Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 64 of 320
Found at i:19241862 original size:31 final size:32
Alignment explanation
Indices: 19241824--19241925 Score: 105
Period size: 26 Copynumber: 3.4 Consensus size: 32
19241814 TAAATGAAAT
19241824 AAATTAAA-AAATGAAATGAAACTAAAAATTG
1 AAATTAAATAAATGAAATGAAACTAAAAATTG
19241855 AAATTAAATTAAATGAAATGAAA-T--AAATT-
1 AAATTAAA-TAAATGAAATGAAACTAAAAATTG
*
19241884 -AA--AAATGAAATGAAATG-AACAAAAAATTG
1 AAATTAAAT-AAATGAAATGAAACTAAAAATTG
*
19241913 AAATGAAATAAAT
1 AAATTAAATAAAT
19241926 AAAAATTGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
25 3 0.05
26 13 0.22
28 7 0.12
30 7 0.12
31 12 0.20
32 5 0.08
33 13 0.22
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (32 bp):
AAATTAAATAAATGAAATGAAACTAAAAATTG
Found at i:19241889 original size:21 final size:22
Alignment explanation
Indices: 19241762--19241850 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
19241752 GAAGTGAAAC
19241762 TAAAAATTGAAATGAAAT-AAAT
1 TAAAAA-TGAAATGAAATAAAAT
* * *
19241784 TCAAAAGGAAATTAAATGAAAAAT
1 TAAAAATGAAATGAAAT--AAAAT
* *
19241808 T-GAAATTAAATGAAAT-AAAT
1 TAAAAATGAAATGAAATAAAAT
19241828 TAAAAAATGAAATGAAACTAAAA
1 T-AAAAATGAAATGAAA-TAAAA
19241851 ATTGAAATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.10
21 9 0.18
22 17 0.33
23 12 0.24
24 8 0.16
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAAAATGAAATGAAATAAAAT
Found at i:19241890 original size:21 final size:22
Alignment explanation
Indices: 19241853--19241997 Score: 87
Period size: 21 Copynumber: 6.8 Consensus size: 22
19241843 AACTAAAAAT
*
19241853 TGAAATTAAATT--AAATGAAA
1 TGAAATAAAATTAAAAATGAAA
19241873 TGAAAT-AAATTAAAAATGAAA
1 TGAAATAAAATTAAAAATGAAA
*
19241894 TGAAATGAACAA--AAAATTGAAA
1 TGAAAT-AA-AATTAAAAATGAAA
19241916 TGAAAT-AAA-TAAAAATTGAAA
1 TGAAATAAAATTAAAAA-TGAAA
* * * *
19241937 TGAAAT-GAGTTGATAATGAAA
1 TGAAATAAAATTAAAAATGAAA
* *
19241958 TGAAAATTTCAAA-T-GAAATGAAA
1 TG-AAA--TAAAATTAAAAATGAAA
19241981 TGAAAT-AAATTAAAAAT
1 TGAAATAAAATTAAAAAT
19241998 TAAAAATTGA
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.10
20 13 0.13
21 37 0.37
22 25 0.25
23 10 0.10
24 4 0.04
25 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (22 bp):
TGAAATAAAATTAAAAATGAAA
Found at i:19242009 original size:34 final size:31
Alignment explanation
Indices: 19241977--19242051 Score: 80
Period size: 34 Copynumber: 2.3 Consensus size: 31
19241967 CAAATGAAAT
*
19241977 GAAATGAAATAAATTAAAAATTAAAAATTGAAAT
1 GAAATGAAATAAA-TAAAAATT-GAAA-TGAAAT
* *
19242011 GAAATGAAATAATTTAAAAGTTGAAATGAAAT
1 GAAATGAAATAA-ATAAAAATTGAAATGAAAT
19242043 GAAAT-AAAT
1 GAAATGAAAT
19242052 TTATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.11
32 11 0.30
33 3 0.08
34 19 0.51
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (31 bp):
GAAATGAAATAAATAAAAATTGAAATGAAAT
Found at i:19242010 original size:6 final size:5
Alignment explanation
Indices: 19241715--19242051 Score: 114
Period size: 5 Copynumber: 66.0 Consensus size: 5
19241705 TAATAATTAA
* * *
19241715 GAAAT GAAA- AAAATT GAAAT GAAAT GAAAT -AAA- -AAAA GAAGT GAAACT
1 GAAAT GAAAT GAAA-T GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T
* * * * *
19241763 AAAAATT GAAAT GAAAT -AAATT CAAAAG GAAAT TAAAT GAAA- -AATT
1 -GAAA-T GAAAT GAAAT GAAA-T -GAAAT GAAAT GAAAT GAAAT GAAAT
* * *
19241809 GAAAT TAAAT GAAAT -AAAT TAAA- -AAAT GAAAT GAAACT AAAAATT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAA-T
* * * *
19241854 GAAAT TAAAT TAAAT GAAAT GAAAT -AAATT AAAAAT GAAAT GAAAT GAACAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAAT GAAAT GAAAT GAA-AT
* * **
19241906 AAAATT GAAAT GAAAT -AAAT AAAAATT GAAAT GAAAT GAGTT GATAAT
1 GAAA-T GAAAT GAAAT GAAAT -GAAA-T GAAAT GAAAT GAAAT GA-AAT
* * *
19241954 GAAAT GAAAATTT CAAAT GAAAT GAAAT GAAAT -AAATT AAAAAT TAAA-
1 GAAAT G-AAA--T GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAAT GAAAT
* * *
19242002 -AATT GAAAT GAAAT GAAAT -AATTT AAAAGTT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAA-AT GAAA--T GAAAT GAAAT GAAAT
19242048 -AAAT
1 GAAAT
19242052 TTATTATTTA
Statistics
Matches: 255, Mismatches: 40, Indels: 75
0.69 0.11 0.20
Matches are distributed among these distances:
3 10 0.04
4 29 0.11
5 157 0.62
6 33 0.13
7 25 0.10
8 1 0.00
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.24
Consensus pattern (5 bp):
GAAAT
Found at i:19242069 original size:66 final size:58
Alignment explanation
Indices: 19241833--19242052 Score: 170
Period size: 59 Copynumber: 3.7 Consensus size: 58
19241823 TAAATTAAAA
* * * * *
19241833 AATGAAATG-AAACTAAAAATTGAAATTAAATTAAATGAAATGAAATAAATTAAAAA-TGA-
1 AATGAAATGAAAATTTAAAA-TGAAATGAAATGAAAT-AAAT-TAA-AAATTAAAAATTGAT
* * *
19241892 AATGAAATGAACAA---AAAATTGAAATGAAAT-AAATAAAAATT-GAAATGAAATGAGTTGAT
1 AATGAAATGAA-AATTTAAAA-TGAAATGAAATGAAAT--AAATTAAAAATTAAA--AATTGAT
*
19241951 AATGAAATGAAAATTTCAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGA-
1 AATGAAATGAAAATTTAAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGAT
19242008 AATGAAATGAAATAATTTAAAAGTTGAAATGAAATGAAATAAATT
1 AATGAAATG-AA-AATTTAAAA--TGAAATGAAATGAAATAAATT
19242053 TATTATTTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
55 7 0.05
57 14 0.10
58 31 0.23
59 33 0.25
60 19 0.14
61 30 0.22
ACGTcount: A:0.60, C:0.01, G:0.12, T:0.26
Consensus pattern (58 bp):
AATGAAATGAAAATTTAAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGAT
Found at i:19242651 original size:20 final size:20
Alignment explanation
Indices: 19242626--19242665 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19242616 CAATATGGTC
*
19242626 AAATATTCACTAATTTATAA
1 AAATATTCACTAATTGATAA
19242646 AAATATTCACTAATTGATAA
1 AAATATTCACTAATTGATAA
19242666 TATATTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTCACTAATTGATAA
Found at i:19246988 original size:6 final size:6
Alignment explanation
Indices: 19246970--19247017 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
19246960 GAAATCTAAG
* *
19246970 AAAATA ACAATA AACATA AAAATA AAAATA AAAATA TAAAATA TAAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA -AAAATA -AAAA
19247018 CAAATGGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:19248629 original size:3 final size:3
Alignment explanation
Indices: 19248621--19248674 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
19248611 CAGTAAAACC
19248621 AAT AAT AAT AA- AAT AAT AAT AAT AAAT AA- AA- AAT AATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT
19248665 AAT AAT AAT A
1 AAT AAT AAT A
19248675 CTAGAGCTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 35 0.74
4 6 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19248640 original size:14 final size:14
Alignment explanation
Indices: 19248621--19248672 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
19248611 CAGTAAAACC
19248621 AATAATAATAAAAT
1 AATAATAATAAAAT
19248635 AATAATAAT-AAAT
1 AATAATAATAAAAT
19248648 AA-AA-AATAATTAAT
1 AATAATAATAA--AAT
19248662 AATAATAATAA
1 AATAATAATAA
19248673 TACTAGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.09
12 3 0.09
13 6 0.18
14 14 0.42
15 2 0.06
16 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:19252987 original size:14 final size:14
Alignment explanation
Indices: 19252956--19253015 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
19252946 TTTTCAACAG
* * *
19252956 TAAACCCTAAATCT
1 TAAATCCTAAACCC
* *
19252970 TAAATCCCAAACCA
1 TAAATCCTAAACCC
*
19252984 TAAA-CCTACACCC
1 TAAATCCTAAACCC
19252997 TAAATCCTAAACCC
1 TAAATCCTAAACCC
19253011 TAAAT
1 TAAAT
19253016 ATATATATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATCCTAAACCC
Found at i:19252998 original size:7 final size:7
Alignment explanation
Indices: 19252956--19253014 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
19252946 TTTTCAACAG
19252956 TAAACCC
1 TAAACCC
* *
19252963 TAAATCT
1 TAAACCC
19252970 TAAATCCC
1 TAAA-CCC
*
19252978 -AAACCA
1 TAAACCC
19252984 TAAA-CC
1 TAAACCC
*
19252990 TACACCC
1 TAAACCC
*
19252997 TAAATCC
1 TAAACCC
19253004 TAAACCC
1 TAAACCC
19253011 TAAA
1 TAAA
19253015 TATATATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
6 6 0.15
7 32 0.82
8 1 0.03
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:19253320 original size:50 final size:50
Alignment explanation
Indices: 19253226--19253320 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
19253216 CCCAAAATAA
* * * * *
19253226 TAAATATTATATCATAAACCCTAAACCCCTAAACCATGAGCATTAAACCT
1 TAAATATTAAATCATAAACCCTAAACCCCAAAACAATAAACATTAAACCT
* *
19253276 TAAATCTTAAATCATAAACCCTAAACCCCAAAATAATAAACATTA
1 TAAATATTAAATCATAAACCCTAAACCCCAAAACAATAAACATTA
19253321 TATCATAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.25
Consensus pattern (50 bp):
TAAATATTAAATCATAAACCCTAAACCCCAAAACAATAAACATTAAACCT
Found at i:19253855 original size:7 final size:7
Alignment explanation
Indices: 19253821--19253932 Score: 95
Period size: 7 Copynumber: 16.1 Consensus size: 7
19253811 CCATATTTAC
19253821 CCCTAAA
1 CCCTAAA
19253828 CCC--AA
1 CCCTAAA
19253833 CCTCTAAA
1 CC-CTAAA
*
19253841 CCCCAAA
1 CCCTAAA
*
19253848 CCTTAAA
1 CCCTAAA
19253855 CCCTAAA
1 CCCTAAA
19253862 CCCTAAA
1 CCCTAAA
*
19253869 CCCCAAA
1 CCCTAAA
*
19253876 CCATAAA
1 CCCTAAA
* *
19253883 CTCTAAG
1 CCCTAAA
19253890 CCCTAAA
1 CCCTAAA
*
19253897 CTCTAAA
1 CCCTAAA
*
19253904 TCCTAAA
1 CCCTAAA
*
19253911 CCTTAAA
1 CCCTAAA
*
19253918 CCAT-AA
1 CCCTAAA
19253924 CCCATAAA
1 CCC-TAAA
19253932 C
1 C
19253933 TAAATTTAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 9
0.74 0.17 0.08
Matches are distributed among these distances:
5 4 0.05
6 5 0.06
7 65 0.80
8 7 0.09
ACGTcount: A:0.43, C:0.39, G:0.01, T:0.17
Consensus pattern (7 bp):
CCCTAAA
Found at i:19253995 original size:40 final size:40
Alignment explanation
Indices: 19253948--19254036 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
19253938 TTAAAAATGT
* * *
19253948 CACTAATGCTCGATCTATGGCGGCATTGTTT-AAAAAGCGC
1 CACTAATGCTCGACCTATAGCAGCATT-TTTCAAAAAGCGC
* *
19253988 CACTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGC
1 CACTAATGCTCGACCTATAGCAGCATTTTTCAAAAAGCGC
*
19254028 CGCTAATGC
1 CACTAATGC
19254037 CACTAAAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.07
40 38 0.93
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (40 bp):
CACTAATGCTCGACCTATAGCAGCATTTTTCAAAAAGCGC
Found at i:19254183 original size:115 final size:114
Alignment explanation
Indices: 19253969--19254266 Score: 418
Period size: 115 Copynumber: 2.6 Consensus size: 114
19253959 GATCTATGGC
* * *
19253969 GGCATTGTTTAAAAAGCGCCACTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAA
1 GGCATTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAA
19254034 TGCCACTAAAGCTCACATAAAACGACGGCATTGTGCTTAATTTTTTTGT-
66 TGCCACTAAAGCTCACATAAAACGACGGCATTGTGCTTAATTTTTTT-TA
* * * *
19254083 GGCATTTTTTAAAAAAGCATCGCTAATAGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTA
1 GGCATTTTTT-AAAAAGCACCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGCCGCTA
*
19254148 ATGCCACTAAAGCTCACATAAAACGACGGCGTTGTGCTTAATTTTTTTTA
65 ATGCCACTAAAGCTCACATAAAACGACGGCATTGTGCTTAATTTTTTTTA
** * * * * * *
19254198 CGGTGTTTTTTAAAAAGCGCCTCTAATGGTCAACCTATAGTAGCATTTTTCAAAAAGCGCCACTA
1 -GGCATTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGCCGCTA
19254263 ATGC
65 ATGC
19254267 TCGATCTATA
Statistics
Matches: 161, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
114 10 0.06
115 143 0.89
116 8 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (114 bp):
GGCATTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAA
TGCCACTAAAGCTCACATAAAACGACGGCATTGTGCTTAATTTTTTTTA
Found at i:19254287 original size:40 final size:40
Alignment explanation
Indices: 19254202--19254287 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
19254192 TTTTTACGGT
* * * *
19254202 GTTTTTTAAAAAGCGCCTCTAATGGTCAACCTATAGTAGC
1 GTTTTTCAAAAAGCGCCACTAATGCTCAACCTATAGCAGC
* * * *
19254242 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGC
1 GTTTTTCAAAAAGCGCCACTAATGCTCAACCTATAGCAGC
19254282 GTTTTT
1 GTTTTT
19254288 AGTCCTAGCG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCACTAATGCTCAACCTATAGCAGC
Found at i:19255707 original size:19 final size:19
Alignment explanation
Indices: 19255676--19255725 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
19255666 TCTAAAGAAA
19255676 TTGAATGGAGATATTCAATC
1 TTGAAT-GAGATATTCAATC
19255696 TTGAATGAGATATTCAATC
1 TTGAATGAGATATTCAATC
*
19255715 TTGAAGGAGAT
1 TTGAATGAGAT
19255726 CCGCTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (19 bp):
TTGAATGAGATATTCAATC
Found at i:19256853 original size:23 final size:21
Alignment explanation
Indices: 19256823--19256868 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
19256813 AATTATTTAT
19256823 AATTTATATATGAAAATATAA
1 AATTTATATATGAAAATATAA
19256844 AATTTATATATGAAAATATAA
1 AATTTATATATGAAAATATAA
19256865 AATT
1 AATT
19256869 CGACCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
AATTTATATATGAAAATATAA
Found at i:19261862 original size:18 final size:19
Alignment explanation
Indices: 19261829--19261866 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19261819 AGACTCCAGG
*
19261829 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
19261848 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
19261866 T
1 T
19261867 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:19268346 original size:40 final size:34
Alignment explanation
Indices: 19268271--19268340 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
19268261 AGTAACAGTC
19268271 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
*
19268305 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
19268339 CA
1 CA
19268341 ATAACAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
Found at i:19276003 original size:34 final size:34
Alignment explanation
Indices: 19275965--19276034 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
19275955 AGTAACAATC
* * * *
19275965 CAGTATCAGTGTGGATCTTAGTCCATTACAATAA
1 CAGTATCAATATGGACCTTAGCCCATTACAATAA
* *
19275999 CAGTATCAATATGGGCCTTAGCCCATTACAGTAA
1 CAGTATCAATATGGACCTTAGCCCATTACAATAA
19276033 CA
1 CA
19276035 ATAACAGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (34 bp):
CAGTATCAATATGGACCTTAGCCCATTACAATAA
Found at i:19276192 original size:21 final size:21
Alignment explanation
Indices: 19276168--19276214 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19276158 CGGCATTATT
19276168 CAGTAATTGCAGCAAAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
* *
19276189 CAGTAATTGTAGCAGAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
19276210 CAGTA
1 CAGTA
19276215 CAGTACACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
CAGTAATTGCAGCAAAGCTGC
Found at i:19279795 original size:43 final size:43
Alignment explanation
Indices: 19279748--19279850 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 43
19279738 TAGAACATGA
19279748 CCTTTAGCGGCGCTTTTACAACAAACACCGCTAAAAAATATGG
1 CCTTTAGCGGCGCTTTTACAACAAACACCGCTAAAAAATATGG
* * * * * ** * *
19279791 CCTTTGGCGACACTTTTCCCACAAACGTCGTTAAAGAATATGG
1 CCTTTAGCGGCGCTTTTACAACAAACACCGCTAAAAAATATGG
* *
19279834 CCTTTAACAGCGCTTTT
1 CCTTTAGCGGCGCTTTT
19279851 CCCATAAACG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (43 bp):
CCTTTAGCGGCGCTTTTACAACAAACACCGCTAAAAAATATGG
Found at i:19280056 original size:34 final size:35
Alignment explanation
Indices: 19280018--19280083 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
19280008 CTATTAAAAT
*
19280018 TTTAACTTTA-AAACTAAATATAA-AAATTAATGAG
1 TTTAAATTTAGAAACTAAA-ATAATAAATTAATGAG
*
19280052 TTTAAATTTAGAATCTAAAATAATAAATTAAT
1 TTTAAATTTAGAAACTAAAATAATAAATTAAT
19280084 AACACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (35 bp):
TTTAAATTTAGAAACTAAAATAATAAATTAATGAG
Found at i:19280178 original size:19 final size:19
Alignment explanation
Indices: 19280133--19280181 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
19280123 TAAATATTAA
* **
19280133 AATAAAAATAAAAATTTAG
1 AATAAAAATTAAAATAAAG
* *
19280152 AATCAAAATTAAAATAAAT
1 AATAAAAATTAAAATAAAG
19280171 AATAAAAATTA
1 AATAAAAATTA
19280182 TCTAATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAAAAATTAAAATAAAG
Found at i:19283007 original size:82 final size:80
Alignment explanation
Indices: 19282890--19283042 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 80
19282880 AATGGGGAAA
* *
19282890 AAAAAGAGAAGAAATTTCAGGCAAAGTTTTAGGATTTCTTTGGGGAG-GGGGAGGGAACCGATTT
1 AAAAAGAGAAGAAATTTCAGCCAAAGTTTTAGGATTTC---GGGGAGAAGGGA-GGAACCGATTT
19282954 TGGGAAAAAGAAAGGAGGG
62 TGGGAAAAAGAAAGGAGGG
* * *
19282973 AAAAA-AGAAGATATTTCATGCCAAA-TTTTGGGATTTCGGGGCGAAGGGAGGAACCGATTTTGG
1 AAAAAGAGAAGAAATTTCA-GCCAAAGTTTTAGGATTTCGGGGAGAAGGGAGGAACCGATTTTGG
19283036 GAAAAAG
65 GAAAAAG
19283043 TCTTAAGGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
79 26 0.41
80 4 0.06
82 23 0.37
83 10 0.16
ACGTcount: A:0.37, C:0.08, G:0.33, T:0.22
Consensus pattern (80 bp):
AAAAAGAGAAGAAATTTCAGCCAAAGTTTTAGGATTTCGGGGAGAAGGGAGGAACCGATTTTGGG
AAAAAGAAAGGAGGG
Found at i:19283233 original size:17 final size:18
Alignment explanation
Indices: 19283200--19283233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19283190 TATTTCTTAA
19283200 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
19283218 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
19283234 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:19283662 original size:15 final size:15
Alignment explanation
Indices: 19283642--19283677 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19283632 GACCCTAACT
19283642 ATAAAACAAAAAACC
1 ATAAAACAAAAAACC
*
19283657 ATAAAACCAAAAACC
1 ATAAAACAAAAAACC
19283672 A-AAAAC
1 ATAAAAC
19283678 TCTAAACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.72, C:0.22, G:0.00, T:0.06
Consensus pattern (15 bp):
ATAAAACAAAAAACC
Found at i:19283669 original size:7 final size:7
Alignment explanation
Indices: 19283644--19283677 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
19283634 CCCTAACTAT
*
19283644 AAAACAA
1 AAAACCA
19283651 AAAACCA
1 AAAACCA
19283658 TAAAACCA
1 -AAAACCA
19283666 AAAACCA
1 AAAACCA
19283673 AAAAC
1 AAAAC
19283678 TCTAAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.74, C:0.24, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAACCA
Found at i:19283675 original size:22 final size:22
Alignment explanation
Indices: 19283644--19283690 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19283634 CCCTAACTAT
19283644 AAAACAAAAAAC-CATAAAACCA
1 AAAACAAAAAACTC-TAAAACCA
* *
19283666 AAAACCAAAAACTCTAAACCCA
1 AAAACAAAAAACTCTAAAACCA
19283688 AAA
1 AAA
19283691 TAATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (22 bp):
AAAACAAAAAACTCTAAAACCA
Found at i:19283727 original size:43 final size:42
Alignment explanation
Indices: 19283667--19283802 Score: 112
Period size: 43 Copynumber: 3.2 Consensus size: 42
19283657 ATAAAACCAA
* *
19283667 AAACCAAAAACTCTAAACCCAAAATAATAAACATTATATCAT
1 AAACCATAAACCCTAAACCCAAAATAATAAACATTATATCAT
* * ** * * * *
19283709 AAACCCTAAACCCCTAAA-CCATGAGCATTAAACCTTAAATCTT
1 AAACCATAAA-CCCTAAACCCA-AAATAATAAACATTATATCAT
* * *
19283752 AAATCATAAACTCTAAACCCCAAAATAATAAACACTATATCAT
1 AAACCATAAACCCTAAA-CCCAAAATAATAAACATTATATCAT
*
19283795 AACCCATA
1 AAACCATA
19283803 TCCCTTAAAC
Statistics
Matches: 67, Mismatches: 23, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
42 17 0.25
43 47 0.70
44 3 0.04
ACGTcount: A:0.51, C:0.26, G:0.01, T:0.22
Consensus pattern (42 bp):
AAACCATAAACCCTAAACCCAAAATAATAAACATTATATCAT
Found at i:19284319 original size:14 final size:14
Alignment explanation
Indices: 19284287--19284336 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
19284277 CCATATTTAC
19284287 CCCTAAA-CCC-AA
1 CCCTAAACCCCAAA
19284299 CCTCTAAACCCCAAA
1 CC-CTAAACCCCAAA
*
19284314 CCCTAAACCCTAAA
1 CCCTAAACCCCAAA
*
19284328 CCCCAAACC
1 CCCTAAACC
19284337 ATAAACTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 2 0.06
13 5 0.15
14 22 0.67
15 4 0.12
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (14 bp):
CCCTAAACCCCAAA
Found at i:19284326 original size:21 final size:21
Alignment explanation
Indices: 19284285--19284371 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
19284275 CACCATATTT
19284285 ACCCCTAAACCC--AACCTCTAA
1 ACCCC-AAACCCTAAACC-CTAA
19284306 ACCCCAAACCCTAAACCCTAA
1 ACCCCAAACCCTAAACCCTAA
* *
19284327 ACCCCAAACCATAAACTCTAA
1 ACCCCAAACCCTAAACCCTAA
* ** * *
19284348 GCCATAAACTCTAAATCCTAA
1 ACCCCAAACCCTAAACCCTAA
19284369 ACC
1 ACC
19284372 TTAAACCATA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 6 0.11
21 44 0.81
22 4 0.07
ACGTcount: A:0.43, C:0.41, G:0.01, T:0.15
Consensus pattern (21 bp):
ACCCCAAACCCTAAACCCTAA
Found at i:19284341 original size:14 final size:14
Alignment explanation
Indices: 19284297--19284391 Score: 77
Period size: 14 Copynumber: 6.7 Consensus size: 14
19284287 CCCTAAACCC
**
19284297 AACCTCTAAACCCCA
1 AACC-CTAAACCATA
*
19284312 AACCCTAAACCCTA
1 AACCCTAAACCATA
*
19284326 AACCCCAAACCATA
1 AACCCTAAACCATA
* *
19284340 AACTCTAAGCCATA
1 AACCCTAAACCATA
*
19284354 AACTCTAAATCC-TA
1 AACCCTAAA-CCATA
*
19284368 AACCTTAAACCAT-
1 AACCCTAAACCATA
19284381 AACCCATAAAC
1 AACCC-TAAAC
19284392 TAAATTTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
13 6 0.09
14 55 0.82
15 6 0.09
ACGTcount: A:0.45, C:0.37, G:0.01, T:0.17
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:19284342 original size:7 final size:7
Alignment explanation
Indices: 19284311--19284391 Score: 51
Period size: 7 Copynumber: 11.6 Consensus size: 7
19284301 TCTAAACCCC
*
19284311 AAACCCT
1 AAACCAT
*
19284318 AAACCCT
1 AAACCAT
**
19284325 AAACCCC
1 AAACCAT
19284332 AAACCAT
1 AAACCAT
19284339 AAACTC-T
1 AAAC-CAT
*
19284346 AAGCCAT
1 AAACCAT
19284353 AAACTC-T
1 AAAC-CAT
19284360 AAATCC-T
1 AAA-CCAT
*
19284367 AAACCTT
1 AAACCAT
19284374 AAACCAT
1 AAACCAT
*
19284381 AACCCAT
1 AAACCAT
19284388 AAAC
1 AAAC
19284392 TAAATTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
6 3 0.05
7 55 0.90
8 3 0.05
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCAT
Found at i:19284468 original size:40 final size:40
Alignment explanation
Indices: 19284416--19284494 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
19284406 CCGGTAATAT
*
19284416 TCGATCTATAGCGGCGTTGTTT-AAAAAGCACCGCTAATGG
1 TCGACCTATAGCGGCGTT-TTTCAAAAAGCACCGCTAATGG
*
19284456 TCGACCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
1 TCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATG
19284495 CCACTAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 3 0.08
40 33 0.92
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (40 bp):
TCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGG
Found at i:19284640 original size:115 final size:115
Alignment explanation
Indices: 19284428--19284725 Score: 445
Period size: 115 Copynumber: 2.6 Consensus size: 115
19284418 GATCTATAGC
* *
19284428 GGCGTTGTTTAAAAAGCACCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAA
1 GGCGTTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAA
* *
19284493 TGCCACTAAAGTTCACATAAAACAACGGCATTGTGCTT-AATTTTTTTGT
66 TGCCACTAAAGCTCACATAAAACAACGGCATTGTGCTTAAATTTTTTTAT
* * *
19284542 GGCGTTTTTTAAAAAAGCACCACTAATAGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGTTA
1 GGCGTTTTTT-AAAAAGCACCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTA
*
19284607 ATGCCACTAAAGCTCACATAAAACGACGGCATTGTGCTTAAATTTTTTTAT
65 ATGCCACTAAAGCTCACATAAAACAACGGCATTGTGCTTAAATTTTTTTAT
* * * * ** *
19284658 GGCATTTTTTAAAAAGCGCTGCTAATGGTCAACCTATAGTAGCGTTTTTCAAAAAGCACCACTAA
1 GGCGTTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAA
19284723 TGC
66 TGC
19284726 TCGATCTATA
Statistics
Matches: 164, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
114 9 0.05
115 136 0.83
116 19 0.12
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (115 bp):
GGCGTTTTTTAAAAAGCACCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAA
TGCCACTAAAGCTCACATAAAACAACGGCATTGTGCTTAAATTTTTTTAT
Found at i:19286194 original size:23 final size:19
Alignment explanation
Indices: 19286135--19286185 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
19286125 TCTAAAGAAA
19286135 TTGAATGGAGATCTTCAAAC
1 TTGAA-GGAGATCTTCAAAC
*
19286155 TTGAAGGAGATCTTCAATC
1 TTGAAGGAGATCTTCAAAC
19286174 TTGAAGGAGATC
1 TTGAAGGAGATC
19286186 CGCTTTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (19 bp):
TTGAAGGAGATCTTCAAAC
Found at i:19287317 original size:21 final size:21
Alignment explanation
Indices: 19287291--19287336 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
19287281 AATTATTTAT
**
19287291 AATTTATATATGAAAATATAA
1 AATTTATATACAAAAATATAA
19287312 AATTTATATACAAAAATATAA
1 AATTTATATACAAAAATATAA
19287333 AATT
1 AATT
19287337 CGACCAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTTATATACAAAAATATAA
Found at i:19294438 original size:21 final size:21
Alignment explanation
Indices: 19294412--19294458 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
19294402 CGACATTATT
* * *
19294412 CAGTAATTGTAGTATAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
19294433 CAGTAATTGCAGCAAAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
19294454 CAGTA
1 CAGTA
19294459 CAGTACACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (21 bp):
CAGTAATTGCAGCAAAGCTGC
Found at i:19294758 original size:17 final size:19
Alignment explanation
Indices: 19294724--19294760 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19294714 AAAGTTCACA
19294724 ACACAGCCCATGTGGGCCC
1 ACACAGCCCATGTGGGCCC
*
19294743 ACAC-GCCCGTGT-GGCCC
1 ACACAGCCCATGTGGGCCC
19294760 A
1 A
19294761 TTAAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.11
Consensus pattern (19 bp):
ACACAGCCCATGTGGGCCC
Found at i:19301103 original size:91 final size:91
Alignment explanation
Indices: 19300943--19301135 Score: 368
Period size: 91 Copynumber: 2.1 Consensus size: 91
19300933 AATATGGGGT
*
19300943 ATTAGCCAAGCCCTTAATAGTCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAATGTACTAG
1 ATTACCCAAGCCCTTAATAGTCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAATGTACTAG
19301008 AAGCTTTTGAACAGCTCAAAACAACA
66 AAGCTTTTGAACAGCTCAAAACAACA
*
19301034 ATTACCCAAGCCCTTAATAGTCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAGTGTACTAG
1 ATTACCCAAGCCCTTAATAGTCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAATGTACTAG
19301099 AAGCTTTTGAACAGCTCAAAACAACA
66 AAGCTTTTGAACAGCTCAAAACAACA
19301125 ATTACCCAAGC
1 ATTACCCAAGC
19301136 ACCATAACTA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 100 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (91 bp):
ATTACCCAAGCCCTTAATAGTCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAATGTACTAG
AAGCTTTTGAACAGCTCAAAACAACA
Found at i:19309821 original size:44 final size:42
Alignment explanation
Indices: 19309755--19309842 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 42
19309745 CTAAACTCAG
*
19309755 AAAAAATATCTTATTTATTTCAAAATAAAAATAAAATAATTA
1 AAAAAATATCTTATTTACTTCAAAATAAAAATAAAATAATTA
*
19309797 AAAAATATAATCTTATTTACTTCAAAATAAAAATATAATAATTA
1 AAAAA-AT-ATCTTATTTACTTCAAAATAAAAATAAAATAATTA
19309841 AA
1 AA
19309843 TTAAGTTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 5 0.12
43 2 0.05
44 35 0.83
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (42 bp):
AAAAAATATCTTATTTACTTCAAAATAAAAATAAAATAATTA
Found at i:19325799 original size:22 final size:22
Alignment explanation
Indices: 19325774--19325821 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
19325764 TGGTAGCAGT
*
19325774 TTTGACAAATACCATTCTGTTA
1 TTTGACAAATACCATTCTATTA
***
19325796 TTTGGTTAATACCATTCTATTA
1 TTTGACAAATACCATTCTATTA
19325818 TTTG
1 TTTG
19325822 GTTTATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTGACAAATACCATTCTATTA
Found at i:19325822 original size:22 final size:22
Alignment explanation
Indices: 19325781--19325824 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19325771 AGTTTTGACA
*
19325781 AATACCATTCTGTTATTTGGTT
1 AATACCATTCTATTATTTGGTT
19325803 AATACCATTCTATTATTTGGTT
1 AATACCATTCTATTATTTGGTT
19325825 TATTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (22 bp):
AATACCATTCTATTATTTGGTT
Found at i:19327961 original size:23 final size:23
Alignment explanation
Indices: 19327934--19327979 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19327924 TAGACTCCAT
19327934 CCAGCTTCCTAAAGTCAAAATCC
1 CCAGCTTCCTAAAGTCAAAATCC
*
19327957 CCAGCTTTCTAAAGTCAAAATCC
1 CCAGCTTCCTAAAGTCAAAATCC
19327980 TACTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (23 bp):
CCAGCTTCCTAAAGTCAAAATCC
Found at i:19328023 original size:12 final size:12
Alignment explanation
Indices: 19328008--19328032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19327998 CTATCCTAAT
19328008 TAAAATCCAAAA
1 TAAAATCCAAAA
19328020 TAAAATCCAAAA
1 TAAAATCCAAAA
19328032 T
1 T
19328033 TCAAATGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAATCCAAAA
Found at i:19329203 original size:16 final size:17
Alignment explanation
Indices: 19329184--19329216 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19329174 GCAAAAAGAT
*
19329184 TACAAGTTAAC-CATAA
1 TACAAGTGAACACATAA
19329200 TACAAGTGAACACATAA
1 TACAAGTGAACACATAA
19329217 CATTACCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (17 bp):
TACAAGTGAACACATAA
Found at i:19347832 original size:13 final size:13
Alignment explanation
Indices: 19347814--19347838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19347804 TAATGGTATA
19347814 TTGAATCCATGAC
1 TTGAATCCATGAC
19347827 TTGAATCCATGA
1 TTGAATCCATGA
19347839 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:19348441 original size:27 final size:27
Alignment explanation
Indices: 19348382--19348557 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
19348372 TAAATTGTAC
19348382 AGCACTAAGTGTGCG-ATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
19348408 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
19348434 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
19348462 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
19348490 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
19348516 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
19348543 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19348558 GCTCAATATA
Statistics
Matches: 126, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
26 37 0.29
27 67 0.53
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:19354173 original size:27 final size:27
Alignment explanation
Indices: 19354143--19354321 Score: 191
Period size: 27 Copynumber: 6.6 Consensus size: 27
19354133 ATATTGAGCC
* * * *
19354143 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAGTCATAT
* * *
19354170 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCATAT
*
19354197 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCATA-T
** *
19354225 CGCACACTTAGTGCCGCATGGTCA-ATT
1 CGCACACTTAGTGCTACATAGTCATA-T
* *
19354252 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCATAT
*
19354279 CGCACACTTAGTGCAACATAGTCATAT
1 CGCACACTTAGTGCTACATAGTCATAT
19354306 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
19354322 TACAATTTAA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCATAT
Found at i:19354282 original size:82 final size:81
Alignment explanation
Indices: 19354169--19354319 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
19354159 TATAATCATC
* *
19354169 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
19354234 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* ** *
19354251 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
19354315 AGTGC
65 AGTGC
19354320 TATACAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:19354885 original size:13 final size:13
Alignment explanation
Indices: 19354867--19354891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19354857 TACTAAATTT
19354867 TCATGGATTCAAG
1 TCATGGATTCAAG
19354880 TCATGGATTCAA
1 TCATGGATTCAA
19354892 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:19365598 original size:51 final size:51
Alignment explanation
Indices: 19365543--19365642 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
19365533 CTACCACATA
*
19365543 ACATGTAA-CACATCCATAATGAACTC-GAACCACTCAACGAGTTCGGATGTT
1 ACATG-AATCACATCCATAATGAACTCAG-ACCACTCAACGAGCTCGGATGTT
* *
19365594 ACATGAATCGCATCCATCATGAACTCAGACCACTCAACGAGCTCGGATG
1 ACATGAATCACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATG
19365643 CTCGCATCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 2 0.05
51 41 0.93
52 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGTT
Found at i:19365649 original size:43 final size:43
Alignment explanation
Indices: 19365601--19365687 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
19365591 GTTACATGAA
*
19365601 TCGCATCCATCATGAACTCAGACCACTCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
* * *
19365644 TCGCATCTATAATGAACTCGGACCTCTCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
19365687 T
1 T
19365688 ACATAACTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
Found at i:19371517 original size:193 final size:191
Alignment explanation
Indices: 19371185--19371563 Score: 548
Period size: 193 Copynumber: 2.0 Consensus size: 191
19371175 GGGAAGAGTG
* * **
19371185 TGCTAATATGGGAAGATTAATGGATTATGATGTGTATGTTAATAAGATTAACCATTTTAGGTTGG
1 TGCTAATATGGGAAGATTAATGGATTAGGATGAGTATGTTAATAAGATTAACCAACTTAGGTTGG
* *
19371250 TGGATTCCGACTGTGCATATAAGAGTGGATGAAATTATAAACAGAGAGGAAATTTTGGGATTTGT
66 TGGATTCCGACTGTGCATATAAGAGTGGATCAAATTATAAACAGAGAGGAAAATTTGGGATTTGT
* * *
19371315 TTACCATTGGGCACTGATTATCTGTGATGGAAATAAGCATTTTATT-AGTATTCTAGTAGAGGA
131 TGACCATTGGGAACTGATTATCTAT-ATGGAAATAAGC-TTTT-TTGAGTATTCTAGTAGAGGA
19371378 TGCTAATATGGGAAGATTAATGGATTAGGATGCAG-ATGTTAATAAGATTAACCAACTTAGGTTG
1 TGCTAATATGGGAAGATTAATGGATTAGGATG-AGTATGTTAATAAGATTAACCAACTTAGGTTG
* * * * *
19371442 GTGGATTCGGACTTTGCTTATAAGAGTGGATCAAATTATAAAGAGGGAGGAAAATTTGGGATTT-
65 GTGGATTCCGACTGTGCATATAAGAGTGGATCAAATTATAAACAGAGAGGAAAATTTGGGATTTG
* *
19371506 TTCGGCCATTGGGAACTGGTTATCTATATGGAAATAAGCTTTTTTGAGTATTCTAGTA
130 TT-GACCATTGGGAACTGATTATCTATATGGAAATAAGCTTTTTTGAGTATTCTAGTA
19371564 AGGGATACTG
Statistics
Matches: 167, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
190 2 0.01
191 16 0.10
192 14 0.08
193 134 0.80
194 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (191 bp):
TGCTAATATGGGAAGATTAATGGATTAGGATGAGTATGTTAATAAGATTAACCAACTTAGGTTGG
TGGATTCCGACTGTGCATATAAGAGTGGATCAAATTATAAACAGAGAGGAAAATTTGGGATTTGT
TGACCATTGGGAACTGATTATCTATATGGAAATAAGCTTTTTTGAGTATTCTAGTAGAGGA
Found at i:19381003 original size:16 final size:16
Alignment explanation
Indices: 19380982--19381013 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19380972 TAATTGGTTG
*
19380982 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
19380998 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
19381014 GATTAATTGA
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:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:19394997 original size:35 final size:36
Alignment explanation
Indices: 19394928--19395046 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
19394918 CCATATACAA
*
19394928 ATATATATTACATATAACACAAAA-C-T-CACACAT
1 ATATATATTATATATAACACAAAACCATGCACACAT
*
19394961 ATATATATTATATATAACA-AAAACCATGCACCCAT
1 ATATATATTATATATAACACAAAACCATGCACACAT
*
19394996 ATTTATATTATATATATA-ACAAAACCATGCACACAT
1 ATATATATTATATATA-ACACAAAACCATGCACACAT
19395032 AT-TAATATTATATAT
1 ATAT-ATATTATATAT
19395047 GCACCTACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
32 4 0.05
33 19 0.25
34 1 0.01
35 23 0.30
36 29 0.38
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.33
Consensus pattern (36 bp):
ATATATATTATATATAACACAAAACCATGCACACAT
Found at i:19396294 original size:28 final size:29
Alignment explanation
Indices: 19396255--19396313 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
19396245 TGCTTCTAAC
*
19396255 TTTTGAACTTAA-TGACTAATTTATAAAT
1 TTTTGAACTTAAGTGACTAAATTATAAAT
* *
19396283 TTTTGAAGTTAAGTGATTAAATTATAAAT
1 TTTTGAACTTAAGTGACTAAATTATAAAT
19396312 TT
1 TT
19396314 ATTAATAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.47
Consensus pattern (29 bp):
TTTTGAACTTAAGTGACTAAATTATAAAT
Found at i:19408836 original size:17 final size:17
Alignment explanation
Indices: 19408810--19408842 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19408800 TAGTAAAGAT
19408810 ATATAAAATTA-TTAAC
1 ATATAAAATTAGTTAAC
19408826 ATATCAAAATTAGTTAA
1 ATAT-AAAATTAGTTAA
19408843 ATTATTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATAAAATTAGTTAAC
Found at i:19422663 original size:40 final size:40
Alignment explanation
Indices: 19422617--19422841 Score: 254
Period size: 40 Copynumber: 5.6 Consensus size: 40
19422607 CTTGCACAAG
* *
19422617 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
19422657 GCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * * * *
19422697 GCCTTCGAGTTTTAGCCCGAATATAATCGCTAGAACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
19422737 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
19422777 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
* *
19422818 GCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
19422842 CATTCGAATA
Statistics
Matches: 153, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 124 0.81
41 28 0.18
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:19422714 original size:80 final size:79
Alignment explanation
Indices: 19422581--19422841 Score: 258
Period size: 80 Copynumber: 3.3 Consensus size: 79
19422571 CTCAAGTAAT
* * * * * * *
19422581 CTTCGGGATTTAG-CCAGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTC-GGTCTTAGCCCGGATATAGT
*
19422644 CACTAGCATAAATGC
65 CACTAGCACAAATGC
* * * * *
19422659 CTTCGGGACTTAGCCCGGATATAATC-GCTAGCACAAATGCCTTCGAGTTTTAGCCCGAATATAA
1 CTTCGGGACTTAGCCCGGATAT-AGCAACTAGCACAAATGCCTTCG-GTCTTAGCCCGGATATAG
* *
19422723 TCGCTAGAACAAATGC
64 TCACTAGCACAAATGC
* * * * *
19422739 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGG-TCTTAGCCCGGATATAGT
*
19422804 CACCTAGCACAAAAGC
65 CA-CTAGCACAAATGC
*
19422820 CTTCGGGACTTAGCCCAGATAT
1 CTTCGGGACTTAGCCCGGATAT
19422842 CATTCGAATA
Statistics
Matches: 148, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
78 12 0.08
79 17 0.11
80 88 0.59
81 31 0.21
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:19443913 original size:92 final size:92
Alignment explanation
Indices: 19443756--19444033 Score: 529
Period size: 92 Copynumber: 3.0 Consensus size: 92
19443746 CTATACATGC
19443756 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
1 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
19443821 CCTATCCCGATTCTCAGGCCGGCTTGT
66 CCTATCCCGATTCTCAGGCCGGCTTGT
19443848 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
1 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
19443913 CCTATCCCGATTCTCAGGCCGGCTTGT
66 CCTATCCCGATTCTCAGGCCGGCTTGT
19443940 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
1 CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
* * *
19444005 CCTATCTCGATTCTCAAGTCGGCTTGT
66 CCTATCCCGATTCTCAGGCCGGCTTGT
19444032 CA
1 CA
19444034 AACCTACAAT
Statistics
Matches: 183, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 183 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (92 bp):
CACATTCAAAATATACAAGCCATTTTACCAATTTAGGTCTTTGGATAGTGTGAACGAGCCTTCGA
CCTATCCCGATTCTCAGGCCGGCTTGT
Found at i:19444894 original size:19 final size:20
Alignment explanation
Indices: 19444857--19444900 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
19444847 CGAGCCTATT
19444857 CCTCGTAAACTTTGTTTTTC
1 CCTCGTAAACTTTGTTTTTC
19444877 CCTCGTAAACTTTGTTTTTC
1 CCTCGTAAACTTTGTTTTTC
19444897 CCTC
1 CCTC
19444901 AATCACGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.30, G:0.09, T:0.48
Consensus pattern (20 bp):
CCTCGTAAACTTTGTTTTTC
Found at i:19454555 original size:43 final size:42
Alignment explanation
Indices: 19454489--19454577 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
19454479 AGCTTGTACC
* * *
19454489 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATAT-G
*
19454532 ATGCC-ACTGTCCCAGATAGGGTCTTACACGAAATCAAATATG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGAAATCAAATATG
19454574 ATGC
1 ATGC
19454578 TGATGTTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 7 0.17
43 34 0.83
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATG
Found at i:19456963 original size:42 final size:42
Alignment explanation
Indices: 19456861--19457005 Score: 139
Period size: 42 Copynumber: 3.4 Consensus size: 42
19456851 AGCTCGTACA
* * ** * *
19456861 ATGCCAAAGTCCCAGACGAGGTCTTACATGTAATTGAATATCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACATAAAT-CATATCG
*
19456904 ATGCCACTGTCCCAGACAAGGTCTTACACA-AAATCATATACG
1 ATGCCAATGTCCCAGACAAGGTCTTACACATAAATCATAT-CG
* * * *
19456946 ATGCCAATGTCCTAGACATGGTCTTACACATAAATCTCAAATCA
1 ATGCCAATGTCCCAGACAAGGTCTTACACATAAA--TCATATCG
*
19456990 ATGCCAACGTCCCAGA
1 ATGCCAATGTCCCAGA
19457006 TGTGGCCTTA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.05
42 32 0.38
43 28 0.33
44 15 0.18
45 5 0.06
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACATAAATCATATCG
Found at i:19468250 original size:12 final size:12
Alignment explanation
Indices: 19468235--19468300 Score: 71
Period size: 12 Copynumber: 5.4 Consensus size: 12
19468225 AAGAAACATT
*
19468235 ATCAGAACTAGA
1 ATCAGAATTAGA
*
19468247 ATCAAAATTAGA
1 ATCAGAATTAGA
19468259 ATCAGAATTAG-
1 ATCAGAATTAGA
* *
19468270 GTGACAGAATCAGA
1 AT--CAGAATTAGA
19468284 ATCAGAATTAGA
1 ATCAGAATTAGA
19468296 ATCAG
1 ATCAG
19468301 TATCAAGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 1 0.02
12 34 0.77
13 8 0.18
14 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (12 bp):
ATCAGAATTAGA
Found at i:19468318 original size:31 final size:31
Alignment explanation
Indices: 19468283--19468360 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
19468273 ACAGAATCAG
*
19468283 AATCAGAATTAGAATCAGTATCAAGTAACAA
1 AATCAAAATTAGAATCAGTATCAAGTAACAA
* * * * *
19468314 AATCAAAATCATAATCAGTATTAGGTAACAG
1 AATCAAAATTAGAATCAGTATCAAGTAACAA
19468345 AATCAAAAATTAGAAT
1 AATC-AAAATTAGAAT
19468361 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 29 0.76
32 9 0.24
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (31 bp):
AATCAAAATTAGAATCAGTATCAAGTAACAA
Found at i:19468318 original size:37 final size:37
Alignment explanation
Indices: 19468244--19468324 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
19468234 TATCAGAACT
* * * *
19468244 AGAATCAAAATTAGAATCAGAATTAGGTGACAGAATC
1 AGAATCAAAATTAGAATCAGAATCAAGTAACAAAATC
* *
19468281 AGAATCAGAATTAGAATCAGTATCAAGTAACAAAATC
1 AGAATCAAAATTAGAATCAGAATCAAGTAACAAAATC
*
19468318 AAAATCA
1 AGAATCA
19468325 TAATCAGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (37 bp):
AGAATCAAAATTAGAATCAGAATCAAGTAACAAAATC
Found at i:19468539 original size:27 final size:26
Alignment explanation
Indices: 19468497--19468596 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 26
19468487 GCTCAGTTAT
* *
19468497 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
19468524 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
19468550 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
19468578 CAGATAATGTGGCAAAGCC
1 CAGATATTGTGGCAGAGCC
19468597 GCTTAACAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
26 7 0.11
27 51 0.77
28 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:19468793 original size:22 final size:22
Alignment explanation
Indices: 19468757--19468821 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
19468747 GCAAATACGT
19468757 TTGGCACACAA-CCATAATCAGG
1 TTGGCACA-AAGCCATAATCAGG
* *
19468779 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
19468801 TTGACAGAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
19468822 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:19469304 original size:27 final size:27
Alignment explanation
Indices: 19469248--19469441 Score: 219
Period size: 27 Copynumber: 7.2 Consensus size: 27
19469238 GGGCAAAATG
* * * * *
19469248 GTAATTTTACCCCACA-AGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
19469274 GTAATTCCACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
19469301 GTAATTCTACCCTACAGAGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
19469328 GTAATTCTACCCTACAGGGGTATTGCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * **
19469355 ATAATTCTACCCTACAAGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
19469382 GTAATTCTACCCTGCAGGGGTATTCCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
19469409 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
19469436 GTAATT
1 GTAATT
19469442 TTGTAAATCG
Statistics
Matches: 138, Mismatches: 29, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
26 13 0.09
27 125 0.91
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:19469334 original size:54 final size:53
Alignment explanation
Indices: 19469248--19469441 Score: 253
Period size: 54 Copynumber: 3.6 Consensus size: 53
19469238 GGGCAAAATG
* * * * **
19469248 GTAATTTTACCCCACAAGGTATCTCGGTAATTCCACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCA
*
19469301 GTAATTCTACCCTACAGAGGTATTTCGGTAATTCTACCCTACAGGGGTATTGCA
1 GTAATTCTACCCTACA-AGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCA
* * *
19469355 ATAATTCTACCCTACAAGGGTATTTTGGTAATTCTACCCTGCAGGGGTATTCCA
1 GTAATTCTACCCTACAA-GGTATTTCGGTAATTCTACCCTACAGGGGTATTCCA
* *
19469409 GTAATTCTACCTTACAGGGGTATTTCGGTAATT
1 GTAATTCTACCCTACA-AGGTATTTCGGTAATT
19469442 TTGTAAATCG
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
53 15 0.12
54 109 0.88
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (53 bp):
GTAATTCTACCCTACAAGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCA
Found at i:19469441 original size:81 final size:81
Alignment explanation
Indices: 19469248--19469441 Score: 246
Period size: 81 Copynumber: 2.4 Consensus size: 81
19469238 GGGCAAAATG
* * * * *
19469248 GTAATTTTACCCCACA-AGGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCCACCCTACAAGGGTATTTTAGTAATTCTACC
* *
19469312 CTACAGAGGTATTTCG
66 CTACAGAGGTATTCCA
* ** * *
19469328 GTAATTCTACCCTACAGGGGTATTGCAATAATTCTACCCTACAAGGGTATTTTGGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCCACCCTACAAGGGTATTTTAGTAATTCTACC
* *
19469393 CTGCAGGGGTATTCCA
66 CTACAGAGGTATTCCA
*
19469409 GTAATTCTACCTTACAGGGGTATTTCGGTAATT
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATT
19469442 TTGTAAATCG
Statistics
Matches: 95, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
80 14 0.15
81 81 0.85
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (81 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCCACCCTACAAGGGTATTTTAGTAATTCTACC
CTACAGAGGTATTCCA
Found at i:19469464 original size:27 final size:27
Alignment explanation
Indices: 19469434--19469511 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
19469424 AGGGGTATTT
*
19469434 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CGGTAATTTTATAAATCGAGGGTAAAA
* * ***
19469461 CGGTAATTCTATAAATCAAGGGTACTT
1 CGGTAATTTTATAAATCGAGGGTAAAA
* *
19469488 TGGTAATTTTATAAGTCGAGGGTA
1 CGGTAATTTTATAAATCGAGGGTA
19469512 TTTCAATAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (27 bp):
CGGTAATTTTATAAATCGAGGGTAAAA
Found at i:19469521 original size:27 final size:27
Alignment explanation
Indices: 19469491--19469582 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
19469481 GGTACTTTGG
*
19469491 TAATTTTATAAGTCGAGGGTATTTCAA
1 TAATTTTACAAGTCGAGGGTATTTCAA
* * *
19469518 TAATTTTACAGGTCGAGGGTATTTTAG
1 TAATTTTACAAGTCGAGGGTATTTCAA
* * ***
19469545 TAATTTCACAAATC-ATGGGTATTTTTG
1 TAATTTTACAAGTCGA-GGGTATTTCAA
19469572 TAATTTTACAA
1 TAATTTTACAA
19469583 ACTAGGGGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 54 0.98
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGGTATTTCAA
Found at i:19469548 original size:81 final size:80
Alignment explanation
Indices: 19469462--19469820 Score: 335
Period size: 81 Copynumber: 4.4 Consensus size: 80
19469452 AGGGTAAAAC
* * * * * *
19469462 GGTAATTCTATAAATCAAGGGTACTTTGGTAATTTTATAAGTCGAGGGTATTTCAATAATTTTAC
1 GGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAA-ACAAGGGTATTTTAATAATTTTAC
** *
19469527 -AGGTCGAGGGTATTTT
65 AAACTAG-GGGTATTTT
* * * * * * * *
19469543 AGTAATTTCACAAATCATGGGTATTTTTGTAATTTTACAAACTAGGGGTATTTTGATGATTTTAC
1 GGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAAC-AAGGGTATTTTAATAATTTTAC
19469608 AAACTAGGGGTATTTT
65 AAACTAGGGGTATTTT
* *
19469624 GGTAATTTTACAAA-CCAGAGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTA
1 GGTAATTTTACAAATCAAG-GGTATTTTGGTAATTTTATAAAC-AAGGGTATTTTAATAATTTTA
19469688 CAAACTAGGGGTATTTT
64 CAAACTAGGGGTATTTT
** * * * * ** * *
19469705 GGTAATTTTGTAAACCAAGGGTATTTTGGTAAATTTACAAACCAGGGGTATTTTGGTGATTTTAT
1 GGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAA-CAAGGGTATTTTAATAATTTTAC
* *
19469770 AAACCAAGGGTATTTT
65 AAACTAGGGGTATTTT
* * * *
19469786 AGTAATTTTATAAACCAGGGGTATTTTGGTAATTT
1 GGTAATTTTACAAATCAAGGGTATTTTGGTAATTT
19469821 GGTAAACTAA
Statistics
Matches: 230, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
80 3 0.01
81 220 0.96
82 7 0.03
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (80 bp):
GGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACAAGGGTATTTTAATAATTTTACA
AACTAGGGGTATTTT
Found at i:19469827 original size:27 final size:27
Alignment explanation
Indices: 19469534--19469820 Score: 358
Period size: 27 Copynumber: 10.6 Consensus size: 27
19469524 TACAGGTCGA
* * * *
19469534 GGGTATTTTAGTAATTTCACAAATCAT
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
19469561 GGGTATTTTTGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
19469588 GGGTATTTTGATGATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
19469615 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * * *
19469642 AGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
19469669 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
19469696 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
*
19469723 GGGTATTTTGGTAAATTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
19469750 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
19469777 GGGTATTTTAGTAATTTTATAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
19469804 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
19469821 GGTAAACTAA
Statistics
Matches: 223, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 223 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:19469827 original size:54 final size:54
Alignment explanation
Indices: 19469480--19469820 Score: 396
Period size: 54 Copynumber: 6.3 Consensus size: 54
19469470 TATAAATCAA
* ** * * * ***
19469480 GGGTACTTTGGTAATTTTATAAGTCGAGGGTATTTCAATAATTTTACAGGTC-G
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* * * * * * *
19469533 AGGGTATTTTAGTAATTTCACAAATCATGGGTATTTTTGTAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* * * * * *
19469588 GGGTATTTTGATGATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* * *
19469642 AGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* * *
19469696 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAAATTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* *
19469750 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
19469804 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
19469821 GGTAAACTAA
Statistics
Matches: 243, Mismatches: 43, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
54 242 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
Found at i:19476464 original size:43 final size:43
Alignment explanation
Indices: 19476398--19476556 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
19476388 AGCTCGTACA
*
19476398 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGTAATCAAATATCG
* * *
19476441 ATGCC-ACTGTCCCAGACAGGGTCTTAAACGAAATCAAATA-CA
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGTAATCAAATATCG
* * * * *
19476483 ATGTCGATGTCCCAGACATGGTCTTACACGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGT-AATCA-AATATCG
19476527 ATGCCAACGTCCCAGAC-GTGGTCTTACACG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACG
19476557 AGAACACATC
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 27 0.28
43 40 0.42
44 28 0.29
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGTAATCAAATATCG
Found at i:19482272 original size:21 final size:22
Alignment explanation
Indices: 19482248--19482288 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19482238 TAGCATCATC
*
19482248 ACCAAA-ACAGTTAAAACCATA
1 ACCAAACACAGTCAAAACCATA
*
19482269 ACCAAACATAGTCAAAACCA
1 ACCAAACACAGTCAAAACCA
19482289 AACTCAGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.56, C:0.27, G:0.05, T:0.12
Consensus pattern (22 bp):
ACCAAACACAGTCAAAACCATA
Found at i:19484829 original size:42 final size:42
Alignment explanation
Indices: 19484699--19484834 Score: 105
Period size: 42 Copynumber: 3.2 Consensus size: 42
19484689 GTCCCAGACG
* ** * * * *
19484699 TGGTCTTACATGGGATCTCACATTGATGCCATATCTAAGATA
1 TGGTCTTACACGAAATCTCATATCGACGCCATATCTCAGATA
* * * * * * * *
19484741 TGGTCTTATATGAAATCTCATTTCGATGACATGTC-CTTGATG
1 TGGTCTTACACGAAATCTCATATCGACGCCATATCTC-AGATA
19484783 TGGTCTTACACGAAATCTCATATC-AGCGCCATATCTCAGATA
1 TGGTCTTACACGAAATCTCATATCGA-CGCCATATCTCAGATA
19484825 TGGTCTTACA
1 TGGTCTTACA
19484835 TGATAACACA
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (42 bp):
TGGTCTTACACGAAATCTCATATCGACGCCATATCTCAGATA
Found at i:19487489 original size:47 final size:48
Alignment explanation
Indices: 19487414--19487545 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 48
19487404 CTCAGTCGAT
* * * *
19487414 AAGTACCTATACCATGGCCCATAACCAAATCAAGGTAATTTATCT-CG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCCA
* * * * *
19487461 GAGTACCTATACTATGGCCCCTAGCCAAATTAAGGTAACTCCTCTCCA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCCA
* *
19487509 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
19487546 TAACTCGCAC
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
47 37 0.53
48 33 0.47
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCCA
Found at i:19487683 original size:21 final size:22
Alignment explanation
Indices: 19487657--19487707 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
19487647 TTTCCAATAC
*
19487657 CAAATCATAGTCGAATCA-TTT
1 CAAATCATAGTAGAATCATTTT
*
19487678 CAAATCATTGTAGAATCATTTT
1 CAAATCATAGTAGAATCATTTT
19487700 CAAATCAT
1 CAAATCAT
19487708 GGTCCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
CAAATCATAGTAGAATCATTTT
Found at i:19488568 original size:58 final size:58
Alignment explanation
Indices: 19488478--19488593 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
19488468 TTTTTTTTAT
*
19488478 TTTATTAACCTTTATTTGTCTTATTACTAATTTACCATTAAAAATAATGCTTATTCAC
1 TTTATTAACCTTTATTTGTCTTATTACTAATTTACCATTAAAAATAATGCATATTCAC
19488536 TTTATTAACCTTTATTTGTCTTATTACTAATTTACCATTAAAAATAATGCATATTCAC
1 TTTATTAACCTTTATTTGTCTTATTACTAATTTACCATTAAAAATAATGCATATTCAC
19488594 ACAAATGCCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (58 bp):
TTTATTAACCTTTATTTGTCTTATTACTAATTTACCATTAAAAATAATGCATATTCAC
Found at i:19492999 original size:11 final size:11
Alignment explanation
Indices: 19492983--19493007 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19492973 ATATGATATT
19492983 TTATTATTTTA
1 TTATTATTTTA
19492994 TTATTATTTTA
1 TTATTATTTTA
19493005 TTA
1 TTA
19493008 GTATATATAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:19497202 original size:27 final size:27
Alignment explanation
Indices: 19497149--19497207 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
19497139 GCATCTAATA
*
19497149 CTGATTCTGTATTGGGCTAAGGCCCAC
1 CTGATTCTGTAATGGGCTAAGGCCCAC
19497176 CTGATTCTGTTAATGGGCTAAGG-CCAC
1 CTGATTCTG-TAATGGGCTAAGGCCCAC
19497203 CTGAT
1 CTGAT
19497208 ACTATTTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (27 bp):
CTGATTCTGTAATGGGCTAAGGCCCAC
Found at i:19507030 original size:26 final size:27
Alignment explanation
Indices: 19506989--19507047 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
19506979 TAAGTTGTAT
*
19506989 AATTACTAAAATACCCTTATAGGGTAG
1 AATTACTAAAATACCCTTATAGGGTAA
* * *
19507016 AATTAC-AAGATACCCTTGTGGGGTAA
1 AATTACTAAAATACCCTTATAGGGTAA
19507042 AATTAC
1 AATTAC
19507048 CATTTGCCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (27 bp):
AATTACTAAAATACCCTTATAGGGTAA
Found at i:19508835 original size:40 final size:40
Alignment explanation
Indices: 19508751--19508934 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
19508741 TTGAATGCTG
* * * *
19508751 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
19508790 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
19508831 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
19508871 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
19508911 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19508935 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:19508888 original size:80 final size:81
Alignment explanation
Indices: 19508751--19508931 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
19508741 TTGAATGCTG
* *
19508751 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
19508815 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
19508831 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
19508892 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
19508911 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
19508932 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:19516757 original size:40 final size:40
Alignment explanation
Indices: 19516673--19516855 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
19516663 TTGAATGCTG
* * * *
19516673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
19516712 ATCCGGACTAAGAT-CCGAATGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
19516753 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
*
19516793 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
19516832 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19516856 GTATGAGTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 35 0.29
40 76 0.62
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:19516849 original size:79 final size:81
Alignment explanation
Indices: 19516673--19516852 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
19516663 TTGAATGCTG
* * *
19516673 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAATGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
*
19516737 TGTGCGAGTTATTAAT
66 TGTGCGAGTTATTAAA
**
19516753 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
19516814 A-TTGTGCGAGTT-TTAAAA
63 ATTTGTGCGAGTTATT-AAA
19516832 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
19516853 ATTGTATGAG
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
78 2 0.02
79 36 0.40
80 42 0.47
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTATTAAA
Found at i:19516864 original size:39 final size:38
Alignment explanation
Indices: 19516673--19516892 Score: 165
Period size: 40 Copynumber: 5.6 Consensus size: 38
19516663 TTGAATGCTG
* * * * *
19516673 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGT-TCTAAA
** * * *
19516713 TCCGGACTAAGAT-CCGAATGCATTTGTGCGAGTTATTAAT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTT-CTAAA
* * *
19516753 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAG-TTCTAAA
*
19516793 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTCT-AAA
**
19516832 TCCGGGTTAAGTCCCGAAGGCATTGTATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTT-CTA-AA
* * *
19516872 -CCGGGCTATGTCTCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
19516893 CTTGAACGAG
Statistics
Matches: 147, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.01
39 63 0.43
40 73 0.50
41 9 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTCTAAA
Found at i:19520321 original size:69 final size:68
Alignment explanation
Indices: 19520247--19520466 Score: 228
Period size: 69 Copynumber: 3.2 Consensus size: 68
19520237 CTTTCAATTG
*
19520247 TAATATCAAGGCTCGCAAGTGAAGAGTCATAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCCCA
1 TAATATCAAGGCTC-CAAGTGAAGAGTCGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCCCA
*
19520312 GCTA
65 ACTA
* * *
19520316 TAATATCAAGGCT-CATAGTTTAAGAGTTGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAGCTCCC
1 TAATATCAAGGCTCCA-AG-TGAAGAGTCGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCCC
*
19520380 AACTG
64 AACTA
* * * * * * * *
19520385 TAAGACCAAGGCT-CATAGGCGAAGAGTCGTAGCCTCCAAAATAGTTAGCGAGAGTAAAGCTCTC
1 TAATATCAAGGCTCCA-A-GTGAAGAGTCGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCCC
* *
19520449 AATTG
64 AACTA
*
19520454 TAAGATCAAGGCT
1 TAATATCAAGGCT
19520467 TGCAAGCAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
67 2 0.02
68 2 0.02
69 126 0.96
70 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (68 bp):
TAATATCAAGGCTCCAAGTGAAGAGTCGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCCCAA
CTA
Found at i:19520557 original size:69 final size:67
Alignment explanation
Indices: 19520245--19520576 Score: 218
Period size: 69 Copynumber: 4.8 Consensus size: 67
19520235 AGCTTTCAAT
* * * * * * * *
19520245 TGTAATATCAAGGCTCGCAAGTGAAGAGTCATAGCCTCCAAAAAAGTTAGCAAGAGCAAAACTCC
1 TGTAAGATCAAGGCTCACAAGCGAAGA-AC-TAACCTCCAAAATAGTTAGCAAGAGTAAAGCTCC
*
19520310 CAGC
64 CAAC
* * * ** ** * * *
19520314 TATAATATCAAGGCTCA-TAGTTTAAGAGTTGTAGCCTCCAAAAAAGTTAGCAAGAGCAAAGCTC
1 TGTAAGATCAAGGCTCACAAG-CGAAGA--ACTAACCTCCAAAATAGTTAGCAAGAGTAAAGCTC
19520378 CCAAC
63 CCAAC
* * * * * * *
19520383 TGTAAGACCAAGGCTCATAGGCGAAGAGTCGTAGCCTCCAAAATAGTTAGCGAGAGTAAAGCTCT
1 TGTAAGATCAAGGCTCACAAGCGAAGA-AC-TAACCTCCAAAATAGTTAGCAAGAGTAAAGCTCC
*
19520448 CAAT
64 CAAC
** * * * *
19520452 TGTAAGATCAAGGCTTGCAAGC-AAAAAGCTGCAACCTCTAAAACAGTTAGCGAGAGTAAAGCTC
1 TGTAAGATCAAGGCTCACAAGCGAAGAA-CT--AACCTCCAAAATAGTTAGCAAGAGTAAAGCTC
19520516 CCAAC
63 CCAAC
* * *
19520521 TGTAAGATTAAGGCTCACAAACGAAGAACTAAAACCTCCAGAATAGTTAGCAAGAG
1 TGTAAGATCAAGGCTCACAAGCGAAGAACT--AACCTCCAAAATAGTTAGCAAGAG
19520577 CAAGGCTTCT
Statistics
Matches: 210, Mismatches: 45, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
67 1 0.00
68 7 0.03
69 196 0.93
70 6 0.03
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (67 bp):
TGTAAGATCAAGGCTCACAAGCGAAGAACTAACCTCCAAAATAGTTAGCAAGAGTAAAGCTCCCA
AC
Found at i:19525085 original size:46 final size:46
Alignment explanation
Indices: 19524971--19525086 Score: 223
Period size: 46 Copynumber: 2.5 Consensus size: 46
19524961 CACAAATCCA
*
19524971 GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
19525017 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
19525063 GACTCAACTCAACGAGTTCGGATG
1 GACTCAACTCAACGAGTTCGGATG
19525087 CCCAAATATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
Found at i:19528382 original size:18 final size:18
Alignment explanation
Indices: 19528359--19528394 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19528349 ATTCGCAACT
19528359 TTCATTTATCATG-CATTA
1 TTCATTTA-CATGTCATTA
19528377 TTCATTTACATGTCATTA
1 TTCATTTACATGTCATTA
19528395 CAATCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
TTCATTTACATGTCATTA
Found at i:19530424 original size:46 final size:46
Alignment explanation
Indices: 19530310--19530425 Score: 214
Period size: 46 Copynumber: 2.5 Consensus size: 46
19530300 CACAAATCCA
* *
19530310 GACTCAACTCAATGAGTTCGGACGTTCGCATCCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
19530356 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
19530402 GACTCAACTCAACGAGTTCGGATG
1 GACTCAACTCAACGAGTTCGGATG
19530426 CCCAAATATC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (46 bp):
GACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCG
Found at i:19548951 original size:26 final size:26
Alignment explanation
Indices: 19548921--19548975 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
19548911 TGAATGCCCA
19548921 TTTAGTTCTGTCTAATGATATCTTGG
1 TTTAGTTCTGTCTAATGATATCTTGG
19548947 TTTAGTTCTGTCTAATGATATCTTGG
1 TTTAGTTCTGTCTAATGATATCTTGG
19548973 TTT
1 TTT
19548976 GTGCCGAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (26 bp):
TTTAGTTCTGTCTAATGATATCTTGG
Found at i:19548987 original size:26 final size:26
Alignment explanation
Indices: 19548932--19548987 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
19548922 TTAGTTCTGT
* * *
19548932 CTAATGATATCTTGGTTTAGTTCTGT
1 CTAATGATATCTTGGTTTAGTGCCGA
19548958 CTAATGATATCTTGGTTT-GTGCCGAA
1 CTAATGATATCTTGGTTTAGTGCCG-A
19548984 CTAA
1 CTAA
19548988 AAGCAAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (26 bp):
CTAATGATATCTTGGTTTAGTGCCGA
Found at i:19551661 original size:42 final size:43
Alignment explanation
Indices: 19551543--19551677 Score: 148
Period size: 42 Copynumber: 3.1 Consensus size: 43
19551533 GGAATGTGAA
* * *
19551543 CATCGATCTGAGATATCGTGTAAGACTGTGTTTGGGACACAGG
1 CATCGATCTGAGATTTCGTGTAAGACCGTGTCTGGGACACAGG
* * * * *
19551586 CTTCGATTTGAGATTTACTTGTAAGACCATGTCTGGGACATAGG
1 CATCGATCTGAGATTT-CGTGTAAGACCGTGTCTGGGACACAGG
* *
19551630 CATCGCATCT-A-ATTTCGTGTAAGACCGTGTCTGAGACAGAGG
1 CATCG-ATCTGAGATTTCGTGTAAGACCGTGTCTGGGACACAGG
19551672 CATCGA
1 CATCGA
19551678 AACTGAATTA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 28 0.37
43 17 0.22
44 27 0.36
45 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CATCGATCTGAGATTTCGTGTAAGACCGTGTCTGGGACACAGG
Found at i:19551705 original size:43 final size:42
Alignment explanation
Indices: 19551600--19551705 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
19551590 GATTTGAGAT
* * * * *
19551600 TTACTTGTAAGACCATGTCTGGGACATAGGCATCGCATCTAA
1 TTACATGTAAGACCATGTCTGAGACAGAGGCATCGAAACTAA
* * *
19551642 TTTCGTGTAAGACCGTGTCTGAGACAGAGGCATCGAAACTGAA
1 TTACATGTAAGACCATGTCTGAGACAGAGGCATCGAAACT-AA
*
19551685 TTACATGTAAGACCACGTCTG
1 TTACATGTAAGACCATGTCTG
19551706 GAACGTCGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 33 0.63
43 19 0.37
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGAGACAGAGGCATCGAAACTAA
Found at i:19555882 original size:16 final size:16
Alignment explanation
Indices: 19555859--19555912 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
19555849 TATTTGGGGG
19555859 ATCAAATTGAGAAGTT
1 ATCAAATTGAGAAGTT
*
19555875 ACCAAATTGAGAAGTT
1 ATCAAATTGAGAAGTT
* *
19555891 ATCAATTTTAGAAGTT
1 ATCAAATTGAGAAGTT
19555907 ATCAAA
1 ATCAAA
19555913 GTATGGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (16 bp):
ATCAAATTGAGAAGTT
Found at i:19560778 original size:25 final size:25
Alignment explanation
Indices: 19560740--19560789 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
19560730 TGTGTAAGGT
19560740 TTGAGGTCAAATTGAATGAATGTGC
1 TTGAGGTCAAATTGAATGAATGTGC
* *
19560765 TTGAGGTCAGATTGAATGGATGTGC
1 TTGAGGTCAAATTGAATGAATGTGC
19560790 CTTACATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (25 bp):
TTGAGGTCAAATTGAATGAATGTGC
Found at i:19562620 original size:24 final size:24
Alignment explanation
Indices: 19562593--19562640 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19562583 ACACATAAGT
19562593 GCCACATATACGTACGTAGCTAAA
1 GCCACATATACGTACGTAGCTAAA
19562617 GCCACATATACGTACGTAGCTAAA
1 GCCACATATACGTACGTAGCTAAA
19562641 ACACTCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (24 bp):
GCCACATATACGTACGTAGCTAAA
Found at i:19565375 original size:39 final size:39
Alignment explanation
Indices: 19565332--19565447 Score: 151
Period size: 39 Copynumber: 3.0 Consensus size: 39
19565322 CCGTACATAT
* * *
19565332 TTCCAGCACGTAGCCTGCGGACCTTAAATATGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAATACGGATATAA
* * * *
19565371 TTCCAGCACATAGCCTGTGGGCCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAATACGGATATAA
* *
19565410 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAATACGGATATA
19565448 CATCACTGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAATACGGATATAA
Found at i:19569829 original size:53 final size:53
Alignment explanation
Indices: 19569634--19569888 Score: 250
Period size: 55 Copynumber: 4.8 Consensus size: 53
19569624 ATTAGGGTTT
* * *
19569634 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAAGTTTCTACGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGT-AAGTTTATAAGGC
* * *
19569689 AAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TATAAGGC
* * *
19569744 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTTATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTATAAGGC
* * * ** *
19569797 AAGGATATCATGTAAGACAATGTCAAGACATGGCAACGGTAAGTTT-CAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTATAAGGC
* * * * *
19569846 AAGGATACCACGTAAGACTATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
19569889 GTACCCGTGT
Statistics
Matches: 169, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
49 37 0.22
52 6 0.04
53 46 0.27
54 5 0.03
55 71 0.42
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTATAAGGC
Found at i:19569840 original size:108 final size:110
Alignment explanation
Indices: 19569641--19569841 Score: 325
Period size: 108 Copynumber: 1.8 Consensus size: 110
19569631 TTTAAGGATA
* *
19569641 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAAGTTTCTACGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAAGTTTATAAGGCAAGGATATCATGTAAGA
* **
19569706 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CAATGTCAAGACATGGCAACGATAAGTTACTATAAGGCAAAGGTC
*
19569751 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGT-GAGTTTATAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAAGTTTATAAGGCAAGGATATCATGTAAGA
*
19569814 CAATGTCAAGACATGGCAACGGTAAGTT
66 CAATGTCAAGACATGGCAACGATAAGTT
19569842 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 51 0.61
109 6 0.07
110 27 0.32
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAAGTTTATAAGGCAAGGATATCATGTAAGA
CAATGTCAAGACATGGCAACGATAAGTTACTATAAGGCAAAGGTC
Found at i:19573496 original size:40 final size:39
Alignment explanation
Indices: 19573452--19573682 Score: 105
Period size: 39 Copynumber: 5.9 Consensus size: 39
19573442 TCACCACCCA
*
19573452 AAAGCATGCAGGACTTTAAGACCAGATATAATACCAGCAC
1 AAAGCATGCAGGACTTT-AGACCAGATATAACACCAGCAC
* * * *
19573492 AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCAC
1 AAAGCATGCAGGACTTTAGACCAGATATAACACCAGCAC
* * * * * * *
19573531 GAATGCCTTCGGGGC-TTAG-CTCGGATATAACACCAACAC
1 -AAAGCATGCAGGACTTTAGAC-CAGATATAACACCAGCAC
* * * * *
19573570 GAATGCCTTCGGGAC-TTAG-CCTGGATATAACACCAGCAC
1 -AAAGCATGCAGGACTTTAGACC-AGATATAACACCAGCAC
* * * * *
19573609 GAATGCCTTCAGGAC-TTAGCCCGGATATAACACCAGCAC
1 -AAAGCATGCAGGACTTTAGACCAGATATAACACCAGCAC
* * * * * *
19573648 GGATGCCTTCAGGAC-TTAGCCCGGATATAACACCA
1 -AAAGCATGCAGGACTTTAGACCAGATATAACACCA
19573683 ACACGAATGC
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 144 0.83
40 28 0.16
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (39 bp):
AAAGCATGCAGGACTTTAGACCAGATATAACACCAGCAC
Found at i:19573528 original size:39 final size:39
Alignment explanation
Indices: 19573476--19573721 Score: 359
Period size: 39 Copynumber: 6.3 Consensus size: 39
19573466 TTTAAGACCA
* * *
19573476 GATATAATACCAGCAC-AAAGCCTGCGGGACTTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCG
* *
19573515 GATATAACACCAGCACGAATGCCTTCGGGGCTTAGCTCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* *
19573554 GATATAACACCAACACGAATGCCTTCGGGACTTAGCCTG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
19573593 GATATAACACCAGCACGAATGCCTTCAGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* *
19573632 GATATAACACCAGCACGGATGCCTTCAGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* * *
19573671 GATATAACACCAACACGAATGCCTTTGGGACTTAGCCCA
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
19573710 GATATAACACCA
1 GATATAACACCA
19573722 TTATAAAGTC
Statistics
Matches: 188, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 177 0.94
40 11 0.06
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
Found at i:19573835 original size:28 final size:28
Alignment explanation
Indices: 19573794--19573866 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
19573784 ATTTAATCAT
* *
19573794 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATCTCGCACACTAAGTGTCATTC
* * *
19573822 TTAATATCTCGCACATTAAGTGTCTTTC
1 TCAATATCTCGCACACTAAGTGTCATTC
* *
19573850 TCAATATTTCGTACACT
1 TCAATATCTCGCACACT
19573867 GAGTACCATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (28 bp):
TCAATATCTCGCACACTAAGTGTCATTC
Found at i:19581069 original size:20 final size:20
Alignment explanation
Indices: 19581003--19581069 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
19580993 ATTTTAGTAA
* *
19581003 ACATGGTATGTATAATATGC
1 ACATGATATGTATGATATGC
* *
19581023 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
19581043 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
19581063 ACATGAT
1 ACATGAT
19581070 GTATTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:19581148 original size:25 final size:25
Alignment explanation
Indices: 19581120--19581199 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
19581110 AGGAAGTGTA
19581120 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
19581145 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
19581169 AAAGGGCTTATGCCCCAGTTATATGAT
1 AAAGGGCTTATGCCCCAG-T-TATGAT
19581196 AAAG
1 AAAG
19581200 CAGTTATTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.36
25 24 0.48
26 4 0.08
27 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:19581177 original size:24 final size:24
Alignment explanation
Indices: 19581118--19581190 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
19581108 GGAGGAAGTG
19581118 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
19581142 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
19581167 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
19581191 ATGATAAAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 23 0.50
25 23 0.50
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:19581419 original size:31 final size:31
Alignment explanation
Indices: 19581384--19581447 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
19581374 CATTTACATT
19581384 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
19581415 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
19581446 AA
1 AA
19581448 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:19582724 original size:18 final size:18
Alignment explanation
Indices: 19582682--19582724 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
19582672 GCCCATTTCG
* *
19582682 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
19582700 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
19582718 AAGTATG
1 AAGTATG
19582725 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:19583229 original size:28 final size:28
Alignment explanation
Indices: 19583191--19583344 Score: 238
Period size: 28 Copynumber: 5.5 Consensus size: 28
19583181 TAAATTGTAC
19583191 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
19583219 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
**
19583247 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* * *
19583275 AGCACTAGGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
19583303 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
19583330 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19583345 GACTTAATAT
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
27 24 0.20
28 95 0.80
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:19590659 original size:13 final size:13
Alignment explanation
Indices: 19590641--19590665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19590631 TAATGGTATA
19590641 TTGAATCCATGAC
1 TTGAATCCATGAC
19590654 TTGAATCCATGA
1 TTGAATCCATGA
19590666 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:19591245 original size:27 final size:27
Alignment explanation
Indices: 19591210--19591388 Score: 182
Period size: 27 Copynumber: 6.6 Consensus size: 27
19591200 TTAAATTGTA
19591210 TAGCACTAAGTGTGCGATATGACTATG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
19591237 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATATGACTATG
*
19591264 -ATGCACTAAGTGTGCGA-ATTGACCATG
1 TA-GCACTAAGTGTGCGATA-TGACTATG
** *
19591291 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TATGACTATG
* * *
19591319 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATATGACTATG
* * * *
19591346 TAGCACTGAGTGTGCGAGATGATTATA
1 TAGCACTAAGTGTGCGATATGACTATG
*
19591373 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
19591389 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 106 0.82
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATATGACTATG
Done.