Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 57 of 84
Found at i:12939527 original size:35 final size:35
Alignment explanation
Indices: 12939486--12939553 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
12939476 CAGCAGAGGT
12939486 TCAACAACTTTAAAATCTCATTTAGAAAAGGCTGC
1 TCAACAACTTTAAAATCTCATTTAGAAAAGGCTGC
12939521 TCAACAACTTTAAAATCTCATTTAGAAAAGGCT
1 TCAACAACTTTAAAATCTCATTTAGAAAAGGCT
12939554 CCTCTTAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (35 bp):
TCAACAACTTTAAAATCTCATTTAGAAAAGGCTGC
Found at i:12939575 original size:83 final size:84
Alignment explanation
Indices: 12939436--12939602 Score: 282
Period size: 83 Copynumber: 2.0 Consensus size: 84
12939426 CTCAGCAGAG
*
12939436 GCTCAACAACTTTAAAATCTCATTTAAAAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTTAAAA
1 GCTCAACAACTTTAAAATCTCATTTAAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
12939501 TCTCATTTAG-AAAAGGCT
66 TCTCATTTAGAAAAAGGCT
* * *
12939519 GCTCAACAACTTTAAAATCTCATTTAGAAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAA
1 GCTCAACAACTTTAAAATCTCATTTAAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
*
12939584 TCTCATTTTGAAAAAGGCT
66 TCTCATTTAGAAAAAGGCT
12939603 CCTCTCAATA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 70 0.90
84 8 0.10
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (84 bp):
GCTCAACAACTTTAAAATCTCATTTAAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
TCTCATTTAGAAAAAGGCT
Found at i:12940009 original size:21 final size:22
Alignment explanation
Indices: 12939980--12940029 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12939970 AAATCTCATC
* *
12939980 TTCTCTTAA-AACTAAGTTCTT
1 TTCTTTTAACAACTAAATTCTT
*
12940001 TTCTTTTAACAAGTAAATTCTT
1 TTCTTTTAACAACTAAATTCTT
*
12940023 CTCTTTT
1 TTCTTTT
12940030 GAAATCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (22 bp):
TTCTTTTAACAACTAAATTCTT
Found at i:12953625 original size:26 final size:26
Alignment explanation
Indices: 12953595--12953649 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12953585 CATCTTTTGA
*
12953595 TTTTTGT-TCTGTCGCTATTTTTTTTT
1 TTTTTGTGTATGTCG-TATTTTTTTTT
* *
12953621 TTTTTTTGTATTTCGTATTTTTTTTT
1 TTTTTGTGTATGTCGTATTTTTTTTT
12953647 TTT
1 TTT
12953650 GTATCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.05, C:0.07, G:0.09, T:0.78
Consensus pattern (26 bp):
TTTTTGTGTATGTCGTATTTTTTTTT
Found at i:12953643 original size:20 final size:20
Alignment explanation
Indices: 12953618--12953675 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 20
12953608 GCTATTTTTT
12953618 TTTTTTTTTTGTATTTCGTA
1 TTTTTTTTTTGTATTTCGTA
12953638 --TTTTTTTT-T-TTT-GTA
1 TTTTTTTTTTGTATTTCGTA
*
12953653 TCTTTTTTTTGTATTTCGTA
1 TTTTTTTTTTGTATTTCGTA
12953673 TTT
1 TTT
12953676 ATATTTATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 9 0.28
18 9 0.28
19 3 0.09
20 5 0.16
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.78
Consensus pattern (20 bp):
TTTTTTTTTTGTATTTCGTA
Found at i:12953660 original size:13 final size:13
Alignment explanation
Indices: 12953642--12953666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12953632 TTCGTATTTT
12953642 TTTTTTTTGTATC
1 TTTTTTTTGTATC
12953655 TTTTTTTTGTAT
1 TTTTTTTTGTAT
12953667 TTCGTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTTTTGTATC
Found at i:12954983 original size:19 final size:19
Alignment explanation
Indices: 12954961--12955018 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
12954951 CTTTATTTGG
12954961 GGTTTCGGGTTTCACTTAA
1 GGTTTCGGGTTTCACTTAA
* * **
12954980 GGTTTAGGGTTTCATTTGG
1 GGTTTCGGGTTTCACTTAA
* *
12954999 GGTTTCGAGTTTCACCTAA
1 GGTTTCGGGTTTCACTTAA
12955018 G
1 G
12955019 ATGTAGGTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (19 bp):
GGTTTCGGGTTTCACTTAA
Found at i:12954997 original size:38 final size:38
Alignment explanation
Indices: 12954938--12955040 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
12954928 TTTGAGCGGA
* * *
12954938 TTAAGGTTTTGGACTTT-ATTTGGGGTTTCGGGTTTCAC
1 TTAAGGTTTAGG-GTTTCATTTGGGGTTTCGAGTTTCAC
12954976 TTAAGGTTTAGGGTTTCATTTGGGGTTTCGAGTTTCAC
1 TTAAGGTTTAGGGTTTCATTTGGGGTTTCGAGTTTCAC
* * * *
12955014 CTAAGATGTA-GGTTTCATTTAGGGTTT
1 TTAAGGTTTAGGGTTTCATTTGGGGTTT
12955041 TGTTTTTAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
37 19 0.33
38 38 0.67
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.46
Consensus pattern (38 bp):
TTAAGGTTTAGGGTTTCATTTGGGGTTTCGAGTTTCAC
Found at i:12957146 original size:44 final size:44
Alignment explanation
Indices: 12957097--12957227 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 44
12957087 CGCAGCCCCC
12957097 CTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTGG
1 CTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTGG
* * * ****
12957141 CTCCTTTCTCTTCC--TTTATTTTTTTCC-C-TTGC--CC-CC---
1 CTCCTTT-GCTGCCAGTTCATGCCATTCCACGTT-CTTCCGCCTGG
12957177 CTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTGG
1 CTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTGG
12957221 CTCCTTT
1 CTCCTTT
12957228 CTCTTCCTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 24
0.62 0.14 0.24
Matches are distributed among these distances:
35 4 0.07
36 7 0.11
37 8 0.13
38 2 0.03
39 4 0.07
40 4 0.07
41 4 0.07
42 2 0.03
43 8 0.13
44 14 0.23
45 4 0.07
ACGTcount: A:0.07, C:0.40, G:0.13, T:0.40
Consensus pattern (44 bp):
CTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTGG
Found at i:12957175 original size:80 final size:80
Alignment explanation
Indices: 12957074--12957255 Score: 330
Period size: 80 Copynumber: 2.3 Consensus size: 80
12957064 TTTTTTATTT
*
12957074 TTTATTTTTTTGCCGC-AGCCCCCCTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCC
1 TTTATTTTTTT-CC-CTTGCCCCCCTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCC
12957138 TGGCTCCTTTCTCTTCC
64 TGGCTCCTTTCTCTTCC
12957155 TTTATTTTTTTCCCTTGCCCCCCTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTG
1 TTTATTTTTTTCCCTTGCCCCCCTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTG
12957220 GCTCCTTTCTCTTCC
66 GCTCCTTTCTCTTCC
12957235 TTTATTTTTTTCCCTTGCCCC
1 TTTATTTTTTTCCCTTGCCCC
12957256 TTTTTCTACT
Statistics
Matches: 99, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
79 1 0.01
80 87 0.88
81 11 0.11
ACGTcount: A:0.07, C:0.39, G:0.12, T:0.43
Consensus pattern (80 bp):
TTTATTTTTTTCCCTTGCCCCCCTCCTTTGCTGCCAGTTCATGCCATTCCACGTTCTTCCGCCTG
GCTCCTTTCTCTTCC
Found at i:12957965 original size:6 final size:6
Alignment explanation
Indices: 12957954--12958031 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
12957944 GAATTTTTTG
* * *
12957954 TTGTTT TTGTTT TTATTTT TTGTGTT TGTTTTT TTGTTT TTG-TT TT-TAT
1 TTGTTT TTGTTT TT-GTTT TTGT-TT T-TGTTT TTGTTT TTGTTT TTGTTT
**
12958003 TT-TTT TTGTTT TCACTTT TTGTTT TTGTT
1 TTGTTT TTGTTT T-TGTTT TTGTTT TTGTT
12958032 ATTTTGTCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
5 11 0.20
6 28 0.50
7 15 0.27
8 2 0.04
ACGTcount: A:0.04, C:0.03, G:0.13, T:0.81
Consensus pattern (6 bp):
TTGTTT
Found at i:12957996 original size:33 final size:32
Alignment explanation
Indices: 12957947--12958031 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
12957937 ATAATGTGAA
*
12957947 TTTTTTGTTGTTTTTGTTTTTATTTTTTGTGT
1 TTTTTTTTTGTTTTTGTTTTTATTTTTTGTGT
*
12957979 TTGTTTTTTTGTTTTTGTTTTTATTTTTTTTGT
1 TT-TTTTTTTGTTTTTGTTTTTATTTTTTGTGT
*
12958012 TTTCACTTTTTGTTTTTGTT
1 TTT--TTTTTTGTTTTTGTT
12958032 ATTTTGTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 3 0.06
33 30 0.64
34 14 0.30
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (32 bp):
TTTTTTTTTGTTTTTGTTTTTATTTTTTGTGT
Found at i:12958010 original size:48 final size:46
Alignment explanation
Indices: 12957947--12958061 Score: 133
Period size: 48 Copynumber: 2.5 Consensus size: 46
12957937 ATAATGTGAA
* * * * *
12957947 TTTTTTGTTGTTTTTGTTTTTATTTTTTGTGTTTGTTTTTTTGTTTT
1 TTTTTTATTTTTTTTGTTTTTACTTTTTGTGTTTGTTATTTTG-TCT
* *
12957994 TGTTTTTATTTTTTTTGTTTTCACTTTTTGTTTTTGTTATTTTGTCT
1 T-TTTTTATTTTTTTTGTTTTTACTTTTTGTGTTTGTTATTTTGTCT
*
12958041 TTTTTTCTTTTTTTT-TTTTTA
1 TTTTTTATTTTTTTTGTTTTTA
12958062 AGATGACCAG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
45 5 0.09
46 13 0.22
47 4 0.07
48 36 0.62
ACGTcount: A:0.04, C:0.03, G:0.10, T:0.82
Consensus pattern (46 bp):
TTTTTTATTTTTTTTGTTTTTACTTTTTGTGTTTGTTATTTTGTCT
Found at i:12958151 original size:31 final size:31
Alignment explanation
Indices: 12958116--12958196 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
12958106 GGATTGAACT
* *** *
12958116 GCAGGTCAAAAGAGGTGATTGGGCTTGAATC
1 GCAGGTCAAATGAGGTGACCAGACTTGAATC
*
12958147 GCAGGTCGAATGAGGTGACCAGACTTGAATC
1 GCAGGTCAAATGAGGTGACCAGACTTGAATC
*
12958178 GCAAGTCAAATGAGGTGAC
1 GCAGGTCAAATGAGGTGAC
12958197 TGTTAATTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (31 bp):
GCAGGTCAAATGAGGTGACCAGACTTGAATC
Found at i:12958282 original size:33 final size:33
Alignment explanation
Indices: 12958231--12958545 Score: 157
Period size: 32 Copynumber: 9.8 Consensus size: 33
12958221 TAAATTTGGC
* * * *
12958231 TTAATTTTTCCTTG-GTGCCAGCTAAACTGGGT
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
* * *
12958263 TTAAATTTTCATTAAGTGCCAACTAAACT-AAC
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
** * *
12958295 TTAAAACTTCATTG-GTGCCAACTAAATTGGGT
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
* * * *
12958327 TTAAA-TTTCATTGGGTGCCAATTAGACTGAAT
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
* * *
12958359 TTAAATTTTCATTGAGTGCTAGCTAAACTGGAC
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
* * * * *
12958392 TCAAATTTT-ACT-AGGTGCCAACTAGACAGAGCT
1 TTAAATTTTCATTGA-GTGCCAACTAAACTG-GAT
* * * * * *
12958425 TAAAACTTT-ATTGGGTGCCAACGAAATTGGAC
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
* * * * *
12958457 TTAAATTTTTATTGGGTACCAACTAAGCTAGG-C
1 TTAAATTTTCATTGAGTGCCAACTAAACT-GGAT
* * * * * *
12958490 TT-AAGTTTCATT-AGTACCAAATAATCTGAAC
1 TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
*
12958521 TTAAATTTTC-TTTAGTGCCAACTAA
1 TTAAATTTTCATTGAGTGCCAACTAA
12958546 TCTAAGCTTA
Statistics
Matches: 211, Mismatches: 60, Indels: 24
0.72 0.20 0.08
Matches are distributed among these distances:
30 1 0.00
31 38 0.18
32 90 0.43
33 80 0.38
34 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (33 bp):
TTAAATTTTCATTGAGTGCCAACTAAACTGGAT
Found at i:12958337 original size:31 final size:32
Alignment explanation
Indices: 12958244--12958415 Score: 123
Period size: 33 Copynumber: 5.3 Consensus size: 32
12958234 ATTTTTCCTT
*
12958244 GGTGCCAGCTAAACTGGGTTTAAATTTTCATTA
1 GGTGCCAACTAAACTGGGTTTAAA-TTTCATTA
* *** * *
12958277 AGTGCCAACTAAACTAACTTAAAACTTCATT-
1 GGTGCCAACTAAACTGGGTTTAAATTTCATTA
* *
12958308 GGTGCCAACTAAATTGGGTTTAAATTTCATTG
1 GGTGCCAACTAAACTGGGTTTAAATTTCATTA
* * **
12958340 GGTGCCAATTAGACTGAATTTAAATTTTCATT-
1 GGTGCCAACTAAACTGGGTTTAAA-TTTCATTA
* * ** * * *
12958372 GAGTGCTAGCTAAACTGGACTCAAATTTTACTA
1 G-GTGCCAACTAAACTGGGTTTAAATTTCATTA
12958405 GGTGCCAACTA
1 GGTGCCAACTA
12958416 GACAGAGCTT
Statistics
Matches: 105, Mismatches: 30, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
31 24 0.23
32 39 0.37
33 42 0.40
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (32 bp):
GGTGCCAACTAAACTGGGTTTAAATTTCATTA
Found at i:12958456 original size:65 final size:64
Alignment explanation
Indices: 12958244--12958465 Score: 178
Period size: 65 Copynumber: 3.4 Consensus size: 64
12958234 ATTTTTCCTT
* * ** * * * *
12958244 GGTGCCAGCTAAACTGGGTTTAAATTTTCATTAAGTGCCAACTAAACTA-ACTTAAAACTTCATT
1 GGTGCCAACTAAATTGGACTTAAATTTT-ACTAGGTGCCAACTAGAC-AGACTTAAAACTTTATT
12958308 -
64 G
** * * * * * * * *
12958308 GGTGCCAACTAAATTGGGTTTAAATTTCATTGGGTGCCAATTAGACTGAATTTAAATTTTCATTG
1 GGTGCCAACTAAATTGGACTTAAATTTTACTAGGTGCCAACTAGACAGACTTAAAACTTT-ATTG
* * * * *
12958373 AGTGCTAGCTAAACTGGACTCAAATTTTACTAGGTGCCAACTAGACAGAGCTTAAAACTTTATTG
1 GGTGCCAACTAAATTGGACTTAAATTTTACTAGGTGCCAACTAGACAGA-CTTAAAACTTTATTG
*
12958438 GGTGCCAACGAAATTGGACTTAAATTTT
1 GGTGCCAACTAAATTGGACTTAAATTTT
12958466 TATTGGGTAC
Statistics
Matches: 121, Mismatches: 33, Indels: 7
0.75 0.20 0.04
Matches are distributed among these distances:
63 22 0.18
64 28 0.23
65 63 0.52
66 8 0.07
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (64 bp):
GGTGCCAACTAAATTGGACTTAAATTTTACTAGGTGCCAACTAGACAGACTTAAAACTTTATTG
Found at i:12958524 original size:31 final size:32
Alignment explanation
Indices: 12958456--12958565 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
12958446 CGAAATTGGA
* * * * *
12958456 CTTAAATTTTTATTGGGTACCAACTAAGCTAGG
1 CTTAAATTTTCATT-AGTACCAAATAATCTAAG
*
12958489 CTT-AAGTTTCATTAGTACCAAATAATCTGAA-
1 CTTAAATTTTCATTAGTACCAAATAATCT-AAG
* * *
12958520 CTTAAATTTTCTTTAGTGCCAACTAATCTAAG
1 CTTAAATTTTCATTAGTACCAAATAATCTAAG
12958552 CTTAAATTTTCATT
1 CTTAAATTTTCATT
12958566 GGGTGGGCTT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
31 17 0.27
32 43 0.68
33 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (32 bp):
CTTAAATTTTCATTAGTACCAAATAATCTAAG
Found at i:12958577 original size:21 final size:21
Alignment explanation
Indices: 12958551--12958591 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
12958541 ACTAATCTAA
12958551 GCTTAAATTTTCATTGGGTGG
1 GCTTAAATTTTCATTGGGTGG
12958572 GCTTAAATTTTCATTGGGTG
1 GCTTAAATTTTCATTGGGTG
12958592 CAACTAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (21 bp):
GCTTAAATTTTCATTGGGTGG
Found at i:12958877 original size:22 final size:22
Alignment explanation
Indices: 12958845--12958903 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
12958835 CAATTTTTAA
*
12958845 CTAATTCGGGCTTACATGCCAG
1 CTAATTTGGGCTTACATGCCAG
** *
12958867 CTAATTTGGGCTTATGTGCTAG
1 CTAATTTGGGCTTACATGCCAG
*
12958889 CTAATTTGAGCTTAC
1 CTAATTTGGGCTTAC
12958904 GTACTAGCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (22 bp):
CTAATTTGGGCTTACATGCCAG
Found at i:12958910 original size:22 final size:22
Alignment explanation
Indices: 12958865--12958914 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
12958855 CTTACATGCC
* * *
12958865 AGCTAATTTGGGCTTATGTGCT
1 AGCTAATTTGAGCTTACGTACT
12958887 AGCTAATTTGAGCTTACGTACT
1 AGCTAATTTGAGCTTACGTACT
12958909 AGCTAA
1 AGCTAA
12958915 ACTAGGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (22 bp):
AGCTAATTTGAGCTTACGTACT
Found at i:12959946 original size:19 final size:20
Alignment explanation
Indices: 12959924--12959984 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
12959914 TTTTCTCCAT
12959924 TTTTTCCTTTTTTCTTTTA-
1 TTTTTCCTTTTTTCTTTTAC
*
12959943 TTTTTCATTTTTTC-TTTAC
1 TTTTTCCTTTTTTCTTTTAC
12959962 TTTTT-CTTTTCATTCTTTTAC
1 TTTTTCCTTTT--TTCTTTTAC
12959983 TT
1 TT
12959985 CTTTTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 8 0.22
19 18 0.50
20 3 0.08
21 7 0.19
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTCCTTTTTTCTTTTAC
Found at i:12959980 original size:26 final size:24
Alignment explanation
Indices: 12959936--12959997 Score: 56
Period size: 26 Copynumber: 2.5 Consensus size: 24
12959926 TTTCCTTTTT
*
12959936 TCTTTTAT-TTTTCATTTTTTCTT-
1 TCTTTT-TCTTTTCATTTTTACTTC
12959959 TACTTTTTCTTTTCATTCTTTTACTTC
1 T-CTTTTTCTTTTCA-T-TTTTACTTC
*
12959986 TTTTTTTCTTTT
1 TCTTTTTCTTTT
12959998 TTATCTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 2 0.06
24 11 0.34
25 1 0.03
26 17 0.53
27 1 0.03
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (24 bp):
TCTTTTTCTTTTCATTTTTACTTC
Found at i:12959988 original size:24 final size:22
Alignment explanation
Indices: 12959934--12959992 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
12959924 TTTTTCCTTT
12959934 TTTCTTTTATTTTTCATTTTTTC
1 TTTCTTTT-TTTTTCATTTTTTC
12959957 TTTACTTTTTCTTTTCATTCTTTTAC
1 TTT-CTTTTT-TTTTCATT-TTTT-C
12959983 -TTCTTTTTTT
1 TTTCTTTTTTT
12959993 CTTTTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 6 0.19
24 19 0.59
25 6 0.19
26 1 0.03
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTCTTTTTTTTTCATTTTTTC
Found at i:12959996 original size:8 final size:8
Alignment explanation
Indices: 12959923--12960006 Score: 51
Period size: 9 Copynumber: 9.5 Consensus size: 8
12959913 CTTTTCTCCA
*
12959923 TTTTTTCC
1 TTTTTTTC
*
12959931 TTTTTTCTT
1 TTTTTT-TC
12959940 TTATTTTTC
1 TT-TTTTTC
*
12959949 ATTTTTTC
1 TTTTTTTC
12959957 TTTACTTTTTC
1 -TT--TTTTTC
*
12959968 TTTTCATTC
1 TTTT-TTTC
*
12959977 TTTTACTTC
1 TTTT-TTTC
12959986 TTTTTTTC
1 TTTTTTTC
12959994 TTTTTTATC
1 TTTTTT-TC
12960003 TTTT
1 TTTT
12960007 AGTGGATCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 23 0.38
9 25 0.42
10 6 0.10
11 6 0.10
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTTC
Found at i:12961177 original size:3 final size:3
Alignment explanation
Indices: 12961169--12961253 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
12961159 CATGTTATAG
* * * * *
12961169 TAT TAT TAT TAT TAG TA- TAT TGT ATAG TAT T-T TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * *
12961213 CAT CAT CAT TAT TAT TAT TAT TAT TA- TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12961254 CATTTTTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
2 6 0.09
3 62 0.90
4 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:12962321 original size:45 final size:47
Alignment explanation
Indices: 12962254--12962354 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 47
12962244 AAATAATTAT
12962254 AAAAAAAATCTTTTCAAATAAGTTTTCAAAATAATA-A-AAAAACAAAAAA
1 AAAAAAAATCTTTT---ATAAGTTTTCAAAA-AATATATAAAAACAAAAAA
12962303 AAAAAAAATCTTTT-TAAGTTTTCAAAAAATATTTATAAAAACAAAAAA
1 AAAAAAAATCTTTTATAAGTTTTCAAAAAATA--TATAAAAACAAAAAA
12962351 AAAA
1 AAAA
12962355 CCCTTTCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
44 4 0.08
45 13 0.27
47 1 0.02
48 16 0.33
49 14 0.29
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (47 bp):
AAAAAAAATCTTTTATAAGTTTTCAAAAAATATATAAAAACAAAAAA
Found at i:12967535 original size:208 final size:208
Alignment explanation
Indices: 12967170--12967550 Score: 439
Period size: 208 Copynumber: 1.8 Consensus size: 208
12967160 TCGATCTTAG
* * * * *
12967170 CTCAATCCAGATTATTTTTTATGAATCGTGGTTTTCTCTTGATCATTTATTTTCGACCTCGACTT
1 CTCAATCCAGATCATTTTTTATGAATCATAGTTTTCTCTCGATCATTTATTTTCGACCTCGACTC
* * * * *
12967235 GATCTTGCTCACTTTATTTTTGACTCGTAGTTTCACCTCAGTCACCTGATCTTAGCTCATTCCAA
66 GATCTAGCTCACTTTATTTTTGACTCATAGTTTCACCTCAATCACCCGATCTTAGCTCAGTCCAA
* * * * *
12967300 ATCATTTCTTATGACTTATGGTTTCATCCTGGTTATTTATTTTCGACTTCGATTCCGTCTTGGCT
131 ATCATTTCTTATGACTCATGATTTCATCCCGATCATTTATTTTCGACTTCGATTCCGTCTTGGCT
12967365 GCTTAATTTTTTA
196 GCTTAATTTTTTA
* * ** *
12967378 CTCAATCCAGATCATTTTTTATGACTTATAG-TTTCATCTCGATCATTTATTTTTTACCTTGACT
1 CTCAATCCAGATCATTTTTTATGAATCATAGTTTTC-TCTCGATCATTTATTTTCGACCTCGACT
* * * *
12967442 CGGTCCTAG-TCACTTTATTTTTTACTCAT-GATTTCGTCC-CAATCACCCGATCTTGGCTCAGT
65 CGAT-CTAGCTCACTTTATTTTTGACTCATAG-TTTC-ACCTCAATCACCCGATCTTAGCTCAGT
* * *
12967504 CTAGATGATTTCTTAT-AGCTCATGATTTCATCCCGATCATTTATTTT
127 CCAAATCATTTCTTATGA-CTCATGATTTCATCCCGATCATTTATTTT
12967551 AAACCTCGAC
Statistics
Matches: 141, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
207 6 0.04
208 130 0.92
209 5 0.04
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (208 bp):
CTCAATCCAGATCATTTTTTATGAATCATAGTTTTCTCTCGATCATTTATTTTCGACCTCGACTC
GATCTAGCTCACTTTATTTTTGACTCATAGTTTCACCTCAATCACCCGATCTTAGCTCAGTCCAA
ATCATTTCTTATGACTCATGATTTCATCCCGATCATTTATTTTCGACTTCGATTCCGTCTTGGCT
GCTTAATTTTTTA
Found at i:12968053 original size:120 final size:118
Alignment explanation
Indices: 12967378--12968040 Score: 611
Period size: 120 Copynumber: 5.6 Consensus size: 118
12967368 TAATTTTTTA
* * * * *
12967378 CTCAATCCAGATCATTTTTTATGACTTATAGTTTCATCTCGATCATTTATTTTTTACCTTGACTC
1 CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
* * * * * **
12967443 GGTCCTAGTCACTTTATTTTTTACTCATGATTTCGTCCCAATCACCCGATCTTGG
66 GATCCTAGTCGCTTCATTTTTGACTCATGGTTT--TCCCGGTCACCCGATCTTGG
* * * * ** *
12967498 CTCAGTCTAGATGATTTCTTAT-AGCTCATGATTTCATCCCGATCATTTATTTTAAACCTCGACT
1 CTCAGTCCAGATCATTTCTTATGA-CTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACT
* * ** * * *
12967562 CTG-TCCTAGTTGCTTCATTTTTTACTTGTGATTTTGCCTCGGTCACCCAATCTTAG
65 C-GATCCTAGTCGCTTCATTTTTGACTCATGGTTTT-CC-CGGTCACCCGATCTTGG
* * ** * * *
12967618 TTCAGTCTAGATCATTTCTTATGACTTGTGATTTCATCCCGATCATTTATTTTTTACCTTGA-TC
1 CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
* * ** * ** * *
12967682 GATCCT-GATTGTTTCATTTTTGACTTGTGATTTTGCCCTAATCACCCAATCTTGA
66 GATCCTAG-TCGCTTCATTTTTGACTCATGGTTTT-CCC-GGTCACCCGATCTTGG
* * * * * * *
12967737 CTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCTCGGTTATTTATTTTTGACATCGACTC
1 CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
* *
12967802 GATCCTAGTCGCTTCATTTTTGACTCATGG--TTCCTGGTCACCCGATCTTTG
66 GATCCTAGTCGCTTCATTTTTGACTCATGGTTTTCCCGGTCACCCGATCTTGG
* * * * * *
12967853 CTTAATCCAGATCATTTCTTATGACTCAT-GATTCATCTTGGTCATTTATTTTCGACCTTGACTC
1 CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
* * *
12967917 GATCTTAGTCACTTCATTTTTGACTCATGGTTTTACTCCGGTCACCTGATCTTGG
66 GATCCTAGTCGCTTCATTTTTGACTCATGGTTTT-C-CCGGTCACCCGATCTTGG
* * *
12967972 CTCAGTCAAAATCATTTCTTATGACTCATGGTTTTATCTCGATCATTTATTTTTGACCTTGACTC
1 CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
12968037 GATC
66 GATC
12968041 TTGGTTGCTT
Statistics
Matches: 449, Mismatches: 79, Indels: 30
0.80 0.14 0.05
Matches are distributed among these distances:
115 57 0.13
116 37 0.08
117 4 0.01
118 7 0.02
119 138 0.31
120 203 0.45
121 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (118 bp):
CTCAGTCCAGATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTTGACTC
GATCCTAGTCGCTTCATTTTTGACTCATGGTTTTCCCGGTCACCCGATCTTGG
Found at i:12968053 original size:235 final size:237
Alignment explanation
Indices: 12967379--12968053 Score: 704
Period size: 235 Copynumber: 2.8 Consensus size: 237
12967369 AATTTTTTAC
* *
12967379 TCAATCCAGATCATTTTTTATGACTTATAGTTTCATCTCGATCATTTATTTTTTACCTTGACTCG
1 TCAATCCAGATCATTTCTTATGACTTAT-GATTCATCTCGATCATTTATTTTTTACCTTGACTCG
* * * * *
12967444 GTCCTAGTCACTTTATTTTTTACTCAT-GATTTCGTCCCAATCACCCGATCTTGGCTCAGTCTAG
65 ATCCTAGTCACTTCATTTTTGACTCATGGTTTTC-T-CCAATCACCCGATCTTGGCTCAGTCAAG
* * * **
12967508 ATGATTTCTTAT-AGCTCATGATTTCATCCCGATCATTTATTTTAAACCTCGACTCTG-TCCTAG
128 ATCATTTCTTATGA-CTCATGGTTTCATCTCGATCATTTATTTTTGACCTCGACTC-GATCCTAG
* ** *
12967571 TTGCTTCATTTTTTACTTGTGATTTTGCCTCGGTCACCCAATCTTAGT
191 TTGCTTCATTTTTGACTCATGA-GTTGCCTCGGTCACCCAATCTTAGT
* * * *
12967619 TCAGTCTAGATCATTTCTTATGACTTGTGATTTCATCCCGATCATTTATTTTTTACCTTGA-TCG
1 TCAATCCAGATCATTTCTTATGACTTATGA-TTCATCTCGATCATTTATTTTTTACCTTGACTCG
*** ** * * * * *
12967683 ATCCT-GATTGTTTCATTTTTGACTTGTGATTTTGC-CCTAATCACCCAATCTTGACTTAGTCCA
65 ATCCTAG-TCACTTCATTTTTGACTCATGGTTTT-CTCC-AATCACCCGATCTTGGCTCAGTCAA
* * * * *
12967746 GATCATTTCTTATGATTCGTGGTTTCATCTCGGTTATTTATTTTTGACATCGACTCGATCCTAGT
127 GATCATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTCGACTCGATCCTAGT
* * *
12967811 CGCTTCATTTTTGACTCATG-GTT-CCT-GGTCACCCGATCTTTGCT
192 TGCTTCATTTTTGACTCATGAGTTGCCTCGGTCACCCAATCTTAG-T
* * * **
12967855 T-AATCCAGATCATTTCTTATGACTCATGATTCATCTTGGTCATTTATTTTCGACCTTGACTCGA
1 TCAATCCAGATCATTTCTTATGACTTATGATTCATCTCGATCATTTATTTTTTACCTTGACTCGA
* ** * *
12967919 TCTTAGTCACTTCATTTTTGACTCATGGTTTTACTCCGGTCACCTGATCTTGGCTCAGTCAAAAT
66 TCCTAGTCACTTCATTTTTGACTCATGGTTTT-CTCCAATCACCCGATCTTGGCTCAGTCAAGAT
* * * *
12967984 CATTTCTTATGACTCATGGTTTTATCTCGATCATTTATTTTTGACCTTGACTCGATCTTGGTTGC
130 CATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTCGACTCGATCCTAGTTGC
12968049 TTCAT
195 TTCAT
12968054 CTCCAAACTC
Statistics
Matches: 352, Mismatches: 72, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
234 25 0.07
235 146 0.41
236 8 0.02
237 2 0.01
238 4 0.01
239 109 0.31
240 57 0.16
241 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.44
Consensus pattern (237 bp):
TCAATCCAGATCATTTCTTATGACTTATGATTCATCTCGATCATTTATTTTTTACCTTGACTCGA
TCCTAGTCACTTCATTTTTGACTCATGGTTTTCTCCAATCACCCGATCTTGGCTCAGTCAAGATC
ATTTCTTATGACTCATGGTTTCATCTCGATCATTTATTTTTGACCTCGACTCGATCCTAGTTGCT
TCATTTTTGACTCATGAGTTGCCTCGGTCACCCAATCTTAGT
Found at i:12968247 original size:3 final size:3
Alignment explanation
Indices: 12968239--12968351 Score: 149
Period size: 3 Copynumber: 38.0 Consensus size: 3
12968229 CATGTTATAG
*
12968239 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
12968287 TAT TAT TAT GAT CAT CAT CAT TAT TAT TAT TAT T-T CTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
*
12968332 TAT TA- TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
12968352 CAATTTTTCT
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
2 3 0.03
3 96 0.96
4 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:12969244 original size:13 final size:13
Alignment explanation
Indices: 12969222--12969259 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12969212 GATTGCAAGG
*
12969222 TTTT-TTTTTTTT
1 TTTTATTTTTTTA
*
12969234 TTTTATTTTTTGA
1 TTTTATTTTTTTA
12969247 TTTTATTTTTTTA
1 TTTTATTTTTTTA
12969260 GCTCATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:12969439 original size:36 final size:35
Alignment explanation
Indices: 12969366--12969444 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 35
12969356 AAAAAATTAT
12969366 AAAA-AAAACAAAAAAATCTTTTCAAATAAGTTTTCAA
1 AAAATAAAACAAAAAAATCTTTT---ATAAGTTTTCAA
12969403 AATAATAAAACAAAAAAAATCTTTT-TAAGTTTTCAA
1 AA-AATAAAAC-AAAAAAATCTTTTATAAGTTTTCAA
12969439 AAAATA
1 AAAATA
12969445 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
35 4 0.10
36 13 0.33
37 2 0.05
38 2 0.05
39 5 0.13
40 13 0.33
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (35 bp):
AAAATAAAACAAAAAAATCTTTTATAAGTTTTCAA
Found at i:12969465 original size:25 final size:27
Alignment explanation
Indices: 12969437--12969489 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
12969427 TTAAGTTTTC
*
12969437 AAAAAATATTT-ATAAA-AACAAAAAA
1 AAAAAACATTTAATAAATAACAAAAAA
*
12969462 AAAAACCATTTCAATAAATAACAAAAAA
1 AAAAAACATTT-AATAAATAACAAAAAA
12969490 TCTTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
27 5 0.22
28 9 0.39
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (27 bp):
AAAAAACATTTAATAAATAACAAAAAA
Found at i:12970399 original size:13 final size:13
Alignment explanation
Indices: 12970381--12970409 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12970371 AAAACTTTCA
12970381 TTTTTTTTATTCT
1 TTTTTTTTATTCT
12970394 TTTTTTTTATTCT
1 TTTTTTTTATTCT
12970407 TTT
1 TTT
12970410 CTCTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTATTCT
Found at i:12970426 original size:14 final size:13
Alignment explanation
Indices: 12970390--12970436 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
12970380 ATTTTTTTTA
*
12970390 TTCTTTT-TTTTT
1 TTCTTTTCTCTTT
12970402 ATTCTTTTCTCTTT
1 -TTCTTTTCTCTTT
12970416 TTCTATTTCTCTTTT
1 TTCT-TTTCTC-TTT
12970431 TTCTTT
1 TTCTTT
12970437 AAGGCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.37
14 12 0.40
15 7 0.23
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTCTCTTT
Found at i:12973855 original size:17 final size:15
Alignment explanation
Indices: 12973807--12973862 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
12973797 CATGCAGCAA
12973807 AATTAAAAAAAT-AT
1 AATTAAAAAAATAAT
*
12973821 AATTAAAATGAATTAAT
1 AATTAAAA--AAATAAT
12973838 AATTCAAAAAAATAAAT
1 AATT-AAAAAAAT-AAT
12973855 AATATAAA
1 AAT-TAAA
12973863 CAATATAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.24
16 6 0.18
17 15 0.44
18 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AATTAAAAAAATAAT
Found at i:12974670 original size:19 final size:20
Alignment explanation
Indices: 12974635--12974672 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12974625 TTTTGAAATA
*
12974635 TATTTTTTGAGACAAAATTT
1 TATTTTTTAAGACAAAATTT
12974655 TATTTTTTAAGA-AAAATT
1 TATTTTTTAAGACAAAATT
12974673 GATACTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
TATTTTTTAAGACAAAATTT
Found at i:12974689 original size:151 final size:150
Alignment explanation
Indices: 12974505--12974792 Score: 377
Period size: 151 Copynumber: 1.9 Consensus size: 150
12974495 TATTTAAGGA
* **
12974505 ATTTATTAAGAAAAATTAATGCTTTCAACTTTTCCTT-AAAATGTTTCTTTTGAAAT-TATTTTT
1 ATTTATTAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAACATTTCTTTTGAAATATA-TTTT
*
12974568 TGAAAAA-AAAATTTCTAAGGAAAATTGATACTTTTAACTTTTT-CTTAAAAATATTTCTTTTGA
65 TGAAAAATAAAATTTCTAAGAAAAATTGATAC-TTTAA-TTTTTCCTT-AAAATATTT-TTTTGA
12974631 AATATATTTTTTGAGACAAAATTTT
126 AATATATTTTTTGAGACAAAATTTT
* * * *
12974656 ATTTTTTAAGAAAAATTGATACTTTTAATTTTTCCTTAAAAACATTTCTTTTGAAATATATTTTT
1 ATTTATTAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAACATTTCTTTTGAAATATATTTTT
** * *
12974721 GAAAAATTTTATTTTCTAAGAAAAATTGATACTTTCATTTTTCCTTAAAATATTTTTTTGAAATA
66 GAAAAA-TAAAATTTCTAAGAAAAATTGATACTTTAATTTTTCCTTAAAATATTTTTTTGAAATA
*
12974786 TGTTTTT
130 TATTTTT
12974793 ATTTTAAGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
151 48 0.40
152 42 0.35
153 9 0.08
154 20 0.17
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (150 bp):
ATTTATTAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAACATTTCTTTTGAAATATATTTTT
GAAAAATAAAATTTCTAAGAAAAATTGATACTTTAATTTTTCCTTAAAATATTTTTTTGAAATAT
ATTTTTTGAGACAAAATTTT
Found at i:12977964 original size:8 final size:8
Alignment explanation
Indices: 12977951--12977994 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
12977941 ATATTTAAAA
12977951 TATTATTT
1 TATTATTT
12977959 TATTATTTT
1 TATTA-TTT
12977968 TATTA-TT
1 TATTATTT
12977975 TATTTAATTT
1 TA-TT-ATTT
12977985 TATTATTT
1 TATTATTT
12977993 TA
1 TA
12977995 AGTTACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.12
8 13 0.41
9 11 0.34
10 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTATTT
Found at i:12977968 original size:9 final size:9
Alignment explanation
Indices: 12977951--12977993 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
12977941 ATATTTAAAA
12977951 TATTA-TTT
1 TATTATTTT
12977959 TATTATTTT
1 TATTATTTT
*
12977968 TATTATTTA
1 TATTATTTT
*
12977977 T-TTAATTT
1 TATTATTTT
12977985 TATTATTTT
1 TATTATTTT
12977994 AAGTTACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 11 0.38
9 18 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:12977971 original size:17 final size:18
Alignment explanation
Indices: 12977951--12977994 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12977941 ATATTTAAAA
*
12977951 TATTATTTTA-TTATTTT
1 TATTATTTTATTTAATTT
12977968 TATTA-TTTATTTAATTT
1 TATTATTTTATTTAATTT
12977985 TATTATTTTA
1 TATTATTTTA
12977995 AGTTACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTATTTTATTTAATTT
Found at i:12978197 original size:12 final size:12
Alignment explanation
Indices: 12978182--12978216 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12978172 TTACCTAAGG
12978182 TTTAGGGTTTTA
1 TTTAGGGTTTTA
12978194 TTTAGGGTTTTA
1 TTTAGGGTTTTA
*
12978206 TTTGGGGTTTT
1 TTTAGGGTTTT
12978217 GGGTTTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.29, T:0.60
Consensus pattern (12 bp):
TTTAGGGTTTTA
Found at i:12978202 original size:19 final size:18
Alignment explanation
Indices: 12978155--12978203 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
12978145 TTTAAACTTC
12978155 ATTTAGGGTTTTAGGTTTT
1 ATTTAGGG-TTTAGGTTTT
** *
12978174 ACCTAAGGTTTAGGGTTTT
1 ATTTAGGGTTTA-GGTTTT
12978193 ATTTAGGGTTT
1 ATTTAGGGTTT
12978204 TATTTGGGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (18 bp):
ATTTAGGGTTTAGGTTTT
Found at i:12978222 original size:50 final size:49
Alignment explanation
Indices: 12978155--12978257 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 49
12978145 TTTAAACTTC
* * * *
12978155 ATTTAGGGTTTTAGGTTTTACCTAAGGTTTAGGGTTTTATTTAGGGTTTT
1 ATTTAGGGTTTTAGGTTTCACCTAAGGTTTA-AGTTTCATTTAAGGTTTT
* * *
12978205 ATTTGGGGTTTTGGGTTTCACTTAAGGTTTAAGTTTCATTTAAGGTTTT
1 ATTTAGGGTTTTAGGTTTCACCTAAGGTTTAAGTTTCATTTAAGGTTTT
12978254 ATTT
1 ATTT
12978258 TTAGGTTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 19 0.41
50 27 0.59
ACGTcount: A:0.18, C:0.05, G:0.24, T:0.52
Consensus pattern (49 bp):
ATTTAGGGTTTTAGGTTTCACCTAAGGTTTAAGTTTCATTTAAGGTTTT
Found at i:12978252 original size:12 final size:12
Alignment explanation
Indices: 12978232--12978302 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
12978222 TCACTTAAGG
12978232 TTTAA-GTTTCA
1 TTTAAGGTTTCA
*
12978243 TTTAAGGTTTTA
1 TTTAAGGTTTCA
*
12978255 TTTTTAGGTTTCAA
1 -TTTAAGGTTTC-A
*
12978269 TTTAGGGTTTCA
1 TTTAAGGTTTCA
* *
12978281 TTTAGGGTCTCA
1 TTTAAGGTTTCA
12978293 CTTT-AGGTTT
1 -TTTAAGGTTT
12978303 TGGGTTAGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
11 5 0.10
12 21 0.44
13 21 0.44
14 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.54
Consensus pattern (12 bp):
TTTAAGGTTTCA
Found at i:12978260 original size:25 final size:26
Alignment explanation
Indices: 12978232--12978283 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12978222 TCACTTAAGG
*
12978232 TTTAAGTTTC-ATTTAAGGTTTTATT
1 TTTAAGTTTCAATTTAAGGTTTCATT
* *
12978257 TTTAGGTTTCAATTTAGGGTTTCATT
1 TTTAAGTTTCAATTTAAGGTTTCATT
12978283 T
1 T
12978284 AGGGTCTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (26 bp):
TTTAAGTTTCAATTTAAGGTTTCATT
Found at i:12981333 original size:50 final size:49
Alignment explanation
Indices: 12981273--12981437 Score: 145
Period size: 50 Copynumber: 3.2 Consensus size: 49
12981263 TCTTTTTGAA
*
12981273 TTTTTAAATTTTAAA-TTTTCACCATTTGGACCTATTTAGAAATTCTTTT
1 TTTTTTAATTTTAAATTTTTCACCATTTGG-CCTATTTAGAAATTCTTTT
**
12981322 TTATTTTAATTTTTATCTCTAAATTTTTCACCATTTGGGTTAATTTAGAAATT-TTTT
1 TT-TTTTAA----T-T-T-TAAATTTTTCACCATTTGGCCT-ATTTAGAAATTCTTTT
** * *
12981379 TTTTGAAAATTTTAAATTTTTTACTATTTGGGCCTATTTAGAAATTCTTTT
1 TTTT-TTAATTTTAAATTTTTCACCATTT-GGCCTATTTAGAAATTCTTTT
12981430 TTTTTTAA
1 TTTTTTAA
12981438 GAAAATAATG
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
49 2 0.02
50 33 0.36
51 12 0.13
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 3 0.03
57 13 0.14
58 25 0.27
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.56
Consensus pattern (49 bp):
TTTTTTAATTTTAAATTTTTCACCATTTGGCCTATTTAGAAATTCTTTT
Found at i:12981333 original size:58 final size:56
Alignment explanation
Indices: 12981265--12981437 Score: 157
Period size: 58 Copynumber: 3.1 Consensus size: 56
12981255 ATATTTTCTC
*
12981265 TTTTTGAATTTTTAAATTTTAAATTTTCACCATTTGGACCTATTTAGAAATTCTTTT
1 TTTTTTAATTTTTAAATTTTAAATTTTCACCATTTGG-CCTATTTAGAAATTCTTTT
* **
12981322 TTATTTTAATTTTT--ATCTCTAAATTTTTCACCATTTGGGTTAATTTAGAAATT-TTTT
1 TT-TTTTAATTTTTAAAT-TTTAAA-TTTTCACCATTTGGCCT-ATTTAGAAATTCTTTT
** * *
12981379 TTTTGAAAATTTTAAA--TT---TTTT-ACTATTTGGGCCTATTTAGAAATTCTTTT
1 TTTTTTAATTTTTAAATTTTAAATTTTCACCATTT-GGCCTATTTAGAAATTCTTTT
12981430 TTTTTTAA
1 TTTTTTAA
12981438 GAAAATAATG
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
50 17 0.18
51 17 0.18
55 1 0.01
56 10 0.11
57 14 0.15
58 36 0.38
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.57
Consensus pattern (56 bp):
TTTTTTAATTTTTAAATTTTAAATTTTCACCATTTGGCCTATTTAGAAATTCTTTT
Found at i:12981776 original size:6 final size:7
Alignment explanation
Indices: 12981764--12981805 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12981754 TTTAATTCCA
12981764 AATTTTT
1 AATTTTT
*
12981771 ATTTTTTT
1 A-ATTTTT
*
12981779 TATTTTT
1 AATTTTT
12981786 -ATTTTT
1 AATTTTT
12981792 AATTTTT
1 AATTTTT
12981799 AATTTTT
1 AATTTTT
12981806 TTGTTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.20
7 19 0.63
8 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
AATTTTT
Found at i:12982045 original size:18 final size:18
Alignment explanation
Indices: 12982024--12982058 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12982014 AACACATAAA
12982024 AATAAAAATACAAAAAAG
1 AATAAAAATACAAAAAAG
* *
12982042 AATAAAATTCCAAAAAA
1 AATAAAAATACAAAAAA
12982059 CGAAACGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (18 bp):
AATAAAAATACAAAAAAG
Found at i:12983020 original size:38 final size:40
Alignment explanation
Indices: 12982955--12983069 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 40
12982945 GTAAACAAAG
* *
12982955 CTCCTCTAAACAGAGGCTCAACT-ACTTTGAAAAAA-ATA-
1 CTCCTCTAAACAGAGGCACCA-TAACTTTGAAAAAATATAT
* *
12982993 CTCCTTTAAACAGAGGCACCATAACTTTTAAAAAATATATT
1 CTCCTCTAAACAGAGGCACCATAACTTTGAAAAAATATA-T
*
12983034 GCTTCTCTAAACAGAGGCACCATAACTTTTGAAAAA
1 -CTCCTCTAAACAGAGGCACCATAAC-TTTGAAAAA
12983070 TAAATTGCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
37 1 0.02
38 29 0.45
39 3 0.05
42 23 0.36
43 8 0.12
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (40 bp):
CTCCTCTAAACAGAGGCACCATAACTTTGAAAAAATATAT
Found at i:12983051 original size:42 final size:42
Alignment explanation
Indices: 12982958--12983205 Score: 202
Period size: 42 Copynumber: 6.0 Consensus size: 42
12982948 AACAAAGCTC
* * * * *
12982958 CTCTAAACAGAGGCTCAACTAC-TTTG-AAAA-AAA-TACTC
1 CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCTT
* * * *
12982996 CTTTAAACAGAGGCACCATAACTTTTAAAAAATATATTGCTT
1 CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCTT
*
12983038 CTCTAAACAGAGGCACCATAACTTTTGAAAAATAAATTGCTT
1 CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCTT
* * * * * *
12983080 ATCTAAATAAAGGTACCACAAC-TTTGAAAAAACAAATTAC-T
1 CTCTAAACAGAGGCACCACAACTTTTG-AAAAATAAATTGCTT
* **** * * * *
12983121 CATATGTTTAGAGGTACCACAACTTTGGAAAAATAAAATTACTC
1 C-TCTAAACAGAGGCACCACAACTTTTGAAAAAT-AAATTGCTT
12983165 CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCT
1 CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCT
12983206 CATCAATAAT
Statistics
Matches: 165, Mismatches: 36, Indels: 14
0.77 0.17 0.07
Matches are distributed among these distances:
38 17 0.10
39 3 0.02
40 4 0.02
41 7 0.04
42 98 0.59
43 35 0.21
44 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (42 bp):
CTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATTGCTT
Found at i:12983659 original size:21 final size:21
Alignment explanation
Indices: 12983622--12983661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12983612 GGTTTCACAC
*
12983622 CTCAAAGATCTTTATTTGAAA
1 CTCAAAGATCTTCATTTGAAA
12983643 CTCAAAGAT-TCTCATTTGA
1 CTCAAAGATCT-TCATTTGA
12983662 GTTTGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
CTCAAAGATCTTCATTTGAAA
Found at i:12983787 original size:58 final size:58
Alignment explanation
Indices: 12983643--12983774 Score: 214
Period size: 58 Copynumber: 2.3 Consensus size: 58
12983633 TTATTTGAAA
*
12983643 CTCAAAGATTCTCATTTGAGTTTGAAGATTCACATTCGAAAAATTTTGGGTTTCACAC
1 CTCAAAGATTCTCATTTGAGTTTGAAGATTCACATTCGAAAAATTTTAGGTTTCACAC
*
12983701 CTCAAAGATTCTCATTTGAGTTTGAAGATTTACATTCGATAAAA-TTTAGG-TTCACAC
1 CTCAAAGATTCTCATTTGAGTTTGAAGATTCACATTCGA-AAAATTTTAGGTTTCACAC
*
12983758 TTCAAAGATTCTCATTT
1 CTCAAAGATTCTCATTT
12983775 AAAATTCAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
57 23 0.33
58 43 0.61
59 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (58 bp):
CTCAAAGATTCTCATTTGAGTTTGAAGATTCACATTCGAAAAATTTTAGGTTTCACAC
Found at i:12984989 original size:22 final size:21
Alignment explanation
Indices: 12984959--12985031 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
12984949 TCAATTTGAG
*
12984959 TCTTTTTTTCTTTTATTTTCA
1 TCTTTTTTTTTTTTATTTTCA
**
12984980 TCTTTTTTTTTTTTTATTTTTT
1 TC-TTTTTTTTTTTTATTTTCA
*
12985002 TCTTTTTCATTTTTTATTTTTTCA
1 TCTTTTT--TTTTTT-TATTTTCA
12985026 TCTTTT
1 TCTTTT
12985032 ACCATCAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
21 7 0.17
22 18 0.43
23 6 0.14
24 11 0.26
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (21 bp):
TCTTTTTTTTTTTTATTTTCA
Found at i:12984992 original size:15 final size:14
Alignment explanation
Indices: 12984961--12985031 Score: 65
Period size: 15 Copynumber: 5.0 Consensus size: 14
12984951 AATTTGAGTC
*
12984961 TTTTTTTC-TTTTA
1 TTTTTTTCATTTTT
**
12984974 TTTTCATC-TTTTT
1 TTTTTTTCATTTTT
*
12984987 TTTTTTTTATTTTT
1 TTTTTTTCATTTTT
12985001 TTCTTTTTCATTTTT
1 TT-TTTTTCATTTTT
12985016 TATTTTTTCATCTTTT
1 T-TTTTTTCAT-TTTT
12985032 ACCATCAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
13 15 0.32
14 7 0.15
15 20 0.43
16 5 0.11
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTCATTTTT
Found at i:12989068 original size:44 final size:45
Alignment explanation
Indices: 12989020--12989115 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 45
12989010 TTTTATTTTA
*
12989020 TTTTTTT-ATCTCTAAATTTTTCACAATTTGGGTCAATTT-AAATT
1 TTTTTTTAAT-TCTAAATTTTTCACAATTTGGGCCAATTTAAAATT
* * *
12989064 TTTTTTTAATTTTAAATTTTTCACCATTTGGGCCTATTTAAAATT
1 TTTTTTTAATTCTAAATTTTTCACAATTTGGGCCAATTTAAAATT
*
12989109 CTTTTTT
1 TTTTTTT
12989116 GTTTTTGGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 32 0.71
45 13 0.29
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.57
Consensus pattern (45 bp):
TTTTTTTAATTCTAAATTTTTCACAATTTGGGCCAATTTAAAATT
Found at i:12990457 original size:9 final size:9
Alignment explanation
Indices: 12990443--12990495 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
12990433 AATTCAACTT
*
12990443 TTTTTTTCG
1 TTTTTTTCA
12990452 TTTTTTTCA
1 TTTTTTTCA
12990461 TTTTTTTCAA
1 TTTTTTTC-A
*
12990471 CTTTTTTTTTA
1 --TTTTTTTCA
12990482 TTTTTTT-A
1 TTTTTTTCA
12990490 TTTTTT
1 TTTTTT
12990496 ATTAACAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 7 0.18
9 23 0.59
10 1 0.03
11 1 0.03
12 7 0.18
ACGTcount: A:0.09, C:0.08, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:12990473 original size:31 final size:29
Alignment explanation
Indices: 12990435--12990495 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 29
12990425 CCAACCTAAA
*
12990435 TTCAACTTTTTTTTTCGTTTTTTTCATTTTT
1 TTCAACTTTTTTTTT-ATTTTTTT-ATTTTT
12990466 TTCAACTTTTTTTTTATTTTTTTATTTTT
1 TTCAACTTTTTTTTTATTTTTTTATTTTT
12990495 T
1 T
12990496 ATTAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.24
30 7 0.24
31 15 0.52
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (29 bp):
TTCAACTTTTTTTTTATTTTTTTATTTTT
Found at i:12993749 original size:21 final size:22
Alignment explanation
Indices: 12993719--12993759 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12993709 ATTTGTGTTC
* *
12993719 AAATATAATT-ATTTAAAATAT
1 AAATAAAATTAATATAAAATAT
12993740 AAATAAAATTAATATAAAAT
1 AAATAAAATTAATATAAAAT
12993760 TTAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAAAATTAATATAAAATAT
Found at i:12994745 original size:8 final size:8
Alignment explanation
Indices: 12994732--12994774 Score: 61
Period size: 8 Copynumber: 5.2 Consensus size: 8
12994722 TTTTTCAAGC
12994732 TTTATTAT
1 TTTATTAT
12994740 TTTATTAT
1 TTTATTAT
12994748 CTTATATTAT
1 -TT-TATTAT
12994758 TTTATTAT
1 TTTATTAT
12994766 TTT-TTAT
1 TTTATTAT
12994773 TT
1 TT
12994775 AATGGCCGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 6 0.18
8 17 0.52
9 4 0.12
10 6 0.18
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTAT
Found at i:12994773 original size:18 final size:18
Alignment explanation
Indices: 12994732--12994773 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12994722 TTTTTCAAGC
12994732 TTTATTATTTTATTATCT
1 TTTATTATTTTATTATCT
* *
12994750 TATATTATTTTATTATTT
1 TTTATTATTTTATTATCT
12994768 TTTATT
1 TTTATT
12994774 TAATGGCCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTATTTTATTATCT
Found at i:12995959 original size:12 final size:13
Alignment explanation
Indices: 12995942--12995970 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12995932 TAAAAAGCTT
12995942 TTTATTTATT-TA
1 TTTATTTATTGTA
12995954 TTTATTTATTGTA
1 TTTATTTATTGTA
12995967 TTTA
1 TTTA
12995971 GAGTAATCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTATTTATTGTA
Found at i:12996543 original size:4 final size:4
Alignment explanation
Indices: 12996534--12996590 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
12996524 ATAAGAGTAC
* * * * * *
12996534 TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA TGTA TGTA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
12996582 TGTA TATA T
1 TATA TATA T
12996591 CTGCAGAGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:12996547 original size:8 final size:8
Alignment explanation
Indices: 12996536--12996590 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
12996526 AAGAGTACTA
*
12996536 TATATATA
1 TATATATG
*
12996544 TATATATA
1 TATATATG
12996552 TATATATG
1 TATATATG
*
12996560 TATGTATG
1 TATATATG
*
12996568 TATGTATG
1 TATATATG
*
12996576 TATGTATG
1 TATATATG
12996584 TATATAT
1 TATATAT
12996591 CTGCAGAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:12996551 original size:12 final size:12
Alignment explanation
Indices: 12996536--12996590 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
12996526 AAGAGTACTA
*
12996536 TATATATATATA
1 TATATATATATG
12996548 TATATATATATG
1 TATATATATATG
* *
12996560 TATGTATGTATG
1 TATATATATATG
* *
12996572 TATGTATGTATG
1 TATATATATATG
12996584 TATATAT
1 TATATAT
12996591 CTGCAGAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:13003927 original size:5 final size:6
Alignment explanation
Indices: 13003912--13003946 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
13003902 CATTCAAGAA
* *
13003912 AAAAAT AAAAAT AAAAAT AAAAAG AAAAAG AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
13003947 GGTTATTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (6 bp):
AAAAAT
Found at i:13004851 original size:2 final size:2
Alignment explanation
Indices: 13004844--13004890 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
13004834 CAGGTTCCTT
13004844 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13004886 TC TC T
1 TC TC T
13004891 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13006951 original size:13 final size:12
Alignment explanation
Indices: 13006914--13006979 Score: 87
Period size: 12 Copynumber: 5.2 Consensus size: 12
13006904 GGGTTTTAAA
*
13006914 TTTCATTTATGG
1 TTTCATTTAAGG
13006926 TTTCATTTAAGG
1 TTTCATTTAAGG
13006938 TTTCATTCTAAGG
1 TTTCATT-TAAGG
*
13006951 TTTTAATTTAAGG
1 -TTTCATTTAAGG
13006964 TTTCATTTTAAGG
1 TTTCA-TTTAAGG
13006977 TTT
1 TTT
13006980 AAAAAACTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
12 22 0.46
13 20 0.42
14 6 0.12
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.55
Consensus pattern (12 bp):
TTTCATTTAAGG
Found at i:13006962 original size:26 final size:25
Alignment explanation
Indices: 13006914--13006979 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
13006904 GGGTTTTAAA
* *
13006914 TTTCATTTATGG-TTTCATTTAAGG
1 TTTCATTTAAGGTTTTAATTTAAGG
13006938 TTTCATTCTAAGGTTTTAATTTAAGG
1 TTTCATT-TAAGGTTTTAATTTAAGG
13006964 TTTCATTTTAAGGTTT
1 TTTCA-TTTAAGGTTT
13006980 AAAAAACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 7 0.19
25 4 0.11
26 24 0.65
27 2 0.05
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.55
Consensus pattern (25 bp):
TTTCATTTAAGGTTTTAATTTAAGG
Found at i:13009750 original size:2 final size:2
Alignment explanation
Indices: 13009745--13009785 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13009735 TACAAGAGAT
*
13009745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13009786 GCGCGCGCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13017125 original size:17 final size:16
Alignment explanation
Indices: 13017095--13017128 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13017085 TTCATTTTAT
*
13017095 TTTTTTTATATTTAAA
1 TTTTATTATATTTAAA
*
13017111 TTTTATTATATTTTAA
1 TTTTATTATATTTAAA
13017127 TT
1 TT
13017129 AAAATTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATATTTAAA
Found at i:13021944 original size:28 final size:26
Alignment explanation
Indices: 13021887--13021957 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
13021877 TATATACAAT
* * * *
13021887 AATAAAAATAAATATGTTAATAAATT
1 AATAAAAATAAAAATATTAAGAAATA
13021913 AATAGAAAATAAAAATATTGAAGAAATA
1 AATA-AAAATAAAAATATT-AAGAAATA
13021941 AATAAAACA-AAAAATAT
1 AATAAAA-ATAAAAATAT
13021958 ATATAATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
27 23 0.61
28 11 0.29
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (26 bp):
AATAAAAATAAAAATATTAAGAAATA
Found at i:13022470 original size:17 final size:19
Alignment explanation
Indices: 13022428--13022478 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 19
13022418 TTAATATATT
*
13022428 TAAATTTAAATTTTATGCA
1 TAAATTTTAATTTTATGCA
*
13022447 AAAATTTTAATTTTA-G-A
1 TAAATTTTAATTTTATGCA
13022464 TAAATTTTAATTTTA
1 TAAATTTTAATTTTA
13022479 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 1 0.03
19 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (19 bp):
TAAATTTTAATTTTATGCA
Found at i:13022508 original size:25 final size:25
Alignment explanation
Indices: 13022479--13022528 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
13022469 TTTAATTTTA
*
13022479 ATTTAAATAA-TTATTCAAAATATTT
1 ATTTAAATAATTTATT-AAAAAATTT
13022504 ATTTAAATAATTTATTAAAAAATTT
1 ATTTAAATAATTTATTAAAAAATTT
13022529 TATTAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTAAATAATTTATTAAAAAATTT
Found at i:13022642 original size:2 final size:2
Alignment explanation
Indices: 13022626--13022660 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13022616 CATGTAATTT
13022626 TA TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13022661 TAGATGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13024527 original size:27 final size:28
Alignment explanation
Indices: 13024497--13024557 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
13024487 AAAAATTTAT
*
13024497 AATTATT-TAATAATTATTCAAATAAAA
1 AATTATTATAATAATCATTCAAATAAAA
* *
13024524 AATTATTATCATAATCATTTAAATAAAA
1 AATTATTATAATAATCATTCAAATAAAA
*
13024552 ATTTAT
1 AATTAT
13024558 GATTGTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTATTATAATAATCATTCAAATAAAA
Found at i:13033864 original size:15 final size:15
Alignment explanation
Indices: 13033844--13033882 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
13033834 ATTTGGACGG
**
13033844 ATAATAAAATTAATT
1 ATAATAAAATTAAAA
13033859 ATAATAAAATTAAAA
1 ATAATAAAATTAAAA
13033874 ATAATAAAA
1 ATAATAAAA
13033883 AATTAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAAAATTAAAA
Found at i:13033908 original size:23 final size:23
Alignment explanation
Indices: 13033878--13033939 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 23
13033868 TTAAAAATAA
*
13033878 TAAAAAATTAATGTAATTGTGAT
1 TAAAAAATTAATATAATTGTGAT
13033901 TAAAAAATTATCACTATAATTGTGAT
1 TAAAAAATTA--A-TATAATTGTGAT
*
13033927 AAAAAAATTAATA
1 TAAAAAATTAATA
13033940 AAAAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.35
24 1 0.03
25 1 0.03
26 20 0.59
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.35
Consensus pattern (23 bp):
TAAAAAATTAATATAATTGTGAT
Found at i:13040041 original size:14 final size:14
Alignment explanation
Indices: 13040024--13040050 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13040014 GCTGCTTGGA
13040024 TTGGGTATAAATGG
1 TTGGGTATAAATGG
13040038 TTGGGTATAAATG
1 TTGGGTATAAATG
13040051 TGATAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (14 bp):
TTGGGTATAAATGG
Found at i:13044750 original size:24 final size:24
Alignment explanation
Indices: 13044722--13044771 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
13044712 TCACAATATT
* *
13044722 AAATTCAAGAATTAAACATTAAAA
1 AAATTCAAAAAATAAACATTAAAA
*
13044746 AAATTTAAAAAATAAACATTAAAA
1 AAATTCAAAAAATAAACATTAAAA
13044770 AA
1 AA
13044772 GAAAAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATTCAAAAAATAAACATTAAAA
Found at i:13045849 original size:31 final size:30
Alignment explanation
Indices: 13045794--13045887 Score: 84
Period size: 32 Copynumber: 3.1 Consensus size: 30
13045784 TATATTAGAT
*
13045794 TTAATA-AAATATAAAAATAT-ATTTTTATA
1 TTAATATAAA-ATAAATATATAATTTTTATA
* * *
13045823 TTAATATAAATTATGATATATAATTTTTAAA
1 TTAATATAAAATA-AATATATAATTTTTATA
* *
13045854 TAAAATATAAAATAAATATATAAATTTTAATA
1 T-TAATATAAAATAAATATAT-AATTTTTATA
13045886 TT
1 TT
13045888 TTACATAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
29 8 0.16
30 8 0.16
31 15 0.30
32 19 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
TTAATATAAAATAAATATATAATTTTTATA
Found at i:13048670 original size:15 final size:15
Alignment explanation
Indices: 13048650--13048696 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
13048640 AATCTATTTC
13048650 TTTTTATTTATTAAT
1 TTTTTATTTATTAAT
*
13048665 TTTTTA-TTATTAAC
1 TTTTTATTTATTAAT
* * *
13048679 ATTTTCTTTGTTAAT
1 TTTTTATTTATTAAT
13048694 TTT
1 TTT
13048697 AATTTCTAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTATTTATTAAT
Found at i:13050987 original size:13 final size:13
Alignment explanation
Indices: 13050971--13050995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13050961 CCCCCCCCCA
13050971 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
13050984 AAAAAAAAAAAA
1 AAAAAAAAAAAA
13050996 TTCCGGATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:13053825 original size:12 final size:14
Alignment explanation
Indices: 13053801--13053833 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
13053791 ACTTATATAA
13053801 ACTTTTTTGTTTTT
1 ACTTTTTTGTTTTT
13053815 A-TTTTTT-TTTTT
1 ACTTTTTTGTTTTT
13053827 ACTTTTT
1 ACTTTTT
13053834 GAATAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 11 0.61
14 1 0.06
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (14 bp):
ACTTTTTTGTTTTT
Found at i:13055356 original size:21 final size:22
Alignment explanation
Indices: 13055332--13055391 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
13055322 TAAAAACTAA
13055332 AAAATATATGTAATATATTTG-
1 AAAATATATGTAATATATTTGT
13055353 AAAATATATGTAATATATTTGT
1 AAAATATATGTAATATATTTGT
13055375 AAAA-ATATGTAAATATA
1 AAAATATATGT-AATATA
13055392 ACTAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
21 27 0.73
22 10 0.27
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (22 bp):
AAAATATATGTAATATATTTGT
Found at i:13055375 original size:11 final size:11
Alignment explanation
Indices: 13055335--13055391 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 11
13055325 AAACTAAAAA
13055335 ATATATGTAAT
1 ATATATGTAAT
* *
13055346 ATATTTG-AAA
1 ATATATGTAAT
13055356 ATATATGTAAT
1 ATATATGTAAT
*
13055367 ATATTTGTAA-
1 ATATATGTAAT
*
13055377 AAATATGTAA-
1 ATATATGTAAT
13055387 ATATA
1 ATATA
13055392 ACTAATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
10 20 0.54
11 17 0.46
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (11 bp):
ATATATGTAAT
Found at i:13061537 original size:18 final size:17
Alignment explanation
Indices: 13061505--13061567 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
13061495 AATTCAAAAA
13061505 AAAAT-TTTAAGAAAATCT
1 AAAATATTTAA-AAAAT-T
13061523 AAAATATTTAAAAAATT
1 AAAATATTTAAAAAATT
*
13061540 ATAAA-AATTAAAAAATAT
1 A-AAATATTTAAAAAAT-T
13061558 AAAAATATTT
1 -AAAATATTT
13061568 TTAGAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 12 0.32
18 17 0.45
19 9 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATTTAAAAAATT
Found at i:13061545 original size:9 final size:9
Alignment explanation
Indices: 13061533--13061592 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
13061523 AAAATATTTA
13061533 AAAAATTAT
1 AAAAATTAT
13061542 AAAAATTA-
1 AAAAATTAT
13061550 AAAAA-TAT
1 AAAAATTAT
*
13061558 AAAAATATTTTT
1 -AAAA-A-TTAT
*
13061570 AGAAATTAT
1 AAAAATTAT
13061579 AAAAATTAT
1 AAAAATTAT
*
13061588 GAAAA
1 AAAAA
13061593 CTTAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 27 0.66
10 2 0.05
11 3 0.07
12 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:13061546 original size:42 final size:42
Alignment explanation
Indices: 13061456--13061546 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
13061446 CCACATAAAA
* *
13061456 TTAAAAGAAAATTTTAAAAAAATTTTAAAATTTCAAAAGAAT
1 TTAAAAAAAAATTTTAAAAAAATTCTAAAATTTCAAAAGAAT
* * *
13061498 TCAAAAAAAAATTTTAAGAAAA-TCTAAAATATTTAAAA-AAT
1 TTAAAAAAAAATTTTAAAAAAATTCTAAAAT-TTCAAAAGAAT
13061539 TATAAAAA
1 T-TAAAAA
13061547 TTAAAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 11 0.27
42 30 0.73
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (42 bp):
TTAAAAAAAAATTTTAAAAAAATTCTAAAATTTCAAAAGAAT
Found at i:13061552 original size:16 final size:16
Alignment explanation
Indices: 13061511--13061563 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 16
13061501 AAAAAAAATT
*
13061511 TTAAGAAAATCTAAAATA
1 TTAA-AAAATATAAAA-A
13061529 TTTAAAAAATTATAAAAA
1 -TTAAAAAA-TATAAAAA
13061547 TTAAAAAATATAAAAA
1 TTAAAAAATATAAAAA
13061563 T
1 T
13061564 ATTTTTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.28
17 8 0.25
18 5 0.16
19 10 0.31
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAAATATAAAAA
Found at i:13061600 original size:37 final size:35
Alignment explanation
Indices: 13061511--13061586 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 35
13061501 AAAAAAAATT
*
13061511 TTAAGAAAATCTAAAATATTTAAAAAATTATAAAAA
1 TTAA-AAAATATAAAATATTTAAAAAATTATAAAAA
* *
13061547 TTAAAAAATATAAAAATATTTTTAGAAATTATAAAAA
1 TTAAAAAATAT-AAAATA-TTTAAAAAATTATAAAAA
13061584 TTA
1 TTA
13061587 TGAAAACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.17
36 10 0.29
37 19 0.54
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (35 bp):
TTAAAAAATATAAAATATTTAAAAAATTATAAAAA
Found at i:13061762 original size:20 final size:20
Alignment explanation
Indices: 13061723--13061764 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13061713 ATAAAAATCT
** *
13061723 AAAATCTAAAATTTTTTTAA
1 AAAATCTAAAAAATTCTTAA
13061743 AAAATCTAAAAAATTCTTAA
1 AAAATCTAAAAAATTCTTAA
13061763 AA
1 AA
13061765 TTTTTCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATCTAAAAAATTCTTAA
Found at i:13061877 original size:20 final size:19
Alignment explanation
Indices: 13061844--13061882 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13061834 TTTGTAGAAA
13061844 TTATAAAAACTAAAAAAAT
1 TTATAAAAACTAAAAAAAT
* *
13061863 TTATGAAAACTTAAAAAAT
1 TTATAAAAACTAAAAAAAT
13061882 T
1 T
13061883 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
TTATAAAAACTAAAAAAAT
Found at i:13061890 original size:19 final size:19
Alignment explanation
Indices: 13061848--13061890 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
13061838 TAGAAATTAT
* *
13061848 AAAAACTAAAAAAATTTAT
1 AAAAACTAAAAAAATTAAA
* *
13061867 GAAAACTTAAAAAATTAAA
1 AAAAACTAAAAAAATTAAA
13061886 AAAAA
1 AAAAA
13061891 TTCAAAAAGT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAACTAAAAAAATTAAA
Found at i:13062433 original size:21 final size:21
Alignment explanation
Indices: 13062409--13062464 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
13062399 TTAAAAAGTG
*
13062409 TTTTAAAATTTTTCTAGAATT
1 TTTTAAAATTTTTCTAGAAAT
** *
13062430 TTTTTGAATTTTT-TTGAAAT
1 TTTTAAAATTTTTCTAGAAAT
* *
13062450 TTTAAAAAATTTTCT
1 TTTTAAAATTTTTCT
13062465 TTTAATAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTAAAATTTTTCTAGAAAT
Found at i:13062740 original size:53 final size:53
Alignment explanation
Indices: 13062621--13062729 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
13062611 AACATCAAAC
*
13062621 TAAAAATTTTATTTCTTTAAATACCAAACTAAAGGAAAATGTAAGTACAAAGG
1 TAAAAATTTTATTTCTTTAAATACCAAACTAAAAGAAAATGTAAGTACAAAGG
13062674 TAAAAATTTTATTTCTTTAAATACCAAACTAAAAGAAAATGTAAGTACAAAGG
1 TAAAAATTTTATTTCTTTAAATACCAAACTAAAAGAAAATGTAAGTACAAAGG
13062727 TAA
1 TAA
13062730 TTTTTATATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.30
Consensus pattern (53 bp):
TAAAAATTTTATTTCTTTAAATACCAAACTAAAAGAAAATGTAAGTACAAAGG
Found at i:13071509 original size:13 final size:13
Alignment explanation
Indices: 13071487--13071528 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
13071477 GATAATTTTG
*
13071487 ATAAATAATACTAT
1 ATAAA-AATAATAT
13071501 ATAAAAATAATAT
1 ATAAAAATAATAT
*
13071514 A-AAAAATCATAT
1 ATAAAAATAATAT
13071526 ATA
1 ATA
13071529 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 9 0.36
14 5 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATAATAT
Found at i:13071717 original size:42 final size:42
Alignment explanation
Indices: 13071633--13071722 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
13071623 TATGAATACG
* *
13071633 TTTAATTTAATTTTATCATATATTTAATATATTTAACATATT
1 TTTAATTTAATTTTATCATATATTTAATATATTAAAAATATT
* *
13071675 TTTATATTT-ATTTTATTATA-ATATTAATATA-TAAAAAT-TA
1 TTTA-ATTTAATTTTATCATATAT-TTAATATATTAAAAATATT
13071715 TTTAATTT
1 TTTAATTT
13071723 TTTATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 4 0.10
40 5 0.12
41 7 0.17
42 22 0.52
43 4 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (42 bp):
TTTAATTTAATTTTATCATATATTTAATATATTAAAAATATT
Found at i:13072180 original size:15 final size:15
Alignment explanation
Indices: 13072109--13072190 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
13072099 TATTTTGATT
13072109 TATATTTATATTAGTA
1 TATATTTATATTA-TA
* *
13072125 -ATATTTAT-TTTTG
1 TATATTTATATTATA
13072138 TATATTTATATTA-A
1 TATATTTATATTATA
*
13072152 TCGTATTTAT-TTATA
1 T-ATATTTATATTATA
*
13072167 TATATTTATATTATT
1 TATATTTATATTATA
*
13072182 TATGTTTAT
1 TATATTTAT
13072191 TCATGTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 21 0.40
15 31 0.58
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (15 bp):
TATATTTATATTATA
Found at i:13072191 original size:29 final size:29
Alignment explanation
Indices: 13072109--13072179 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
13072099 TATTTTGATT
* * *
13072109 TATATTTATATTAGTAATATTTATTTTTG
1 TATATTTATATTAATAATATTTATTTATA
**
13072138 TATATTTATATTAATCGTATTTATTTATA
1 TATATTTATATTAATAATATTTATTTATA
13072167 TATATTTATATTA
1 TATATTTATATTA
13072180 TTTATGTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (29 bp):
TATATTTATATTAATAATATTTATTTATA
Found at i:13072199 original size:19 final size:19
Alignment explanation
Indices: 13072140--13072199 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
13072130 TATTTTTGTA
* *
13072140 TATTTATAT-TAATCGTATT
1 TATTTATATATATTCATA-T
*
13072159 TATTTATATATATTTATAT
1 TATTTATATATATTCATAT
* * *
13072178 TATTTATGTTTATTCATGT
1 TATTTATATATATTCATAT
13072197 TAT
1 TAT
13072200 AATTAAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTCATAT
Found at i:13072303 original size:17 final size:18
Alignment explanation
Indices: 13072278--13072328 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
13072268 TTCATTCATG
*
13072278 TTTAAAATTTAAA-AATA
1 TTTATAATTTAAATAATA
* *
13072295 TTTATAATTCAAATTATA
1 TTTATAATTTAAATAATA
*
13072313 TTTAT-ATTTTAATAAT
1 TTTATAATTTAAATAAT
13072329 TATATCTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATAATTTAAATAATA
Found at i:13076822 original size:19 final size:18
Alignment explanation
Indices: 13076798--13076841 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
13076788 ACAAACTTTC
13076798 AAAATTAATGTAATTAAGT
1 AAAATTAAT-TAATTAAGT
*
13076817 AAAATTTCATTAATTAAGT
1 AAAA-TTAATTAATTAAGT
13076836 AAAATT
1 AAAATT
13076842 TCATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (18 bp):
AAAATTAATTAATTAAGT
Found at i:13076842 original size:19 final size:19
Alignment explanation
Indices: 13076808--13076848 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
13076798 AAAATTAATG
13076808 TAATTAAGTAAAATTTCAT
1 TAATTAAGTAAAATTTCAT
13076827 TAATTAAGTAAAATTTCAT
1 TAATTAAGTAAAATTTCAT
13076846 TAA
1 TAA
13076849 ATTAGACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TAATTAAGTAAAATTTCAT
Found at i:13077417 original size:22 final size:23
Alignment explanation
Indices: 13077392--13077434 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13077382 ATTTTGATTG
* *
13077392 AAACTTGTG-CAAAATTTGTGGA
1 AAACGTGTGCCAAAATATGTGGA
13077414 AAACGTGTGCCAAAATATGTG
1 AAACGTGTGCCAAAATATGTG
13077435 CTATTGTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (23 bp):
AAACGTGTGCCAAAATATGTGGA
Found at i:13077773 original size:5 final size:5
Alignment explanation
Indices: 13077763--13077867 Score: 56
Period size: 5 Copynumber: 20.2 Consensus size: 5
13077753 CTATTAGTAT
* * *
13077763 TATTA TATTA TATTA TATAATA TAATA TATTA TATCA TATTA GTA--C
1 TATTA TATTA TATTA TAT--TA TATTA TATTA TATTA TATTA -TATTA
* * *
13077809 TATTA TACTTA T-TTA T-TTA TCATTA TTAGTA TATCA TATCA TATTA
1 TATTA TA-TTA TATTA TATTA T-ATTA -TATTA TATTA TATTA TATTA
13077855 TTATTA TTATTA T
1 -TATTA -TATTA T
13077868 TTACATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
3 2 0.03
4 8 0.10
5 42 0.52
6 23 0.29
7 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:13077791 original size:17 final size:17
Alignment explanation
Indices: 13077766--13077802 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13077756 TTAGTATTAT
*
13077766 TATATTATATTATATAA
1 TATAATATATTATATAA
*
13077783 TATAATATATTATATCA
1 TATAATATATTATATAA
13077800 TAT
1 TAT
13077803 TAGTACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATATTATATAA
Found at i:13077889 original size:11 final size:11
Alignment explanation
Indices: 13077873--13077897 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13077863 ATTATTTACA
13077873 TTTTTTTCTTT
1 TTTTTTTCTTT
13077884 TTTTTTTCTTT
1 TTTTTTTCTTT
13077895 TTT
1 TTT
13077898 GTTTGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:13078713 original size:17 final size:17
Alignment explanation
Indices: 13078691--13078740 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
13078681 TAAGGCTTTC
*
13078691 TTTTTTA-TTTTATTTTA
1 TTTTTTAGTTTT-TATTA
13078708 TTTTTTAGTTTTTATTA
1 TTTTTTAGTTTTTATTA
* *
13078725 TTTTTTTGGTTTTATT
1 TTTTTTAGTTTTTATT
13078741 TTTGAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTTTAGTTTTTATTA
Found at i:13078937 original size:19 final size:19
Alignment explanation
Indices: 13078905--13078946 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
13078895 TTGTAAAAAC
13078905 AAAAAAATTCTTTC-AATA
1 AAAAAAATTCTTTCAAATA
*
13078923 AAAAAAATCTTTTTCAAATA
1 AAAAAAAT-TCTTTCAAATA
13078943 AAAA
1 AAAA
13078947 TACCTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAAAATTCTTTCAAATA
Found at i:13080017 original size:184 final size:183
Alignment explanation
Indices: 13079692--13080025 Score: 399
Period size: 184 Copynumber: 1.8 Consensus size: 183
13079682 TTTTGAAGGA
* * * *
13079692 AAAAAGAAATTTTTGTTATATTGAAGTTTTTTATAAATATTTCAATACACTGATAATATTTAAAA
1 AAAAAGAAAATTTTATTATATTGAAATTTTTTATAAATATTCCAATACACTGATAATATTTAAAA
* * * *
13079757 AAAATCTTATCACCTAGGGATTTCGTAAAGCATCACTACTTGGAATACTTTTAGAGTCCTATCAT
66 AAAATCTTATCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACATTTAGAATCCTATCAT
* *
13079822 TGGATAAATTTTT-TTTTCTCATTTATATTATTATTAATTATTTTTTATTTAC
131 GGGAAAAATTTTTCTTTTCTCATTTATATTATTATTAATTATTTTTTATTTAC
* * * *
13079874 AAAAAGATAAATTTTATTGTATTGTAAATTTTTTATAAAATATTCCAATACACTGGTAGTA-TTG
1 AAAAAGA-AAATTTTATTATATTG-AAATTTTTTAT-AAATATTCCAATACACTGATAATATTTA
* * * * *
13079938 AAAAAAATCTTCTCACCTAGAGATTTTGT-AGGCATCACTACTCGGAGTTCATTT-GAAT-CTCA
63 AAAAAAATCTTATCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACATTTAGAATCCT-A
*
13080000 TCGTCGGGTAAAAATTTTTCTTTTCT
127 TCAT-GGG-AAAAATTTTTCTTTTCT
13080026 TTTTTTATTA
Statistics
Matches: 125, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
181 2 0.02
182 14 0.11
183 35 0.28
184 47 0.38
185 27 0.22
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (183 bp):
AAAAAGAAAATTTTATTATATTGAAATTTTTTATAAATATTCCAATACACTGATAATATTTAAAA
AAAATCTTATCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACATTTAGAATCCTATCAT
GGGAAAAATTTTTCTTTTCTCATTTATATTATTATTAATTATTTTTTATTTAC
Found at i:13080070 original size:12 final size:12
Alignment explanation
Indices: 13080055--13080082 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13080045 TATTATTAAG
13080055 TTTATTTTTTAT
1 TTTATTTTTTAT
13080067 TTTATTTTTTAT
1 TTTATTTTTTAT
13080079 TTTA
1 TTTA
13080083 AAAATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:13080981 original size:23 final size:23
Alignment explanation
Indices: 13080950--13080998 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
13080940 TTTATAGAGC
13080950 TTTTAGGGATTCAAATCCCATAT
1 TTTTAGGGATTCAAATCCCATAT
* **
13080973 TTTTTGGGATTTGAATCCCATAT
1 TTTTAGGGATTCAAATCCCATAT
13080996 TTT
1 TTT
13080999 CAATAGGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
TTTTAGGGATTCAAATCCCATAT
Found at i:13081418 original size:89 final size:89
Alignment explanation
Indices: 13081325--13081570 Score: 309
Period size: 89 Copynumber: 2.8 Consensus size: 89
13081315 TAAAGGCTCC
* ** * *
13081325 AGAAGTTCAACAACATTTTTTAAATTTAAATAG-GCTCCTCTAAGCAAAGTCTCAACAACTTTTA
1 AGAAGCTCAACAAC-TTTTAAAAATTTAAAAAGAGCTCCTCTAAGCAAAGGCTCAACAACTTTTA
13081389 AAAATTTAAAAAGGTTCCTCTAAGT
65 AAAATTTAAAAAGGTTCCTCTAAGT
* * * *
13081414 AGAAGCTCAACAACTTTTAAAAATTTAAAAAGAGCTCCTCTAAGTAGAGGCTTAACAACTTTTGA
1 AGAAGCTCAACAACTTTTAAAAATTTAAAAAGAGCTCCTCTAAGCAAAGGCTCAACAACTTTTAA
13081479 AAATTTAAAAAGGTTCCTCTAAGT
66 AAATTTAAAAAGGTTCCTCTAAGT
* * * ** * *
13081503 AGAGGCTCAACAACTTTTGAAAATTTAAAAAAAGCTATTTTAAGTAGAA-GCTCAACAA-TTTTA
1 AGAAGCTCAACAACTTTTAAAAATTTAAAAAGAGCTCCTCTAAGCA-AAGGCTCAACAACTTTTA
13081566 AAAAT
65 AAAAT
13081571 CTATCTTGAA
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
88 24 0.18
89 112 0.82
90 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (89 bp):
AGAAGCTCAACAACTTTTAAAAATTTAAAAAGAGCTCCTCTAAGCAAAGGCTCAACAACTTTTAA
AAATTTAAAAAGGTTCCTCTAAGT
Found at i:13081471 original size:45 final size:44
Alignment explanation
Indices: 13081331--13081570 Score: 293
Period size: 44 Copynumber: 5.4 Consensus size: 44
13081321 CTCCAGAAGT
** * * * *
13081331 TCAACAACATTTTTTAAATTTAAATAGGCTCCTCTAAGCAAAGTC
1 TCAACAAC-TTTTAAAAATTTAAAAAGGCTCCTCTAAGTAGAGGC
* *
13081376 TCAACAACTTTTAAAAATTTAAAAAGGTTCCTCTAAGTAGAAGC
1 TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGTAGAGGC
13081420 TCAACAACTTTTAAAAATTTAAAAAGAGCTCCTCTAAGTAGAGGC
1 TCAACAACTTTTAAAAATTTAAAAAG-GCTCCTCTAAGTAGAGGC
* * *
13081465 TTAACAACTTTTGAAAATTTAAAAAGGTTCCTCTAAGTAGAGGC
1 TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGTAGAGGC
* * ** * *
13081509 TCAACAACTTTTGAAAATTTAAAAAAAGCTATTTTAAGTAGAAGC
1 TCAACAACTTTTAAAAATTT-AAAAAGGCTCCTCTAAGTAGAGGC
13081554 TCAACAA-TTTTAAAAAT
1 TCAACAACTTTTAAAAAT
13081571 CTATCTTGAA
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
44 99 0.58
45 73 0.42
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (44 bp):
TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGTAGAGGC
Found at i:13081698 original size:49 final size:49
Alignment explanation
Indices: 13081552--13082107 Score: 571
Period size: 48 Copynumber: 11.5 Consensus size: 49
13081542 TTAAGTAGAA
* * *
13081552 GCTCAACAATTTTAAAAATC-TATCTTGAAAAAGCTCTTCTAAGCAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
** * *
13081600 TTTCAACAACTTT-AAAAT-TCATCTTGAAAAA-CTTCCTTTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGC-TCCTCTCAGCAGAG
* * * * *
13081647 GCTCAATAATTTTAAAAATCTTATCTTGAAAAAGCTCATCTTAGCATAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
** * * *
13081696 GCTCAGTAACTTT-AAAAT-TTCATCTTGAAAAAAGCTCATCTCAGTAGAA
1 GCTCAACAACTTTAAAAATCTT-ATCTTG-AAAAAGCTCCTCTCAGCAGAG
* * * *
13081745 GCTCAACAATTTTAAAAATC-TATCTTCAAAAAGCTCCTCTCAACAAAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
* * * * * *
13081793 GGTCAACAACTTT-AAAATCTTATCTTCAAAAAGCTCATATCAACAGAA
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
* * * * * *
13081841 GCTTAACAATTTTAAAAAT-TCATCTTGAAAAAGCTCATTTCATCAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
*
13081889 GCTTAACAACTTT-AAAAT-TTCATCTTGAAAAAAGCTCCTCTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTT-ATCTTG-AAAAAGCTCCTCTCAGCAGAG
* *
13081938 GTTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTTTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
* * * * * *
13081987 GCTTAACAACTTT-AAATTTTTATTTTGAAAAAAGCTCCTCTTAGTAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTG-AAAAAGCTCCTCTCAGCAGAG
* *
13082036 GCTCAACAATTTTAAAAAT-TCATCTTGAAAAAGCTCCTCTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
13082084 GCTCAACAACTTTAAAAATCTTAT
1 GCTCAACAACTTTAAAAATCTTAT
13082108 TTGTTCTCGA
Statistics
Matches: 420, Mismatches: 70, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
46 1 0.00
47 50 0.12
48 177 0.42
49 168 0.40
50 22 0.05
51 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (49 bp):
GCTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTCTCAGCAGAG
Found at i:13081868 original size:193 final size:192
Alignment explanation
Indices: 13081545--13082100 Score: 695
Period size: 193 Copynumber: 2.9 Consensus size: 192
13081535 AGCTATTTTA
* **
13081545 AGTAGAAGCTCAACAATTTTAAAAATCTATCTTGAAAAAGCTCTTCT-AAGCAGAGTTTCAACAA
1 AGTAGAAGCTCAACAATTTTAAAAATCTATCTTGAAAAAGCTCCTCTCAA-CAGAGGCTCAACAA
* * * * *
13081609 CTTTAAAATTCATCTTGAAAAA-CTTCCTTTCAGCAGAGGCTCAATAATTTTAAAAATCTTATCT
65 CTTTAAAATTTATCTTAAAAAAGC-TCCTATCAGCAGAGGCTCAACAATTTTAAAAAT-TCATCT
* **
13081673 TGAAAAAGCTCATCTTAGCATAGGCTCAGTAACTTTAAAATTTCATCTTGAAAAAAGCTCATCTC
128 TGAAAAAGCTCATCTTAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAAGCTCATCTC
* * *
13081738 AGTAGAAGCTCAACAATTTTAAAAATCTATCTTCAAAAAGCTCCTCTCAACAAAGGGTCAACAAC
1 AGTAGAAGCTCAACAATTTTAAAAATCTATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAAC
* * * * *
13081803 TTTAAAATCTTATCTTCAAAAAGCTCATATCAACAGAAGCTTAACAATTTTAAAAATTCATCTTG
66 TTTAAAAT-TTATCTTAAAAAAGCTCCTATCAGCAGAGGCTCAACAATTTTAAAAATTCATCTTG
* * *
13081868 AAAAAGCTCAT-TTCATCAGAGGCTTAACAACTTTAAAATTTCATCTTGAAAAAAGCTCCTCTC
130 AAAAAGCTCATCTT-AGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAAGCTCATCTC
* * * * * * *
13081931 AGCAGAGGTTCAACAACTTTAAAAATCTTATCTTGAAAAAGCTCCTTTCAGCAGAGGCTTAACAA
1 AGTAGAAGCTCAACAATTTTAAAAATC-TATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAA
* * * * *
13081996 CTTTAAATTTTTATTTTGAAAAAAGCTCCTCTTAGTAGAGGCTCAACAATTTTAAAAATTCATCT
65 CTTTAAA-ATTTATCTT-AAAAAAGCTCCTATCAGCAGAGGCTCAACAATTTTAAAAATTCATCT
* *
13082061 TGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
128 TGAAAAAGCTCATCTTAGCAGAGGCTCAACAACTTTAAAA
13082101 ATCTTATTTG
Statistics
Matches: 311, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
192 2 0.01
193 149 0.48
194 84 0.27
195 75 0.24
196 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (192 bp):
AGTAGAAGCTCAACAATTTTAAAAATCTATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAAC
TTTAAAATTTATCTTAAAAAAGCTCCTATCAGCAGAGGCTCAACAATTTTAAAAATTCATCTTGA
AAAAGCTCATCTTAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAAGCTCATCTC
Found at i:13082907 original size:8 final size:8
Alignment explanation
Indices: 13082894--13082934 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
13082884 AAATGAGTTA
13082894 TTATTTTT
1 TTATTTTT
13082902 TTATTTTT
1 TTATTTTT
**
13082910 TTAACTTT
1 TTATTTTT
*
13082918 TTATTTAT
1 TTATTTTT
13082926 TTATTTTT
1 TTATTTTT
13082934 T
1 T
13082935 AAGTAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (8 bp):
TTATTTTT
Done.