTATAGTA
* * *
2063639 TATAGTATATAAATATCAACTATAGTATATAGTTTATATATAAATTATATTTAATGTAGTTTATA
1 TATAGTATATAAATATCAACTATAGTATATAGTTTATATACAAATTATATTTAATATAGTATATA
*
2063704 TATATAGTTCATATGTAAACTATACTATATATA-TATATAT
66 TATATAGTTCATATATAAACTATACTATATATACTATATAT
2063744 TATAGTATATAAATATCAACTATAGTATATAGTTTATATACAAATTATAGTTTATATATA-TATA
1 TATAGTATATAAATATCAACTATAGTATATAGTTTATATACAAATTATA-TTTA-ATATAGTATA
*
2063808 TATATATA-TAT-ATATATATA-TCATTAC-ATATATACTATATA
64 TATATATAGT-TCATATATAAACT-A-TACTATATATACTATATA
2063849 AATAGTTTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
104 1 0.01
105 64 0.68
106 25 0.27
107 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (106 bp):
TATAGTATATAAATATCAACTATAGTATATAGTTTATATACAAATTATATTTAATATAGTATATA
TATATAGTTCATATATAAACTATACTATATATACTATATAT
Found at i:2063862 original size:9 final size:9
Alignment explanation
Indices: 2063850--2063897 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
2063840 TACTATATAA
2063850 ATAGTTTAT
1 ATAGTTTAT
*
2063859 ATAGTTATAC
1 ATAGTT-TAT
***
2063869 ATAAACTAT
1 ATAGTTTAT
2063878 ATAGTTTAT
1 ATAGTTTAT
2063887 ATAGTTTAT
1 ATAGTTTAT
2063896 AT
1 AT
2063898 GTGAACTACC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 25 0.83
10 5 0.17
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (9 bp):
ATAGTTTAT
Found at i:2063993 original size:96 final size:93
Alignment explanation
Indices: 2063817--2063993 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 93
2063807 ATATATATAT
2063817 ATATATATATATCATTACATATATACTATATAAATAGTTTATATAGTTATACATAAACTATATAG
1 ATATATATATATCATTACATATATACTATATAAATAGTTTATATAGTTATACATAAACTATATAG
* *
2063882 TTTATATAGTTTATATGTGAACTACCTA
66 TATATATAGTGTATATGTGAACTACCTA
* * * **
2063910 ATATATATATATTA-TATATATATA-TATATATATAGTTTATACATTTAGTTCATATGTAAACTA
1 ATATATATATATCATTACATATATACTATATAAATAGTTTAT--A--TAGTT-ATACATAAACTA
2063973 TATAGTATATATAGTGTATAT
61 TATAGTATATATAGTGTATAT
2063994 ATAATTCATA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
91 15 0.21
92 9 0.12
93 14 0.19
95 5 0.07
96 29 0.40
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (93 bp):
ATATATATATATCATTACATATATACTATATAAATAGTTTATATAGTTATACATAAACTATATAG
TATATATAGTGTATATGTGAACTACCTA
Found at i:2064034 original size:11 final size:11
Alignment explanation
Indices: 2063978--2064016 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2063968 AACTATATAG
* *
2063978 TATATATAGTG
1 TATATATAATT
2063989 TATATATAATT
1 TATATATAATT
*
2064000 CATATATAATT
1 TATATATAATT
2064011 TATATA
1 TATATA
2064017 AAAATATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (11 bp):
TATATATAATT
Found at i:2064106 original size:82 final size:82
Alignment explanation
Indices: 2064076--2064288 Score: 194
Period size: 79 Copynumber: 2.6 Consensus size: 82
2064066 TAGTTCATAT
2064076 ATAAACTATATAGTTTATATATATATATATACTATATATATATATATATATAAACTATAGAGTTT
1 ATAAACTATATAGTTTATATATATATATATACTATATATATATATATATATAAACTATAGAGTTT
*
2064141 ATATATAGTTTATATTA
66 ATATATAGTTAATATTA
* ** *
2064158 ATAAACTATATAGTTATACATAATATATATATTTTTTATATAATATATAATAATATAAA-TAT-G
1 ATAAACTATATAGTT-TATAT-ATATATATATACTATATAT-ATATAT-AT-ATATAAACTATAG
*
2064221 A----ACTATATAGTT--TA-TC
61 AGTTTA-TATATAGTTAATATTA
* *
2064237 ATAATA-TATATAGTTTATATATATAAATATAAACTATATAGTATTTATATAT
1 ATAA-ACTATATAGTTTATATATAT--ATATATACTATATA-TATATATATAT
2064289 TATATATGGA
Statistics
Matches: 110, Mismatches: 11, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
77 6 0.05
78 6 0.05
79 29 0.26
80 4 0.04
81 1 0.01
82 24 0.22
83 4 0.04
84 16 0.15
85 8 0.07
86 5 0.05
87 7 0.06
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (82 bp):
ATAAACTATATAGTTTATATATATATATATACTATATATATATATATATATAAACTATAGAGTTT
ATATATAGTTAATATTA
Found at i:2064308 original size:2 final size:2
Alignment explanation
Indices: 2063724--2064295 Score: 140
Period size: 2 Copynumber: 278.5 Consensus size: 2
2063714 ATATGTAAAC
*
2063724 TA TA CTA TA TA TA TA TA TA T- TA TA GTA TA TA AA TA TCA -A CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA
* * * *
2063766 TA GTA TA TA GTT TA TA TA CA AA T- TA TA GTT TA TA TA TA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
2063808 TA TA TA TA TA TA TA TA TA TA TCA T- TA CA TA TA TA CTA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA
* * * * *
2063851 TA GTT TA TA TA GT- TA TA CA TA AA CTA TA TA GTT TA TA TA GTT TA
1 TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA
* **
2063895 TA TG TGA -A CTA CC TA -A TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2063936 TA TA TA TA GTT TA TA CA TT TA GT- TCA TA TG TA AA CTA TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA -TA TA TA -TA
* * * *
2063980 TA TA TA GTG TA TA TA TA -A T- TCA TA TA TA -A TT TA TA TA AA AA
1 TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * * *
2064021 TA TA CA -A TT TA TA T- TA -A TA AA CTA TG TA GTT TA TA TA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA
* *
2064062 TCA -A TA GT- TCA TA TA TA AA CTA TA TA GTT TA TA TA TA TA TA TA
1 T-A TA TA -TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * *
2064105 TA CTA TA TA TA TA TA TA TA TA TA AA CTA TA GA GTT TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * *
2064148 GTT TA TA T- TA -A TA AA CTA TA TA GT- TA TA CA TA -A TA TA TA
1 -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
2064187 TA T- TT TT TA TA TA -A TA TA TA -A TA -A TA TA AA TA TGA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA
* * *
2064226 TA TA GTT TA TCA TA -A TA TA TA TA GTT TA TA TA TA TA AA TA TA
1 TA TA -TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
2064268 AA CTA TA TA GTA TT TA TA TA T- TA TA TA T
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA T
2064296 GGACTATATA
Statistics
Matches: 414, Mismatches: 83, Indels: 146
0.64 0.13 0.23
Matches are distributed among these distances:
1 29 0.07
2 335 0.81
3 50 0.12
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2071564 original size:101 final size:102
Alignment explanation
Indices: 2071389--2071592 Score: 392
Period size: 101 Copynumber: 2.0 Consensus size: 102
2071379 CTATGGCTAT
*
2071389 ATTCTAGATTGATATTATGCATGCATATGGTCGGATTAATTCACTTCAAGTCAGCCATTGTCCAA
1 ATTCTAGATTGATATTATGCATGCATATGGTCGAATTAATTCACTTCAAGTCAGCCATTGTCCAA
2071454 CCTAGGGCCTTTCTGTGTTGTGATAAAAC-TTCTACA
66 CCTAGGGCCTTTCTGTGTTGTGATAAAACATTCTACA
2071490 ATTCTAGATTGATATTATGCATGCATATGGTCGAATTAATTCACTTCAAGTCAGCCATTGTCCAA
1 ATTCTAGATTGATATTATGCATGCATATGGTCGAATTAATTCACTTCAAGTCAGCCATTGTCCAA
2071555 CCTAGGGCCTTTCTGTGTTGTGATAAAACATTCTACA
66 CCTAGGGCCTTTCTGTGTTGTGATAAAACATTCTACA
2071592 A
1 A
2071593 ACTATTCTCC
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 93 0.92
102 8 0.08
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (102 bp):
ATTCTAGATTGATATTATGCATGCATATGGTCGAATTAATTCACTTCAAGTCAGCCATTGTCCAA
CCTAGGGCCTTTCTGTGTTGTGATAAAACATTCTACA
Found at i:2073019 original size:20 final size:21
Alignment explanation
Indices: 2072981--2073019 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2072971 CATCAAGGTC
* *
2072981 TTTGTGGAGGCCATGAAATCT
1 TTTGTCGAGACCATGAAATCT
2073002 TTTGTCGAGACCAT-AAAT
1 TTTGTCGAGACCATGAAAT
2073020 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
TTTGTCGAGACCATGAAATCT
Found at i:2074630 original size:108 final size:108
Alignment explanation
Indices: 2074441--2074656 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
2074431 ATCGCTTGTA
2074441 AAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGATGCAAGTAATATAGTAG
1 AAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGATGCAAGTAATATAGTAG
2074506 TGAGTGAGTTATCGTCTCCTCAGGGATTAGTTTAGAAATTTAT
66 TGAGTGAGTTATCGTCTCCTCAGGGATTAGTTTAGAAATTTAT
2074549 AAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGATGCAAGTAATATAGTAG
1 AAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGATGCAAGTAATATAGTAG
2074614 TGAGTGAGTTATCGTCTCCTCAGGGATTAGTTTAGAAATTTAT
66 TGAGTGAGTTATCGTCTCCTCAGGGATTAGTTTAGAAATTTAT
2074657 CCTCACCACA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (108 bp):
AAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGATGCAAGTAATATAGTAG
TGAGTGAGTTATCGTCTCCTCAGGGATTAGTTTAGAAATTTAT
Found at i:2081568 original size:85 final size:85
Alignment explanation
Indices: 2081420--2081585 Score: 199
Period size: 85 Copynumber: 2.0 Consensus size: 85
2081410 ATACAATCAC
* * * * * * *
2081420 GACACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTTAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACAAGCAATGCAAGTCATA
* *
2081485 CATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* **
2081505 GACACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACAATCAATGCGTGTCAT
1 GACACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACAAGCAATGCAAGTCAT
*
2081569 AAATGTGCGTCATAAAT
65 AAATGCGCGTCATAAAT
2081586 GTAAGTCATA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 64 0.96
86 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACAAGCAATGCAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:2081580 original size:13 final size:13
Alignment explanation
Indices: 2081564--2081608 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
2081554 ATCAATGCGT
2081564 GTCATAAATGTGC
1 GTCATAAATGTGC
**
2081577 GTCATAAATGTAA
1 GTCATAAATGTGC
*
2081590 GTCATAAATGCGC
1 GTCATAAATGTGC
2081603 GTCATA
1 GTCATA
2081609 GATTTATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (13 bp):
GTCATAAATGTGC
Found at i:2093439 original size:60 final size:61
Alignment explanation
Indices: 2093325--2093444 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 61
2093315 GGGATTAAAG
* *
2093325 AAAGCTTAAAAGTAATTAATGATAGATGAAAAGATGGAAAGATACAAAGCTAAAA-AATAT
1 AAAGCTTAAAAGTAATTAATGATAGATGAAAAGATGGAAAGAGACAAAGATAAAATAATAT
*
2093385 AAAGCTTAAAAGTAATTAATGATAGTTGAAAAGATGGAAAGAGA-AAAGAATAAAATAATA
1 AAAGCTTAAAAGTAATTAATGATAGATGAAAAGATGGAAAGAGACAAAG-ATAAAATAATA
2093445 AAGTAGTGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 4 0.07
60 47 0.85
61 4 0.07
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.22
Consensus pattern (61 bp):
AAAGCTTAAAAGTAATTAATGATAGATGAAAAGATGGAAAGAGACAAAGATAAAATAATAT
Found at i:2101337 original size:95 final size:95
Alignment explanation
Indices: 2101170--2101392 Score: 272
Period size: 95 Copynumber: 2.3 Consensus size: 95
2101160 TACTGATGAG
* * * * *
2101170 GTAGTATCGATACTATGGTGAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTGTCGAT
1 GTAGTATCGATACCATGGTGAGGGCATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGAT
* *
2101235 ACAGAAAGGGGGTATCGATACCCTA-TCATA
66 ACAGAAAGGGGGTATCAATACCATAGT-ATA
* * * * *
2101265 GTAGTATCGATACCATGGTGAGGGCATTGATACCAAGCCACGTCGAAGCTAATTTTGGTATTGAT
1 GTAGTATCGATACCATGGTGAGGGCATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGAT
*
2101330 ATC-GAAAGGGGGTATCAATACCATAGTATG
66 A-CAGAAAGGGGGTATCAATACCATAGTATA
*
2101360 GTAGTATCGATACCATGGT-AGGGGTATCGATAC
1 GTAGTATCGATACCATGGTGA-GGGCATCGATAC
2101393 TAAAGGGCCA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
94 1 0.01
95 107 0.97
96 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTGAGGGCATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGAT
ACAGAAAGGGGGTATCAATACCATAGTATA
Found at i:2101388 original size:20 final size:21
Alignment explanation
Indices: 2101338--2101392 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2101328 ATATCGAAAG
*
2101338 GGGGTATCAATACCATAGTAT
1 GGGGTATCGATACCATAGTAT
* *
2101359 GGTAGTATCGATACCATGGTA-
1 GG-GGTATCGATACCATAGTAT
2101380 GGGGTATCGATAC
1 GGGGTATCGATAC
2101393 TAAAGGGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.34
21 4 0.14
22 15 0.52
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (21 bp):
GGGGTATCGATACCATAGTAT
Found at i:2101792 original size:59 final size:59
Alignment explanation
Indices: 2101714--2102118 Score: 616
Period size: 59 Copynumber: 6.9 Consensus size: 59
2101704 ATTACCAAAT
* *
2101714 GGCACTAAGTGTGCAAAAATGATAAGGAAATCATAGTAAGTGTATGAATTTCTAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* * *
2101773 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATGCTAAGTGTATGAATTTCCAAATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* * *
2101832 AGCACAAAGTGTGATAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* *
2101891 GGAACTAAGTATGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* * * * *
2101950 GGTACTAAGTGTACTAAACTGATAAGGAAATCATATTAAGTGTATGAATTTCCAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* *
2102009 GGCACTAAGTGTGCTAAAATGGTAAGAAAATCATACT-AGTGTATGAATTTCTAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
* *
2102067 GGCACTTCA-TGTGCTAAAATGATAAGGAAATCATACTAATTGTATGAATTTC
1 GGCAC-TAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTC
2102119 CTATTGAATT
Statistics
Matches: 311, Mismatches: 33, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
58 51 0.16
59 260 0.84
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (59 bp):
GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
Found at i:2108013 original size:95 final size:95
Alignment explanation
Indices: 2107888--2108063 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 95
2107878 TACTGATGAG
* * *
2107888 GTAGTATCGATACCATGGTGAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCAAT
1 GTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCAAT
* *
2107953 ACTGGAAGGGGGTATCAGTACCCTAGCATA
66 ACCGGAAGCGGGTATCAGTACCCTAGCATA
* ** * *
2107983 GTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCCACATCAAAGGTAATTTTTGTATCGAT
1 GTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCAAT
2108048 ACCGGAAGCGGGTATC
66 ACCGGAAGCGGGTATC
2108064 GATACCATTG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 71 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCAAT
ACCGGAAGCGGGTATCAGTACCCTAGCATA
Found at i:2108082 original size:20 final size:19
Alignment explanation
Indices: 2108040--2108088 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
2108030 GGTAATTTTT
2108040 GTATCGATACCGGAAGCGG
1 GTATCGATACCGGAAGCGG
*
2108059 GTATCGATACCATTGAAG-GG
1 GTATCGATACC--GGAAGCGG
2108079 GTATCGATAC
1 GTATCGATAC
2108089 TAAAGGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 12 0.44
21 4 0.15
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (19 bp):
GTATCGATACCGGAAGCGG
Found at i:2108570 original size:59 final size:59
Alignment explanation
Indices: 2108409--2108861 Score: 563
Period size: 59 Copynumber: 7.9 Consensus size: 59
2108399 ATTACCAAAT
* * * *
2108409 GGCACTAAGTGTGTTAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATAT
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2108468 GGCACTAAGTGTGCT-AAATGATAAGG-AA--AT--TAAGTGTATGAATTTCTAGACAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2108521 GGCACTAAGTATGCTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2108580 GGCACCAAGTGTGCTAAAATGATAAGCAAATCATACTAAGTGTATGAATTT-C---T--
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * *
2108633 CG-ACGAAGTGTACTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
** * * *
2108691 GGCACTTTGTGCGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
** ** * * *
2108750 GGCACTTCGTGCCCTAAACTGATAAGGAAATCATACTAAGTGTAAGAATTTCCAGATAT
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
** *
2108809 GGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAATTGTATGAATTTCC
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCC
2108862 TATTGAATTT
Statistics
Matches: 345, Mismatches: 36, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
52 45 0.13
53 34 0.10
54 10 0.03
55 5 0.01
56 1 0.00
57 4 0.01
58 13 0.04
59 233 0.68
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (59 bp):
GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:2108725 original size:170 final size:171
Alignment explanation
Indices: 2108409--2108861 Score: 499
Period size: 170 Copynumber: 2.6 Consensus size: 171
2108399 ATTACCAAAT
* * * * *
2108409 GGCACTAAGTGTGTTAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATATGGCACT
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTT-C-----TCGAACG
* *
2108474 AAGTGTGCT-AAATGATAAGG-AA--AT--TAAGTGTATGAATTTCTAGACAGGGCACTAAGTAT
60 AAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGACAGGGCACTAAGTAC
*
2108533 GCTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
125 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2108580 GGCACCAAGTGTGCTAAAATGATAAGCAAATCATACTAAGTGTATGAATTTCTCG-ACGAAGTGT
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTCGAACGAAGTGT
* * ** *
2108644 ACTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGCGCTAAA
66 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGACAGGGCACTAAGTACGCTAAA
* *
2108709 CTGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAG
131 ATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
** ** * * *
2108750 GGCACTTCGTGCCCTAAACTGATAAGGAAATCATACTAAGTGTAAGAATTTC-CAGATATGGCAC
1 GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTC-GA-A-CG-A-
* *
2108814 TTCGTGTGCTAAAATGATAAGGAAATCATACTAATTGTATGAATTTCC
61 --AGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCC
2108862 TATTGAATTT
Statistics
Matches: 240, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
164 10 0.04
165 13 0.05
166 2 0.01
168 2 0.01
169 1 0.00
170 119 0.50
171 47 0.20
172 1 0.00
173 1 0.00
174 1 0.00
177 43 0.18
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (171 bp):
GGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTCGAACGAAGTGT
GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGACAGGGCACTAAGTACGCTAAA
ATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:2108823 original size:229 final size:223
Alignment explanation
Indices: 2108423--2108860 Score: 633
Period size: 229 Copynumber: 1.9 Consensus size: 223
2108413 CTAAGTGTGT
* *
2108423 TAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATATGGCACTAAGTGTGCTAAATG
1 TAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATAGGGCACTAAGTGCGCTAAATG
** *
2108488 ATAAGGAAATTAAGTGTATGAATTTCTAGACAGGGCACTAAGTATGCTAAAATGTTAAGGAAATC
66 ATAAGGAAATTAAGTGTATGAATTTCTAGACAGGGCACTAAGTACCCTAAAATGATAAGGAAATC
*
2108553 ATACTAAGTGTATGAATTTCCAGATAGGGCACCAAGTGTGCTAAAATGATAAGCAAATCATACTA
131 ATACTAAGTGTAAGAATTTCCAGATAGGGCACCAAGTGTGCTAAAATGATAAGCAAATCATACTA
2108618 AGTGTATGAATTTCTCGACGAAGTGTAC
196 AGTGTATGAATTTCTCGACGAAGTGTAC
* * **
2108646 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGCGCTAAACT
1 TAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATAGGGCACTAAGTGCGCTAAA-T
* ** * *
2108711 GATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGTGCCCTAAACTGATAAG
65 GATAAGG-AA--AT--TAAGTGTATGAATTTCTAGACAGGGCACTAAGTACCCTAAAATGATAAG
* *** *
2108776 GAAATCATACTAAGTGTAAGAATTTCCAGATATGGCACTTCGTGTGCTAAAATGATAAGGAAATC
125 GAAATCATACTAAGTGTAAGAATTTCCAGATAGGGCACCAAGTGTGCTAAAATGATAAGCAAATC
*
2108841 ATACTAATTGTATGAATTTC
190 ATACTAAGTGTATGAATTTC
2108861 CTATTGAATT
Statistics
Matches: 188, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
223 57 0.30
224 8 0.04
225 2 0.01
227 2 0.01
229 119 0.63
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (223 bp):
TAAAATGATAAGGAAATCATACTAAGTGTATAAATTTACAGATAGGGCACTAAGTGCGCTAAATG
ATAAGGAAATTAAGTGTATGAATTTCTAGACAGGGCACTAAGTACCCTAAAATGATAAGGAAATC
ATACTAAGTGTAAGAATTTCCAGATAGGGCACCAAGTGTGCTAAAATGATAAGCAAATCATACTA
AGTGTATGAATTTCTCGACGAAGTGTAC
Found at i:2110635 original size:17 final size:18
Alignment explanation
Indices: 2110613--2110647 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2110603 AACCATGAAA
*
2110613 ATAAAATTA-TTTAAAAT
1 ATAAAATAATTTTAAAAT
2110630 ATAAAATAATTTTAAAAT
1 ATAAAATAATTTTAAAAT
2110648 TTTAAATGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATAATTTTAAAAT
Found at i:2114601 original size:20 final size:20
Alignment explanation
Indices: 2114558--2114603 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
2114548 CAACCTTAAT
2114558 TCCTAAAAATAATAAATCTGA
1 TCCTAAAAATAATAAATC-GA
*
2114579 TCCTAAAAGATAATTAATC-A
1 TCCTAAAA-ATAATAAATCGA
2114599 TCCTA
1 TCCTA
2114604 TATTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.30
Consensus pattern (20 bp):
TCCTAAAAATAATAAATCGA
Found at i:2120055 original size:11 final size:11
Alignment explanation
Indices: 2120039--2120088 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
2120029 AAATTTTGGC
*
2120039 TTTTTTGGCTT
1 TTTTTTGCCTT
**
2120050 TTTTTTGTTTTT
1 TTTTTTG-CCTT
2120062 TTTTTTGCCTT
1 TTTTTTGCCTT
2120073 TTTTTTGCCTT
1 TTTTTTGCCTT
2120084 TTTTT
1 TTTTT
2120089 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:2120099 original size:11 final size:11
Alignment explanation
Indices: 2120039--2120098 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
2120029 AAATTTTGGC
*
2120039 TTTTTTGGCTT
1 TTTTTTGTCTT
*
2120050 TTTTTTGTTTTT
1 TTTTTTG-TCTT
*
2120062 TTTTTTGCCTT
1 TTTTTTGTCTT
*
2120073 TTTTTTG-CCT
1 TTTTTTGTCTT
2120083 TTTTTTGT-TT
1 TTTTTTGTCTT
2120093 TTTTTT
1 TTTTTT
2120099 TAAAATAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
10 16 0.39
11 16 0.39
12 9 0.22
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (11 bp):
TTTTTTGTCTT
Found at i:2122899 original size:4 final size:4
Alignment explanation
Indices: 2122882--2122936 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
2122872 AGTTCATGCA
* * *
2122882 ATTT ATTT -TATT ATTT ATTT ATTT GTTA ATTT ATTT -TAGT ATTT ATTT
1 ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT
2122930 ATTT ATT
1 ATTT ATT
2122937 AAAATAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 2 0.05
4 37 0.90
5 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2122912 original size:28 final size:28
Alignment explanation
Indices: 2122881--2122938 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2122871 AAGTTCATGC
* *
2122881 AATTTATTTTATTATTTATTTATTTGTT
1 AATTTATTTTAGTATTTATTTATTTATT
2122909 AATTTATTTTAGTATTTATTTATTTATT
1 AATTTATTTTAGTATTTATTTATTTATT
2122937 AA
1 AA
2122939 AATAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (28 bp):
AATTTATTTTAGTATTTATTTATTTATT
Found at i:2123832 original size:43 final size:43
Alignment explanation
Indices: 2123785--2123941 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 43
2123775 AAATGCCTCA
* * * *
2123785 AAATCTCAACACTTATTGCGGTGTTTGTGATAAAAATGCTGCT
1 AAATATCAACACCTATTGCGGCGTTTGTGAGAAAAATGCTGCT
* * * * *
2123828 AAATCTCAACACCTATTGCGACGTTTGTGGGAAAAACGCCGCT
1 AAATATCAACACCTATTGCGGCGTTTGTGAGAAAAATGCTGCT
* * *
2123871 AAATATCAACACCTATTACGGCGTTTATGAGACAAATGCTGCT
1 AAATATCAACACCTATTGCGGCGTTTGTGAGAAAAATGCTGCT
*** *
2123914 AAATATCGTTACCTATTGCGGTGTTTGT
1 AAATATCAACACCTATTGCGGCGTTTGT
2123942 TCAACAAACG
Statistics
Matches: 93, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 93 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (43 bp):
AAATATCAACACCTATTGCGGCGTTTGTGAGAAAAATGCTGCT
Found at i:2123928 original size:86 final size:86
Alignment explanation
Indices: 2123785--2123982 Score: 209
Period size: 86 Copynumber: 2.3 Consensus size: 86
2123775 AAATGCCTCA
* * * * * *
2123785 AAATCTCAACACTTATTGCGGTGTTTGTGATAAAAATGCTGCTAAATCTCAACACCTATTGCGAC
1 AAATATCAACACCTATTGCGGCGTTTATGAGAAAAATGCTGCTAAATATCAACACCTATTGCGAC
*
2123850 GTTTGTGGGAA-AAACGCCGCT
66 GTTTGT-GCAACAAACGCCGCT
* * *** **
2123871 AAATATCAACACCTATTACGGCGTTTATGAGACAAATGCTGCTAAATATCGTTACCTATTGCGGT
1 AAATATCAACACCTATTGCGGCGTTTATGAGAAAAATGCTGCTAAATATCAACACCTATTGCGAC
*
2123936 GTTTGTTCAACAAACGCCGCT
66 GTTTGTGCAACAAACGCCGCT
* ***
2123957 ATATATCGTTACCTATTGCGGCGTTT
1 AAATATCAACACCTATTGCGGCGTTT
2123983 TTCGTTAACA
Statistics
Matches: 91, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
85 2 0.02
86 89 0.98
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (86 bp):
AAATATCAACACCTATTGCGGCGTTTATGAGAAAAATGCTGCTAAATATCAACACCTATTGCGAC
GTTTGTGCAACAAACGCCGCT
Found at i:2126149 original size:20 final size:20
Alignment explanation
Indices: 2126121--2126158 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2126111 TTTTTGGGAG
*
2126121 TATCGATACTAGATGAACAT
1 TATCAATACTAGATGAACAT
2126141 TATCAATACTAGATGAAC
1 TATCAATACTAGATGAAC
2126159 TAGGATGAAT
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:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (20 bp):
TATCAATACTAGATGAACAT
Found at i:2127779 original size:167 final size:167
Alignment explanation
Indices: 2127502--2127837 Score: 627
Period size: 167 Copynumber: 2.0 Consensus size: 167
2127492 CCGTTCTAGT
2127502 CTTCTTGAAAATATTTCTCAAAACAATTTTGAAAAAAGAAAATTGCTCTGAACCGGGTCAATTGA
1 CTTCTTGAAAATATTTCTCAAAACAATTTTGAAAAAAGAAAATTGCTCTGAACCGGGTCAATTGA
* * *
2127567 GTAGAGGCCAAATGATTTCGTAGAGGTTAGGATTCGAATTGTTTGTTACTATTTCCGAATTGTTG
66 GTAGAGGCCAAATGATTTCGTAGAGGTTAGGATTCGAACTGTTTGTCACTATTGCCGAATTGTTG
* *
2127632 TTATTCCAAGAACCCTAGGTATATCTCGTAACTCTTC
131 TTATTCCAAGAACCCAAGGTATATATCGTAACTCTTC
2127669 CTTCTTGAAAATATTTCTCAAAACAATTTTGAAAAAAGAAAATTGCTCTGAACCGGGTCAATTGA
1 CTTCTTGAAAATATTTCTCAAAACAATTTTGAAAAAAGAAAATTGCTCTGAACCGGGTCAATTGA
2127734 GTAGAGGCCAAATGATTTCGTAGAGGTTAGGATTCGAACTGTTTGTCACTATTGCCGAATTGTTG
66 GTAGAGGCCAAATGATTTCGTAGAGGTTAGGATTCGAACTGTTTGTCACTATTGCCGAATTGTTG
2127799 TTATTCCAAGAACCCAAGGTATATATCGTAACTCTTC
131 TTATTCCAAGAACCCAAGGTATATATCGTAACTCTTC
2127836 CT
1 CT
2127838 CCTGAATTTG
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 164 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (167 bp):
CTTCTTGAAAATATTTCTCAAAACAATTTTGAAAAAAGAAAATTGCTCTGAACCGGGTCAATTGA
GTAGAGGCCAAATGATTTCGTAGAGGTTAGGATTCGAACTGTTTGTCACTATTGCCGAATTGTTG
TTATTCCAAGAACCCAAGGTATATATCGTAACTCTTC
Found at i:2145089 original size:17 final size:18
Alignment explanation
Indices: 2145057--2145091 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2145047 ATTGATAATG
*
2145057 ACCCTTGAGTATCGATAC
1 ACCCTTGAGTAGCGATAC
2145075 ACCCTT-AGTAGCGATAC
1 ACCCTTGAGTAGCGATAC
2145092 TAAAAATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (18 bp):
ACCCTTGAGTAGCGATAC
Found at i:2146100 original size:20 final size:20
Alignment explanation
Indices: 2146071--2146108 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2146061 AGCAAGGTGG
* *
2146071 GTATCGATACTCAAGGGTCA
1 GTATCAATACTAAAGGGTCA
2146091 GTATCAATACTAAAGGGT
1 GTATCAATACTAAAGGGT
2146109 TTATTATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (20 bp):
GTATCAATACTAAAGGGTCA
Found at i:2148805 original size:75 final size:76
Alignment explanation
Indices: 2148681--2148832 Score: 227
Period size: 75 Copynumber: 2.0 Consensus size: 76
2148671 TACTAATATA
* *
2148681 ATGAAATGCTAATTCACGAATTCATTATGAATACAATTGATGCACACATAGTACCGAAAGTACAC
1 ATGAAATGCTAATTCACGAATTCATTATGAATACAATGGATGCACACATAGTACCGAAAGAACAC
2148746 AAAGTACTGAT
66 AAAGTACTGAT
* * **
2148757 ATGAAATGGTAATTCAC-AACTT-ATTATGAATACCATGGATGCACACATAGTGTCGAAAGAACA
1 ATGAAATGCTAATTCACGAA-TTCATTATGAATACAATGGATGCACACATAGTACCGAAAGAACA
2148820 CAAAGTACTGAT
65 CAAAGTACTGAT
2148832 A
1 A
2148833 CAAAAATTCA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 51 0.74
76 18 0.26
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (76 bp):
ATGAAATGCTAATTCACGAATTCATTATGAATACAATGGATGCACACATAGTACCGAAAGAACAC
AAAGTACTGAT
Found at i:2150483 original size:16 final size:15
Alignment explanation
Indices: 2150462--2150491 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2150452 TAAGAAAGAA
2150462 ATGATTAAGTAAATGG
1 ATGATTAAG-AAATGG
2150478 ATGATTAAGAAATG
1 ATGATTAAGAAATG
2150492 AAATGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (15 bp):
ATGATTAAGAAATGG
Found at i:2150502 original size:6 final size:6
Alignment explanation
Indices: 2150486--2150536 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
2150476 GGATGATTAA
2150486 GAAAT- GAAATG GAAATG GAAATG GAAATG GAAA-- GAAAT- GAAAT-
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
2150529 GAAATG GA
1 GAAATG GA
2150537 TAGAAATGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.09
5 15 0.35
6 24 0.56
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:2150534 original size:20 final size:21
Alignment explanation
Indices: 2150497--2150544 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2150487 AAATGAAATG
2150497 GAAATGGAAATGGAAATGGAAA
1 GAAAT-GAAATGGAAATGGAAA
*
2150519 GAAATGAAAT-GAAATGGATA
1 GAAATGAAATGGAAATGGAAA
2150539 GAAATG
1 GAAATG
2150545 TTATCAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.60
21 5 0.20
22 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (21 bp):
GAAATGAAATGGAAATGGAAA
Found at i:2156681 original size:75 final size:76
Alignment explanation
Indices: 2156559--2156715 Score: 199
Period size: 75 Copynumber: 2.1 Consensus size: 76
2156549 TACTAATATA
* * * *
2156559 AGGAAATGATAATTCACAAATTTATTATGAATACCATGAATGAACACATAGTGCCAAAAGTATAC
1 AGGAAATGATAATTCACAAACTCATTATGAATACCATGAATGAACACATAGTGCCAAAAGAACAC
2156624 AAAGTACTGAT
66 AAAGTACTGAT
* * * * * *
2156635 AGGAAATGGTAATTCAC-AACTCATTGTGAATACCATGGATGCACACATAGTGTCGAAAGAACAC
1 AGGAAATGATAATTCACAAACTCATTATGAATACCATGAATGAACACATAGTGCCAAAAGAACAC
*
2156699 ATAGTACTGAT
66 AAAGTACTGAT
*
2156710 ACGAAA
1 AGGAAA
2156716 ATACAACATA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 53 0.77
76 16 0.23
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (76 bp):
AGGAAATGATAATTCACAAACTCATTATGAATACCATGAATGAACACATAGTGCCAAAAGAACAC
AAAGTACTGAT
Found at i:2157033 original size:13 final size:13
Alignment explanation
Indices: 2157015--2157047 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2157005 ACTCACCTGA
2157015 TATGCCTCACTAT
1 TATGCCTCACTAT
2157028 TATGCCTCACTAT
1 TATGCCTCACTAT
2157041 TATGCCT
1 TATGCCT
2157048 TATTGTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.39
Consensus pattern (13 bp):
TATGCCTCACTAT
Found at i:2162639 original size:60 final size:60
Alignment explanation
Indices: 2162575--2162708 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
2162565 AGGATGAAAA
* *
2162575 TCATAGCTTGGGGATGAAAATGAAATGT-TCAAAATTTTAAGGACTAATTT-AAAGTAATAG
1 TCATAGATTGGGGATGAAAATGAAATGTCT-AAAATTTTAAGGACTAATTTGAAA-TAAGAG
* *** * * *
2162635 TCATAGTTTAATGATGAAATTGAAATGTCTAAAATTTTAGGGACTAATTTGAAATAAGGG
1 TCATAGATTGGGGATGAAAATGAAATGTCTAAAATTTTAAGGACTAATTTGAAATAAGAG
2162695 TCATAGATTGGGGA
1 TCATAGATTGGGGA
2162709 CATATGATGC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
60 56 0.93
61 4 0.07
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.33
Consensus pattern (60 bp):
TCATAGATTGGGGATGAAAATGAAATGTCTAAAATTTTAAGGACTAATTTGAAATAAGAG
Found at i:2162891 original size:16 final size:15
Alignment explanation
Indices: 2162870--2162903 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2162860 AAAAATTCGA
*
2162870 GTTATTTTCGATTTAG
1 GTTATTTTCAATTT-G
2162886 GTTATTTTCAATTTG
1 GTTATTTTCAATTTG
2162901 GTT
1 GTT
2162904 GCTTTCGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (15 bp):
GTTATTTTCAATTTG
Found at i:2162919 original size:31 final size:32
Alignment explanation
Indices: 2162875--2162957 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 32
2162865 TTCGAGTTAT
* * * *
2162875 TTTCGATTTAGGTTATTTTCAATTTGG-TTGC
1 TTTCGGTTCAGGTTACTTTCAATTTGGATTAC
2162906 TTTCGGTTCAGGTTACTTTCAATTTGGATTAC
1 TTTCGGTTCAGGTTACTTTCAATTTGGATTAC
2162938 TCTT--GTTCAGGTTACTTTCA
1 T-TTCGGTTCAGGTTACTTTCA
2162958 GTTTAGCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 40 0.87
32 4 0.09
33 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.51
Consensus pattern (32 bp):
TTTCGGTTCAGGTTACTTTCAATTTGGATTAC
Found at i:2165494 original size:59 final size:58
Alignment explanation
Indices: 2165400--2165572 Score: 231
Period size: 59 Copynumber: 3.0 Consensus size: 58
2165390 ATTACCAAAT
* * * * * *
2165400 GGCACTTTGTATGCAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTCAGTATAG
1 GGCACCTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAG
* *
2165458 GGCA-CTTCGTGTGCTAACGTGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATCG
1 GGCACCTT-GTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAG
* *
2165517 GGCACCTTGTGTGCTAAATGATAAGAAATTCATACTAAATGTAGGAATTTCTGTAT
1 GGCACCTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
2165573 GGAAAATATA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.02
58 47 0.47
59 49 0.49
60 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (58 bp):
GGCACCTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAG
Found at i:2166061 original size:68 final size:68
Alignment explanation
Indices: 2165946--2166267 Score: 520
Period size: 68 Copynumber: 4.8 Consensus size: 68
2165936 AATAAAGGTA
*
2165946 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
1 TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
2166011 GCC
66 GCC
* * * *
2166014 TACCTATGCATATGGCAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGATTAAGTGTCTTTAAG
1 TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
2166079 GCC
66 GCC
* *
2166082 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAGTGTCTTTAAG
1 TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
2166147 GCC
66 GCC
* * * *
2166150 TAACTAGGCAT-TGACAAAAAGGTGTCATTTATCCCAGTTAGATGAAAGACTAAGTGTTTTTAAG
1 TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
*
2166214 GCT
66 GCC
*
2166217 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGAC
1 TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGAC
2166268 CTTTGAGGTC
Statistics
Matches: 231, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
67 60 0.26
68 171 0.74
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (68 bp):
TAACTATGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
GCC
Found at i:2166140 original size:32 final size:32
Alignment explanation
Indices: 2166104--2166206 Score: 77
Period size: 32 Copynumber: 3.1 Consensus size: 32
2166094 TGACAGAAAG
2166104 GTGTCATTTATGCCAGTTAGATGAAAAACTAA
1 GTGTCATTTATGCCAGTTAGATGAAAAACTAA
* ** *
2166136 GTGTC-TTTAAGGCCTAACTAGGCATTGACAAAA--AG
1 GTGTCATTT-ATGCC-AGTTA-G-A-TGA-AAAACTAA
* *
2166171 GTGTCATTTATCCCAGTTAGATGAAAGACTAA
1 GTGTCATTTATGCCAGTTAGATGAAAAACTAA
2166203 GTGT
1 GTGT
2166207 TTTTAAGGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 18
0.65 0.12 0.22
Matches are distributed among these distances:
30 3 0.06
31 6 0.12
32 15 0.29
33 4 0.08
34 4 0.08
35 10 0.19
36 6 0.12
37 4 0.08
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (32 bp):
GTGTCATTTATGCCAGTTAGATGAAAAACTAA
Found at i:2166236 original size:135 final size:136
Alignment explanation
Indices: 2165946--2166264 Score: 559
Period size: 135 Copynumber: 2.4 Consensus size: 136
2165936 AATAAAGGTA
*
2165946 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTAAG
1 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAGTGTCTTTAAG
* * * * *
2166011 GCCTACCTATGCATATGGCAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGATTAAGTGTCTTT
66 GCCTAACTAGGCATATGACAAAAAGGTGTCATTTATCCCAGTTAGATGAAAGACTAAGTGTCTTT
2166076 AAGGCC
131 AAGGCC
2166082 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAGTGTCTTTAAG
1 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAGTGTCTTTAAG
*
2166147 GCCTAACTAGGCAT-TGACAAAAAGGTGTCATTTATCCCAGTTAGATGAAAGACTAAGTGTTTTT
66 GCCTAACTAGGCATATGACAAAAAGGTGTCATTTATCCCAGTTAGATGAAAGACTAAGTGTCTTT
*
2166211 AAGGCT
131 AAGGCC
2166217 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAA
1 TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAA
2166265 GACCTTTGAG
Statistics
Matches: 175, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
135 99 0.57
136 76 0.43
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (136 bp):
TAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAGTGTCTTTAAG
GCCTAACTAGGCATATGACAAAAAGGTGTCATTTATCCCAGTTAGATGAAAGACTAAGTGTCTTT
AAGGCC
Found at i:2166423 original size:81 final size:80
Alignment explanation
Indices: 2166277--2166513 Score: 262
Period size: 81 Copynumber: 3.0 Consensus size: 80
2166267 CCTTTGAGGT
* *
2166277 CTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATAAACAGTTAAATACCATTGA
1 CTAACTGTG-AATTGGCAAAAATGTGTCAATTATGCCAGTTAGATAAACAGTTAAATACCATTGA
2166342 GTAAAAGAATAATGGC
65 GTAAAAGAATAATGGC
* * * * * *
2166358 CTAACTGTGAAATTGGCAAAAATGTGTCAATTATGCCAGTTGGATGAA-TGATTAAGTATCGTTG
1 CTAACTGTG-AATTGGCAAAAATGTGTCAATTATGCCAGTTAGATAAACAG-TTAAATACCATTG
2166422 AGTAAAAGAATAATGGC
64 AGTAAAAGAATAATGGC
* * * * * ** * **
2166439 CTAATTGTGCATTGGCATAAAGGTGTCAATTATACCAGTTAGACGAAC-GTTAAACACTGTTGAG
1 CTAACTGTGAATTGGCAAAAATGTGTCAATTATGCCAGTTAGATAAACAGTTAAATACCATTGAG
*
2166503 TAAGAGAATAA
66 TAAAAGAATAA
2166514 ATAAATTATA
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 21 0.16
80 34 0.26
81 78 0.59
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (80 bp):
CTAACTGTGAATTGGCAAAAATGTGTCAATTATGCCAGTTAGATAAACAGTTAAATACCATTGAG
TAAAAGAATAATGGC
Found at i:2171063 original size:20 final size:20
Alignment explanation
Indices: 2171028--2171083 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
2171018 GCCATTTTTA
* *
2171028 GTATCGGTAC-CAAGGGTGG
1 GTATCGATACTCAAGGGTCG
* *
2171047 GTATTGATACTCAAGGGTCT
1 GTATCGATACTCAAGGGTCG
*
2171067 GTATCGATACTAAAGGG
1 GTATCGATACTCAAGGG
2171084 CATGGTATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCAAGGGTCG
Found at i:2172591 original size:69 final size:69
Alignment explanation
Indices: 2172477--2172626 Score: 178
Period size: 69 Copynumber: 2.2 Consensus size: 69
2172467 TTGTATCGAT
* * * *
2172477 ATCACAATTAATATACCACCCAAGCATACATCAAACACTCATACAAGTAAGTAAATAACCATAAA
1 ATCACAAATAATACACCACCCAAACATACATCAAACACTCATACAAGTAAATAAATAACCATAAA
*
2172542 ATGA
66 ACGA
* * * * * *
2172546 ATCACAAGTAATACACCACCTAAATATGCATCAAACACT-AGTACAAGTAAATAAATCAGCATAA
1 ATCACAAATAATACACCACCCAAACATACATCAAACACTCA-TACAAGTAAATAAATAACCATAA
2172610 AACGA
65 AACGA
2172615 AT-ACAAATAATA
1 ATCACAAATAATA
2172627 GAGATGAGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
68 10 0.14
69 59 0.86
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (69 bp):
ATCACAAATAATACACCACCCAAACATACATCAAACACTCATACAAGTAAATAAATAACCATAAA
ACGA
Found at i:2175468 original size:118 final size:117
Alignment explanation
Indices: 2175329--2175555 Score: 303
Period size: 118 Copynumber: 1.9 Consensus size: 117
2175319 ACATGATTAG
* ** *
2175329 ATTTAATTCAAAATTTAATGAATAAATAAGAGAAAT-GGAAAAGATGGCCAAAAACTAAACATTT
1 ATTTAATTCAAAATTGAATGAATAAATAAGAGAAATAAAAAAAGAGGGCCAAAAACTAAA-ATTT
* * *
2175393 TGTGAAATTATAAAAATTAAAGATTCTAATTATAAATATTAAAAACCGGTTAA
65 TATGAAATTATAAAAATTAAAGATTATAATTATAAATATAAAAAACCGGTTAA
* * ***
2175446 ATTTAATTCAAAAATTGAATGAATTAATAAGAGAAATAAAAAAAGAGGGTCAAATGGTAAAATTT
1 ATTTAATTC-AAAATTGAATGAATAAATAAGAGAAATAAAAAAAGAGGGCCAAAAACTAAAATTT
* *
2175511 TATGAAATTATAAAAATTAAGGGTTATAATTATAAATATAAAAAA
65 TATGAAATTATAAAAATTAAAGATTATAATTATAAATATAAAAAA
2175556 TTAAAAGTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
117 9 0.10
118 69 0.73
119 16 0.17
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (117 bp):
ATTTAATTCAAAATTGAATGAATAAATAAGAGAAATAAAAAAAGAGGGCCAAAAACTAAAATTTT
ATGAAATTATAAAAATTAAAGATTATAATTATAAATATAAAAAACCGGTTAA
Found at i:2175557 original size:29 final size:29
Alignment explanation
Indices: 2175522--2175606 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
2175512 ATGAAATTAT
*
2175522 AAAAATTAAGGGTTATAATTATAAATATA
1 AAAAATTAAGAGTTATAATTATAAATATA
*
2175551 AAAAATTAAAAGTTATAATTATAAATATA
1 AAAAATTAAGAGTTATAATTATAAATATA
* * *
2175580 AAAGATTAAGAATTCTAATTATAAATA
1 AAAAATTAAGAGTTATAATTATAAATA
2175607 CGGAAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAAATTAAGAGTTATAATTATAAATATA
Found at i:2178941 original size:22 final size:22
Alignment explanation
Indices: 2178911--2178961 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2178901 CTGGACATAT
*
2178911 ACAATATACAAAGGTCATTTGGG
1 ACAA-ATACAAAGGTCATTCGGG
* *
2178934 ACAAATACAATGGTCCTTCGGG
1 ACAAATACAAAGGTCATTCGGG
2178956 ACAAAT
1 ACAAAT
2178962 TTCACATGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (22 bp):
ACAAATACAAAGGTCATTCGGG
Found at i:2181579 original size:42 final size:41
Alignment explanation
Indices: 2181505--2181714 Score: 118
Period size: 44 Copynumber: 4.9 Consensus size: 41
2181495 TTTATAGGAT
* *
2181505 CTTTAATTTTTTTTATTTTATTTATTA-TTTTATAATTAAGAC
1 CTTTAATTTTTTTAATTTT-TTT-TTACCTTTATAATTAAGAC
* *
2181547 CTTTAATTTTTTTAAATTTTTTTTTACCTTTATAATTGAGGC
1 CTTTAATTTTTTT-AATTTTTTTTTACCTTTATAATTAAGAC
* * * ** *
2181589 TTTTAAATTTTATAATTTCACCTTTTACTTTTATAATTAA-ATC
1 CTTTAATTTTTTTAATTT--TTTTTTACCTTTATAATTAAGA-C
** ** * *
2181632 CCCTAATTTTTTTCAATTCCGCTTTTTACCTTTATAATTGAGGCC
1 CTTTAATTTTTTT-AATT--TTTTTTTACCTTTATAATT-AAGAC
*** *
2181677 CCAAAATTTTTTCAATCTTATTTTTTACCTTTATAATT
1 CTTTAATTTTTTTAAT-TT-TTTTTTACCTTTATAATT
2181715 GAAGTCCCTA
Statistics
Matches: 129, Mismatches: 27, Indels: 22
0.72 0.15 0.12
Matches are distributed among these distances:
41 8 0.06
42 38 0.29
43 30 0.23
44 40 0.31
45 13 0.10
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (41 bp):
CTTTAATTTTTTTAATTTTTTTTTACCTTTATAATTAAGAC
Found at i:2181669 original size:44 final size:44
Alignment explanation
Indices: 2181533--2181750 Score: 142
Period size: 44 Copynumber: 5.0 Consensus size: 44
2181523 TATTTATTAT
* ** * **
2181533 TTTATAATTAAGACCTTTAATTTTTTTAAATT--TTTTTTTACC
1 TTTATAATTAAGTCCCCTAATTTTTTTCAATTCCACTTTTTACC
* * *** * * * * *
2181575 TTTATAATTGAGGCTTTTAAATTTTAT-AATTTCACCTTTTACT
1 TTTATAATTAAGTCCCCTAATTTTTTTCAATTCCACTTTTTACC
* *
2181618 TTTATAATTAAATCCCCTAATTTTTTTCAATTCCGCTTTTTACC
1 TTTATAATTAAGTCCCCTAATTTTTTTCAATTCCACTTTTTACC
* * * * * *
2181662 TTTATAATTGAGGCCCCAAAATTTTTTCAA-TCTTATTTTTTACC
1 TTTATAATTAAGTCCCCTAATTTTTTTCAATTC-CACTTTTTACC
* *
2181706 TTTATAATTGAAGT-CCCT-ATTTTTTTCAATTTCACCTTTTACC
1 TTTATAATT-AAGTCCCCTAATTTTTTTCAATTCCACTTTTTACC
2181749 TT
1 TT
2181751 GAGGCCCTAT
Statistics
Matches: 133, Mismatches: 37, Indels: 11
0.73 0.20 0.06
Matches are distributed among these distances:
41 4 0.03
42 22 0.17
43 47 0.35
44 58 0.44
45 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.53
Consensus pattern (44 bp):
TTTATAATTAAGTCCCCTAATTTTTTTCAATTCCACTTTTTACC
Found at i:2181684 original size:87 final size:87
Alignment explanation
Indices: 2181567--2181750 Score: 212
Period size: 87 Copynumber: 2.1 Consensus size: 87
2181557 TTTAAATTTT
**** *
2181567 TTTTTACCTTTATAATTGAGGCTTTTAAATTTTAT-AAT-TTCACCTTTTACTTTTATAATT-AA
1 TTTTTACCTTTATAATTGAGGCCCCAAAATTTTATCAATCTT-ACCTTTTACCTTTATAATTGAA
*
2181629 ATCCCCTAATTTTTTTCAATTCCGC
65 AT-CCCT-ATTTTTTTCAATTCCAC
* ** *
2181654 TTTTTACCTTTATAATTGAGGCCCCAAAATTTTTTCAATCTTATTTTTTACCTTTATAATTGAAG
1 TTTTTACCTTTATAATTGAGGCCCCAAAATTTTATCAATCTTACCTTTTACCTTTATAATTGAAA
*
2181719 TCCCTATTTTTTTCAATTTCAC
66 TCCCTATTTTTTTCAATTCCAC
*
2181741 CTTTTACCTT
1 TTTTTACCTT
2181751 GAGGCCCTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
87 54 0.66
88 23 0.28
89 5 0.06
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (87 bp):
TTTTTACCTTTATAATTGAGGCCCCAAAATTTTATCAATCTTACCTTTTACCTTTATAATTGAAA
TCCCTATTTTTTTCAATTCCAC
Found at i:2181746 original size:43 final size:43
Alignment explanation
Indices: 2181602--2181750 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 43
2181592 TAAATTTTAT
* *
2181602 AATTTCACCTTTTACTTTTATAATT-AAATCCCCTAATTTTTTTC
1 AATTTCACCTTTTACCTTTATAATTGAAGT-CCCT-ATTTTTTTC
* * * * * * *
2181646 AATTCCGCTTTTTACCTTTATAATTGAGGCCCCAAAATTTTTTC
1 AATTTCACCTTTTACCTTTATAATTGAAGTCCC-TATTTTTTTC
**
2181690 AATCTT-ATTTTTTACCTTTATAATTGAAGTCCCTATTTTTTTC
1 AAT-TTCACCTTTTACCTTTATAATTGAAGTCCCTATTTTTTTC
2181733 AATTTCACCTTTTACCTT
1 AATTTCACCTTTTACCTT
2181751 GAGGCCCTAT
Statistics
Matches: 83, Mismatches: 18, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 21 0.25
44 58 0.70
45 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.50
Consensus pattern (43 bp):
AATTTCACCTTTTACCTTTATAATTGAAGTCCCTATTTTTTTC
Found at i:2183075 original size:104 final size:104
Alignment explanation
Indices: 2182895--2183095 Score: 402
Period size: 104 Copynumber: 1.9 Consensus size: 104
2182885 ATCTATCAAG
2182895 AGCATATTACATGCTTAAGACTAATGTTCCTTAGAGGCATCAATACAATGCAATAATGATCAAAG
1 AGCATATTACATGCTTAAGACTAATGTTCCTTAGAGGCATCAATACAATGCAATAATGATCAAAG
2182960 TTGTTGAATATGTGCAATGAGAGAACTAATTATTGTGTA
66 TTGTTGAATATGTGCAATGAGAGAACTAATTATTGTGTA
2182999 AGCATATTACATGCTTAAGACTAATGTTCCTTAGAGGCATCAATACAATGCAATAATGATCAAAG
1 AGCATATTACATGCTTAAGACTAATGTTCCTTAGAGGCATCAATACAATGCAATAATGATCAAAG
2183064 TTGTTGAATATGTGCAATGAGAGAACTAATTA
66 TTGTTGAATATGTGCAATGAGAGAACTAATTA
2183096 GAACAATTTC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (104 bp):
AGCATATTACATGCTTAAGACTAATGTTCCTTAGAGGCATCAATACAATGCAATAATGATCAAAG
TTGTTGAATATGTGCAATGAGAGAACTAATTATTGTGTA
Found at i:2185857 original size:118 final size:118
Alignment explanation
Indices: 2185649--2185885 Score: 474
Period size: 118 Copynumber: 2.0 Consensus size: 118
2185639 GGCATGAGCC
2185649 AAACGAGCATGCCAAACACTTATTTCGTTAACAAAAGATGGAATACAATGAGAAGGCAACACATT
1 AAACGAGCATGCCAAACACTTATTTCGTTAACAAAAGATGGAATACAATGAGAAGGCAACACATT
2185714 ATTTTTTGGGAAAAACTGTGAAGAAAACAAACTAGACTCTTTATCTTTTTATG
66 ATTTTTTGGGAAAAACTGTGAAGAAAACAAACTAGACTCTTTATCTTTTTATG
2185767 AAACGAGCATGCCAAACACTTATTTCGTTAACAAAAGATGGAATACAATGAGAAGGCAACACATT
1 AAACGAGCATGCCAAACACTTATTTCGTTAACAAAAGATGGAATACAATGAGAAGGCAACACATT
2185832 ATTTTTTGGGAAAAACTGTGAAGAAAACAAACTAGACTCTTTATCTTTTTATG
66 ATTTTTTGGGAAAAACTGTGAAGAAAACAAACTAGACTCTTTATCTTTTTATG
2185885 A
1 A
2185886 GGACCCAGCC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (118 bp):
AAACGAGCATGCCAAACACTTATTTCGTTAACAAAAGATGGAATACAATGAGAAGGCAACACATT
ATTTTTTGGGAAAAACTGTGAAGAAAACAAACTAGACTCTTTATCTTTTTATG
Found at i:2187497 original size:17 final size:17
Alignment explanation
Indices: 2187475--2187510 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2187465 ATACATGTAC
2187475 AACCAGCTAAGCTAACT
1 AACCAGCTAAGCTAACT
*
2187492 AACCAGCTATGCTAACT
1 AACCAGCTAAGCTAACT
2187509 AA
1 AA
2187511 TAACTAACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (17 bp):
AACCAGCTAAGCTAACT
Found at i:2190101 original size:170 final size:169
Alignment explanation
Indices: 2189774--2190112 Score: 669
Period size: 170 Copynumber: 2.0 Consensus size: 169
2189764 ATACTCTATT
2189774 CATAGAGTATCTATATTGTTCCTCAGGTATCGATACCCAAGGGTGGGATATTGGTACCATCGTTA
1 CATAGAGTATCTATATTGTTCCTCAGGTATCGATACCCAAGGGTGGGATATTGGTACCATCGTTA
2189839 AGTTACAAATTCCATAGCTAAAATTAATATTTTTACTCGAGGAGTATCAACACCACACAAAGCAT
66 AGTTACAAATTCCATAGCTAAAATTAATATTTTTACTCGAGGAGTATCAACACCACACAAAGCAT
2189904 AAGTACGAATACACTAAGTAAGGCATTAATAGTGATTTA
131 AAGTACGAATACACTAAGTAAGGCATTAATAGTGATTTA
2189943 CATAGAGTATCTATATTGTTCCTCAGGTATCGATACCCAAGGGTGGGATATTGGTACCATCGTTA
1 CATAGAGTATCTATATTGTTCCTCAGGTATCGATACCCAAGGGTGGGATATTGGTACCATCGTTA
2190008 AGTTACAAATTCCAGTAGCTAAAATTAATATTTTTACTCGAGGAGTATCAACACCACACAAAGCA
66 AGTTACAAATTCCA-TAGCTAAAATTAATATTTTTACTCGAGGAGTATCAACACCACACAAAGCA
2190073 TAAGTACGAATACACTAAGTAAGGCATTAATAGTGATTTA
130 TAAGTACGAATACACTAAGTAAGGCATTAATAGTGATTTA
2190113 TTTTCTCAAG
Statistics
Matches: 169, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 79 0.47
170 90 0.53
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (169 bp):
CATAGAGTATCTATATTGTTCCTCAGGTATCGATACCCAAGGGTGGGATATTGGTACCATCGTTA
AGTTACAAATTCCATAGCTAAAATTAATATTTTTACTCGAGGAGTATCAACACCACACAAAGCAT
AAGTACGAATACACTAAGTAAGGCATTAATAGTGATTTA
Found at i:2198135 original size:17 final size:17
Alignment explanation
Indices: 2198113--2198145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2198103 TAAGATTTAA
2198113 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
2198130 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
2198146 CTTCCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:2202636 original size:16 final size:16
Alignment explanation
Indices: 2202615--2202646 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2202605 AATTAATAAT
*
2202615 AAAAAAATAACCTCAC
1 AAAAAAAAAACCTCAC
2202631 AAAAAAAAAACCTCAC
1 AAAAAAAAAACCTCAC
2202647 CAGACACTCC
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:0.66, C:0.25, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAACCTCAC
Found at i:2202969 original size:9 final size:8
Alignment explanation
Indices: 2202950--2202980 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2202940 CTCTTTAAAC
*
2202950 TTTTTTCT
1 TTTTTTAT
2202958 TTTTTTAT
1 TTTTTTAT
2202966 TTTTTTAT
1 TTTTTTAT
2202974 TTTTTTA
1 TTTTTTA
2202981 CTAACTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:2204301 original size:17 final size:17
Alignment explanation
Indices: 2204272--2204321 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
2204262 TAAGAGTTAA
*
2204272 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
*
2204289 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
2204306 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
2204322 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:2224630 original size:20 final size:20
Alignment explanation
Indices: 2224598--2224635 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2224588 AATTTATAAT
2224598 TTGTTTAGATTAT-TAAAAA
1 TTGTTTAGATTATATAAAAA
*
2224617 TTGTTTATATTTATATAAA
1 TTGTTTAGA-TTATATAAA
2224636 TACGATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (20 bp):
TTGTTTAGATTATATAAAAA
Found at i:2225079 original size:24 final size:24
Alignment explanation
Indices: 2225052--2225107 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2225042 CGTTCATTTA
2225052 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
2225076 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
2225100 CGTTCGGT
1 CGTTCGGT
2225108 TATCTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:2225081 original size:14 final size:14
Alignment explanation
Indices: 2225062--2225110 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
2225052 CGTTCGTGAA
2225062 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2225076 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2225090 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2225100 CGTTCGGTTAT
1 CGTTCGGTTAT
2225111 CTTCATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.08, C:0.14, G:0.27, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2225108 original size:24 final size:24
Alignment explanation
Indices: 2225063--2225124 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
2225053 GTTCGTGAAC
*
2225063 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
2225087 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
* *
2225111 CTTCATTTATGTTC
1 GTTCGTTTATGTTC
2225125 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:2225652 original size:11 final size:11
Alignment explanation
Indices: 2225636--2225760 Score: 88
Period size: 11 Copynumber: 10.6 Consensus size: 11
2225626 TGGTGCAATG
2225636 TCGAGCTTGAA
1 TCGAGCTTGAA
**
2225647 TCGAGCTCAAAA
1 TCGAGCT-TGAA
2225659 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
2225670 TTGAGCTCAGAA
1 TCGAGCT-TGAA
*
2225682 TCAAGCTTGAAAGAA
1 TCGAGCTT----GAA
*
2225697 TTGAGCTTGAA
1 TCGAGCTTGAA
* *
2225708 TTGAGCTCAGAA
1 TCGAGCT-TGAA
2225720 TCGAGCTTGAA
1 TCGAGCTTGAA
*
2225731 TCGAGCTCAGAA
1 TCGAGCT-TGAA
*
2225743 TCGAGCTTTAA
1 TCGAGCTTGAA
2225754 TCGAGCT
1 TCGAGCT
2225761 CGAGTCTCGG
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
11 44 0.49
12 36 0.40
15 9 0.10
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2225666 original size:23 final size:23
Alignment explanation
Indices: 2225636--2225692 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2225626 TGGTGCAATG
2225636 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
* *
2225659 TCGAGCTTGAATTGAGCTCAGAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
2225682 TCAAGCTTGAA
1 TCGAGCTTGAA
2225693 AGAATTGAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAAAA
Found at i:2225725 original size:23 final size:23
Alignment explanation
Indices: 2225693--2225761 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
2225683 CAAGCTTGAA
* *
2225693 AGAATTGAGCTTGAATTGAGCTC
1 AGAATCGAGCTTGAATCGAGCTC
2225716 AGAATCGAGCTTGAATCGAGCTC
1 AGAATCGAGCTTGAATCGAGCTC
*
2225739 AGAATCGAGCTTTAATCGAGCTC
1 AGAATCGAGCTTGAATCGAGCTC
2225762 GAGTCTCGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (23 bp):
AGAATCGAGCTTGAATCGAGCTC
Found at i:2226114 original size:199 final size:199
Alignment explanation
Indices: 2225774--2226164 Score: 737
Period size: 199 Copynumber: 2.0 Consensus size: 199
2225764 GTCTCGGTTA
* * * *
2225774 TAATCGAGCTCTTAAATTTTTTTTGAGTTCGAGCCTTTTCGAGTTCGAGTTGATTTTCAATATTA
1 TAATCGAGCTCTTAAATTTTTTTTGAGTTCAAGCCTTTTCGAGTTCGAGTCGAGTTTCAACATTA
2225839 TATTTCGAGTTCGATTCGAACTTGATAATTTTAAGCTCGCGAGTTTTCGAGTCGAGCTGACTTTG
66 TATTTCGAGTTCGATTCGAACTTGATAATTTTAAGCTCGCGAGTTTTCGAGTCGAGCTGACTTTG
2225904 AAAGTTTTTTCGAGTTCGAGTCGAGCTCAGCAATACTCGAGCTTGACTCGGCTCGTTTACACAGA
131 AAAGTTTTTTCGAGTTCGAGTCGAGCTCAGCAATACTCGAGCTTGACTCGGCTCGTTTACACAGA
2225969 GTTT
196 GTTT
2225973 TAATCGAGCTCTTAAATTTTTTTTGAGTTCAAGCCTTTTCGAGTTCGAGTCGAGTTTCAACATTA
1 TAATCGAGCTCTTAAATTTTTTTTGAGTTCAAGCCTTTTCGAGTTCGAGTCGAGTTTCAACATTA
*
2226038 TATTTCGAGTTCGATTCGAACTTGATAATTTTAAGCTCGCGAGTTTTCGAGTTGAGCTGACTTTG
66 TATTTCGAGTTCGATTCGAACTTGATAATTTTAAGCTCGCGAGTTTTCGAGTCGAGCTGACTTTG
2226103 AAAGTTTTTTCGAGTTCGAGTCGAGCTCAGCAATACTCGAGCTTGACTCGGCTCGTTTACAC
131 AAAGTTTTTTCGAGTTCGAGTCGAGCTCAGCAATACTCGAGCTTGACTCGGCTCGTTTACAC
2226165 TCCTAGGTAG
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 187 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (199 bp):
TAATCGAGCTCTTAAATTTTTTTTGAGTTCAAGCCTTTTCGAGTTCGAGTCGAGTTTCAACATTA
TATTTCGAGTTCGATTCGAACTTGATAATTTTAAGCTCGCGAGTTTTCGAGTCGAGCTGACTTTG
AAAGTTTTTTCGAGTTCGAGTCGAGCTCAGCAATACTCGAGCTTGACTCGGCTCGTTTACACAGA
GTTT
Found at i:2226124 original size:101 final size:101
Alignment explanation
Indices: 2225809--2226127 Score: 273
Period size: 101 Copynumber: 3.2 Consensus size: 101
2225799 AGTTCGAGCC
* * *
2225809 TTTTCGAGTTCGAGTTGATTTTCAATATTATATTTCGAGTTCGATTCGAACTTGATAATTTTAAG
1 TTTTCGAGTTCGAGTCGAGTTTCAACATTATATTTCGAGTTCGATTCGAACTTGATAATTTTAAG
*
2225874 CTCGCGAGTTTTCGAGTCGAGCTGACTTTGAAAGTT
66 CTCGCGAGTTTTCGAGTTGAGCTGACTTTGAAAGTT
* * * * ** * *
2225910 TTTTCGAGTTCGAGTCGAG-CTCAGCA--ATA-CTCGAGCTT-GACTCGGCTCGTTTACACAGAG
1 TTTTCGAGTTCGAGTCGAGTTTCAACATTATATTTCGAG-TTCGATTC-GAAC--TT-GATA-A-
* ** * **** * * **
2225970 TTTTAA--T--CGAGCTCTTAAATTTTTTTTGA-GTT-CAAGCC
59 TTTTAAGCTCGCGAG-TTTTCGAGTTGAGCTGACTTTGAAAGTT
2226008 TTTTCGAGTTCGAGTCGAGTTTCAACATTATATTTCGAGTTCGATTCGAACTTGATAATTTTAAG
1 TTTTCGAGTTCGAGTCGAGTTTCAACATTATATTTCGAGTTCGATTCGAACTTGATAATTTTAAG
2226073 CTCGCGAGTTTTCGAGTTGAGCTGACTTTGAAAGTT
66 CTCGCGAGTTTTCGAGTTGAGCTGACTTTGAAAGTT
2226109 TTTTCGAGTTCGAGTCGAG
1 TTTTCGAGTTCGAGTCGAG
2226128 CTCAGCAATA
Statistics
Matches: 155, Mismatches: 44, Indels: 38
0.65 0.19 0.16
Matches are distributed among these distances:
96 6 0.04
97 10 0.06
98 32 0.21
99 22 0.14
100 20 0.13
101 49 0.32
102 10 0.06
103 6 0.04
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (101 bp):
TTTTCGAGTTCGAGTCGAGTTTCAACATTATATTTCGAGTTCGATTCGAACTTGATAATTTTAAG
CTCGCGAGTTTTCGAGTTGAGCTGACTTTGAAAGTT
Found at i:2226215 original size:16 final size:16
Alignment explanation
Indices: 2226190--2226248 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
2226180 CCAACGTTTA
2226190 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2226206 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
2226222 TGTTCTTTTATGTTCA
1 TGTTCGTTTATGTTCG
2226238 TGTTCGTTTAT
1 TGTTCGTTTAT
2226249 TTATTAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Done.